Highlights of Biological Physics (DBIO) Talks @ APS 2021 March Meeting
American Physics Society (APS) March meeting is one of the largest physics meetings in the world. In 2021, the meeting will be held online due to COVID-19.
To help the community quickly catch up on the work to be presented in this meeting, Paper Digest Team processed all talk abstracts, and generated one highlight sentence (typically the main topic) for each. Readers are encouraged to read these machine generated highlights / summaries to quickly get the main idea of each talk. This article is on the talks related to Biological Physics (DBIO).
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TABLE : Biological Physics (DBIO)
| Title | Authors | Highlight | Session | |
|---|---|---|---|---|
| 1 | Swimming in Elastic Liquids: Faster or Slower than their Newtonian Counterparts? | Shaqfeh, Eric S | In this talk, I will review the field including how large scale numerical simulation can predict mechanisms of speed enhancement or retardation. | Session 1: Active Colloids |
| 2 | Microorganism locomotion in viscoelastic fluids | Thomases, Becca | We use computational models of swimmers in viscoelastic fluids to investigate and provide mechanistic explanations for emergent swimming behaviors. | Session 1: Active Colloids |
| 3 | Pairwise and collective behavior of dumbbell swimmers at intermediate Reynolds numbers | Dombrowski, Thomas; Nguyen, Hong; Klotsa, Daphne | We computationally investigate the pairwise and collective behavior of simple, reciprocal dumbbell swimmers composed of two unequally sized spheres at intermediate Reynolds numbers (0.1 < Re < 100). | Session 1: Active Colloids |
| 4 | Sedimenting chiral swimmers | Fadda, Federico; Molina, John; Yamamoto, Ryoichi | The squirmer model is a theoretical model introduced to study microorganisms like algae and bacteria [1]. | Session 1: Active Colloids |
| 5 | Chiral propulsion: the method of effective boundary conditions | Korneev, Leonid; Kharzeev, Dmitri; Abanov, Alexandre | We revisit a problem of computing the chiral propulsion for bodies with helical symmetry in a fluid at low Reynolds numbers. | Session 1: Active Colloids |
| 6 | Effect of inertia on the collective dynamics of an active suspension of mesoscale model swimmers | Nguyen, Hong; Dombrowski, Thomas; Klotsa, Daphne | We computationally examine how the collective behaviors emerge in a collection of simple model swimmers immersed in a viscous incompressible fluid as the impact of inertia, characterized by the Reynolds number (Re), gradually increases. | Session 1: Active Colloids |
| 7 | Enhanced hydrodynamic performance of biomimetic tapered propulsor | Demirer, Ersan; Oshinowo, Oluwafikayo; Alexeev, Alexander | Using three-dimensional fully coupled fluid-structure interaction simulations, we showed that fin tapering is an effective approach to generate travelling waves in underwater propulsors. | Session 1: Active Colloids |
| 8 | Command of active droplets in a nematic liquid crystal by an electric field | Rajabi, Mojtaba; Lavrentovich, O | Here we report real-time control of both the propulsion direction and the speed of active droplets in a nematic by an ac electric field. | Session 1: Active Colloids |
| 9 | Reconfigurable Artificial Microswimmers with Internal Feedback | Alvarez Frances, Laura; Fernandez-Rodriguez, Migue Angel; Alegria, Angel; Arrese-Igor, Silvia; Zhao, Kai; Kröger, Martin; Isa, Lucio | Here, we create a new class of responsive microswimmers, powered by induced-charge electrophoresis, which can adapt their motility to external stimuli via internal feedback. | Session 1: Active Colloids |
| 10 | Viscoelastic burrowing locomotion in nematodes reveal transition to complex postural dynamics | Pierce, Christopher; Sun, Gongchen; Lu, Hang; Goldman, Daniel | We observed C. elegans burrowing within non-Newtonian gels with tunable viscoelasticity – models of conditions in rotting fruit. | Session 1: Active Colloids |
| 11 | Quantifying the Spatiotemporal Dynamics of Locomotory Waves | Ahamed, Tosif; Asuka Guan, Sihui; Hung, Wesley; Zhen, Mei | Here, we develop methods to quantify locomotor wave dynamics at a high spatiotemporal resolution. | Session 1: Active Colloids |
| 12 | Is fluid friction enough to counteract the active drive in ciliary oscillations? | Mondal, Debasmita; Adhikari, Ronojoy; Sharma, Prerna | We combine these experimental insights with theoretical modeling of active filaments to illustrate that ciliary oscillations indeed exist in the presence of internal friction as the sole source of dissipation. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 13 | Measuring the Stokes’ drag in a microtubule-kinesin active gel | Durey, Guillaume; Luo, Wan; Dalal, Shibani; Duclos, Guillaume; Pelcovits, Robert; Powers, Thomas; Breuer, Kenneth | Combined with theoretical and numerical frameworks, we present the statistics of the bead trajectories and develop the form of the Stokes drag for active media. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 14 | Phase diagram of microtubule and end-directed motor proteins | Dogic, Zvonimir; Lemma, Bezia; Mitchell, Noah; Subramanian, Radhika; Needleman, Daniel | Extensive efforts over the past few years have focused on understanding the non-equilibrium macroscale behaviors of filamentous biopolymers such as microtubules and actin filaments that are driven by associated molecular motors. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 15 | Bifurcations and the nature of transition to turbulence in active nematic channel flow | Wagner, Caleb; Norton, Michael; Park, Jae Sung; Grover, Piyush | In this work, we explore these states and the transitions between them in a 2D channel from a dynamical systems point of view using the nemato-hydrodynamic equations. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 16 | Liquid to Gel Transitions in 3D Active Networks | Najma, Bibi; Duclos, Guillaume | We are investigating the origin of self-amplifying deformations in 3D active networks composed of cytoskeletal filaments (microtubules), crosslinkers and molecular motors. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 17 | Confinement-induced flow patterns in microtubule-based active fluids | Jarvis, Edward | Here, we demonstrate two flow patterns induced by confinement. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 18 | Active self-organization and division of nematic droplets | Schwarzendahl, Fabian; Weirich, Kimberly; Ronceray, Pierre; Dasbiswas, Kinjal | We present a continuum model that accounts for the activity of myosin motors that slide actin filaments according to their polarity. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 19 | Biomimetic active droplets via enzymatically driven reactions | Testa, Andrea | Here, we introduce a model system to mimic the high crowding and metabolic rates found in living cytoplasm, while maintaining relatively simple compositions. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 20 | Elastically confined polar active filaments | Peterson, Matthew; Hagan, Michael; Baskaran, Aparna | We discuss simple scaling models that reveal the mechanisms underlying these emergent behaviors. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 21 | Dynamics of the cytokinetic ring during cell division | Chatterjee, Mainak; Chatterjee, Arkya; Nandi, Amitabha; Sain, Anirban | Within a continuum gel theory framework, we explore the coupled dynamics of the flow and the degree of alignment in the acto-myosin network (the order parameter). | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 22 | Emerging Periodic Behaviour in three-dimensional Active Nematics | Keogh, Ryan | In this talk, I will describe our recent simulations of three-dimensional active nematic flows in microfluidic channels. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 23 | Active nematics near walls | Doré, Claire; Hardoüin, Jérôme; Ignés-Mullol, Jordi; Sagués, Francesc; Lopez-Leon, Teresa | Here we show that geometrical confinement can be an effective means to achieve control on the dynamical defect configuration of an active system. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 24 | Interfacial dynamics of active microtubule nematics | Adkins, Raymond; Kolvin, Itamar; Witthaus, Sven; You, Zhihong; Marchetti, M Cristina; Dogic, Zvonimir | We developed an experimental system for studying the fluctuations of a soft interface between an active and passive fluid. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 25 | How fluid flows influence defect dynamics in active nematic films | Angheluta, Luiza; Bowick, Mark; Chen, Zhitao; Marchetti, M Cristina | Using the hydrodynamic description of active nematics, we derive how the defect velocity and the orientational dynamics of the defects depend on both fluid flow and flow-induced alignment. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 26 | Understanding mesoscopic consequences of microscopic driving in active nematics | Redford, Steven; Ruijgrok, Paul; Zemsky, Sasha; Molaei, Mehdi; Colen, Jonathan; Vitelli, Vincenzo; Bryant, Zev; Gardel, Margaret | Understanding mesoscopic consequences of microscopic driving in active nematics | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 27 | Confinement of active nematics using virtual boundaries imposed by submerged rectangular structures | Khaladj, Dimitrius; Gharbi, Mohamed Amine; Fraden, Seth; Hirst, Linda | In this work, we report phenomena where we introduce submerged retactangular structures, trenches and via microfabrication. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 28 | Optimal Braiding of Active Nematic Microtubule Defects on the Sphere | Smith, Spencer; Frasier, Ekaterina | In this study, we consider four +1/2 defects on a sphere. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 29 | Role of confinement in stabilizing 3D Active nematic droplets | Alam, Salman; Duclos, Guillaume | We study how the critical radius depends on the activity and nematic elasticity. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 30 | Tunable spontaneous circulation of microtubule-based active fluid confined in a compressed water-in-oil droplet using milli-fluidic devices | Chen, Yen-Chen (Anderson); Jolicoeur, Brock; Chueh, Chih-Che; Wu, Kun-Ta | We found that the formation of circulatory flows depended on the thickness of the oil layer surrounding the droplet, implying that the fluid dynamics between the active fluid within the droplet and the oil outside the droplet were coupled. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 31 | Defect dynamics on active nematic ellipsoids | Clairand, Martina; Mozaffari, Ali; Hardoüin, Jérôme; Zhang, Rui; Ignés-Mullol, Jordi; Sagués, Francesc; De Pablo, Juan; Lopez-Leon, Teresa | In the current work, we build biomimmetic structural units by coating ellipsoidal droplets of smectic liquid crystal with an active nematic obtained from a cytoskeletal gel. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 32 | Active Multi-Particle Collision Dynamics: Collision Operators for Coarse Grained Simulation of Active Nematic Liquid Crystals | Kozhukhov, Timofey; Shendruk, Tyler | In this work, we present collision operators which extend MPCD to active systems. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 33 | Theory of activity-powered interfacial fluctuations | You, Zhihong; Adkins, Raymond; Kolvin, Itamar; Witthaus, Sven; Dogic, Zvonimir; Marchetti, M Cristina | Motivated by experimental studies of the dynamics of active interfaces in microtubule-based active matter, we formulate a hydrodynamic model that describes the non-equilibrium fluctuations of soft interfaces observed in liquid-liquid phase separation. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 34 | Orientational Order of Active Nematic Defects: From Flat Space to Curved Geometries | Nambisan, Jyothishraj; Pearce, Daniel; Giomi, Luca; Fernandez-Nieves, Alberto | In this talk, we explain how we confine this system to flat 2D cells and shapes of varying Gaussian curvature, K, like ellipsoids and tori. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 35 | Design of Defect Dynamics and Flows in Active Liquid Crystal Systems | Zhang, Rui | In this talk, I will discuss several recent experimental and simulation efforts which demonstrate that nucleation and self-propulsion of defects can be manipulated through, for example, spatiotemporal patterning of activity. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 36 | Active Surfaces and Defect-Mediated Morphogenesis | Hoffmann, Ludwig; Giomi, Luca | We present an analytic theory describing the dynamics of an active surface, a two-dimensional deformable surface coupled to an active liquid crystal on the surface. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 37 | Active Cell Divisions Generate Four-Fold Orientational Order in Living Tissue | Cislo, Dillon; Qin, Haodong; Yang, Fengshuo; Bowick, Mark; Streichan, Sebastian | We uncover a four-fold orientationally ordered phase in the crustacean Parhyale hawaiensis and provide a quantitative profile of the tissue dynamics through which this order emerges. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 38 | Liquid-crystal organization of liver tissue | Morales-Navarette, Hernan; Nonaka, Hidenori; Scholich, Andre; Segovia-Miranda, Fabian; de Back, Walter; Meyer, Kirstin; Bogorad, Roman; Kotelianski, Victor; Brusch, Lutz; Kalaidizidis, Yannis; Julicher, Frank; Friedrich, Benjamin; Zerial, Marino | We computationally reconstructed 3D tissue geometry from microscopy images of mouse liver tissue and analyzed it using concepts from biaxial liquid crystal theory. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 39 | No large-scale demixing due to differences in diffusivity in a model for confluent tissues | McCarthy, Erin; Damavandi, Ojan; Manning, M. Lisa | In this study, we ask whether a similar demixing via diffusivity persists in a confluent model for biological tissue. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 40 | A microbial hare and tortoise story: interactions between topological defects in biofilms favour bacteria that move more slowly | Meacock, Oliver; Doostmohammadi, Amin; Foster, Kevin; Yeomans, Julia; Durham, William | Using cell tracking, active nematic theory, and simulations of self-propelled rods, we show that this phenomenon is caused by the behaviour of +1/2 topological defects within the collective. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 41 | Liquid crystal elastomer substrates with predesigned splay and bend to control growth and migration of fibroblast cells | Koizumi, Runa; Rajabi, Mojtaba; Kim, Min-Ho; Lavrentovich, O | This work demonstrates that the active force caused by gradients of the orientational order in tissues triggers polar migration of cells. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 42 | Confinement Discerns Swarmers from Planktonic Bacteria | CHEN, WEIJIE; Tang, Jay | Here, we show that when confined by microwells of specific sizes mounted on an agar surface, novel bacterium Enterobacter sp. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 43 | Topological defects patterns in monolayers of cells | Serra, Francesca | We can thus analyze the alignment of cells in the vicinity of the topological defects under different conditions and observe multiple possible solutions that the cells utilize to adapt to the boundaries. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 44 | Multi-scale multi-species modeling of emergent flows andactive mixing in confined bacterial swarms | Fylling, Cayce; Gopinath, Arvind; theillard, maxime | Here we present a new method for modeling such fluids under confinement. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 45 | Interaction of active droplets with director gradients in nematic liquid crystal | Baza, Hend; Wang, Yuhan; Lavrentovich, O | We use the plasmonic metamasks technique to pattern the director in a one-dimensionally periodic sequence of splay and bend deformations and in the form of defects, such as semi-integer singular disclinations and integer nonsingular disclinations. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 46 | Phase transitions in growing bacteria colonies at liquid interfaces | Langeslay, Blake; Juarez, Gabriel | We present a growing colony of motile E. coli at an oil-water interface in which system evolution can be directly and continuously observed using time-lapse microscopy over eight hours. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 47 | Space and time cluster tomography of active systems | Matoz Fernandez, Daniel; Edblom Dougherty, Sean Patrick; Blackwell, Brendan; Driscoll, Michelle; Kovacs, Istvan; Olvera De La Cruz, Monica | As an alternative, here we propose to perform cluster tomography in space and time by measuring the spatial gap size distribution 3 and inter-event time distribution 4 within particle clusters. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 48 | Global order and lane formation in Microtubule-based active matter | Memarian, Fereshteh; Lopes, Joseph; Hirst, Linda | In this project, we investigated MT-kinesin-based transportation by performing experiments using kinesin motors coupled to a lipid bilayer. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 49 | Active self-organization in actin cytoskeleton | Mirza, Waleed; Corato, Marco de; Sánchez, Alejandro; Arroyo, Marino; Caicoya, Guillermo | In this study, we use a continuum model to explain an out-of-equilibrium self-assembly of such regularly spaced actin bundles. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 50 | Active Matter Self-Organization Simulator (AMSOS): Combining biophysics and mechanics on HPC | Yan, Wen; Lamson, Adam; Ansari, Saad; Betterton, Meredith; Shelley, Michael | We use a new numerical method based on geometrically constrained optimization to guarantee that steric interactions and crosslinker binding forces between filaments are properly and efficiently handled. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 51 | Collective motion of vinegar eels: metachronal waves and induced flows | Peshkov, Anton; McGaffigan, Sonia; Wright, Esteban; Quillen, Alice | We experimentally study the collective motion of the free-swimming nematode Turbatrix Aceti also known as the vinegar eel. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 52 | Rotation and propulsion in 3D active chiral droplets | Negro, Giuseppe; Carenza, Livio Nicola; Gonnella, Giuseppe; Marenduzzo, Davide | Here we consider a system which is inherently chiral and apolar and that can be modelled – in the passive limit – as a Cholesteric Liquid Crystal. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 53 | Dynamical renormalizatin group approach to the collective behaviour of swarms | Cavagna, Andrea; Di Carlo, Luca; Giardina, Irene; Grigera, Tomas; Pisegna, Giulia | We study the critical behavior of a model with nondissipative couplings aimed at describing the collective behavior of natural swarms, using the dynamical renormalization group under a fixed-network approximation. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 54 | Linear stability analysis for asymmetric contraction of the cytokinetic ring | Chatterjee, Arkya; Chatterjee, Mainak; Nandi, Amitabha; Sain, Anirban | In a previous work [1], using a continuum gel theory framework in a weak flow coupling regime, we obtained exact analytical solutions for the quasi-static dynamics of the radially symmetric ring contraction. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 55 | Finite wave number instability interrupts motility-induced phase separation | MA, ZHAN; Ni, Ran | In this work, we formulate a continuum theory for cABPs, and the fluctuation dispersion relation reveals two types of instabilities, i.e. at low torque intensity, type I instability refers to the zero wave number starting unstable mode inducing the MIPS; for large enough torque, type II instability refers to the finite wave number starting unstable modes, which results in the dynamical clustering state and interrupts the conventional MIPS. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 56 | Active cholesterics and smectics are hydrodynamically distinct | Kole, Swapnil; Alexander, Gareth; Ramaswamy, Sriram; Maitra, Ananyo | We show theoretically that active cholesterics, by contrast, display striking signatures of chirality, and are thus qualitatively distinct from smectics, even in their asymptotic long-wavelength dynamics. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 57 | Emergent task-driven cooperation in ant collectives | S, Ganga Prasath; Mandal, Souvik; Giardina, Fabio; Murthy, Venkatesh; Mahadevan, L. | We find that ant collectives that have multiple castes are more efficient than those made of a single caste – and show how the task creates an emergent dynamic division of labor determined by the interaction with the environment that cuts across morphological and physiological distinctions. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 58 | Sparse Identification of Continuum Theories of 2D Active Nematics | Joshi, Chaitanya; Lemma, Linnea; Dogic, Zvonimir; Baskaran, Aparna; Hagan, Michael | In this work, we employ a recently developed method to automatically identify the optimal continuum models, along with their parameters, directly from the spatio-temporal director and velocity data, via sparse fitting of the coarse-grained fields on to generic low order PDEs. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 59 | Strategies for Collective Adaptive Workload Distribution in Varying Work Conditions | Aina, Kehinde; Kuan, Hui-Shun; Goldman, Daniel; Betterton, Meredith | In this work, we model how behavior changes if individual ants optimize an objective in a changing environment. | Session 2: Active Matter and Liquid Crystals in Biological and Bio-Inspired Systems |
| 60 | Clogging Dynamics of Active and Passive Disks in Complex Environments | Reichhardt, Cynthia; Reichhardt, Charles | We study the directional locking and clogging of passive disks and active run-and-tumble particles interacting with a periodic array of obstacles. | Session 3: Active Matter in Complex Environments |
| 61 | Breakdown of Ergodicity and Self-Averaging in Polar Flocks with Quenched Disorder | Duan, Yu; Mahault, Benoît; Shi, Xiaqing; Chate, Hugues | We show that quenched disorder affects polar active matter in ways more complex and far-reaching than believed heretofore. | Session 3: Active Matter in Complex Environments |
| 62 | Life in a tight spot: How bacteria move in porous media | Bhattacharjee, Tapomoy; Amchin, Daniel; Ott, Jenna; Kratz, Felix; Datta, Sujit | To address this gap in knowledge, we combine microscopy, materials fabrication, and microbiology to investigate how E. coli moves in 3D porous media. | Session 3: Active Matter in Complex Environments |
| 63 | Chemotaxis strategies of bacteria with multiple run modes in complex environments | Alirezaeizanjani, Zahra; Großmann, Robert; Pfeifer, Veronika; Hintsche, Marius; Beta, Carsten | Here, we discuss the chemotactic motion of the bacterium Pseudomonas putida as a model organism [2]. | Session 3: Active Matter in Complex Environments |
| 64 | Chemotaxis of cargo-carrying self-propelled particles | Vuijk, Hidde; Merlitz, Holger; Lang, Michael; Sharma, Abhinav; Sommer, Jens-Uwe | We show that self-propelled particles display chemotaxis and move into regions of higher activity, if the particles perform work on passive objects, or cargo, to which they are bound. | Session 3: Active Matter in Complex Environments |
| 65 | Active Matter Commensuration and Frustration Effects on Periodic Substrates | Reichhardt, Charles; Reichhardt, Cynthia | We show that self-driven particles coupled to a periodic obstacle array exhibit novel active matter commensuration effects that are absent in the Brownian limit. | Session 3: Active Matter in Complex Environments |
| 66 | Trapping in porous microstructure suppresses magnetotactic bacterial transport | Dehkharghani, Amin; Waisbord, Nicolas; Guasto, Jeffrey | Using microfluidic experiments complemented by Langevin simulations, we investigate the effect of porous microstructure and the role of disorder in dictating cell transport. | Session 3: Active Matter in Complex Environments |
| 67 | Enhanced bacterial motility in colloidal media | Kamdar, Shashank; Shin, Seunghwan; Kim, Youngjun; Francis, Lorraine; Cheng, Xiang | Here, we investigate the motility of E. coli, a flagellated bacterium, in colloidal media. | Session 3: Active Matter in Complex Environments |
| 68 | Emergence of collective states in suspensions of swimming bacteria in confined geometries | Ghosh, Dipanjan; Cheng, Xiang | Imaging these suspensions using bright-field microscopy, we observe the emergence of three distinct collective states, dependent on the density of bacteria and their swimming velocity: a disordered state, a state characterized by lanes with long-ranged orientational nematic order, and a state of swarming clusters with short-ranged polar order. | Session 3: Active Matter in Complex Environments |
| 69 | Attractors in disordered active matter and using disorder to control active matter | Peruani, Fernando | Attractors in disordered active matter and using disorder to control active matter | Session 3: Active Matter in Complex Environments |
| 70 | Separating Motile and Immotile Bacteria through Confined Chemotaxis | CHIU, SHANG-HUAN; Zumpano, Francesca; Lushi, Enkeleida | We will present a model that couples individual run-and-tumble bacterial motion to the chemical gradient while the entire colony is inside a circular confinement. | Session 3: Active Matter in Complex Environments |
| 71 | Aligning self-propelling particles in confinement | Lushi, Enkeleida; Wall, Katherine; Netznik, Nathaniel; Chiu, Shang-Huan | We present a model for self-propelling aligning particles and look at the collective motion for such swimmers in non-trivial confined domains. | Session 3: Active Matter in Complex Environments |
| 72 | Bacterial motion and spread in porous media | Almoteri, Yasser; Lushi, Enkeleida | We will present a continuum model that describes the collective dynamics of micro-swimmers such as bacteria through a porous wet material. | Session 3: Active Matter in Complex Environments |
| 73 | Nonequillibrium shape fluctuations and motility of a droplet enclosing active particles | Kokot, Gasper; Faizi, Hammad; Pradillo, Gerardo; Snezhko, Alexey; Vlahovska, Petia | We study the collective dynamics of the Quincke rollers in soft confinement by enclosing the rollers inside a liquid droplet sandwiched between two surfaces. | Session 3: Active Matter in Complex Environments |
| 74 | States of active nematics confined to annuli | Zarei, Zahra; Joshi, Chaitanya; . Norton, Michael; Hagan, Michael; Fraden, Seth | In this study, we investigate a 2D active nematic confined in an annulus in which the plus and minus half defects exhibit rich dynamical behavior. | Session 3: Active Matter in Complex Environments |
| 75 | Optimal navigation strategies for microswimmers on curved manifolds | Piro, Lorenzo; Tang, Evelyn; Golestanian, Ramin | We study this problem by building an analytical formalism for overdamped microswimmers on curved manifolds and arbitrary flows. | Session 3: Active Matter in Complex Environments |
| 76 | Slip and ypsotaxis of catalytically self-propelled particles near surfaces | Ketzetzi, Stefania; de Graaf, Joost; Kraft, Daniela | In this talk, I will demonstrate that the choice of the substrate material has a strong influence on the microswimmer speed through slippage [1]. | Session 3: Active Matter in Complex Environments |
| 77 | Spontaneous propulsion of an isotropic colloid in a phase-separating medium | Decayeux, Jeanne; Dahirel, Vincent; Illien, Pierre; Jardat, Marie | We consider an isotropic colloid in a bath of small solute particles. | Session 3: Active Matter in Complex Environments |
| 78 | Interplay of flow and swimmer’s polar orientation in confined active suspensions | Gulati, Paarth; Shankar, Suraj; Marchetti, M Cristina | We examine the dynamics of a continuum model of confined active bacterial suspensions where flows driven by active stresses are coupled to the tendency of microorganism to propel themselves along their orientation axis. | Session 3: Active Matter in Complex Environments |
| 79 | Unravel the transport and rotation properties of a squirmer in viscoelastic fluids | Qi, Kai; Corato, Marco de; Pagonabarraga, Ignacio | We study the rotational motion and transport peculiarities of a single swimmer in a viscoelastic fluid via Lattice Boltzmann (LB) simulations. | Session 3: Active Matter in Complex Environments |
| 80 | Viscoelasticity enables self-organization of bacterial active matter | Liu, Song; Shankar, Suraj; Marchetti, M Cristina; Wu, Yilin | Here we found that tuning the rheological properties of bacterial active fluids enables large-scale spatial and temporal self-organization. | Session 3: Active Matter in Complex Environments |
| 81 | Effective thermodynamic properties of inertial active microswimmers with alignment interaction | Karmakar, Soumen; Ganesh, Rajaraman | We demonstrate that the alignment dynamics bring in important changes in the effective thermodynamic-like features. | Session 3: Active Matter in Complex Environments |
| 82 | Dynamic structures in concentrated suspensions of spherical squirmers | Brumley, Douglas; Ishikawa, Takuji; Pedley, Timothy | This work suggests that lubrication theory, based on near-field interactions alone, contains most of the relevant physics, and successfully connects microscale structural features in the suspension with bulk rheological attributes. | Session 3: Active Matter in Complex Environments |
| 83 | Design principles for transport of vesicles by enclosed active particles | Uplap, Sarvesh; Hagan, Michael; Baskaran, Aparna | In this work, we seek to leverage these phenomena to identify design principles for optimal transport of flexible compartments that enclose active particles. | Session 3: Active Matter in Complex Environments |
| 84 | The dynamic steady-states of polar self-propelled filaments confined in 2D flexible vesicles | Ma, Yingyou; Baskaran, Aparna; Hagan, Michael | In this work we investigate the relationship between boundary and agent degrees of freedom, by simulating self-propelled semiflexible filaments confined within flexible vesicles in two dimensions. | Session 3: Active Matter in Complex Environments |
| 85 | Survival time of active Brownian particles on flat curves | Herrera, Pedro; Sandoval, Mario | We find the average time for an overdamped active Brownian particle (OABP) moving on any flat curve with metric, to first reach a given point on the curve (so called mean-first passage time, MFPT). | Session 3: Active Matter in Complex Environments |
| 86 | Spontaneous demixing of mixed active-passive suspensions | Jeanneret, Raphaël; Williams, Stephen; Tuval, Idan; Polin, Marco | We show that this can be used to induce the system to de-mix spontaneously. | Session 3: Active Matter in Complex Environments |
| 87 | Interaction of microswimmers with elastic interfaces | Nambiar, Sankalp; Wettlaufer, John | Simulations and theories have shown that microswimmers subject to confinement between parallel rigid boundaries exhibit an excess accumulation near the boundary; in turn, there is an associated enhancement of the active pressure forces on the wall. | Session 3: Active Matter in Complex Environments |
| 88 | Crowding-Enhanced Diffusion: An Exact Theory for Highly Entangled Self-Propelled Stiff Filaments | Mandal, Suvendu; Kurzthaler, Christina; Franosch, Thomas; Löwen, Hartmut | We predict a scaling theory for the effective diffusivity as a function of the Peclet number and the filament number density. | Session 3: Active Matter in Complex Environments |
| 89 | Dynamics of entangled active polymers | Tejedor, Andrés; Ramirez, Jorge | In this work, we extend the theory to consider the effect of an active force (drift) that drives the polymer along the tube in a certain direction. | Session 3: Active Matter in Complex Environments |
| 90 | Can activity in a suspension cause thickening or dethickening? | Ong, Edward; Liarte, Danilo; Griniasty, Itay; Ramaswamy, Meera; Ness, Christopher; Sethna, James; Cohen, Itai | We describe our investigations into the ability of active matter to tune shear thickening and jamming in colloidal suspensions. | Session 3: Active Matter in Complex Environments |
| 91 | Active colloidal gel | Wei, Mengshi; Ben Zion, Matan Yah; Dauchot, Olivier | At the microscopic level, we look into the short time vibrational dynamics and long-time dynamical correlations and analyze how they depend on the local structure of the gel. | Session 3: Active Matter in Complex Environments |
| 92 | Doping of a Sedimented Column of Passive Particles | Chen, Moyuan; Morin, Alexandre; Palacci, Jeremie | Here, we explore, via numerical experiments, the effect of active stirring by letting the active particle swim in a density gradient of passive particles, unveiling unexpected dynamics that warrant further investigations. | Session 3: Active Matter in Complex Environments |
| 93 | What can kinetic Monte Carlo do for active Matter? | Klamser, Juliane; Dauchot, Olivier; Tailleur, Julien | We focus on a kinetic MC version for the simplest kind of active matter: persistently moving, non-polar, interacting particles. | Session 3: Active Matter in Complex Environments |
| 94 | A reinforcement learning approach to optical control of active matter | Falk, Martin; Murugan, Arvind | Here, we apply a reinforcement learning approach; a reinforcement learning agent identifies time-varying patterns of a scalar activity parameter which induce net transport in a chosen direction in a simulated system of self-propelled spheres. | Session 3: Active Matter in Complex Environments |
| 95 | Energetics of critical oscillators in active bacterial baths | Roldan, Edgar; Gopal, Ashwin; Ruffo, Stefano | We investigate the nonequilibrium energetics near a critical point of a non-linear driven oscillator immersed in an active bacterial bath. | Session 3: Active Matter in Complex Environments |
| 96 | Swimming behavior of Paramecium in crowded environments | Escoubet, Nicolas; Brette, Romain; Prevost, Alexis; Pontani, Léa-Laetitia | Here, we report on extensive measurements of the trajectories of P aramecium t etraurelia in engineered environments with and without obstacles. | Session 3: Active Matter in Complex Environments |
| 97 | Using unsupervised machine learning to detect depinning and clustering transitions in active matter driven across quenched disorder | McDermott, Danielle; Reichhardt, Cynthia; Reichhardt, Charles | Using large-scale numerical simulations of active disks, we demonstrate that a machine learning order parameter can detect depinning transitions and different dynamic flow phases in systems driven far from equilibrium. | Session 3: Active Matter in Complex Environments |
| 98 | Modeling collective cell migration on substrates with topological defects | Kaiyrbekov, Kurmanbek; Sullivan, Kyle; Camley, Brian | In this work we perform 2D active Monte Carlo simulations to investigate cell arrangements and motion on a substrate patterned with ridges that induce a +1 defect. | Session 3: Active Matter in Complex Environments |
| 99 | Extracted Active Fluctuations from an Active-Passive Mixture Reveal the Dynamic Class of Active Materials | Shen, Chong; Ou-Yang, H Daniel | We developed a deconvolution method to extract the active fluctuations from that of a mixture. | Session 3: Active Matter in Complex Environments |
| 100 | Inverse Solidification Induced by Active Janus Particles | Misko, Vyacheslav | In contrast to this classical scenario, we demonstrate [1] a counter-intuitive occurrence of crystalline long-range order in an initially disordered matrix of passive colloidal particles accommodating chemically active defects – photocatalytic Janus particles (JP). | Session 3: Active Matter in Complex Environments |
| 101 | Slow Diffusion in Active Bath: Theoretical Description of the Activity-induced Energy Landscape | Chaki, Subhasish; Chakrabarti, Rajarshi | In this context, we have studied a prototype model for diffusion in an activity-induced rugged energy landscape to describe the dynamics of a tagged particle in a dense active environment. | Session 3: Active Matter in Complex Environments |
| 102 | First passage of an active particle in the presence of passive crowders | Biswas, Animesh; Cruz, J. M.; Parmananda, Punit; Das, Dibyendu | We experimentally study the stochastic transport of a self-propelled camphor boat, driven by Marangoni forces, through a crowd of passive paper discs floating on water. | Session 3: Active Matter in Complex Environments |
| 103 | A General 3D Model for the Dynamics of Rod-Like Sensory-Growth Systems and their Mechanical Interaction with the Environment | Porat, Amir; Meroz, Yasmine | In order to emulate these dynamics in a 3D environment, we recently developed a general model for the growth of rod-like organs, adopting the Cosserat rod model. | Session 4: Animal Behavior |
| 104 | Integration of applied force by bean stems determines initiation of twining behavior around supporting structures: | Ohad, Amir; Meroz, Yasmine | Our study suggests that this decision is determined by an integration of the force applied on the plant during contact with the support, a force that is driven by the circumnutational movement. | Session 4: Animal Behavior |
| 105 | Encounter rates involving elongated marine microorganisms | Slomka, Jonasz; Alcolombri, Uria; Secchi, Eleonora; Fernandez, Vicente; Stocker, Roman | Later, we describe the encounters between bacteria and sinking particles of organic matter. | Session 4: Animal Behavior |
| 106 | Bridging time scales in C. elegans behavior | Costa, Antonio Carlos; Ahamed, Tosif; Jordan, David; Stephens, Greg | We use a recently developed transfer operator approach, akin to a Fokker-Planck description, to perform a top-down coarse-graining of C. elegans posture dynamics: from long timescale “roaming’’ and “dwelling’’ states (minutes), to a “run’’ and “pirouette’’ description (seconds), down to fine scale movements (milliseconds). | Session 4: Animal Behavior |
| 107 | C. elegans turns in heterogeneous environments | Diaz, Kelimar; Chong, Baxi; Ding, Jimmy; Lu, Hang; Goldman, Daniel | To discover if such “omega turns” are effective in heterogeneous environments, we conducted laboratory experiments in fluid filled PDMS multi-post arrays. | Session 4: Animal Behavior |
| 108 | Measuring large obstacle traversal over large spatiotemporal scales | Othayoth Mullankandy, Ratan Sadanand; Francois, Evains; Li, Chen | Here, we used a novel terrain treadmill to study cockroach traversal of large pillar obstacles over large spatiotemporal scales. | Session 4: Animal Behavior |
| 109 | Active sensing becomes rhythmic during oscillatory behaviour in electric fish | Melanson, Alexandre; Longtin, Andre | Here, we report on and characterize an hitherto unknown behavioural state of pulse-type weakly electric fish during which electrosensory acquisition becomes rhythmic and is coupled to low-frequency movement. | Session 4: Animal Behavior |
| 110 | A low energy effective theory for larval Drosophila behaviour | Loveless, Jane; Garner, Alastair; Issa, Abdul; Roberts, Ruairi; Webb, Barbara; Prieto-Godino, Lucia; Ohyama, Tomoko; Alonso, Claudio | As a basis for understanding the physics of behaviour in fruitfly larvae, we here develop an effective theory for the animals’ motion. | Session 4: Animal Behavior |
| 111 | Spotted lanternfly nymphs use multiple self-righting behaviors during landing | Kane, Suzanne Amador; Bien, Theodore; Contreras-Orendain, Luis; Ochs, Michael; Hsieh, Tonia | We used high-speed video to study whether immature SLFs (nymphs) land upright more often than expected by chance, and, if so, whether they do so via active or passive mechanisms. | Session 4: Animal Behavior |
| 112 | Stochastic insect navigation in complex rapidly fluctuating odor plumes | Demir, Mahmut; Kadakia, Nirag; Anderson, Hope; Clark, Damon; Emonet, Thierry | Combining measurements, dynamical models, and statistical inference we found that navigation was stochastic, and did not rely on the continuous modulation of speed or orientation. | Session 4: Animal Behavior |
| 113 | Behavioral quantification of freely moving mice | Bergeler, Silke; Klibaite, Ugne; Verpeut, Jessica; Wang, Samuel; Shaevitz, Joshua | As a second approach, we identify change points in the temporal dynamics, and locally fit the data to autoregressive models, which also can be clustered to assign behaviors. | Session 4: Animal Behavior |
| 114 | How snakes traverse large obstacles in complex 3-D terrain | Fu, Qiyuan; Astley, Henry; Li, Chen | Here, we hypothesized that vertical body bending is important for traversal of more complex rubble-like terrain and tested it using the generalist corn snake P. guttatus ( N = 2 animals, n = 23 trials). | Session 4: Animal Behavior |
| 115 | Multi-timescale representation of rat behavior | Jain, Kanishk; Menichini, Elena; Muzzu, Tomaso; Macke, Jakob; Saleem, Aman; Berman, Gordon | We use activation values from each layer to create multiple two-dimensional density maps of behavioral states. | Session 4: Animal Behavior |
| 116 | Functional consequences of microscopic skin features on snake locomotion | Rieser, Jennifer; Li, Tai-De; Tingle, Jessica; Goldman, Daniel; Mendelson, Joseph | We hypothesize that these microstructures affect the frictional interaction with the substrate and we use resistive force theory to model the effects of frictional anisotropy on snake locomotion. | Session 4: Animal Behavior |
| 117 | Measuring and modeling the thermotactic learning behavior of C. elegans. | Roman, Ahmed; Palanski, Konstantine; Nemenman, Ilya; Ryu, William | We build a predictive model with multiple time scales and utilize mutants to detangle the various learning processes. | Session 4: Animal Behavior |
| 118 | Drops: A bio-inspired tool to fabricate granular materials | Amstad, Esther | In this talk, I will demonstrate how we convert individually dispersed emulsion drops into selectively permeable viscoelastic capsules that enable controlled localized release of reagents. | Session 5: Biomaterials |
| 119 | Determining Structure and Action Mechanism of Artificial Peptide LBF14 by Molecular Simulation | Solbach, Florian; Faller, Roland | We analyze the structure of this peptide in free solution and bound to a lipid membrane. | Session 5: Biomaterials |
| 120 | Origin of Viscoelasticity in Protein-RNA Condensates | Alshareedah, Ibraheem; Banerjee, Priya | Here, we perform quantitative rheological characterization of protein-RNA condensates using active and passive optical tweezer-based microrheology. | Session 5: Biomaterials |
| 121 | Diffusion of water through palm leaf materials | mohanty, debapriya pinaki; Udupa, Anirudh; Dayananda, Mysore; Chandrasekar, Srinivasan | Here, we report on a study of diffusion of water through the sheath since water penetration affects the structural integrity of the material, controlling product life. | Session 5: Biomaterials |
| 122 | Understanding red blood cell behavior in contracting clot | Sun, Yueyi; Myers, David; Lam, Wilbur; Alexeev, Alexander | We use experiments and mesoscale modeling to examine the biophysics of clot contraction. | Session 5: Biomaterials |
| 123 | E-Cadherin-mediated adhesion in the absence of the cytoskeletal machinery | Nagendra, Kartikeya; IZZET, Adrien; Friedman, Leah; Harrison, Oliver; Pontani, Léa-Laetitia; Shapiro, Larry; Honig, Barry; Brujic, Jasna | We develop a biomimetic emulsion[1] to probe the physical basis of cadherin adhesion and characterize the role of lateral cis interactions in cadherin recruitment. | Session 5: Biomaterials |
| 124 | Microfluidics & Algorithm for Comprehensive Small Volume Blood Diagnostics via Rapid Solidification of μL Drops into Homogeneous Thin Film Solid Films and XRF | Balasooriya, Thilina; Peng, Wesley; Suresh, Nikhil; Gurijala, Aashi; Sahal, Mohammed; Culbertson, Eric; Culbertson, Robert; Herbots, Nicole | Microfluidics & Algorithm for Comprehensive Small Volume Blood Diagnostics via Rapid Solidification of μL Drops into Homogeneous Thin Film Solid Films and XRF | Session 5: Biomaterials |
| 125 | Influence of NaCl Concentration on Phospholipid Membranes | Jaksch, Sebastian; Frielinghaus, Henrich; Holderer, Olaf; Koutsioubas, Alexandros; Zolnierczuk, Piotr | We previously showed the structure (neutron reflectometry, GISANS) and the dynamic behavior (GINSES) of L-α-phosphatidylcholine (SoyPC) phospholipid membranes, [1,2] and established a multi-lamellar structure as well as a surface mode, attributed to transient waves in the membranes. | Session 5: Biomaterials |
| 126 | Evolution and engineering of avian eggs | Stoddard, Mary; Jia, Zian; Deng, Zhifei; Weaver, James; Li, Ling | Here, we explore these questions through the lenses of evolutionary biology, biophysics and mechanical engineering, which together provide an integrative picture of the form and function of avian eggs. | Session 5: Biomaterials |
| 127 | Modeling Kinetoplast Dynamics | Garcia, Edgar; Polson, James; Klotz, Alexander | Here, we discuss the scaling behavior of the planar and transverse components of the gyration tensor and compare them to existing models of elastic membranes, to determine the physical effects of linked-ring connectivity. | Session 5: Biomaterials |
| 128 | Active Elasto-Capillarity Determines the Wetting Dynamics of Living Droplets | Yousafzai, Sulaiman; Yadav, Vikrant; Amiri, Sorosh; Staddon, Michael; Tabatabai, Alan; Errami, Youssef; Jaspard, Gwillherm; Amiri, Sirine; Banerjee, Shiladitya; Murrell, Michael | Here, we model the adhesion and spreading (wetting) of living cell aggregates as ‘active droplets’, with a non-equilibrium surface energy that depends upon internal stress generated by the actomyosin cytoskeleton. | Session 5: Biomaterials |
| 129 | Patterns in skeletal biomineralization | Porter, Susannah; Moore, John; Riedman, Leigh Anne | Earlier work showed that the choice of carbonate mineralogy (aragonite vs. calcite) in animals reflects the chemistry of seawater at the time the skeleton evolved. | Session 5: Biomaterials |
| 130 | Applications of molecular taphonomy to the invertebrate fossil record | Myers, Corinne; Bergmann, Kristin; Gilbert, Pupa | Future work on the utility of hyperspectral imaging, the geography of preservation, influence of large-scale ocean-climate regimes (e.g., icehouse vs. greenhouse; calcite vs. aragonite seas) and complementary analyses (e.g., Raman spectroscopy), will provide additional clues into the molecular and structural preservation of biominerals, as well as their evolution through geologic time. | Session 5: Biomaterials |
| 131 | Probabilistic Modeling of Hyaluronan Synthesis and Secretion | Scrimgeour, Jan | I present a probabilistic model that allows an examination of secretion of HA by the synthase enzyme. | Session 5: Biomaterials |
| 132 | First structural study of gel inside the electro sensory organs of cartilaginous fishes | Wheeler, Alauna; Phillips, Molly; Jia, Manping; Rolandi, Marco; Amemiya, Chris; Hirst, Linda | Using data collected from atomic force microscopy (AFM), proton conductivity, and x-ray scattering experiments, we present the first microscopic descriptions of the AoL gel structure. | Session 5: Biomaterials |
| 133 | Resonance Raman measurements on fossilized remains show ancient heme-globin complex | Long, Brandon; zheng, wenxia; Schweitzer, Mary; Hallen, Hans | Doubly selective resonant Raman techniques confirms the co-location of a heme moiety onto a larger globin protein by probing both heme vibrational modes and a excitation-resonant bond simultaneously. | Session 5: Biomaterials |
| 134 | Ptychography of diatoms reveals chemically inhomogeneous biosilica cell walls | Li, Jiaqi; Gilbert, Pupa | Here, we studied the biosilica coordination and the morphology of diatom BCWs using the synchrotron-based x-ray spectromicroscopy (ptychography), with a 10nm spatial resolution. | Session 5: Biomaterials |
| 135 | Inhomogeneous degree of connectivity preference and computational efficiency in the olfactory system of the fruit fly | Cheng, Lishan; Charng, Ching-Che; Feng, Kuan-Lin; Chu, Li-An; Lo, Chung-Chan; Chiang, Ann-Shyn; Lee, Ting-Kuo | Inhomogeneous degree of connectivity preference and computational efficiency in the olfactory system of the fruit fly | Session 5: Biomaterials |
| 136 | Remote Data Processing Using Crowd-Sourced Cloud-Computing | Fordyce, Benjamin; Gilbert, Pupa | To adjust our model for remote data processing to correct this error and make findings more rigorous, we introduce a model of “crowd-sourced” data processing using cloud computing. | Session 5: Biomaterials |
| 137 | Inelastic neutron scattering of perdeuterated cellulose | Wang, Howard; Nishiyama, Yoshiharu; Zhang, Xin; Briber, Robert; russell, robert; Chen, Siqian; zhang, Yanjun | Inelastic neutron scattering of perdeuterated cellulose | Session 5: Biomaterials |
| 138 | Nanoscale crystal orientations in tooth enamel in monsters of the past and their modern counterparts | Stifler, Cayla; Chopdekar, Rajesh; Gilbert, Pupa | We used PIC (polarization-dependent imaging contrast) mapping at the calcium L-edge (https://doi.org/10.1021/jacs.8b05547) to reveal the crystal orientations of enamel(oid) crystals in monsters of the past, including T. rex, megalodon and ancient and modern sharks and bears. | Session 5: Biomaterials |
| 139 | Curvature-mediated feedback leads to turbulence of growing interfaces | Würthner, Laeschkir; Frey, Erwin | Motivated by this work, we have studied the dynamics of a growing interface driven by the local density of membrane proteins. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 140 | Phase Diagram and Interfacial Instabilities in the Driven Widom-Rowlinson Lattice Gas | Dickman, Ronald; Zia, Royce; Lavrentovich, Maxim; Chate, Hugues | These are now eliminated using a new method in which particles are slowly added to the evolving system, allowing a pattern of the preferred wavelength to emerge spontaneously. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 141 | Microemulsions in the driven Widom-Rowlinson lattice gas | Lavrentovich, Maxim; Dickman, Ronald; Zia, Royce | We study this model at low particle densities in two- and three-dimensions, where we find a disordered phase with a characteristic length scale (similar to a “microemulsion”). | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 142 | Strong current response to slow modulation: A metabolic case-study | Forastiere, Danilo; Falasco, Gianmaria; Esposito, Massimiliano | We study the current response to periodic driving of a crucial biochemical reaction network, namely, substrate inhibition. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 143 | Controlling the velocity of DNA base in nanopores using flossing | Mahalik, Jyoti; Muthukumar, Murugappan | We propose a DNA flossing technique for controlling the DNA base motion inside the nanopore and we demonstrate this using Langevin dynamics simulation. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 144 | Combining Statistical Thermodynamics, Control Theory and Reinforement Learning to Predict Regulation and Post-translational Control of Metabolism | Britton, Samuel; Cannon, William; Alber, Mark | We use two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 145 | No synchronization for coupled oscillators on small-world networks | Liu Rodrigues, Kevin; Dickman, Ronald | In this work, we show that one such model may fail to achieve synchronization even when the dynamics occur on networks with non-local coupling and even long-range interactions. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 146 | Recent Advances in the Understanding of Dynamic Phase Transitions in Ferromagnetic Thin Films | Quintana, Mikel; Marín Ramírez, Juan; Berger, Andreas | Here, we present some of our most recent experimental results, specifically related to our studies of the vector nature of Q in thin films with uniaxial anisotropy, as well as work on the general definition of the conjugate field of Q. [1] P. Riego, P. Vavassori, A. Berger, Physica B 549, 13 (2018) | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 147 | Barrier-Controlled Non-Equilibrium Criticality in Random Organization | Lei, Qun-li; Hu, Hao; Ni, Ran | A mean-field theory is proposed to explain this phenomenon, which suggests that the transition at finite thermal noise belongs to the Ising universality. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 148 | Control of the surface roughness during a growth process described by the Kardar-Parisi-Zhang equation | Priyanka, Priyanka; Pleimling, Michel; Tauber, Uwe | Control theory is a widely used tool in engineering to develop controlled, stable models of dynamical systems. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 149 | Ensemble reservoir equivalence in driven lattice gases | Calazans, Leonardo; Dickman, Ronald | We consider NESS in the driven lattice gas with nearest-neighbor exclusion. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 150 | Dynamical Transitions in Aperiodically Kicked Tight Binding Models | Ravindranath, Vikram; M. S., Santhanam | Considering a 2-band model, we have found that this behaviour is related to the existence of flat bands, and the mechanism for asymptotic diffusion is similar to that of a classical random walk. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 151 | Field-theoretic approach to study a class of reaction-diffusion models | Sharma, Prashant | We present a field-theoretic derivation of a class of models of reaction-diffusion systems of which the Gray-Scott model is a special case. | Session 6: Control of Noisy Non-Linear Dynamical Systems |
| 152 | DBIO Happy Hour | DBIO Happy Hour | Session 7: DBIO Happy Hour | |
| 153 | DBIO Short Course: Machine Learning for Biological Physics | DBIO Short Course: Machine Learning for Biological Physics | Session 8: DBIO Short Course: Machine Learning for Biological Physics | |
| 154 | Error-speed correlations in biopolymer synthesis | Chiuchiu, Davide; Tu, Yuhai; Pigolotti, Simone | We show here that the fluctuations in the error rate and the speed of a replicative enzyme can reveal details of its error-correction mechanisms. | Session 9: DNA and RNA Biophysics |
| 155 | DNA transport and conformational dynamics in active cytoskeleton composites | Garamella, Jonathan; Adalbert, Serenity; Aguirre, Gina; McGorty, Ryan; Robertson-Anderson, Rae | DNA transport and conformational dynamics in active cytoskeleton composites | Session 9: DNA and RNA Biophysics |
| 156 | Nucleic acid melting under small tension | Hart, Derek; Jeong, Jiyoun; Kim, Harold | To investigate the effect of ~pN axial force on nucleic acid duplex stability, we developed a novel single-molecule force assay, which utilizes the intrinsic bending rigidity of DNA to exert weak pulling forces down to the entropic force limit. | Session 9: DNA and RNA Biophysics |
| 157 | First passage time study of DNA strand displacement | Cook, Alexander; Broadwater, Bo; Kim, Harold | Here, we describe a single-molecule FRET assay dubbed “fission” which allows us to study the first passage time of strand displacement directly. | Session 9: DNA and RNA Biophysics |
| 158 | Data-driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization | Zhang, Bin | We introduce a polymer model to study the organization of the diploid human genome: it is data-driven as all parameters can be derived from Hi-C data; it is also a mechanistic model since the energy function is explicitly written out based on a few biologically motivated hypotheses. | Session 9: DNA and RNA Biophysics |
| 159 | Field theories for density estimation on sequence space | Chen, Wei-Chia; Zhou, Juannan; Sheltzer, Jason; Kinney, Justin; McCandlish, David | We present a novel solution to this problem based on Bayesian field theory and spectral graph theory. | Session 9: DNA and RNA Biophysics |
| 160 | Observation of Stochastic Resonance in Transport of the DNA between Entropic Traps | Lame, Shayan | We describe a nanofluidic system in which stochastic resonance (SR) could be observed in the motion of single DNA molecules. | Session 9: DNA and RNA Biophysics |
| 161 | Anharmonic bending of DNA base-pair mismatches | Ryan, Michael; Jeong, Jiyoun; Lemos, Tony; Kim, Harold | We propose a simple anharmonic model for DNA mismatch bending, which would better serve to explain not only our data but also the bend-weakening seen in recent molecular dynamic simulations. | Session 9: DNA and RNA Biophysics |
| 162 | Mechanically bent DNA molecules as sensing amplifiers for probing interactions of DNA with metal ions and small organic molecules | Wang, Yong; Freeland, Jack; Zhang, Lihua; Wang, Shih-Ting; Ruiz, Mason | Here, we present our development of this concept of exploiting mechanical energies/forces to amplify the interactions between DNA and inorganic salts or small organic molecules. | Session 9: DNA and RNA Biophysics |
| 163 | Decoding DNA barcodes using a Cylindrical Nanopore | Bhattacharya, Aniket; Seth, Swarnadeep | We use Brownian dynamics simulation on a model coarse-grained dsDNA to estimate the marker (barcode) locations using the dwell time information. | Session 9: DNA and RNA Biophysics |
| 164 | Theory of the Overestimation of Protein-RNA Binding Energies obtained by Molecular Dynamics Simulations with Umbrella Sampling. | Gvildys, Zachary; Bruinsma, Robijn | We compare the theory with MD simulations of protein-RNA interactions and present a method to obtain binding free energy by the systematic application of constraints. | Session 9: DNA and RNA Biophysics |
| 165 | Polymer Single File Diffusion: A phase diagram | Wang, Hanyang; Slater, Gary | We propose a phase diagram describing different diffusion regimes. | Session 9: DNA and RNA Biophysics |
| 166 | Integrating double stranded RNA binding proteins into RNA secondary structure prediction | Shatoff, Elan; Bundschuh, Ralf | Here, we introduce a quantitative model that allows calculation of the effective affinity of dsRBPs to any RNA given a base affinity and the sequence of the RNA, while fully taking into account the entire secondary structure ensemble of the RNA. | Session 9: DNA and RNA Biophysics |
| 167 | Biophysics of centrosome separation and centrosome-nucleus association | KABACAOGLU, GOKBERK; Farhadifar, Reza; Fabig, Gunar; Yu, Che-Hang; Wu, Hai-Yin; Needleman, Daniel; Müller-Reichert, Thomas; Shelley, Michael | Three alternative models have been proposed: pushing forces between antiparallel overlapping microtubules from the two centrosomes, pulling forces from cortically-bound force generators, and pulling forces from nuclear-bound force generators. | Session 9: DNA and RNA Biophysics |
| 168 | Intrinsic Rashba coupling due to hydrogen bonding in DNA and Oligopeptides | Torres, Juan; Hidalgo, Raul; Varela, Solmar; Mujica, Vladimiro; Berche, Bertrand; Medina, Ernesto | Here we derive an analytical tight-binding Hamiltonian model for oligopeptides that contemplates both intrinsic SO and Rashba interaction induced by hydrogen bonding. | Session 9: DNA and RNA Biophysics |
| 169 | Deep Learning for Dynamical Systems | Brunton, Steven | In this talk, we will discuss several deep learning approaches to simultaneously discover coordinate transformations and parsimonious models of the dynamics. | Session 10: Data Science for Dynamical Systems and Real World Networks |
| 170 | The spectra of small-world random networks | Larson, Elizabeth; Kirst, Christoph; Vucelja, Marija | Here we present a practical tool to verify whether a network can be considered a small-world based on its eigenvalue spectrum properties. | Session 10: Data Science for Dynamical Systems and Real World Networks |
| 171 | Machine Learning for Partial Differential Equations | Brenner, Michael | I will discuss several ways in which machine learning can be used for solving and understanding the solutions of nonlinear partial differential equations. | Session 10: Data Science for Dynamical Systems and Real World Networks |
| 172 | Digital Twin: A Theorist’s Playground for APXPS and Surface Science | Qian, Jin; Crumlin, Ethan | As daunting as it sounds, I will explain the challenges along with the milestones: 1) developing physically accurate quantum chemistry methods that improve the numerical accuracy of XPS binding energy (BE) calculation; 2) realizing that a central piece of chemical reaction network (CRN) is universal in the chemical systems of interest, such as reactors and heterogeneous catalysis 3) sharing a user-friendly, natural chemical language syntax Digital Twin v.01 software package, which we welcome collaboration and feedback in any form. | Session 10: Data Science for Dynamical Systems and Real World Networks |
| 173 | TBA | Gonzalez, Marta | TBA | Session 10: Data Science for Dynamical Systems and Real World Networks |
| 174 | Cascading Failure From Targeted Road Network Disruptions | Vivek, Skanda | Guided by microscopic traffic simulations, we develop a theoretical framework for predicting the growth in cascading traffic jams around disruptions. | Session 10: Data Science for Dynamical Systems and Real World Networks |
| 175 | Experimental Realization of Reservoir Computing with Wave Chaotic Systems | Ma, Shukai; Antonsen, Thomas; Ott, Edward; Anlage, Steven | We propose unique techniques to create virtual RC nodes by both spectral and spatial perturbation. | Session 10: Data Science for Dynamical Systems and Real World Networks |
| 176 | Investment vs. reward in a competitive knapsack problem | Neumann, Oren; Gros, Claudius | Our goal is to investigate the balance between the metabolic costs of larger brains compared to the advantage they provide in solving general and combinatorial problems. | Session 10: Data Science for Dynamical Systems and Real World Networks |
| 177 | Max Delbruck Prize in Biological Physics (2021): From individual motion to group behavior: what regulates collective dynamics in natural swarms of insects | Giardina, Irene | I will discuss how, when modeling these systems starting from the data, three crucial ingredients must be incorporated in their theoretical description: activity, behavioral inertia, and mutual alignment. | Session 11: Delbruck Prize Symposium |
| 178 | Max Delbruck Prize in Biological Physics (2021): Equilibrium to off-equilibrium crossover in homogeneous active matter near its ordering transition | Cavagna, Andrea; Di Carlo, Luca; Giardina, Irene; Grigera, Tomas; Pisegna, Giulia | I will present simulations of the compressible Vicsek model in the homogeneous near-ordering regime and find that critical slowing down indeed changes with activity, displaying two exponents that are in good agreement with the RG prediction. | Session 11: Delbruck Prize Symposium |
| 179 | Hydrodynamics of collective cell migration: the good, the bad and the chiral | Giomi, Luca | In this talk, I will review our recent theoretical and experimental efforts towards modelling the collective motion of cells at the large scale using active hydrodynamics. | Session 11: Delbruck Prize Symposium |
| 180 | Flow, fluctuate and freeze: Epithelial cell sheets as soft active matter | Henkes, Silke | Soft and active matter provides a theoretical and computational framework to understand the mechanics and dynamics of these tissues. | Session 11: Delbruck Prize Symposium |
| 181 | Solvent vapor annealing of diblock copolymer thin films with a solvent mixture | Papadakis, Christine; Jung, Florian; Berezkin, Anatoly; Posselt, Dorthe; Smilgies, Detlef | We used a setup with two bubblers to investigate thin films from a cylinder-forming polystyrene- block-poly(dimethylsiloxane) (PS- b-PDMS) diblock copolymer in mixtures of the vapors of toluene, which is nearly non-selective for the PS matrix and the PDMS cylinders, and n-heptane, which is selective for PDMS [1]. | Session 12: Developments in Reflectivity for Thin Film Characterization |
| 182 | Introducing the CANDOR polychromatic reflectometer | Hoogerheide, David; Grutter, Alexander; Maranville, Brian; Majkrzak, Charles | In this talk, I will describe the instrument features of CANDOR and compare its performance to that of conventional reflectometers. | Session 12: Developments in Reflectivity for Thin Film Characterization |
| 183 | Characterization of anisotropic organic layered films by resonant soft x-ray reflectivity | Pasquali, Luca; Capelli, Raffaella; Bonfatti, Matteo; Mezzadri, Francesco; Galligani, Emanuele; Verna, Adriano; Ruocco, Alessandro; Mahne, Nicola; Nannarone, Stefano | In particular, we developed a protocol to get simultaneous quantitative information on the structure, interface morphology, chemical properties and optical anisotropies of layered organic materials with sub-nm depth resolution. | Session 12: Developments in Reflectivity for Thin Film Characterization |
| 184 | Probing Buried Interfaces in Polymers with Soft X-ray Reflectivity | Sunday, Daniel; Thelen, Jacob; Zhou, Chun; Ren, Jiaxing; Kline, R. Joseph; Nealey, Paul | This technique is applied to two systems of BCP multilayers with different affinities for a surface. | Session 12: Developments in Reflectivity for Thin Film Characterization |
| 185 | Development of spin-contrast-variation neutron reflectometry for structural analysis of multilayer films | Kumada, Takayuki; Akutsu, Kazuhiro; Miura, Daisuke; Suzuki, Jun-ichi; Torikai, Naoya | The spin-contrast-variation neutron reflectometry technique was developed for the structural analysis of multilayer films. | Session 12: Developments in Reflectivity for Thin Film Characterization |
| 186 | Information Content and Experimental Design in Neutron Reflectometry | Heinrich, Frank | We have introduced a quantitative framework to determine the gain in information from neutron reflectometry (NR) experiments using information theory and Bayesian statistics [1]. | Session 12: Developments in Reflectivity for Thin Film Characterization |
| 187 | Determining Lamellar Structure with Soft X-ray Reflectivity | Loo, Whitney; Feng, Hongbo; Sunday, Daniel; Nealey, Paul | We have devised a model block copolymer system to systematically tune χ through use of modular A- b-(B- r-C) copolymers. | Session 12: Developments in Reflectivity for Thin Film Characterization |
| 188 | Depth profiling molecular orientation with polarized resonant soft X-ray reflectivity | Ferron, Thomas; Thelen, Jacob; Bagchi, Kushal; Fiori, Marie; Ediger, Mark; DeLongchamp, Dean; Sunday, Daniel | Here we will discuss progress in developing polarized resonant soft X-ray reflectivity (P-RSoXR) for molecular orientation depth profiling in soft matter thin-films. | Session 12: Developments in Reflectivity for Thin Film Characterization |
| 189 | Probing interactions at the polymer thin film/substrate interface using Kelvin probe force microscopy | Wenderott, Jill; Dong, Ban; Amonoo, Jojo; Green, Peter | Here, we utilized Kelvin probe force microscopy (KPFM) to better understand interactions at the polymer thin film/substrate interface. | Session 12: Developments in Reflectivity for Thin Film Characterization |
| 190 | Hydrodynamic Interactions in Topologically Linked Ring Polymers | Rauscher, Phillip; Rowan, Stuart; De Pablo, Juan | We show that the symmetry of ring polymers leads to a hydrodynamic decoupling of ring dynamics. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 191 | Dynamics and rheology of bidisperse polymer melts through a simplified molecular model | Adeyemi, Oluseye; Xi, Li | In this study, we focused on bidisperse polymers of different compositions as an idealized model system and used a coarse-grained molecular model to explore their dynamics and rheology. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 192 | Recovery of stress overshoot under orthogonal shear after interrupted shear flow | Galvani, Marco; Olmsted, Peter; Robbins, Mark | Previous experimental work shows that melts subjected to interrupted shear flows exhibit a smaller overshoot when sheared again after allowing for some relaxation. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 193 | Predicting the plateau modulus from molecular parameters of conjugated polymers | Fenton, Abigail; Gomez, Enrique; Colby, Ralph | Using small angle neutron scattering, oscillatory shear rheology, in-situ polarized optical rheology, along with the freely rotating chain model, we have shown that twelve polymers with aromatic backbones, including conjugated polymers, populate a large part of this gap. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 194 | Model for flow-induced crystallization of industrial-grade LLDPEs | Andreev, Marat; Nicholson, David; Rutledge, Gregory; Kotula, Anthony; Kearns, Kenneth; Moore, Jonathan; den Doelder, Jaap | In this work, we combine information from atomistic molecular dynamics simulations, mesoscale slip-link modeling, rheo-Raman measurements and fast scanning chip calorimetry to build a model for flowing LLDPE melts undergoing crystallization. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 195 | Solvent-induced Collapse Transition in Kinetoplast DNA sheets | Holling, Dave; Klotz, Alexander | We aimed to observe the 2D version of the coil-globule transition by measuring diffusivity and radius of gyration of kinetoplasts as a function of ethanol concentration. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 196 | Dynamic transistion to isostaticity induces complex stress response in DNA nanostar networks | Conrad, Nathaniel; Bevier, Alexander; Fygenson, Deborah; Saleh, Omar | Here, we perform oscillatory rheology on networks made of 6-armed DNA nanostars (NS) whose designable interactions allow us to investigate the role of cross-linker lifetime on the complex stress response. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 197 | Local Hydrodynamics and Chain Architecture in Flowing Semidilute Polymer Solutions | Young, Charles; Sing, Charles | We developed an iterative conformational-averaging (CA) method for performing these calculations, circumventing a number of computational bottlenecks to enable the large-scale simulation of polymer solutions in flow. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 198 | Macromolecular engineering of pinching dynamics, extensional rheology and processability | Sharma, Vivek; Dinic, Jelena; Jimenez, Leidy; Martinez, Carina | We distill out how length, diameter and number of Kuhn segments affects macromolecular dynamics, rheological response and processability, and infer that the ratio of packing length to Kuhn length, a parameter we term as segmental dissymmetry, helps to hone in on the contrast related to flexibility and extensibility, that are determined by chemical structure for macromolecules comparable molecular weight. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 199 | Dynamics and Rheology of Polymers and Polyelectrolytes | Vermant, Jan | Dynamics and Rheology of Polymers and Polyelectrolytes | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 200 | Heterogeneous Rouse Model for Polymer Dynamics and Linear Rheology in the Time-Temperature-Superposition-Breakdown Regime | Simmons, David; Yu, Peijing | The Heterogeneous Rouse Model predicts a compression of the Rouse regime in complex and relaxation moduli with increasing dynamic heterogeneity at lower temperatures. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 201 | Crossover from Rouse to entangled polyisoprene dynamics: a multiscale simulation approach | Li, Wei; Behbahani, Alireza; Burkhart, Craig; Polinska, Patrycja; Harmandaris, Vagelis; Doxastakis, Manolis | The crossover from the low molecular limit described by the Rouse model to dynamics prescribed by entanglements has long been the subject of extensive research with significant challenges present. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 202 | Crossover from Rouse to Reptation Dynamics in Salt-Free Polyelectrolyte Complex Coacervates | Yu, Boyuan; Rauscher, Phillip; Jackson, Nicholas; Rumyantsev, Artem; De Pablo, Juan | A central question is whether the classical Rouse and reptation models can be applied to these systems. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 203 | Chain models for the simulation of polyelectrolytes in combination of flow and electric fields | Gulati, Shreyash; Setaro, Angelo C.; Underhill, Patrick | We use chain models to overcome this problem. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 204 | Fast Dynamics and its Role in Conductivity of Polymerized Ionic Liquids | bocharova, Vera; Genix, Anne-Caroline; Osti, Naresh; Mamontov, Eugene; Sokolov, Alexei | In this work, we provide new insights into the roles of various microscopic parameters controlling ion transport in these polymers, which are crucial for their rational design and practical applications. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 205 | Shear Response of THF Swollen Ionic Polymer Melts: Molecular Dynamics Simulations Study | Meedin, Shalika; Senanayake, Manjula; Mohottalalage, Supun; Kosgallana, Chathurika; Perahia, Dvora; Grest, Gary | We find that the shear viscosity is higher for the polyelectrolyte regime compared with ionomer one, due to large continuous ionic assemblies in polyelectrolytes. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 206 | Dynamics of liquid coacervates: Higher charged density polyelectrolytes are in entangled semiflexible regime | Aponte-Rivera, Christian; Rubinstein, Michael | Here, we consider the case in which the electrostatic persistence length of the high charge density polymer is larger than the diameter of a confining tube by low charge density polymers. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 207 | A critical Assessment of Linear Viscoelasticity and Time-Temperature-Salt and Other Superpositions in Polyelectrolyte Coacervates | Larson, Ronald; Liu, Ying; Li, Huiling | A critical Assessment of Linear Viscoelasticity and Time-Temperature-Salt and Other Superpositions in Polyelectrolyte Coacervates | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 208 | Molecular Basis for Elasticity and Viscoelasticity in Chitosan-Surfactant Hydrogels | Gotla, Suhas; Matysiak, Silvina | In this work, we employ multiscale molecular dynamics to identify the molecular phenomena that underpin these distinct mechanical behaviours. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 209 | Nonlinear Elongation Flows Effects on Aggregation in Associating Polymer Melts | Mohottalalage, Supun; Senanayake, Manjula; O’Connor, Thomas; Grest, Gary; Perahia, Dvora | Here, we use molecular dynamics (MD) simulations of bead-spring chains to identify how associating groups alter the structure and dynamics of linear polymer melts in uniaxial elongation flows. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 210 | Determination of the Number-Average Molecular Weight of Polyelectrolytes | Han, Aijie; Uppala, Shravan; Madsen, Louis; Colby, Ralph | We developed four methods using the chain dynamics in the semidilute unentangled regime to determine the number-average molecular weight (M n) of polyelectrolytes. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 211 | Rheology and Pinching Dynamics of Polyelectrolyte Solutions | Jimenez, Leidy; Martinez, Carina; Dinic, Jelena; Sharma, Vivek | Here focus on the characterization of capillary thinning and pinch-off dynamics, extensional rheology and printability of two model systems: sodium (polystyrene sulfonate) and poly(acrylic acid) by using dripping-onto-substrate (DoS) rheometry technique. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 212 | Effect of counterion and solvent type on the scattering and rheology of polyelectrolyte solutions | Gulati, Anish; Lopez, Carlos; Richtering, Walter | Here we use Small-Angle neutron Scattering (SANS) and rheology to study solutions of carboxymethyl cellulose (CMC) with different counterions of varying size and hydrophobicity in aqueous and organic media. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 213 | Polyelectrolyte solutions in complex macro- and micro-scale flows | Metaxas, Athena; Panwar, Vishal; Dutcher, Cari | In this study, a cationic polyacrylamide was used to modify the elasticity of the solution, and with varying concentrations of NaCl to alter the ionic strength of the solution. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 214 | Dynamic mechanical response of solid polyelectrolyte complexes at varying temperature, humidity and pH | Lalwani, Suvesh; Lutkenhaus, Jodie | Here, we describe the dynamic mechanical behavior of PAA-PAH solid PECs at different pH values, hydration and temperature. | Session 13: Dynamics and Rheology of Polymers and Polyelectrolytes |
| 215 | Three Pillars to Stochastic Control: Autoregulation, Noise and Feeback | May, Michael; Munsky, Brian | We explore how an “Optogenetic Maxwell Demon” could selectively amplify noise to control multiple cells using single-input-multiple-output (SIMO) feedback. | Session 14: Dynamics of Gene Regulation |
| 216 | A Generalized Langevin Approach to Modeling Protein Migration | Bailey, Alana; Stanton, Liam | Here, we propose a generalized Langevin model to describe the migration of KRas (and other proteins) along the membrane, thus mitigating many of the computational constraints of traditional MD simulations. | Session 14: Dynamics of Gene Regulation |
| 217 | Stochastic transcription-error correction by backtracking and repelling RNA polymerases | Zuo, Xinzhe; Chou, Tom | We derive analytic solutions for a stochastic model that allows for locally interacting RNAPs to explicitly show how a trailing RNAP influences the probability that an error is corrected or incorporated by the leading backtracking RNAP. | Session 14: Dynamics of Gene Regulation |
| 218 | Restricted mobility and jamming of densely packed DNA exiting a viral capsid | Fizari, Mounir; Keller, Nicholas; Smith, Douglas | At DNA packing densities higher than ~0.3 g/ml, we observe a sharp decrease in exit velocity, highly heterogenous dynamics, and long pauses. | Session 14: Dynamics of Gene Regulation |
| 219 | Switch-like mRNA localization to mitochondria arises from nonequilibrium protein translation effects | Brown, Aidan; Garcia-Arceo, Ximena; Tsuboi, Tatsuhisa; Zid, Brian; Koslover, Elena | To understand the distinct localization behaviours for mRNA of nuclear-encoded mitochondrial genes, we use a quantitative model of mRNA diffusion around the cell, protein translation along mRNA, and nascent polypeptide tethering. | Session 14: Dynamics of Gene Regulation |
| 220 | Live measurements of transcriptional bursting and dynamic gene regulation in early fly embryos | Chen, Po-Ta; Zoller, Benjamin; Levo, Michal; Gregor, Thomas | We have developed an optimized two-photon microscope to measure real-time gene activity in early fly embryos. | Session 14: Dynamics of Gene Regulation |
| 221 | A computational framework to study single-molecule canonical and non-canonical translation dynamics. | Aguilera, Luis; Raymond, William; Koch, Amanda; Lyon, Kenneth; Morisaki, Tatsuya; Stasevich, Timothy; Munsky, Brian | Here, we combine fluorescence microscopy and stochastic modeling to study canonical and non-canonical ribosomal translation processes. | Session 14: Dynamics of Gene Regulation |
| 222 | Rationalizing the abundance statistics of feed-forward loop motifs: an evolutionary strategy mediated by control on fluctuations | Momin, Md; Biswas, Ayan | We construct a theoretical framework hypothesizing the rationale behind this phenomenon. | Session 14: Dynamics of Gene Regulation |
| 223 | Diffusiophoresis of passive particles in the presence of protein patterns | Goychuk, Andriy; Ramm, Beatrice; Khmelinskaia, Alena; Blumhardt, Philipp; Eto, Hiromune; Ganzinger, Kristina; Schwille, Petra; Frey, Erwin | To answer this question, we combined theory and experiment, and have shown that this transport phenomenon originates from diffusiophoresis. | Session 14: Dynamics of Gene Regulation |
| 224 | Jamming-free crowded transport through the nuclear pore complex | Zheng, Tiantian; Gu, Chad; Zilman, Anton | We show that the regime of jamming-free transport is possible if (and only if) FG nups within the NPC are spatially arranged into “vestibule” and “barrier” regions, as previously suggested by experiments. | Session 14: Dynamics of Gene Regulation |
| 225 | Using genetic data to predict clinical outcomes in emergent antibody therapies against HIV. | LaMont, Colin | We can use this analysis to determine how many different antibodies would be needed to successfully prevent the emergence of HIV resistance. | Session 14: Dynamics of Gene Regulation |
| 226 | Estimating the Role of Active Matter and Population Genetic Dynamics in Enhancing Antibiotic Resistance in Expanding Bacterial Colonies via Lattice Simulations | Gonzalez, Jimmy; Beller, Daniel; Gopinath, Arvind | In this work, we employ 2D lattice models combing population genetics and hydrodynamic interactions to study the effects of active matter dynamics on genetic structure in bacterial colonies, as well as statistically characterize the role that mixing, genetic drift, cell motility, and mutation have on the emergence of antibiotic resistance in active bacterial populations. | Session 14: Dynamics of Gene Regulation |
| 227 | Trading bits in the readout from a genetic network | Bauer, Marianne; Bialek, William; Gregor, Thomas; Petkova, Mariela; Wieschaus, Eric | We explore this trading between bits of precision in measuring concentration and bits of relevant information that can be extracted, using the gap gene network in the early fruit fly embryo as an example. | Session 14: Dynamics of Gene Regulation |
| 228 | Top-down analysis of gene-regulatory networks using global coordination method | Atias, Eyal; Amit, Guy; Bashan, Amir | Here, we systematically analyse the performance and limitations of the GCL using real and simulated gene expression data. | Session 14: Dynamics of Gene Regulation |
| 229 | Influence of controlled ionic conductivity on melt electrospinning of polyethylene | Sheoran, Neelam; Boland, Brenton; Thornton, Samuel; Gorga, Russell; Bochinski, Jason; Clarke, Laura | We discuss results from two commercial formulations of linear low-density polyethylene as a function of additive concentration and correlate changes in fluid properties with the time to first fluid perturbation, the number of jets, the capillary length (due to the electric force), the cone and jet sizes and the resulting fiber diameter. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 230 | Using Multiplexed Electrosprays To Manipulate Fluids and (soft) Materials | Gomez, Sandro | Using fluid mechanics and electrostatics, we a) developed criteria for compact multiplexing to increase flow rate drastically, b) microfabricated systems with high packing densities (1.1 10 4 sources/cm 2), reducing the cost per electrospray source, and c) demonstrated successful operation of these devices in the synthesis of (soft) materials (e.g., polymer nanoparticles of controlled shape for drug delivery and battery materials) and in microchip cooling. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 231 | Finite Element Method Modeling of Self-Limiting Electrospray Deposition | Nachtigal, Catherine; Kovacevich, Dylan; Lei, Lin; Singer, Jonathan | To model the SLED process, COMSOL was used to create a model of the spray needle, target, and electric field, creating a particle trace representing the spray. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 232 | Self-limiting electrospray deposition to create bioactive coating | Park, Sarah; Lei, Lin; Lallow, Emran; Nachtigal, Catherine; Lin, Hao; Singer, Jonathan | Here, I will discuss opportunities to create bioactive conformal coatings on medically-relevant architectures with blending, self-assembly, and complex geometries. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 233 | The Influence of Charge Injection on Melting Gels Delivered via Electrospray Deposition | Grzenda, Michael; Gamboa, Arielle Marie; Lei, Lin; Mercado, James; Samateh, Alfusainey; Klein, Lisa; Jitianu, Andrei; Singer, Jonathan | The Influence of Charge Injection on Melting Gels Delivered via Electrospray Deposition | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 234 | Stability limit of droplets in combined fields | Beroz, Justin; Hart, A. John; Bush, John | Here we present the experimental results for a droplet’s stability limit under combined electrostatic and gravitational fields – a nonlinear system in which the droplet takes various non-elementary shapes at different combined field strengths. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 235 | The transition from induced charge electroosmotic flow to electrothermal flow in a constriction microchannel | Malekanfard, Amirreza; Liu, Zhijian; Xuan, Xiangchun | We present a combined experimental and numerical study of the transition from the induced charge electroosmotic flow in a low-conductivity fluid to the electrothermal flow in a high-conductivity fluid. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 236 | Using Electrohydrodynamic Deposition for In-Space Manufacture of Perovskite Solar Cells | Erickson, Samuel; Delmas, William; DiBenedetto, Albert; McMillon-Brown, Lyndsey; Peshek, Timothy; Ghosh, Sayantani | We have developed a thin film preparation technique utilizing electrohydrodynamic deposition (EHD) for in situ fabrication of photovoltaic (PV) devices during space missions. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 237 | Electrohydrodynamic Thermal Oscillators for Waste Heat Harvesting Applications | Ma, Tianxing; Dsouza, Darrel; Ryerson, Kyrsten McKenzie; Signorelli, Matthew; Singer, Jonathan; Zhong, Mingjiang; Loewenberg, Michael; Osuji, Chinedum | This work attempts to design and test the efficiency of a novel liquid-based thermal oscillator, which utilizes periodic electrohydrodynamic (EHD) capillary bridging and debridging between two coaxial droplets in a parallel plate capacitor under an electric field. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 238 | Dynamic Modulation of Dielectrophoretic Force Using Resonant Feedback | Padhy, Punnag; Zaman, Mohammad; Jensen, Michael; Hesselink, Lambertus | To overcome this problem, we propose to connect the trap electrodes in series with an external resistor and an inductor to form a resonant RLC circuit. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 239 | Interfacial and bulk assembly of ellipsoidal microparticles under the influences of external electric fields | Trevenen, Samuel; Beltramo, Peter | This talk will present recent work using Mirau Interferometry to accurately map the interfacial deformation around polymer microellipsoids pinned to an air-water interface under various external fields. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 240 | Interfacial Tension Hysteresis in Oxidizing Eutectic Gallium-Indium | Hillaire, Keith; Song, Minyung; Kiani, Abolfazl; Rashid-Nadimi, Sahar; Dickey, Michael; Daniels, Karen | We examine the interfacial tension’s dependence on voltage, voltage sweep rate and direction, and on time, and present a model of the droplet’s surface free energy as dependent on charge density and molecular composition of the interface to describe the voltage history dependence of the interfacial tension. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 241 | Electrospray Deposition of Polyimide with Passive Material Focusing | Kingsley, Bryce; Pawliczak, Emma; Hurley, Thomas; Chiarot, Paul | Electrospray Deposition of Polyimide with Passive Material Focusing | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 242 | Linking electrostatic charging profiles to patterns on peeled tape | Reiter, Mary; Shinbrot, Troy | We contextualize these findings within industry and nature and describe new avenues for this field. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 243 | Measuring charge loss in acoustically-levitated, airborne materials | McGrath, Jake; Mendez, Joshua; Huang, Tianshu; Harvey, Dana; Burton, Justin | Now, we have constructed an acoustic levitation device capable of suspending dense materials such as copper. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 244 | Nanosheets and Hydrogels of Self-assembled 2-nm Metal-Organic Cages with Electrostatic interaction | Yang, Yuqing; Rehak, Pavel; Xie, Ting-Zheng; Feng, Yi; Sun, Xinyu; Chen, Jiahui; Li, Hui; Král, Petr; Liu, Tianbo | We report a hydrogel formation process from 2-nm emissive, low molecular-weight metal-organic cages at low concentrations (>15 mg/mL) based on counterion-mediated attraction, π-π/hydrophobic interactions as well as σ-π interactions. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 245 | Capture of semi-flexible polyelectrolytes by a Nanopore: A Lattice Boltzmann Simulation Study | Qiao, Le; Slater, Gary | In this talk, we compare LD results to those obtained when Hydrodynamic Interactions (HI) and explicit salt are added. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 246 | Coarse grained modeling of ion transport through a hydrophobic nanopore | Gubbiotti, Alberto; Tinti, Antonio; Camisasca, Gaia; Giacomello, Alberto | Based on the data from RMD simulations, we developed a coarse grained model for the dynamics of the water inside the pore and computed the conductivity of both ions as a function of the number of water molecules inside the pore. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 247 | Exact polarization energy for contacting dielectrics | Lian, Huada; Qin, Jian | We propose a parameterized form of the electrostatic energy, which generalizes the known logarithmic singularity for conductors to dielectrics. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 248 | Electro-optic demonstration of ferroelectricity in the thermotropic nematic liquid crystal DIO | MacLennan, Joseph; Chen, Xi; Korblova, Eva; Glaser, Matthew; Walba, David; Clark, Noel | In the search for additional ferroelectric nematic liquid crystals, we studied the liquid crystal DIO, which was previously reported to be ferroelectric-like [2]. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 249 | Electro-optic response of a spontaneously twisted ferroelectric nematic structure in an anti-parallel rubbed cell | Chen, Xi; Korblova, Eva; Shao, Renfan; Glaser, Matthew; MacLennan, Joseph; Walba, David; Clark, Noel | Here we report an N F twist structure with two possible chiralities stabilized by polar anchoring at the cell surfaces that forms spontaneously in anti-parallel rubbed cells. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 250 | Advanced material science of clay minerals: from capture of carbon dioxide to non-iridescent structural coloration. | Fossum, Jon Otto | Advanced material science of clay minerals: from capture of carbon dioxide to non-iridescent structural coloration. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 251 | How Electrostatic Interactions Determine the Shape of Chiral Assemblies | Mccourt, Joseph; Kewalramani, Sumit; Valencia, Dulce; Gao, Changrui; Bedzyk, Michael; Olvera De La Cruz, Monica | We combine in situ small-/wide-angle X-ray scattering (SAXS/WAXS), cryo-transmission electron microscopy (TEM) and atomic force microscopy (AFM) to analyze the self-assembly of charged chiral amphiphiles consisting of an amino acid (lysine) head group coupled to alkyl tails (C n=12,14,16). | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 252 | A new scaling theory for polyelectrolyte brushes | Chen, Guang; Stone, Howard | In this work, we introduce new scaling laws for the brush height H as a function of the grafting density σ, salt concentration c s, and charge fraction φ, by employing a cell model to provide a detailed analysis of the electrostatic interactions between the charged monomers and mobile ions based on the Poisson-Boltzmann theory. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 253 | Electro-optic study of the phase behavior of mixtures of two ferroelectric nematic liquid crystals | Zhu, Zhecong; Park, Cheol; Chen, Xi; Korblova, Eva; Glaser, Matthew; MacLennan, Joseph; Walba, David; Clark, Noel | We have shown previously that the second nematic phase (N F) of the thermotropic liquid crystal RM374 is ferroelectric [1]. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 254 | Electrophoretic mobility of highly charged macroions in aqueous electrolytes with multivalent coions | Guerrero-Garcia, Guillermo; Gonzalez-Tovar, Enrique | In order to determine if such a dominance can be observed dynamically, in this work we study the electrophoretic mobility of highly charged spherical colloids immersed in several 1:z electrolytes, when the counterions have the same properties. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter |
| 255 | Lessons from molecular evolution: from origin of life to phage-based nanomaterials | Chen, Irene | I will present our work examining the effect of encapsulation inside protocells and the role of chance during RNA evolution. | Session 16: Evolution of Cellular Complexity |
| 256 | Our evolving view of cell motility | Fritz-Laylin, Lillian | We use this approach to predict alpha-motility in the amphibian-killing chytrid fungus Batrachochytrium dendrobatidis, a prediction we have verified using microscopy and small molecule inhibitors of actin cytoskeletal components. | Session 16: Evolution of Cellular Complexity |
| 257 | The role of large-scale gene duplication in the evolution of the eukaryotic membrane traffic system | Thattai, Mukund; Purkanti, Ramya; Laxman, Sunil | Biophysical and phylogenetic analyses suggest that the evolution of organelles with new compositions requires gene family expansion. | Session 16: Evolution of Cellular Complexity |
| 258 | Drift, Mutation, and the Origin of Cellular Features | Lynch, Mike | Drift, Mutation, and the Origin of Cellular Features | Session 16: Evolution of Cellular Complexity |
| 259 | The evolution of cell division: from archaea to eukaryotes | Baum, Buzz | In this talk, by looking at features of the cell division machinery that we (eukaryotes) share with our cellular relatives, the archaea, we will attempt to shed light on the origins of our cell division machinery. | Session 16: Evolution of Cellular Complexity |
| 260 | Dynamics of growth, death, and resource competition in sessile organisms | Lee, Edward; Kempes, Christopher; West, Geoffrey | We build on a minimal dynamical model of metabolic growth where the tension between individual growth and mortality determines population size distribution. | Session 17: Evolutionary and Ecological Dynamics |
| 261 | Emerging spatio-temporal patterns in cyclic predator-prey systems with habitats | Mir, Hana; Stidham, James; Pleimling, Michel | In this study, we analyze a structured heterogeneous system which gives one species an advantage to escape predation in an area, we refer to as a habitat, and study the effect on species coexistence and spatio-temporal patterns. | Session 17: Evolutionary and Ecological Dynamics |
| 262 | Universality classes for fixation-time distributions in stochastic evolutionary games | Hathcock, David; Strogatz, Steven | Stochastic models in evolutionary biology and ecology are often described by birth-death dynamics where absorption times are the key quantity of interest: how long does it take for a mutation to become fixed or for a fluctuating population to go extinct? | Session 17: Evolutionary and Ecological Dynamics |
| 263 | Differences in bacteria killing rates are mitigated by finite size effects | Copeland, Raymond; Yunker, Peter | To determine the impact of finite size effects on deadly competitions within biofilms, we perform individual based simulations of bacteria confined to different sized environments. | Session 17: Evolutionary and Ecological Dynamics |
| 264 | Improve it or lose it: evolvability costs of competition for expression | Moran, Jacob; Finlay, Devon; Tikhonov, Mikhail | Using a minimal model to study this in the context of a changing environment, we demonstrate that one unexpected consequence of such a feedback loop is that a slow switch to a new environment can allow genomes to reach higher fitness sooner than direct exposure. | Session 17: Evolutionary and Ecological Dynamics |
| 265 | Population boundary across an environmental gradient: Effects of quenched disorder | Kovacs, Istvan; Juhasz, Robert | Here, we capture the effects of quenched heterogeneities on the ecological boundary with the disordered contact process in one and two dimensions with a linear spatial trend in the local control parameter. | Session 17: Evolutionary and Ecological Dynamics |
| 266 | Fluctuations in population density change topology of genealogical trees in range expansions | Birzu, Gabriel; Hallatschek, Oskar; Korolev, Kirill | Here, we show that different growth dynamics lead to qualitative changes in the topology of genealogies at the front. | Session 17: Evolutionary and Ecological Dynamics |
| 267 | Self-Organization of Lifelike Behaviors | England, Jeremy | In this talk, we will report recent progress in understanding what physical conditions are required for the spontaneous emergence of these various lifelike behaviors from assemblages of simple, interacting components. | Session 17: Evolutionary and Ecological Dynamics |
| 268 | Modeling the ecology of parasitic plasmids | Lopez, Jaime; Wingreen, Ned; Donia, Mohamed | We propose that this tragedy of the commons is averted by selection between competing populations and demonstrate this effect in a metapopulation model. | Session 17: Evolutionary and Ecological Dynamics |
| 269 | Inducing stable spiral structures and population diversity in the asymmetric May–Leonard model | Serrao, Shannon; Tauber, Uwe | We qualitatively describe the spiral stabilization in the asymmetric patch down to the injection of periodic wavefronts from the adjacent symmetric region. | Session 17: Evolutionary and Ecological Dynamics |
| 270 | Transition states of two-cycle ecological oscillators: Blume-Capel representation | Nareddy, Vahini Reddy; Machta, Jonathan; Abbott, Karen; Esmaeili-Wellman, Shadi Sadat; Hastings, Alan | We model the spatially-extended ecological systems with coupled lattice maps in two-cycle regime and represent them with the Blume-Capel model. | Session 17: Evolutionary and Ecological Dynamics |
| 271 | Time-Dependent Effective Sampling Bias in Populations with Broad Offspring Number Distributions | Okada, Takashi; Hallatschek, Oskar | Here, we establish several new scaling relations about the fixation probability, the extinction time, the allele-frequency fluctuations, and the site frequency spectrum, when offspring numbers are distributed according to a fat-tailed distribution with a divergent variance (1/u α+1 with 1<α<2). | Session 17: Evolutionary and Ecological Dynamics |
| 272 | Playing it safe: information constraints bias living systems towards less risky strategies | Fleig, Philipp; Balasubramanian, Vijay | We argue that strategies employed by organisms are fundamentally probabilistic, and define a probability of survival in terms of a distance measure between an organism’s strategy and the statistics of the environment. | Session 17: Evolutionary and Ecological Dynamics |
| 273 | Inferring the effects of mutations on SARS-CoV-2 transmission | Lee, Brian; Ahmed, Syed; Finney, Elizabeth; Quadeer, Ahmed; Sohail, Saqib; Mckay, Matthew; Barton, John | Here we develop a model for disease spread in a localized population that accounts for both the possibility of a long tailed distribution for the number of people infected by a single individual, and that pathogen genetic variation may affect the probability of transmission, i.e., transmission fitness. | Session 17: Evolutionary and Ecological Dynamics |
| 274 | Stochastic birth of de novo genes | Mani, Somya; Tlusty, Tsvi | Through this study, we aim to infer the relationship between the mutational and epigenetic dynamics at intergenic regions, and the probability and timing of gene birth in natural populations. | Session 17: Evolutionary and Ecological Dynamics |
| 275 | Power-Law Memory in Living Species and the Distribution of Lifespans | Edelman, Mark; Jacobi, Rachel | Models with power-law memory may explain the observed decrease at very large ages of the rate of increase of the force of mortality and they imply limited lifespans. | Session 17: Evolutionary and Ecological Dynamics |
| 276 | Curvature Driven Dynamics in Ecological Coupled Lattice Maps | Shneer, Tom; Machta, Jonathan | In this talk, we will demonstrate that these two systems share two properties, both of which have been well studied in the zero temperature Ising model [2,3,4]: (1) both evolve with curvature driven dynamics and, (2) both freeze into final states with probabilities agreeing reasonably well with predictions from percolation theory. | Session 17: Evolutionary and Ecological Dynamics |
| 277 | Noise-induced versus intrinsic oscillations in ecological systems | Esmaeili-Wellman, Shadi Sadat; Hastings, Alan; Abbott, Karen; Machta, Jonathan; Nareddy, Vahini Reddy | We numerically investigated the dynamics of coupled, noisy oscillators, as we slowly change the parameter from the steady state to the two-cycle regime. | Session 17: Evolutionary and Ecological Dynamics |
| 278 | Population Extinction on a Random Fitness Seascape | Ottino-Loffler, Bertrand; Kardar, Mehran | We explore the role of stochasticity and noise in the statistical outcomes of commonly studied population dynamics models within a space-independent (mean-field) perspective. | Session 17: Evolutionary and Ecological Dynamics |
| 279 | A simple metabolic architecture allows near-optimal adaptation to rapidly fluctuating environments | Landmann, Stefan; Holmes, Caroline; Tikhonov, Mikhail | Here, we use a model of metabolism to show that a simple generalization of a ubiquitous regulatory motif (end-product inhibition) is sufficient both for learning complex continuous-valued features of the environment and for translating this information into predictive behavior; moreover, it accomplishes these tasks near-optimally. | Session 17: Evolutionary and Ecological Dynamics |
| 280 | Effects of demographic stochasticity on eco-evolutionary dynamics and trait-space patterning of complex communities | Wu, Jim; Mehta, Pankaj; Schwab, David | Within this model, we explore the factors that determine the evolutionary fate of the ecosystem. | Session 17: Evolutionary and Ecological Dynamics |
| 281 | A pandemic risk model for viruses | Doelger, Julia; Kardar, Mehran; Chakraborty, Arup | We investigate the pandemic risk for different viral types, using an analytical model. | Session 17: Evolutionary and Ecological Dynamics |
| 282 | Antagonism between toxin-secreting yeast strains as an experimental model for biological nucleation dynamics | Giometto, Andrea; Nelson, David; Murray, Andrew | We developed mathematical models that predict the experimental population dynamics of antagonistic competition in both well-mixed and spatially structured populations. | Session 17: Evolutionary and Ecological Dynamics |
| 283 | Optimal evolutionary control for artificial selection on molecular phenotypes | Nourmohammad, Armita; Eksin, Ceyhun | Here, we propose a feedback control formalism to devise globally optimal artificial selection protocol to direct evolution of molecular phenotypes. | Session 17: Evolutionary and Ecological Dynamics |
| 284 | Transitions in body wave dynamics in lizards with varying body and limb proportions | Chong, Baxi; Erickson, Eva; Goldman, Daniel; Bergmann, Philip | Here we studied the locomotion patterns of three species of Brachymeles skinks ( B. kadwa with effective hind leg lengths (HLL)=0.17 relative to snout-vent length (SVL) , B. taylori with HLL= 0.15 SVL , and B. mungtingkamay with the HLL=0.09 SVL) and compared them with stereotypical lizards, Uma scoparia (HLL=0.33 SVL) and Callisaurus draconoides (HLL=0.44 SVL), and an almost legless lizard, Lerista praepedita. | Session 17: Evolutionary and Ecological Dynamics |
| 285 | Balancing spatial heterogeneity and migration to slow the evolution of resistance in a bacterial pathogen. | Huynh, Anh; Sharma, Anupama; De Jong, Max; Wood, Kevin | In this work, we combine lab evolution experiments in spatially connected, computer-controlled chemostats with mathematical models to investigate resistance evolution in E. faecalis, an opportunistic bacterial pathogen. | Session 17: Evolutionary and Ecological Dynamics |
| 286 | Maintaining unused traits by interconnecting trait networks | Kingma, Enzo; Laan, Liedewij | We found that in both environments, repair of the cell polarity defect was accompanied by a better ability to perform diauxic growth. | Session 17: Evolutionary and Ecological Dynamics |
| 287 | Evolution of collective predator evasion: Putting the criticality hypothesis to the test | Klamser, Pascal; Romanczuk, Pawel | Complex systems theory predicts that collective information processing becomes optimal at the border between order and disorder, i.e. at a critical point. | Session 17: Evolutionary and Ecological Dynamics |
| 288 | The fitness landscapes of translation | Josupeit, Mario; Krug, Joachim | Motivated by recent experiments on an antibiotic resistance gene, in this work we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. | Session 17: Evolutionary and Ecological Dynamics |
| 289 | Fluctuation relations and universal constraints on divisions, growth and fitness in lineage trees | Genthon, Arthur; Lacoste, David | We construct a pathwise formulation of a growing population of cells, based on two samplings of the lineages within the population, namely the forward and backward samplings. | Session 17: Evolutionary and Ecological Dynamics |
| 290 | Fitness inference from deep mutational scanning data | Hong, Zhenchen; Barton, John | Here, we combined methods from statistical physics and population genetics to interpret the functional effects of mutations from DMS data. | Session 17: Evolutionary and Ecological Dynamics |
| 291 | Influence of State Reopening Policies in COVID-19 Mortality | Moreno, Juana; Walker, Nicholas; Tam, Ka-Ming | To address this question, we compare the hypothetical case in which the mitigation measures are left intact to the actual data. | Session 17: Evolutionary and Ecological Dynamics |
| 292 | Does selfish runaway or cohesive movement of the entire prey swarm be favourable to escape a predator attack? | Chakraborty, Dipanjan; De, Rumi | Using a simple particle-based model, incorporating the essential attractive and repulsive interactions between the prey and the predator, we investigate the effect of cooperative interactions on the survival chances of a prey swarm attacked by a nearby predator. | Session 17: Evolutionary and Ecological Dynamics |
| 293 | Quasi-strategies in evolutionary games | Adami, Chris | The theory can be extended to describe stochastic strategies and predicts that the stable stochastic strategy is determined by probabilities that reflect the corresponding mixture of deterministic strategies. | Session 17: Evolutionary and Ecological Dynamics |
| 294 | Ruggedness of ecological landscapes informs community optimization | George, Ashish; Korolev, Kirill | We investigate how the success of a heuristic search for the optimal combination of microbes depends on community ecology. | Session 17: Evolutionary and Ecological Dynamics |
| 295 | Synergistic effects of nitrogen and phosphorous on the growth of algal cells reveled by a microfluidic platform | Liu, Fangchen; Yazdani, Mohammad; Wagner, Nicole; Ahner, Beth; Wu, MingMing | In this presentation, we studied the growth of a model algal strain, Chlamydomonas reinhardtii, under a dual concentration gradient of nitrogen (N) and phosphorous (P) and found that N and P synergistically promoted algal cell growth. | Session 17: Evolutionary and Ecological Dynamics |
| 296 | Closed microbial communities self-organize to persistently cycle carbon | Kuehn, Seppe; de Jesús Astacio, Luis; PRABHAKARA, KAUMUDI; Li, Zeqian; Mickalide, Harry | We develop a new technique for quantifying carbon cycling in hermetically sealed microbial communities and show that CES comprised of an alga and diverse bacterial consortia self-organize to cycle carbon. | Session 17: Evolutionary and Ecological Dynamics |
| 297 | Self-organization and criticality in species-rich metacommunities | Denk, Jonas; Hallatschek, Oskar | For global coupling we derive a mean field theory that yields analytic expressions for the species abundances. | Session 17: Evolutionary and Ecological Dynamics |
| 298 | Abundance transitions in multispecies stochastic Lotka-Volterra | Rothschild, Jeremy; Leibovich, Nava; Zilman, Anton; Goyal, Sidhartha | Neutral theories of biodiversity assume that all individuals are functionally identical regardless of the species, whereas symmetrical non-neutral (i.e “niche”) theories forego the assumption of equivalent individuals and distinguish solely between self and non-self interactions. | Session 17: Evolutionary and Ecological Dynamics |
| 299 | Interplay between phenotypic variability and population genetics in bacteria | Jafarpour, Farshid; Levien, Ethan | In this talk, we discuss what aspects of variability in growth and divisions of single cells affect population genetics and are in turn under selection pressure. | Session 17: Evolutionary and Ecological Dynamics |
| 300 | Robust heritability of collective traits via the maximum entropy principle | Day, Thomas; Zamani Dahaj, Seyed Alireza; Ratcliff, William; Yunker, Peter | Here, we propose that stochasticity supplied by random cell division can directly lead to highly heritably group traits. | Session 17: Evolutionary and Ecological Dynamics |
| 301 | Coalescent trees in the oceans | Pigolotti, Simone; Villa Martin, Paula | In this talk, I will introduce a spatial coalescence model that predict the impact of oceanic turbulence on the diversity of these communities. | Session 17: Evolutionary and Ecological Dynamics |
| 302 | To die or not to die: Cell decision-making in the face of viral threat | Oyler-Yaniv, Jennifer | We show that the activation of antagonistic pathways changes the properties of cell fate decision transitioning cells from a “slow and accurate” to “fast and error-prone” decision mode. | Session 18: Immune Sensing and Response |
| 303 | A data-driven model for somatic hypermutation of B-cell | Spisak, Natanael; Walczak, Aleksandra; Mora, Thierry | We describe preferential targeting of motifs and regions along the sequence and observe that mutations occurring concomitantly along B-cell lineages tend to co-localise, suggesting a possible mechanism for accelerating affinity maturation Reference: Natanael Spisak, Aleksandra M Walczak, Thierry Mora, Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data, Nucleic Acids Research, gkaa825, doi.org/10.1093/nar/gkaa825 | Session 18: Immune Sensing and Response |
| 304 | Statistical analysis of sharing in antibody repertoires | Ruiz Ortega, Maria; Mora, Thierry; Walczak, Aleksandra | Here we present a statistical approach defined in terms of a probabilistic V(D)J recombination model enhanced by a selection factor that describes repertoire diversity and that predicts with high accuracy its level of publicness, i.e. the number of sequences that will be shared between any number of individuals. | Session 18: Immune Sensing and Response |
| 305 | How the T cell signaling network processes information to discriminate between self and agonist ligands. | Ganti, Raman; Lo, Wan-Lin; McAffee, Darren B.; Groves, Jay; Weiss, Arthur; Chakraborty, Arup | Using channel capacity, we constructed numerically substantiated hypotheses to explain the discriminatory role of a recently identified slow LAT Y132 phosphorylation step. | Session 18: Immune Sensing and Response |
| 306 | Statistics of large scale insertions in B-cell receptors | Lupo, Cosimo; Mora, Thierry; Walczak, Aleksandra | We introduce a statistical model for the occurrence of these indels, inferring the parameters of such a model from real data through maximum-likelihood approaches. | Session 18: Immune Sensing and Response |
| 307 | Modularity optimizes target recognition in the CRISPR-Cas immune system | Bonomo, Melia | Here, a stochastic model is developed to study the targeting activity of the endogenous CRISPR-Cas immune system in bacteria against viruses. | Session 18: Immune Sensing and Response |
| 308 | A scaling law in CRISPR repertoire sizes arises from the avoidance of autoimmunity | Chen, Hanrong; Mayer, Andreas; Balasubramanian, Vijay | We show that balancing viral defense against auto-immunity predicts a scaling law relating spacer length and CRISPR repertoire size. | Session 18: Immune Sensing and Response |
| 309 | Stochasticity influences the efficacy of simulated bacteriotherapies | Jones, Eric; Sivak, David | We use concepts from transition path theory to investigate how the role of noise affects these bacteriotherapies, and probe the relationship between the deterministic and stochastic systems by comparing isocommittor surfaces of the stochastic system to the separatrix of the deterministic system. | Session 18: Immune Sensing and Response |
| 310 | Inferring T-cells repertoire dynamics for healthy individuals. | Bensouda Koraichi, Meriem; Dupic, Thomas; Mora, Thierry; Walczak, Aleksandra | Using a model that has shown good consistency with stationary data and longitudinal data from different Repertoire Sequencing (RepSeq) techniques, we use Bayesian Inference to learn parameters underlying the healthy T-cells population dynamics for individuals of various ages and both sexes. | Session 18: Immune Sensing and Response |
| 311 | Learning and memory in molecular recognition: from olfactory to immune system | Schnaack, Oskar; Peliti, Luca; Nourmohammad, Armita | To probe the emergence of distinct memory strategies, we propose a dynamical Hebbian network model that can efficiently learn and store memory against evolving patterns. | Session 18: Immune Sensing and Response |
| 312 | Deep generative selection models of T and B cell receptor repertoires with soNNia | Isacchini, Giulio; Mora, Thierry; Walczak, Aleksandra; Nourmohammad, Armita | I will show how to leverage biophysical models of receptor generation with machine learning models of selection to identify specific sequence features characteristic of functional lymphocyte repertoires and subrepertoires. | Session 18: Immune Sensing and Response |
| 313 | A coarse-grained view of biochemical feedback and cell-to-cell communication | Erez, Amir | We consider this mechanism by developing a coarse-grained model of sense-and-secrete feedback. | Session 18: Immune Sensing and Response |
| 314 | Viral surface geometry shapes the coronavirus and influenza virus spike evolution through antibody pressure | Amitai, Assaf | Hence, we offer a geometry-based approach to estimate and assess whether a pandemic virus is changing its mutational pattern to that indicative of a circulating virus. | Session 18: Immune Sensing and Response |
| 315 | Bonds, Catch Bonds, and Statistics | Nelson, Phil | So the recent discovery of catch-bond behavior in T-cell activation is a very good starting point to motivate study of many molecular biophysics ideas. | Session 18: Immune Sensing and Response |
| 316 | Detection of a multi-disease biomarker in Saliva with Graphene Field Effect Transistors | Kumar, Narendra; Gray, Mason; Ortiz-Marquez, Juan C.; Weber, Andrew; Desmond, Cameron R.; Argun, Avni; van Opijnen, Tim; Burch, Kenneth | In this work, we realized a label-free electronic biosensor for detection of CA1 utilizing highly sensitive graphene field effect transistors (G-FETs) as a transducer and specific RNA aptamers as a probe. | Session 18: Immune Sensing and Response |
| 317 | Modeling antigen presentation and immune recognition with Restricted Boltzmann Machines | Bravi, Barbara; Cocco, Simona; Monasson, Rémi; Mora, Thierry; Walczak, Aleksandra | The approach is able to discriminate responses specific to different antigens and highlights amino acid patterns that are central to such specificity at the molecular level. | Session 18: Immune Sensing and Response |
| 318 | Overcoming the sensitivity vs. throughput tradeoff in Coulter counters: a novel side counter design | Bacheschi, Daniel; Polsky, William; Kobos, Zachary; Yosinski, Shari; Menze, Lukas; Chen, Jie; Reed, Mark | We present a simple microfluidic coplanar Coulter counter device design that overcomes constriction clogging and is capable of operating in microfluidic channels filled entirely with highly conductive sample while being cost effective. | Session 18: Immune Sensing and Response |
| 319 | Affinity maturation and germinal centers: how mechanism determines strategy against antigenically variable pathogens | McGough, Lauren; Cobey, Sarah | In this talk, we analyze how the biophysical properties of the germinal center response enable and constrain the immune system’s ability to carry out effective strategies against pathogens, emphasizing that said strategies must account for the coupling between the dynamics of the memory repertoire and the evolution of the pathogens it protects against. | Session 18: Immune Sensing and Response |
| 320 | Antigen-mediated antibody interference shapes polyclonal fate | Wang, Shenshen; Yan, Le | We present an ecological model to account for mediated interactions between B cell lineages, which stem from physical coupling of eptiopes via an antigen molecule. | Session 18: Immune Sensing and Response |
| 321 | B cells use mechanical energy to distinguish affinity and speed up adaptation | Jiang, Hongda; Wang, Shenshen | Here we study the stochastic process of antigen extraction using theory and simulations. | Session 18: Immune Sensing and Response |
| 322 | Optimal response to pathogen evolution in immune repertoires | Chardès, Victor; Mora, Thierry; Walczak, Aleksandra | Here we assume that the immune system follows a strategy that maximizes the long term immune coverage and minimizes the short term metabolic costs associated with affinity maturation. | Session 18: Immune Sensing and Response |
| 323 | The size of the immune repertoire of bacteria | Bradde, Serena; Nourmohammad, Armita; Goyal, Sidhartha; Balasubramanian, Vijay | Here, we identify a fundamental trade-off between the size of the bacterial immune repertoire and effectiveness of response to a given threat, and show how this tradeoff imposes a limit on the optimal size of the CRISPR cassette. | Session 18: Immune Sensing and Response |
| 324 | Multi-modal Single-molecule Imaging with Continuously Controlled Spectral-resolution (CoCoS) Microscopy | Jeffet, Jonathan; Michaeli, Yael; Torchinsky, Dmitry; Israel-Elgali, Ifat; Shomron, Noam; Craggs, Timothy; Ebenstein, Yuval | Here we introduce Continuously Controlled Spectral-resolution (CoCoS) microscopy, an imaging scheme that encodes color into spatial read-out in the image plane, with continuous control over the spectral resolution. | Session 19: Instrumentation and Techniques |
| 325 | Optimal Signal Transduction with Silicon Transistors Enable Therapeutic Enzyme Regulation | Balijepalli, Arvind; Le, Son; Morris, Michelle; Pant, Harish; Richter, Curt | We used commercially sourced n-channel silicon field-effect transistors (nFETs) operating under PID control to demonstrate pH measurements with a resolution of (7.2+/-0.3)x10^-3 at 10 Hz. | Session 19: Instrumentation and Techniques |
| 326 | Characterizing the Simulated Anomalous Diffusion of Proteins in Relation to the Nanoporous Structure of Extracellular Matrix-Relevant Hydrogels | Yoshida, Shawn; Schmid, William; Vo, Nam; Kisley, Lydia | Conventional methods are unable to quantify both nanoscale structure and diffusion, but we overcame these limitations with a technique known as "fluorescence correlation spectroscopy super-resolution optical fluctuation imaging" (fcsSOFI), which can quantify local anomaleity and diffusion dynamics, along with the size, shape, and frequency of nanopore structures. | Session 19: Instrumentation and Techniques |
| 327 | Distinguishing Catalytic and Noncatalytic Motions of Individual Taq Polymerase Molecules | Taulbee, Jeffrey; Turvey, Mackenzie; Lau, Calvin; Lee, Wonbae; Gabriel, Kristin; Chen, Cynthia; Vargas, Rebecca; Weiss, Gregory; Collins, Philip | This presentation will summarize the Taq immobilization orientations and analysis methods that best recorded and differentiated between catalytic and noncatalytic motions, producing detailed single-molecule kinetics and energy landscapes for the two processes. | Session 19: Instrumentation and Techniques |
| 328 | Synthetic Electrophysiology: Manipulating and measuring bioelectric pattern formation with light | McNamara, Harold | Here we present a new strategy to study electrophysiological pattern formation by building synthetic bioelectrical tissues from the bottom-up. | Session 19: Instrumentation and Techniques |
| 329 | DNA Flossing in a Dual Pore Device | Vuong, An; Capaldi, Xavier; Seth, Swarnadeep; Zimny, Philip; Nagel, Roland; Bhattacharya, Aniket; Dunbar, William; Reisner, Walter | We have developed a feedback-driven dynamic control approach based on Field Programmable Gate Arrays that can adjust the opposing forces during translocation so as to scan the DNA molecule back and forth (“DNA flossing” [1-3]) This multi-scanning capability reduces random error by enabling averaging over repeated scans of linearized molecules. | Session 19: Instrumentation and Techniques |
| 330 | The Origin of Conductive-Pulse Sensing Inside a Nanopore and the Role of Electro-Hydrodynamics | Lastra, Lauren; Freedman, Kevin | Here, we discuss how current-enhancing DNA events could be the result of a flux imbalance between anions and cations. | Session 19: Instrumentation and Techniques |
| 331 | Parameter estimation for correlated Ornstein-Uhlenbeck processes | Strey, Helmut | In many fields of science, we observe time-series of a fluctuating quantity: local density fluctuations of a liquid, or fluctuations of neural activity as measured by fMRI. | Session 19: Instrumentation and Techniques |
| 332 | Electroosmotic Flow and Pressure Influences DNA Configuration in Nanopores | Lastra, Lauren | We describe how λ-DNA configurations can fluctuate depending on pore size, voltage applied, and method of translocation (i.e. EOF or electrophoretically). | Session 19: Instrumentation and Techniques |
| 333 | How stochastic thermodynamics changes in systems with multiple interacting components | Wolpert, David | In this talk I summarize the many ways that the form of that directed graph modifies the standard results of stochastic thermodynamics. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 334 | A minimal one-dimensional model of pattern formation in bacterial community phototaxis | Vallomparambath PanikkasserySu, Ritwika; Man Wah Chau, Rosanna; Ursell, Tristan; Bhaya, Devaki; Huang, Kerwyn; Gopinathan, Ajay | We propose a one-dimensional analytical model to predict the critical value of the phototactic bias force for instabilities to manifest as finger-like projections. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 335 | Scale invariance of bacterial cell size fluctuations during starvation | Shimaya, Takuro; Okura, Reiko; Wakamoto, Yuichi; Takeuchi, Kazumasa | Here, by developing a microfluidic device that realizes a uniform and switchable environment for dense bacterial populations, we observe the morphological response of growing E. coli cells against abrupt starvation [2]. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 336 | Spatio-Temporal Supercontinuum Growth Spectroscopy of Rhodobacter Sphaeroides | Kilinc, Mehmet; Wan, Jacky; Kuhlman, Thomas; Gabor, Nathaniel; Cogdell, Richard | Here, we present a novel method, called Spatio-Temporal Supercontinuum Growth Spectroscopy (STSGS), that combines broadband supercontinuum excitation and real-time laser probes of microbial growth in highly controlled environments. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 337 | Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms | Steinbach, Gabi; Crisan, Cristian; Ng, Siu; Hammer, Brian; Yunker, Peter | Instead, we find that contact killing can facilitate coexistence between nominally antagonistic strains. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 338 | Age-related loss of gene-to-gene transcriptional coordination among single cells. | Levy, Orr; Amit, Guy; Vaknin, Dana; Snir, Tom; Efroni, Sol; Castaldi, Peter; Liu, Yang-Yu; Cohen, Haim; Bashan, Amir | Here, we propose a new approach for analysing transcriptional regulation in single-cell RNA sequencing data by focusing on the global coordination between the genes rather than the variability of individual genes or correlations between pairs of genes. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 339 | Who Is to Thank for the Rhythms of My Tail? – A Mathematical Study of Circadian Rhythmicity in Poly(A) Tail Length | Yao, Xiangyu; Kojima, Shihoko; Chen, Jing | Here we constructed a parsimonious model to investigate rhythmic control of poly(A) tail length as a coupled process to rhythmic mRNA expression. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 340 | Development of phenotypic heterogeneity in different environmental niches in Mycobacterium tuberculosis | Aldridge, Bree; Amir, Ariel; Levien, Ethan; Kar, Prathitha; McNellis, Morgan; Chung, Eun Seon; Kamkaew, Maliwan; Smith, Trever | We describe how mycobacteria deterministically generate diversity in their growth characteristics through asymmetric growth and division. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 341 | Biophysical principles of the Chlamydomonas reinhardtii CO2-concentrating mechanism | Fei, Chenyi; Wilson, Alexandra; Mangan, Niall; Jonikas, Martin; Wingreen, Ned | To better understand how this CCM works, we developed a multi-compartment reaction-diffusion model. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 342 | E. coli Bacteria near "Black Hole" | Phan, Trung; Austin, Robert; Gou, Buming; Chaikin, Paul; Martiniani, Stefano | In microfluidic environment, we create hydrodynamic horizon from which no E. coli bacteria can escape ("black hole") to study the collective behaviors of those organisms under the influence of such background, probing for their strategy to avoid potentially harmful region where part of the population disappears. | Session 20: Irreversible Dynamics, Aging and Death: From Cells to Organisms |
| 343 | Processing information by flow: the smart slime mold Physarum | Alim, Karen | We find that flows are the mean to propagate information about the location of a nutrient source. | Session 21: Learning without Neurons |
| 344 | Learning in Physical Networks: From Machine Learning to Learning Machines | Stern, Menachem | By exploiting the advances of statistical learning theory in the real world, we propose the plausibility of new classes of smart metamaterials, adapting in-situ to users’ needs. | Session 21: Learning without Neurons |
| 345 | Prediction and learning in immune repertoires | Walczak, Aleksandra | In this light, I will present a view of the adaptive immune system as a dynamic Bayesian machinery that updates its memory repertoire by balancing evidence from new pathogen encounters against past experience of infection to predict and prepare for future threats. | Session 21: Learning without Neurons |
| 346 | Evolutionary principles of protein structure and function | Ranganathan, Rama | In this talk, I will present new approaches for probing the physical mechanisms implied by the evolution-based models and present ideas for how such mechanisms are constrained by the dynamics of the evolutionary process. | Session 21: Learning without Neurons |
| 347 | How ecosystems and gene regulatory networks can learn? | Szathmáry, Eörs | How ecosystems and gene regulatory networks can learn? | Session 21: Learning without Neurons |
| 348 | A Model For Chromatin Organization Through Liquid-Liquid Phase Separation | Rosen, Michael | In my talk I will discuss our finding that polynucleosome arrays, which mimic the multivalent chromatin polymer, have an intrinsic capacity to undergo LLPS. | Session 22: Liquid Phases, Spatial Genome Organization, and Transcription |
| 349 | The dynamics of gene expression, from the nucleus to mitochondria | Churchman, L. Stirling | In this talk I will discuss our ongoing efforts to investigate gene regulatory processes occurring throughout the cell, from the nucleus to the mitochondria. | Session 22: Liquid Phases, Spatial Genome Organization, and Transcription |
| 350 | No membrane, no problem: Condensing bacterial organelles | Weber, Stephanie | Using fluorescence imaging and single-molecule tracking, we show that E. coli RNA polymerase (RNAP) organizes into clusters through liquid-liquid phase separation (LLPS). | Session 22: Liquid Phases, Spatial Genome Organization, and Transcription |
| 351 | Action at a distance in transcriptional regulation | Gregor, Thomas | An approach based on high-resolution multi-color imaging is presented to discriminate the specificity of various DNA elements in establishing and maintaining discrete chromosomal configurations at the single cell level. | Session 22: Liquid Phases, Spatial Genome Organization, and Transcription |
| 352 | Super-resolution imaging of transcription in living cells | Cisse, Ibrahim | We will discuss the latest efforts in our laboratory to develop highly sensitive methods of microscopy, to go directly inside living cells and uncover the behavior of single biomolecules as they effect their function in transcription. | Session 22: Liquid Phases, Spatial Genome Organization, and Transcription |
| 353 | The physics of firefly communications: Principles and predictions | Peleg, Orit | In this talk, I will explore how fireflies approach this problem while using physics and information-theory concepts, e.g., energetic cost and compression (minimization of bits representing information) and detectability (high signal-to-noise-ratio). | Session 23: Living timekeepers: Precision measurements, emergent simplicities and physics theory |
| 354 | Where and when microtubules are nucleated in the cell | Shaevitz, Joshua | I will discuss recent work on the nucleation of microtubules in space and time. | Session 23: Living timekeepers: Precision measurements, emergent simplicities and physics theory |
| 355 | The rhythmic day of malaria parasites | Rijo-Ferreira, Filipa | Thus, we propose malaria parasites to have intrinsic clocks. | Session 23: Living timekeepers: Precision measurements, emergent simplicities and physics theory |
| 356 | The Circadian Clock in Cyanobacteria Ensures Successful DNA Replication | Rust, Michael; Liao, Yi | Using numerical simulations, we argue that a stable oscillator is a biochemically viable solution to the problem of inferring the metabolic state hours in the future based on past metabolic information. | Session 23: Living timekeepers: Precision measurements, emergent simplicities and physics theory |
| 357 | From frozen to flowing time, and back | Iyer-Biswas, Srividya | In this talk I will address how life shapes time in a simple bacterial cell, and examine the interplay between homeostasis and adaptation in this context. | Session 23: Living timekeepers: Precision measurements, emergent simplicities and physics theory |
| 358 | Topology-Driven Completion of Chemical Data | Zubarev, Dmitry; Ristoski, Petar | We introduce an approach that identifies lacunae in the chemical data and completes them in a targeted manner. | Session 24: Machine Learning and Data in Polymer Physics |
| 359 | Chemically informed fragment choices to improve the property prediction for polymer systems | Dumi, Amanda; Lambrecht, Daniel | We propose an automatic fragmentation approach in which each fragment is chosen according to quantitative criteria based on electronic-structure information achieving a systematically improvable molecular partitioning. | Session 24: Machine Learning and Data in Polymer Physics |
| 360 | A Machine Learning Approach to the Design of Polymer Electrolyte Membranes | Shen, Kuan-Hsuan; Tran, Huan; Kim, Chiho; Ramprasad, Rampi | Proton exchange membrane fuel cells (PEMFCs) have been the subject of considerable research due to their potential as eco-friendly energy conversion systems. | Session 24: Machine Learning and Data in Polymer Physics |
| 361 | Identifying Accelerated Ageing Pathways for Cross-Linked Polyethylene Pipes Through Machine Learning | Damico, Joseph; Hiles, Melanie; Grossutti, Michael; Wareham, Callum; Dutcher, John | We used these results, together with decision tree and random forest classification algorithms, to identify different modes of pipe degradation and to better understand ageing effects on the long-term stability of PEX pipes. | Session 24: Machine Learning and Data in Polymer Physics |
| 362 | Dielectric properties of polymer nanocomposite interphases from electrostatic force microscopy using machine learning | Gupta, Praveen Kumar; Schadler, Linda; Sundararaman, Ravishankar | In this work, we report a protocol of coupling experimental measurements and numerical simulations of EFM through machine learning to extract interphase dielectric permittivity in tailored silica-based nanocomposites. | Session 24: Machine Learning and Data in Polymer Physics |
| 363 | Secondary structure of very large RNAs via high-throughput oligonucleotide-binding microarrays | Kimchi, Ofer; Garmann, Rees; Chiang, Timothy; Engel, Megan; Manoharan, Vinothan; Brenner, Michael | I will describe how we use the non-equilibrium nature of RNA hybridization as a lens to examine the equilibrium structures of large RNA molecules. | Session 24: Machine Learning and Data in Polymer Physics |
| 364 | Reading-out DNA translocation experiments with (un)supervised Machine Learning | Carral, Ángel; Ostertag, Magnus; Radenovic, Aleksandra; Fyta, Maria | In this work, we train machine learning (ML) models on experimental ionic blockade data from DNA nucleotide translocation through 2D pores of different diameters. | Session 24: Machine Learning and Data in Polymer Physics |
| 365 | Understanding sequence-dependent DNA dynamics through self-associative machine learning and temperature-jump spectroscopy | Jones, Mike; Tokmakoff, Andrei; Ferguson, Andrew; Ashwood, Brennan | In this work, we investigate these dynamics by performing equilibrium coarse-grained simulations of oligonucleotide sequences with varied G:C placement. | Session 24: Machine Learning and Data in Polymer Physics |
| 366 | Machine-guided template-based polymer retrosynthesis planning | Chen, Lihua; Lightstone, Jordan; Ramprasad, Rampi | In this work, several thousands of polymer polymerization paths were manually accumulated from various resources to extract hundreds of synthetic templates and used as a knowledge base. | Session 24: Machine Learning and Data in Polymer Physics |
| 367 | Active Learning of Coarse Grained Models for Free Energy Surfaces | Duschatko, Blake; Vandermause, Jonathan; Molinari, Nicola; Kozinsky, Boris | In the present work, we explore how Gaussian processes can be used in determining the optimal complexity of coarse grained free energy surfaces. | Session 24: Machine Learning and Data in Polymer Physics |
| 368 | An Autonomous Liquid-Handling Platform for ML-Driven Industrial Formulation Discovery | Beaucage, Peter; Martin, Tyler | To enable rational design of these materials, we must leverage theory, simulation, and machine learning (ML) tools to greatly reduce the expense of creating phase diagrams. | Session 24: Machine Learning and Data in Polymer Physics |
| 369 | Hybrid machine learning/materials science modeling for semi-crystalline polymer during film fabrication process | Yang, Jian; Karjala, Teresa; Mendenhall, Jonathan; Ginzburg, Valeriy; Patel, Rajen; Hamad, Fawzi; Lugo, Elva; Valavala, Pavan | In this report, we developed a new hybrid approach to combine the power of machine learning and fundamental materials science to characterize semi-crystalline PE, develop structure-property relationship and study the effect of fabrication conditions on physical properties during blown film fabrication process and to inform the design of new polymer structures. | Session 24: Machine Learning and Data in Polymer Physics |
| 370 | Machine Learning of Phase Transitions and Dynamical Crossovers in Polymers | Patra, Tarak; Bhattacharya, Debjyoti; Bale, Ashwin | We demonstrate this framework for coil to globule transition, crystallization and glass formation during cooling of polymers, and provide new physical insights of these processes. | Session 24: Machine Learning and Data in Polymer Physics |
| 371 | Rheology-Informed Neural Networks (RhINNs) for direct and inverse complex fluid modeling | Mahmoudabadbozchelou, Mohammadamin; Jamali, Safa | We present Rheology-Informed Neural Networks (RhINNs) architectures as alternative platforms to solve systems of Ordinary Differential Equations (ODEs) commonly used in rheological constitutive modeling of complex fluids. | Session 24: Machine Learning and Data in Polymer Physics |
| 372 | Design of Polymers for Energy Storage Capacitors Using Machine Learning and Evolutionary Algorithms | Kern, Joseph; Chen, Lihua; Kim, Chiho; Ramprasad, Rampi | By utilizing a genetic algorithm approach, we have designed hypothetical polymers with bandgaps above 5 eV, glass transition temperatures above 500 K, and dielectric constants above 4 at 100 Hz. | Session 24: Machine Learning and Data in Polymer Physics |
| 373 | Phase diagrams of polymer-containing liquid mixtures with a theory-embedded neural network | Nakamura, Issei | In this talk, we discuss our new built-in function that is constructed through coarse-grained mean-field theory and the scaling laws in polymer physics. | Session 24: Machine Learning and Data in Polymer Physics |
| 374 | Neural Network Prediction of Polymer-Solvent Coexistence Curves | Ethier, Jeffrey; Casukhela, Rohan; Latimer, Josh; Jacobsen, Matthew; Vaia, Richard | Focusing on available data (>2500 cloud points) on polystyrene in various solvents, we examine the precision of upper and lower critical solution co-existence predictions with various feature descriptors. | Session 24: Machine Learning and Data in Polymer Physics |
| 375 | Prediction of Block Copolymer Phase Behavior Using Machine Learning | Rebello, Nathan; Arora, Akash; Lin, Tzyy-Shyang; Av-Ron, Sarah; Olsen, Bradley | Given the challenges in physics-based methods, we develop a purely data-driven model to predict phase behavior for neat diblock copolymers and compare with SCFT. | Session 24: Machine Learning and Data in Polymer Physics |
| 376 | Deep Learning and Self-Consistent Field Theory: A Path Towards Accelerating Polymer Phase Discovery | Xuan, Yao; Delaney, Kris; Ceniceros, Hector; Fredrickson, Glenn | A new framework that leverages data obtained from self-consistent field theory (SCFT) simulations with deep learning to accelerate the exploration of parameter space for block copolymers is presented. | Session 24: Machine Learning and Data in Polymer Physics |
| 377 | Thermal conductivity, heat capacity and speed of sound of epoxy resins | lyu, guangxin; Evans, Christopher; Cahill, David | We established one efficient way (less than 8 minutes for each sample) to measure thermal conductivity, heat capacity and speed of sound of epoxy resin by frequency domain probe beam deflection (FD-PBD) and time domain thermoreflectance (TDTR). | Session 24: Machine Learning and Data in Polymer Physics |
| 378 | Using Machine Learning to Predict the Glass Transition Temperature of Polyimides | Wen, Chengyuan; Liu, Binghan; Wolfgang, Josh; Long, Timothy; Odle, Roy; Cheng, Shengfeng | To expedite the process of discovering new polyimides, an important high-temperature polymer, we apply a machine learning approach to predict their glass transition temperature (T g), which controls their processability and possible temperature window of applications. | Session 24: Machine Learning and Data in Polymer Physics |
| 379 | BoltzmaNN: Predicting effective pair potentials and equations of state using neural networks | Berressem, Fabian; Nikoubashman, Arash | We find that the NNs provide much more accurate results compared to the analytic low-density limit estimate of the second virial coefficient. | Session 24: Machine Learning and Data in Polymer Physics |
| 380 | Data-driven tools to “fingerprint” soft material structuring in complex processing flows | Corona, Patrick; Berke, Barbara; Leal, L. Gary; Liebi, Marianne; Helgeson, Matthew | We introduce a new experimental methodology to “fingerprint” the microstructural response of complex fluids to nearly arbitrary flows and enable an alternative approach of data-driven modeling and design. | Session 24: Machine Learning and Data in Polymer Physics |
| 381 | Gaussian Processes and Deep Learning for Experimental Data | Ushizima, Daniela | This talk will give an introduction to the inner workings of the algorithms, how to use it, and will present a handful of examples. | Session 24: Machine Learning and Data in Polymer Physics |
| 382 | Meta-Reinforcement Learning as the Driver of Data Acquisition in Autonomous Polymer Discovery | Swaminathan, Sarath; Piunova, Victoria; Lionti, Krystelle; Nwabugwu, Chinyere; Sanders, Daniel; Zubarev, Dmitry | We report development of an end-to-end RL approach applied to preparation of spin-on-glasses (SOGs). | Session 24: Machine Learning and Data in Polymer Physics |
| 383 | Rational optimization of drug-membrane selectivity by computational screening | Mohr, Bernadette; Shmilovich, Kirill; Bereau, Tristan; Ferguson, Andrew | Our goal is to find compounds with high selectivity that can act as CL probes. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 384 | Learning molecular models from simulation and experimental data | Clementi, Cecilia | We present our efforts to bridge these gaps, by combining statistical physics with state-of-the-art machine-learning methods to design optimal coarse models for complex macromolecular systems. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 385 | Toward Transferable Deep Learning Atomistic Potential for Biomolecular Simulations | Isayev, Olexandr | The new model, dubbed ANI-2x, is trained to sulfur and halogens. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 386 | Accurate Molecular Polarizabilities with Coupled Cluster Theory and Machine Learning | Yang, Yang; Lao, Ka Un; Wilkins, David; Grisafi, Andrea; Ceriotti, Michele; Distasio, Robert | In this work, we present a benchmark database [1] of highly accurate static dipole polarizability tensors of 7,211 small organic molecules computed using linear response coupled cluster singles and doubles theory (LR-CCSD). | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 387 | Machine Learning on a Quantum Hamiltonian shows that DNA is Much Stretchier than Classical Simulations Suggest | Berryman, Joshua | Thermodynamic calculations are made in explicit water using a machine learning molecular dynamics method, trained on a novel dataset of quantum calculations making an advanced treatment of dispersion interactions. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 388 | Machine learning for DNA self-assembly: a numerical case study | Appeldorn, Jörn; Nikoubashman, Arash; Speck, Thomas | We study the spontaneous self-assembly of two single-stranded DNA (ssDNA) fragments using the coarse-grained oxDNA2 implementation [1]. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 389 | Predicting Protein Developability via Convolutional Sequence Representation | Golinski, Alexander; Johnson, Bryce; Laxminarayan, Sidharth; Saha, Diya; Appiah, Sandhya; Hackel, Benjamin; Martiniani, Stefano | In this work, we evaluate the ability of neural networks to learn a developability representation from the HT dataset and transfer the knowledge to predict recombinant expression beyond the observed sequences. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 390 | Supremum modeling to extend model transferability in systems biology | Petrie, Cody; Anderson, Christian; Transtrum, Mark | I describe an approach to improve the transferablility of these reduced models. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 391 | Prospective experimental validation of machine learning for biological sequence design | Colwell, Lucy | In this setting, I will discuss model-based optimization approaches that allow us to take advantage of sample inefficient methods and find diverse optimal sequence candidates for experimental evaluation. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 392 | Recurrent networks for protein structure prediction using Frenet-Serret equations and latent residue representations | Bouatta, Nazim | We use a transfer matrix formalism, which enables reasoning over protein backbones using a discrete version of the Frenet-Serret equations (dFSE) that leverages the fact that protein backbones are intrinsically discrete one-dimensional curves. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 393 | Multi-fidelity integrated computational-experimental design of self-assembling π-conjugated optoelectronic peptides | Shmilovich, Kirill; Panda, Sayak; Tovar, John D.; Ferguson, Andrew | In this work we employ multi-fidelity Bayesian optimization to fuse experimental and computational datastreams for the design of self-assembling π-conjugated peptides with emergent optoelectronic properties. | Session 25: Machine Learning for Biomolecular Design and Simulation |
| 394 | Decoding the physical principles of biomolecular phase separation | Zhang, Yaojun; Xu, Bin; Weiner, Benjamin; Meir, Yigal; Wingreen, Ned | We combined coarse-grained molecular dynamics simulations and analytical theory to investigate how the macroscopic phase boundaries and physical properties of condensates depend on the microscopic properties of the polymers and the concentration ratio between polymer species. | Session 26: Macromolecular Phase Separation |
| 395 | Reentrant transitions in protein phase-separation: segregation vs. association | Deviri, Dan; Safran, Samuel | We use Flory Huggins theory to predict the phase diagrams of scaffold-client-solvent ternary solutions. | Session 26: Macromolecular Phase Separation |
| 396 | Fusion of Biomolecular Condensates | Ijavi, Mahdiye; Sturzenegger, Flurin; Schuler, Benjamin; Dufresne, Eric | To identify the limitations of this technique, we compare the dynamics of fusion for droplets in contact with a surface to droplets in the bulk of a solution. | Session 26: Macromolecular Phase Separation |
| 397 | Novel “dark state” phosphate cluster formation in aqueous solution | Straub, Joshua; Nowotarski, Mesopotamia; Lu, Jiaqi; Helgeson, Matthew; Jerschow, Alexej; Han, Songi | We present novel studies in which the behavior of phosphates with increasing temperature via 31P NMR exhibit anomalous relaxation, indicating the presence of a novel phosphate state. | Session 26: Macromolecular Phase Separation |
| 398 | Non-equilibrium regulation and organization of transcriptional condensates by RNA synthesis | Shrinivas, Krishna; Henninger, Jonathan; Oksuz, Ozgur; Schede, Halima; Sharp, Phillip; Young, Richard; Chakraborty, Arup | We leverage approaches from non-equilibrium statistical physics and complex coacervates to propose a model by which RNA, the product of gene expression, regulates transcriptional condensate dynamics. | Session 26: Macromolecular Phase Separation |
| 399 | Quantitative Theory for the Diffusive Exchange Dynamics of Liquid Condensates | Hubatsch, Lars; Jawerth, Louise; Love, Celina; Bauermann, Jonathan; Tang, TY; Bo, Stefano; Hyman, Anthony; Weber, Christoph | Using the theory of phase separation we derive a framework that quantitatively captures the diffusive transport of labeled droplet components. | Session 26: Macromolecular Phase Separation |
| 400 | Surface condensation of a pioneer transcription factor on DNA | Morin, Jose; Wittmann, Sina; Choubey, Sandeep; Klosin, Adam; Golfier, Stefan; Hyman, Anthony; Julicher, Frank; Grill, Stephan | Here we investigate the role of DNA in nucleation of condensates, using the pioneer transcription factor KLF-4. | Session 26: Macromolecular Phase Separation |
| 401 | Quantitative phase microscopy enables precise and efficient determination of biomolecular condensate composition | McCall, Patrick; Kim, Kyoohyun; Fritsch, Anatol; Iglesias-Artola, Juan; Jawerth, Louise; Wang, Jie; Ruer, Martine; Poznyakovskiy, Andrey; Peychl, Jan; Guck, Jochen; Alberti, Simon; Hyman, Anthony; Brugués, Jan | Here we combined quantitative phase microscopy and the physics of sessile droplets to measure the shape and composition of individual model condensates. | Session 26: Macromolecular Phase Separation |
| 402 | Elastically limited liquid-liquid phase separation | Ronceray, Pierre; Mao, Sheng; Kosmrlj, Andrej; Haataja, Mikko | We propose simple criteria for which scenario is preferred, introducing a phase diagram controlled by the trade-off between elastic modulus, liquid-liquid surface tension, and liquid-network wetting properties. | Session 26: Macromolecular Phase Separation |
| 403 | Phase separation controlled by molecular transitions | Bartolucci, Giacomo; Adame-Arana, Omar; Zhao, Xueping; Weber, Christoph | Here, we derive a minimal model of a phase-separating ternary mixture where two components can convert into each other. | Session 26: Macromolecular Phase Separation |
| 404 | Liquid condensates increase potency of amyloid fibril inhibitors | Michaels, Thomas; Mahadevan, Lakshminarayanan; Weber, Christoph | Here we study the interplay between protein aggregation, its inhibition and liquid-liquid phase separation. | Session 26: Macromolecular Phase Separation |
| 405 | Characterization of the functional relevance of intranuclear transcription factor aggregates in living fly embryos | Munshi, Rahul; Levo, Michal; Wieschaus, Eric; Gregor, Thomas | Here, we employ live imaging and quantitative analyses in early fly embryos to visualize and characterize such TF aggregates and simultaneously measure target gene activity. | Session 26: Macromolecular Phase Separation |
| 406 | Phase-separated compartments as biochemical reactors | Laha, Sudarshana; Michaels, Thomas; Weber, Christoph | Here, we derive a theoretical framework to study fuel driven chemical reactions in the presence of compartments. | Session 26: Macromolecular Phase Separation |
| 407 | Aging of Protein Condensates | Jawerth, Louise | Here, we present our efforts to quantify these new materials as they age in vitro. | Session 26: Macromolecular Phase Separation |
| 408 | Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components | Espinosa, Jorge; Joseph, Jerelle; Sanchez-Burgos, Ignacio; Garaizar, Adiran; Frenkel, Daan; Collepardo-Guevara, Rosana | Using a minimal coarse-grained model that allows us to simulate thousands of interacting multivalent proteins, we provide predictive rules governing the stability and composition of multicomponent biomolecular condensates. | Session 26: Macromolecular Phase Separation |
| 409 | Sequence dependence of biomolecular condensates | Weiner, Benjamin; Meir, Yigal; Wingreen, Ned | Using lattice-polymer simulations and mean-field theory, we show that the sequence of binding motifs strongly affects a polymer’s ability to phase separate, influencing both phase boundaries and condensate properties (e.g. viscosity and polymer extension). | Session 26: Macromolecular Phase Separation |
| 410 | Guiding growing droplets through the cytoskeleton | Boeddeker, Thomas; Rosowski, Kathryn; Dufresne, Eric | Here, we study the interactions of stress granules, a phase-separated protein-RNA droplet in the cytosol, with the heterogeneous networks of actin and microtubules. | Session 26: Macromolecular Phase Separation |
| 411 | Round Tubulin Droplet Formation in Presence of Cross-linkers | Sahu, Sumon; Ross, Jennifer | Surprisingly, we have observed that tubulin, a well-characterized enzyme that polymerizes into microtubules, can display droplet-like phase separation in the presence of a small molecule crosslinker, Sulfo-SMCC, and a microtubule-associated protein, MAP65. | Session 26: Macromolecular Phase Separation |
| 412 | BIAPSS – comprehensive bioinformatic analysis of liquid-liquid phase separating sequences | Badaczewska-Dawid, Aleksandra Elzbieta; Potoyan, Davit | The bioinformatic analysis provides us with the knowledge about sequence conservation, secondary structure preferences, solvent accessibility, contacts, charge decoration, AA composition, and short linear motifs detection. | Session 26: Macromolecular Phase Separation |
| 413 | Cavitation controls droplet sizes in elastic media | Vidal, Estefania; Zwicker, David | We show that large droplets only form when they fracture the surrounding matrix in a cavitation event. | Session 26: Macromolecular Phase Separation |
| 414 | Hierarchical assembly encodes functional structure within liquid condensates | Bhandari, Kamal; Schmit, Jeremy | We propose a general model in which functional structure can be embedded with a liquid when the molecules assemble hierarchically via interactions that vary widely in affinity. | Session 26: Macromolecular Phase Separation |
| 415 | Systematic investigation of a two-fluid model describing ion-induced volume phase transition in polyelectrolyte gels | Mussel, Matan; Lewis, Owen; Basser, Peter; Horkay, Ferenc | Here we report a systematic investigation of a two-fluid model describing the dynamic response of the coupled components (polymer network, solvent, and charged ions). | Session 26: Macromolecular Phase Separation |
| 416 | Liquid-Liquid Phase Separation of Inorganic Polyphosphate; the Complexities of a Simple Model | Seppala, Hannah; Banerjee, Priya | Here, we will present data depicting the phase behavior of polyP, showing that it forms a wide variety of condensates through liquid-liquid phase separation with numerous cations, including divalent salts, polyamines, and proteins. | Session 26: Macromolecular Phase Separation |
| 417 | Specific recognition and recruitment of client molecules by a liquid phase | Bhandari, Kamal; Schmit, Jeremy | Based on theoretical modeling, we propose that molecules are highly aligned to form zipper structures and these zippers have defects in the bonding structure that allow for the subsequent formation of a network. | Session 26: Macromolecular Phase Separation |
| 418 | Computational modeling of liquid-liquid phase separation and cargo encapsulation in self-assembling microcompartments | Mohajerani, Farzaneh; Sayer, Evan; Neil, Christopher; Inlow, Koe; Hagan, Michael | We develop equilibrium theory and dynamical computational model to describe assembly of a protein shell around cargo and scaffold molecules, with cargo coalescence and encapsulation provided by scaffold-mediated interactions. | Session 26: Macromolecular Phase Separation |
| 419 | ATPase-Dependent Enzyme Activity Modulates the Dynamics of a Model Biological Condensate | Coupe, Sebastian; Fakhri, Nikta | Here, we use the model phase-separating DEAD-box helicase LAF-1. | Session 26: Macromolecular Phase Separation |
| 420 | Finite-size transitions in membranes | Girard, Martin; Bereau, Tristan | In this talk, I will show that by carefully extending the 2D Ising model to N states, finite-size effects drive the system to adopt a critical composition. | Session 26: Macromolecular Phase Separation |
| 421 | Signaling outcomes driven by critical fluctuations | Schaffner, Taylor; Machta, Benjamin | Here we present a model and Monte-Carlo simulation framework for proteins coupled to their surrounding lipid membrane using a modified 2D Ising model. | Session 26: Macromolecular Phase Separation |
| 422 | Gelation and phase separation in LAT membrane complexes | GrandPre, Trevor; Limmer, David | We have developed a particle based reaction diffusion model of LAT that incorporates multivalent bonding and diffusive dynamics to study the kinetics and thermodynamics of condensate formation. | Session 26: Macromolecular Phase Separation |
| 423 | Molecular Model of Multi-Phasic Biomolecular Condensates | Kaur, Taranpreet; Raju, Muralikrishna; Alshareedah, Ibraheem; Davis, Richoo; Potoyan, Davit; Banerjee, Priya | Using a minimalistic system, comprising of a Prion-like disordered polypeptide (PDP), an Arginine-rich disordered polypeptide (RDP), and RNA, we investigate the thermodynamics of multicomponent intracellular phase behavior. | Session 26: Macromolecular Phase Separation |
| 424 | Effects of Membrane-Curvature on Amyloid-Beta Aggregation | Sahoo, Abhilash | In this work, we have explored the effects of membrane curvature on Aβ 16–22 aggregation, using physics-based coarse-grained molecular simulations of model membranes composed of phosphatidylcholine lipids. | Session 26: Macromolecular Phase Separation |
| 425 | Diffusion in a membrane in the presence of immobile obstacles: the role of disorder | Ilow, Nicholas; Slater, Gary | We present a study of transient and steady-state molecular diffusion in two-dimensional ”Fuzzy” systems of immobile obstacles, i.e., systems which bridge the gap between the ideal periodic and random limits. | Session 26: Macromolecular Phase Separation |
| 426 | Towards Understanding Antibiotic Permeation Across The Gram-negative Bacteria Outer Membrane Using Molecular Dynamics Simulations | Deylami, Javad; Chng, Shu Sin; Yong, Ee Hou | To shed light on the energetics of antibiotic permeation across the outer membrane, we employed a molecular dynamics (MD) simulation approach to obtain the free energy profiles as various clinically important antibiotics were pulled across an Escherichia coli outer membrane model. | Session 26: Macromolecular Phase Separation |
| 427 | Miscibility tricritical points in asymmetric lipid bilayers | Wang, Anjiabei; Machta, Benjamin; Graf, Isabella | To investigate the conditions under which such a tricritical point occurs, we consider an Ising-type lattice model with two coupled layers representing the two leaflets of cell membranes. | Session 26: Macromolecular Phase Separation |
| 428 | Interaction and assembly of graphene oxide nano-flakes in lipid membranes | MANDAL, PRIYA; Giri, Rajendra; Bhattacharya, Gourav; Bhattacharyya, Arpan; Roy, Susanta; Murphy, Bridget; Ghosh, Sajal | Interaction and assembly of graphene oxide nano-flakes in lipid membranes | Session 26: Macromolecular Phase Separation |
| 429 | Constructing molecularly-informed field theories from bottom-up coarse-graining: Rethinking how we engineer soft matter formulations | Sherck, Nick; Shen, Kevin; Nguyen, My; Yoo, Brian; koehler, Stephan; Speros, Joshua; Delaney, Kris; Shell, M. Scott; Fredrickson, Glenn | To overcome the weaknesses of both, we use small-scale, atomistic simulations to parameterize the statistical field theory models. | Session 26: Macromolecular Phase Separation |
| 430 | Surface Phases in Polymer Mixtures and Critical Membranes | Rouches, Mason; Veatch, Sarah; Machta, Benjamin | Here we explore the physical underpinnings of these domains. | Session 26: Macromolecular Phase Separation |
| 431 | Chromatin Mechanics Dictates Subdiffusion and Coarsening Dynamics of Embedded Condensates | Lee, Daniel; Wingreen, Ned; Brangwynne, Cliff | Here, we utilize a powerful optogenetic strategy to examine the interplay of droplet coarsening with the surrounding chromatin network. | Session 26: Macromolecular Phase Separation |
| 432 | Quantifying Phase Behavior and Material Properties of Multicomponent Biomolecular Condensates | Pullara, Paul; Alshareedah, Ibraheem; Banerjee, Priya | Here we study how variations in RNA-to-protein stoichiometry modulate the phase behavior and condensed phase fluid dynamics. | Session 26: Macromolecular Phase Separation |
| 433 | Reversed trends for the isotropic-nematic transition density in confined semiflexible polymer solutions with repulsive or ideal nanoparticle additives | Roy, Supriya; Chen, Yeng-Long | We investigated how nanoparticle additives with extremely different inter-particle interactions affected the phase transition of strongly confined semiflexible polymer (SFC) solutions. | Session 26: Macromolecular Phase Separation |
| 434 | Relating Solvent Properties of Coexisting Aqueous Phases to Interfacial Tension | Titus, Amber; Ferreira, Luisa; Belgovskiy, Alexander; Kooijman, Edgar; Mann, Elizabeth; Mann Jr., J; Meyer, William; Smart, Anthony; Uversky, Vladimir; Zaslavsky, Boris | Based on our current measurements and literature data, we propose a mechanism for phase separation in aqueous two-phase systems. | Session 26: Macromolecular Phase Separation |
| 435 | Multiphase DNA Nanostar Liquids and their Morphologies | Chaderjian, Aria; Jeon, Byoung-jin; Nguyen, Dan; Saleh, Omar | Inspired by the core-shell structures of various membrane-less organelles, we seek to better understand the thermodynamic limits to the number of phases which can simultaneously exist outside the confines of a cell, and the complex morphological structures they can create. | Session 26: Macromolecular Phase Separation |
| 436 | Thermodynamic and transport properties of amoxicillin | Khanal, Shyam; Adhikari, Narayan | In this work, we have performed classical molecular dynamics simulations of amoxicillin in two solvents: water and ethanol. | Session 26: Macromolecular Phase Separation |
| 437 | Modelling liquid-liquid phase separation in an elastic network | Wei, Xuefeng; Zhou, Jiajia; Wang, Yanting; Meng, Fanlong | We propose a continuum theory of the liquid-liquid phase separation in an elastic network where phase-separated microscopic droplets rich in one fluid component can form as an interplay of fluids mixing, droplet nucleation, network deformation, thermodynamic fluctuation, etc. | Session 26: Macromolecular Phase Separation |
| 438 | Stochastic dynamics of single molecules across phase boundaries | Bo, Stefano; Hubatsch, Lars; Weber, Christoph; Julicher, Frank | Starting from a continuum theory of macroscopic phase separation we derive a Langevin equation for molecular trajectories that takes into account thermal fluctuations. | Session 26: Macromolecular Phase Separation |
| 439 | Fluid Droplet growth in a cross-linked network | Lin, Chen; Levine, Alex; Bruinsma, Robijn | We investigated such a phase separation process by a Brownian dynamics simulation of a size-changeable disk, where the disk size depends on the mechanical forces from the network and chemical potential of the minority phase. | Session 26: Macromolecular Phase Separation |
| 440 | Compressing collagen fibrils attached to an elastic substrate: buckling and torsional instabilities | Peacock, Chris; Lee, Eva; Beral, Theo; Cisek, Richard; Tokarz, Danielle; Kreplak, Laurent | We observe both the well-characterized short wavelength sinewave buckling mode and two types of torsional instabilities, writhing and bird-caging. | Session 26: Macromolecular Phase Separation |
| 441 | Surface Phase Transitions with Membrane Binding | Zhao, Xueping; Bartolucci, Giacomo; Julicher, Frank; Weber, Christoph | Here, we derive the corresponding continuum theory for a three-dimensional bulk in the presence of a two-dimensional membrane. | Session 26: Macromolecular Phase Separation |
| 442 | Comparison of Conformational Phase Behavior for Flexible and Semiflexible Polymers | Aierken, Dilimulati; Bachmann, Michael | We use this method to extend previous simulation studies of a coarse-grained model for flexible polymers [2] and analyze structural transitions in semiflexible polymers. | Session 26: Macromolecular Phase Separation |
| 443 | Frank-Kasper Phases of Diblock Copolymer Melts Studied with the DPD Model | He, Juntong; Wang, Qiang(David) | Here we present reciprocal-space self-consistent field (SCF) calculations of the Frank-Kasper (FK) phases formed by diblock copolymer (DBC) melts based on the model used in dissipative particle dynamics (DPD) simulations, following the method of Matsen (Macromolecules 45, 8502 (2012)). | Session 26: Macromolecular Phase Separation |
| 444 | Designing a New Lattice Model to Simulate Low-Molecular-Weight Block Copolymers for Nanolithographic Applications | Wu, Jiaping; Li, Baohui; Wang, Qiang | A new lattice model is designed to be suitable for simulating low-molecular-weight block copolymer (BCP) melts currently used in experiments to achieve sub-10nm domain sizes ( i.e., having an invariant degree of polymerization between 10 2 and 10 3). | Session 26: Macromolecular Phase Separation |
| 445 | Cilia driven flows: Linking micro- with macroscopic dynamics | Ramirez-San Juan, Guillermina | I will present complementary analyses we have performed in ciliated protists to understand the origin and significance of collective cilia beating patterns, e.g. metachronal waves, observed in diverse biological contexts. | Session 27: Mechanics of Cells and Tissues |
| 446 | Planarian Asexual Reproduction via Mechanical Tearing – One Problem, Multiple Solutions | Goel, Tapan; Ireland, Danielle; Shetty, Vir; Diamond, Patrick; Collins, Eva-Maria | Surprisingly, we found that other planarian species – Schmidtea mediterranea and Girardia tigrina, found different solutions to the same problem. | Session 27: Mechanics of Cells and Tissues |
| 447 | Peristaltic pumping with valves in low Reynolds numbers | Winn, Aaron; Katifori, Eleni | A simple model for valves is proposed to understand the nonlinear fluid-structure interaction. | Session 27: Mechanics of Cells and Tissues |
| 448 | Fluid dynamics of flow networks with fluid-storage function | Luo, Yongtian; Ho, Che-Ling; Helliker, Brent; Katifori, Eleni | We develop a spatially explicit capacitive model which is able to capture the local changes of flow rate and fluid status (such as water potential and fluid content). | Session 27: Mechanics of Cells and Tissues |
| 449 | Vertex Modelling of Cephalic Furrow Formation | Niloy, Redowan Ahmed; thomas, Jeffrey; Blawzdziewicz, Jerzy | In the current research, this question has been addressed to discover critical mechanical cues for cephalic furrow formation in Drosophila melanogaster. | Session 27: Mechanics of Cells and Tissues |
| 450 | Measuring mechanical stress in Myxococcus xanthus monolayers with traction force microscopy | Han, Endao; Copenhagen, Katherine; Shaevitz, Joshua | Using traction force microscopy, we map out the spatial distribution of forces exerted by M. xanthus cells on a soft hydrogel substrate and link the position of defects to the distribution of stresses. | Session 27: Mechanics of Cells and Tissues |
| 451 | Wings deployment in Drosophila melanogaster | Hadjaje, Simon; Andrade-Silva, Ignacio; Clement, Raphael; Dalbe, Marie-Julie; Brun, Pierre-Thomas; Marthelot, Joel | We study the wing expansion in Drosophila melanogaster. | Session 27: Mechanics of Cells and Tissues |
| 452 | Viscoelasticity of Myxococcus xanthus Fruiting Bodies | Black, Matthew; Shaevitz, Joshua | We use atomic force microscope-based microrheology to characterize the mechanical state of these structures throughout their development. | Session 27: Mechanics of Cells and Tissues |
| 453 | Fruit Morphogenesis in Arabidopsis thaliana | Parel, Kurien; Gomez-Felipe, Andre; Kierzkowski, Daniel; Gosselin, Frederick; Routier-Kierzkowska, Anne-Lise | We propose that organ shape emerges from the differences in specified growth between tissues. | Session 27: Mechanics of Cells and Tissues |
| 454 | Award for Outstanding Doctoral Thesis Research in Biological Physics (2020): Vortex arrays and chaotic mixing by swimming invertebrate larvae | Gilpin, William | Using starfish larvae as a model system, we study the fluid dynamics of ciliary bands, and discover that they create a beautiful pattern of slowly-evolving vortices around swimming invertebrate larvae. | Session 27: Mechanics of Cells and Tissues |
| 455 | Environmental Influence on the Ventilation Mechanism of Termite Mounds: A Computational Study | Saxena, Saurabh; Yaghoobian, Neda | Here, we develop and employ an energy balance-based model that simulates the spatiotemporally variable surface temperatures in high resolutions and dynamically couple it with a computational fluid dynamic (CFD) model to investigate the effect of the diurnally variable surface temperatures on the mound internal flow characteristics. | Session 27: Mechanics of Cells and Tissues |
| 456 | Developing epithelial tissues as active materials: Tracking cell dynamics in dorsal closure using machine learning | Haertter, Daniel; Fogerson, Stephanie; Crawford, Janice; Kiehart, Daniel; Schmidt, Christoph | We utilized deep learning to automatically and robustly detect and temporally track various features, even in noisy microscopy movies: individual cell shapes in two distinct tissue types, cell junctions and edge lengths, and tissue topology. | Session 27: Mechanics of Cells and Tissues |
| 457 | Emergent multi-cellular network structures due to mechanical interactions | Noerr, Patrick; Golnaraghi, Farnaz; Gopinathan, Ajay; Dasbiswas, Kinjal | Using an agent-based model of adherent elastically interacting cells, we explore structure formation in multicellular assemblies on a soft substrate by using quantitative metrics such as percolation, number of junctions, branch length, and orientational order to make structure predictions as a function of mechanical characteristics including compressibility and rigidity. | Session 27: Mechanics of Cells and Tissues |
| 458 | Cell cycle dependent mechanics drive epithelial stratification | Devany, John; Harmon, Robert; Gardel, Margaret | Here we focus on skin as a model system which can build these compartments starting from a single layer of stem cells. | Session 27: Mechanics of Cells and Tissues |
| 459 | Non-equilibrium Rigidity Transitions in Embryonic Tissues | Kim, Sangwoo; Pochitaloff, Marie; Stooke-Vaughan, Georgina; Campas, Otger | Here, we present a computational framework that includes key features at the cellular level, namely the presence of extracellular spaces, complex cell shapes and tension fluctuations that enables the description of non-equilibrium dynamics and emergent mechanics in embryonic tissues. | Session 27: Mechanics of Cells and Tissues |
| 460 | Unified theoretical framework for epithelial mechanics, rheology and 3D shaping by upscaling active gels models of the actin cortex | Ouzeri, Adam; Kale, Sohan; Torres-Sánchez, Alejandro; Arroyo, Marino | We address this gap by developing a formalism which bridges the active-gel models of the cortex and vertex-like models at a tissue scale. | Session 27: Mechanics of Cells and Tissues |
| 461 | Collective pack size during cell migration modulated by an apparent cell-substrate friction | Vazquez, Kelly; Notbohm, Jacob | Here we conduct experiments to test two physics-based theoretical models that relate cell-substrate friction to either the size of a collective pack within the monolayer or the size of a protrusion at the leading edge. | Session 27: Mechanics of Cells and Tissues |
| 462 | Predictive understanding of discrete cell-fate decision in early embryonic development | Zhao, Jiaxi; Perkins, Mindy; Norstad, Matthew; Bothma, Jacques; Garcia, Hernan | Specifically, we apply recently developed single-cell live imaging techniques to quantify transcriptional and protein dynamics of the Drosophila pair-rule gene fushi tarazu as cells decide whether to commit to the expression of the gene. | Session 27: Mechanics of Cells and Tissues |
| 463 | Engineering biological machines from living tissues | Sakar, Mahmut Selman | In this talk, I am going to explain how physical principles of morphogenesis can be harnessed for the controlled self-assembly of tissues with complex equilibrium shapes. | Session 27: Mechanics of Cells and Tissues |
| 464 | Multi-tissue mosaics of homotypic and heterotypic cell monolayers | Heinrich, Matthew; Wolf, Avi; Cohen, Daniel; Kosmrlj, Andrej | We developed a framework for predicting the interaction of multiple expanding cell monolayers that fuse into one large monolayer. | Session 27: Mechanics of Cells and Tissues |
| 465 | Tissue pressure and cell traction compensate to drive robust aggregate spreading | Yousafzai, Muhammad Sulaiman; Yadav, Vikrant; Amiri, Sorosh; Staddon, Michael; Tabatabai, Alan; Errami, Youssef; Jaspard, Gwilherm; Amiri, Sirine; Banerjee, Shiladitya; Murrell, Michael | In this work, using a combination of experimental measurements and modeling, we show the surface tension of cell aggregates, as models of active liquid droplets, depends upon the size of the aggregate and the magnitude of applied load, which alters the wetting dynamics. | Session 27: Mechanics of Cells and Tissues |
| 466 | Regulation of Three-Dimensional Epithelial Cell Shape in a Two-Dimensional Tissue | Chmiel, Theresa; Gardel, Margaret | By examining the relationship between cell height, density and biological components of the actin cytoskeleton, we explore the mechanisms by which the epithelial tissue regulates shape and volume. | Session 27: Mechanics of Cells and Tissues |
| 467 | Controlled neighbor exchanges drive glassy behavior, intermittency and cell streaming in epithelial tissues | Das, Amit; Sastry, Srikanth; Bi, Dapeng | We study how this rate-limiting process affects the mechanics and collective behavior of cells by introducing this biological constraint in a vertex-based model as an intrinsic single-cell property. | Session 27: Mechanics of Cells and Tissues |
| 468 | Scaling mechanical response and proliferation rate with cell size using apical stress fibers | Lubensky, David; Lopez-Gay, Jesus; Nunley, Hayden; Bellaiche, Yohanns | By examining how a Drosophila epithelium responds to morphogenetic forces, we identified a class of apical stress fibers (aSFs) anchored to adherens junctions. | Session 27: Mechanics of Cells and Tissues |
| 469 | Temperature induced variations in cell volume and elastic modulus for neuronal cells | Staii, Cristian | We quantify the change in soma volume with temperature and propose a simple theoretical model that relates this change with variations in elastic modulus. | Session 27: Mechanics of Cells and Tissues |
| 470 | A morphometric analysis of cell shape and cytoskeletal form | Prasad, Ashok | Using these images we demonstrated that cell morphology at the single cell level is a sensitive readout of cell state, and lower-dimensional projections can identify similar and dissimilar changes in cellular morphology[1]. | Session 27: Mechanics of Cells and Tissues |
| 471 | Vimentin intermediate filaments mediate cell shape on visco-elastic substrates | Swoger, Maxx; Gupta, Sarthak; Bates, Michael; Charrier, Elisabeth; Hehnly, Heidi; Patteson, Alison | To investigate vimentin’s role in substrate sensing, we designed polyacrylamide hydrogels that mimic the elastic and viscoelastic nature of in vivo tissues. | Session 27: Mechanics of Cells and Tissues |
| 472 | Vimentin mediates nuclear shape and position to affect cell speed and polarity in confinement. | Gupta, Sarthak; Patteson, Alison; Schwarz, J. M. | We develop a minimal model of cells moving through confined geometries that effectively includes all three types of cytoskeletal filaments. | Session 27: Mechanics of Cells and Tissues |
| 473 | Unraveling the interplay between cell shape organization and rheology in epithelial tissues | Huang, Junxiang; Cochran, James; Fielding, Suzanne; Marchetti, M Cristina; Bi, Dapeng | In this work, we use a minimal cell-based computational model to investigate the rheology of confluent epithelial tissues. | Session 27: Mechanics of Cells and Tissues |
| 474 | Label-free Cell Tracking and Dynamic Rearrangements in Epithelial Monolayers | GU, SHUYAO; Lee, Rachel; Benson, Zackery; Vitolo, Michele; Martin, Stuart; Chalfoun, Joe; Losert, Wolfgang | Here we describe the use of deep learning to identify cell nuclei based on a UNet convolutional neural network for nucleus segmentation. | Session 27: Mechanics of Cells and Tissues |
| 475 | Multicellular traction alignment affects collective pack size during collective migration | Saraswathibhatla, Aashrith; Henkes, Silke; Sknepnek, Rastko; Notbohm, Jacob | To test this hypothesis, we used the self-propelled Voronoi model and experimental data on cell tractions and motion. | Session 27: Mechanics of Cells and Tissues |
| 476 | Energetics and irreversibility of Rho-GTP protein patterns on the membrane of starfish oocytes | Chao, Yu-Chen; Liu, Jinghui; Fakhri, Nikta | Here we use chaotic dynamics of Rho-GTP patterns on the membrane of starfish oocytes as a model system to answer these crucial thermodynamic questions. | Session 27: Mechanics of Cells and Tissues |
| 477 | Energy budget model for bacterial growth and shape maintenance | Serbanescu, Diana; Banerjee, Shiladitya | To understand how a bacterium regulate its growth rate, cell shape and size in different environmental conditions, we develop a mechanistic model based on the budgeting of energy contributions for key cellular functions: nutrient import into the cell, energy expended for growth, cellular metabolism, shape maintenance and energy loss due to dissipation. | Session 27: Mechanics of Cells and Tissues |
| 478 | An elastic shell model for animal cells | Golshaei, Behzad; Rezvani, Samaneh; Albarran, Octavio; Schmidt, Christoph | To relate this response to cell material properties we use finite-element modeling to model the cell as a weakly pressurized elastic shell. | Session 27: Mechanics of Cells and Tissues |
| 479 | Traction force microscopy: Force measurement determines the direction of cell migration | Sakaomto, Takeshi | Here, we have employed fluorescent superparamagnetic beads as detection markers. | Session 27: Mechanics of Cells and Tissues |
| 480 | Optical probing of light localization properties to quantify the probiotic effect on chronic alcoholic brain cells via confocal imaging | Adhikari, Prakash; Shukla, Pradeep; Rao, Radhakrishna; Pradhan, Prabhakar | We construct optical lattices based on the confocal images and quantify the degree of structural disorder ( Ld). | Session 27: Mechanics of Cells and Tissues |
| 481 | Correlated Dilution of Filamentous Networks Leads to Reentrant Rigidity Percolation | Michel, Jonathan; Wyse Jackson, Thomas; von Kessel, Gabriel; Bonassar, Lawrence; Cohen, Itai; Das, Moumita | We again find a peak in the measure of non-affinity of network displacement to coincide with rigidity percolation, but observe that this peak becomes higher and broader with increasing correlation. | Session 27: Mechanics of Cells and Tissues |
| 482 | Detecting force transmission pathways in 3D fibrin networks | Hu, Qingda; Botvinick, Elliot | Here we detect which fibers respond to an applied force using fluorescence confocal microscopy and optical tweezers in a 3D fibrin hydrogel. | Session 27: Mechanics of Cells and Tissues |
| 483 | Rigidity and fracture of biopolymer double networks | Lwin, Pancy; Sindermann, Andrew; Sutter, Leo; Wyse Jackson, Thomas; Cohen, Itai; Bonassar, Lawrence; Das, Moumita | We study a model that combines two structure-function frameworks – a double network (DN) made of a stiff network and a flexible network, and rigidity percolation theory. | Session 27: Mechanics of Cells and Tissues |
| 484 | Optimal elasticity of biological networks | Ronellenfitsch, Henrik | Inspired by the hierarchically organized scaffolding networks found in plant leaves, here we model networks of bending beams that capture the discrete and non-uniform nature of natural materials. | Session 27: Mechanics of Cells and Tissues |
| 485 | Mechanobiology of hyaluronan-rich glycocalyx: How do giant polymers modulate cell adhesion. | Jing, Yu; Cohen, Shlomi; Faubel, Jessica; Wei, Wenbin; Curtis, Jennifer | To examine the physical role of HA glycocalyx, we developed a biomimetic glycocalyx consisting of a microns-thick hyaluronan polymer brush. | Session 27: Mechanics of Cells and Tissues |
| 486 | Role of cellular rearrangement time delays on the rheology of vertex models for confluent tissues | Erdemci-Tandogan, Gonca; Manning, M. Lisa | In this work, we incorporate this idea by augmenting vertex models to require a fixed, finite time for T1 transitions, which we call the “T1 delay time”. | Session 27: Mechanics of Cells and Tissues |
| 487 | A Rigidity Percolation Framework to Understand How Biologically Induced Changes in Constituent Composition Alter Cartilage Shear Mechanics | Wyse Jackson, Thomas; Michel, Jonathan; Lwin, Pancy; Bartell, Lena; Fortier, Lisa; Das, Moumita; Bonassar, Lawrence; Cohen, Itai | We present experiments and theory in support of a rigidity percolation framework that explains how the shear properties of cartilage depend on the concentrations of both constituents. | Session 27: Mechanics of Cells and Tissues |
| 488 | Variations in the extensibility of fibrin fibers | Helms, Christine | We found that conditions during fiber formation play a significant role in fibrin extensibility. | Session 27: Mechanics of Cells and Tissues |
| 489 | Membrane deflection due to ultrasound results in cellular depolarization | Vasan, Aditya; Orosco, Jeremy; Magaram, Uri; Ramirez, Mark; Chalasani, Sreekanth; Friend, James | We have developed a model that predicts membrane deflection due to an ultrasound stimulus, and verified the results of this model with novel measurements of the membrane’s motion using high-speed digital holographic microscopy. | Session 27: Mechanics of Cells and Tissues |
| 490 | Real-time imaging of fibrin-bead networks under compression | Carroll, Bobby; Patteson, Alison | Here, we develop a custom compression device that allows for real-time imaging of the local micro-structure in the fibrin-bead network. | Session 27: Mechanics of Cells and Tissues |
| 491 | Viscoelastic properties of tissues in the vertex model | Tong, Sijie; Singh, Navreeta; Sknepnek, Rastko; Kosmrlj, Andrej | It was previously demonstrated that the vertex model can describe both the solid- and fluid-like behavior by tuning the target cell-shape parameter p 0=P 0/sqrt[A 0], where P 0 and A 0 are the preferred perimeter and area of cells, respectively. | Session 27: Mechanics of Cells and Tissues |
| 492 | Frustration and compromise in collectively moving cell clusters | Gopinathan, Ajay | In this talk, I shall describe a few examples of our work on modeling such clusters, highlighting how frustration can arise at the group level because of heterogeneity in behavior among members of the cluster. | Session 27: Mechanics of Cells and Tissues |
| 493 | Learning the dynamics of cell-cell interactions in confined cell migration | Brückner, David; Arlt, Nicolas; Fink, Alexandra; Ronceray, Pierre; Rädler, Joachim; Broedersz, Chase | Our approach reveals that interacting non-cancerous MCF10A cells can be described by repulsion and friction interactions. | Session 27: Mechanics of Cells and Tissues |
| 494 | Modeling cell motility at mechanical interfaces | Bose, Subhaya; Noerr, Patrick; Gopinath, Arvind; Dasbiswas, Kinjal | We use agent-based Brownian dynamics simulations to study the mechanical interactions between motile cells. | Session 27: Mechanics of Cells and Tissues |
| 495 | Recursive Feedback Between Matrix Dissipation and Chemo-mechanical Signaling Drives Oscillatory Growth of Cancer Cell Invadopodia | Gong, Ze; Wisdom, Katrina; McEvoy, Eoin; Chang, Julie; Adebowale, Kolade; Chaudhuri, Ovijit; Shenoy, Vivek | Here, we develop a chemo-mechanical model to predict the impact of matrix plasticity on the dynamics of invadopodia, the protrusive structures that cancer cells use to facilitate invasion. | Session 27: Mechanics of Cells and Tissues |
| 496 | Not only proteins: The role of compressed sugars in cell migration | Cohen, Shlomi; Kotowska, Patrycja; Chang, Patrick; Jing, Yu; Keate, Rebecca; Zhou, Dennis; Garcia, Andres; Nie, Shuyi; Curtis, Jennifer | In this work, we study three cell types to address the mechanics of cell adhesion in the presence of hyaluronan-rich glycocalyx, with a focus on its implications for cell migration. | Session 27: Mechanics of Cells and Tissues |
| 497 | VELOMIR: Fast microrheology sensor with high temporal and spatial resolution reveals onset of drug effects on single cell level | Pfeil, Jonas; Geiger, Daniel; Neckernuss, Tobias; Marti, Othmar | We present VELOMIR, VEry LOngtime MIcroRheology, a compact tool that tracks multiple particles in real time with up to 10 kHz sampling rate for almost infinite long tracking times. | Session 27: Mechanics of Cells and Tissues |
| 498 | Myosin motors regulate Drosophila stretch receptors | Guan, Chonglin; Nishi, Kengo; Kreis, Christian; Baeumchen, Oliver; Goepfert, Martin; Schmidt, Christoph | We found that the extracellular matrix surrounding the cap cells maintains the basic resting tension. | Session 27: Mechanics of Cells and Tissues |
| 499 | Correlation Studies of Cells’ Velocimetry on Micropatterned Substrates | Hughes, Keontré; Hallfors, Nicholas; Teo, Jeremy; Isakovic, Abdel F. | We analyzed the cells kinematics on micropatterned substrates using cells velocimetry and fluorescence microscopy for human foreskin fibroblast (HFF) cells. | Session 27: Mechanics of Cells and Tissues |
| 500 | Dynamic Mechanotransductive Self-Reinforcement of Transcription Factors Induces Memory of Gene Expression | Price, Chris; Mathur, Jairaj; Pathak, Amit; Shenoy, Vivek | We develop a dynamic self-reinforcement model, posed as a series of Waddington landscapes, to explain mechanical memory during cooling which depends on the priming time and the priming stiffness. | Session 27: Mechanics of Cells and Tissues |
| 501 | WKB solutions to the wave equation for the cochlea and for acoustic rainbow sensors | Marrocchio, Riccardo; Karlos, Angelis; Elliott, Stephen | The WKB method is used to derive an approximate solution to the cochlear wave equation, which results from the interaction between the passive dynamics of the basilar membrane and the 1D fluid coupling in the scalae, including both fluid viscosity and compressibility. | Session 27: Mechanics of Cells and Tissues |
| 502 | DNA Supercoiling Drives the Switch between Long-range Cooperative and Antagonistic RNAP Dynamics | Chatterjee, Purba; Goldenfeld, Nigel; Kim, Sangjin | Here we introduce a continuum deterministic model for RNAP translocation where the elongation velocity of an RNAP is coupled to the local supercoiling and RNAP density. | Session 27: Mechanics of Cells and Tissues |
| 503 | Biophysical modeling of membrane-actin interactions governing the morphology of dendritic spines | Alimohamadi, Haleh; Bell, Miriam; Halpain, Shelley; Rangamani, Padmini | In this study, we developed a minimal biophysical model to investigate the role of membrane-actin interactions in governing dendritic spine geometries. | Session 27: Mechanics of Cells and Tissues |
| 504 | Investigating Bacterial Deformation Upon Surface Attachment Using Finite Element Modeling | Wong, Yu-Chern; Gordon, Vernita | Hence, we develop finite element modeling to estimate the bacterial deformations due to adhesion. | Session 27: Mechanics of Cells and Tissues |
| 505 | Award for Outstanding Doctoral Thesis Research in Biological Physics (2019): studying cellular behavior in jammed microgel growth media | Bhattacharjee, Tapomoy | Here, I will present a new approach to 3D bioprinting and 3D culture of cellular communities that utilizes jammed, granular polyelectrolyte microgels as a support medium. | Session 27: Mechanics of Cells and Tissues |
| 506 | Tissue cell behavior in packed microgel media | Subramaniam, Vignesh; Angelini, Thomas | In this presentation, I will present work investigating the shape-evolution of non-spherical mono-culture liver tissue models embedded in packed microgel culture media. | Session 27: Mechanics of Cells and Tissues |
| 507 | Compression stiffening of fibrous networks with stiff inclusions | Shivers, Jordan; Feng, Jingchen; van Oosten, Anne; Levine, Herbert; Janmey, Paul; MacKintosh, Frederick | Utilizing a coarse-grained model, we generate predictive phase diagrams for compression-driven stiffening and particle jamming as a function of particle volume fraction, network critical strain, and applied compression, which we test by simulating the rheology of disordered fiber networks containing rigid particles. | Session 27: Mechanics of Cells and Tissues |
| 508 | Fluid versus solid behaviour in a rheological constitutive model of tissue mechanics | Cochran, James; Huang, Junxiang; Bi, Dapeng; Marchetti, M Cristina; Fielding, Suzanne | In this work, we construct a continuum constitutive model of biological tissue rheology, aimed at describing the mechanics of a monolayer of confluent cells. | Session 27: Mechanics of Cells and Tissues |
| 509 | Intracellular Wave Dynamics Perturbed by Electric Fields and Nano-topography | Yang, Qixin; Hourwitz, Matt; Campanello, Leonard; Devreotes, Peter; Fourkas, John; Losert, Wolfgang | In this study, we explore the roles of these intracellular waves during electrotaxis, by monitoring the dynamics of actin waves in response to EFs. | Session 27: Mechanics of Cells and Tissues |
| 510 | Collective Motility and Mechanical Waves in Cell Clusters: A Molecular Clutch Model | Deng, Youyuan; Levine, Herbert | We formulate a simplified mechanical model which explains these effects in a straight-forward manner. | Session 27: Mechanics of Cells and Tissues |
| 511 | Mapping single cell mechanics as a function of environment geometry using Brillouin microscopy and optical tweezers microrheology | Nikolic, Milos; Scarcelli, Giuliano; Tanner, Kandice | To measure cell mechanics on a sub-micrometer scale we use Brillouin microscopy (~GHz) and broadband frequency optical tweezer microrheology (3Hz-15kHz). | Session 27: Mechanics of Cells and Tissues |
| 512 | Improved Chemotaxis by Repeated Stimulation | Karanam, Aravind Rao | Here, we study chemotaxis in the social amoeba Dictyostelium discoideum, which secretes and relays cyclic adenosine monophosphate (cAMP) during starvation. | Session 27: Mechanics of Cells and Tissues |
| 513 | Bending instability of rod-shaped bacteria | Qiu, Luyi; Amir, Ariel; Hutchinson, John | Motivated by rod-shaped bacteria such as E. coli, whose cell walls are much thinner than their radii and are subject to a substantial internal pressure, we study, theoretically, how such instability is affected by this internal pressure. | Session 27: Mechanics of Cells and Tissues |
| 514 | Multi-fractal analysis of the ossification process in developing skull bone | Bahadorian, Mohammadreza; Modes, Carl | We employ 2D multi-fractal analyses to study the ossification pattern of skull bone in developing mouse embryos. | Session 27: Mechanics of Cells and Tissues |
| 515 | Talin manipulation in cell adhesion through an improved clutch model | venturini, chiara; Roca-Cusachs, Pere; Saez, Pablo | Here, we extend the classical clutch model with a detailed description of talin. | Session 27: Mechanics of Cells and Tissues |
| 516 | Topological braiding and bosonic phases on the cell membrane | Liu, Jinghui; Totz, Jan; Miller, Pearson; Hastewell, Alasdair; Dunkel, Jorn; Fakhri, Nikta | Braiding of topological structures in complex matter fields provides a robust framework for encoding and processing information, and has been extensively studied in the context of topological quantum computation. | Session 27: Mechanics of Cells and Tissues |
| 517 | An analytical model describing the E. coli cell wall as a pressurized elastic cylinder | Albarran, Octavio; Garces, Renata; Schmidt, Christoph | We here introduce a simplified analytical model to rationalize our experiments that compress E. coli between parallel plates while monitoring shapes, forces and indentation depths. | Session 27: Mechanics of Cells and Tissues |
| 518 | Quantifying the flexural rigidity of cyanobacteria using a microfluidic flow cell | Faluweki, Mixon; Goehring, Lucas | Quantifying the flexural rigidity of cyanobacteria using a microfluidic flow cell | Session 28: Microbiological Physics |
| 519 | Altering competition outcomes of a pair of gut bacterial species via manipulation of spatial and temporal structure | Sundarraman, Deepika; Smith, Jarrod; Kast, Jade; Guillemin, Karen; Parthasarathy, Raghuveer | To clarify the still poorly understood forces that shape community composition, especially general consequences of spatial and temporal structure, we have made use of larval zebrafish with controlled combinations of intestinal microbes. | Session 28: Microbiological Physics |
| 520 | Dynamics of commensal gut bacterial colonization in larval zebrafish populations | Ramakrishna, Vivek; Parthasarathy, Raghuveer | Here, we present an imaging-based assay to study the dynamics of colonization of larval zebrafish hosts by multiple species of fluorescently labelled bacteria. | Session 28: Microbiological Physics |
| 521 | Bacterial species abundance covariance structure in C. elegans shows signatures of bacteria-bacteria and host-bacteria interactions | Michael, K.; Taylor, Megan; Nemenman, Ilya; Vega, Nicole | We analyze a simplified microbiome in the gut of Caenorhabditis elegans, a roundworm. | Session 28: Microbiological Physics |
| 522 | Investigating structural stability of SARS-CoV-2 virus like particles. | Sharma, Abhimanyu; Preece, Benjamin; Swann, Heather; Fan, Xyu; McKenney, Richard; Ori-McKenney, Kassandra; Saffarian, Saveez; Vershinin, Michael | I will present our Atomic Force Microscopy (AFM) imaging of SARS-CoV-2 VLPs, the effect of nanoscale forces on the structure of these particles, and the effect of temperature variation on the stability of VLP in liquid and dry conditions. | Session 28: Microbiological Physics |
| 523 | Utilizing massively parallel CRISPRi assays to investigate persistence during antibiotic exposure | Stevenson, Keiran; Lambert, Guillaume | We show that the CRISPRi can replace the function of the toxin-antitoxin systems, inhibiting the cells metabolism and improving survival under certain antibiotics. | Session 28: Microbiological Physics |
| 524 | Vimentin binds to SARS-2 spike protein and antibodies targeting extracellular vimentin block uptake of SARS-2 virus-like particles | Swoger, Maxx; Gupta, Sarthak; Bucki, Robert; Janmey, Paul; Schwarz, J. M.; Patteson, Alison | Here, we present evidence that extracellular vimentin might acts as a critical component of the SARS-CoV-2 spike protein-ACE2 complex in mediating SARS-2 cell entry. | Session 28: Microbiological Physics |
| 525 | Chemotaxis in run-reversing bacterial species | Antani, Jyot; Sumali, Anita; Lele, Tanmay; Lele, Pushkar | I will present our novel approach to characterize the chemotaxis signaling output in one such polar-flagellate, Helicobacter pylori. | Session 28: Microbiological Physics |
| 526 | Growth Curves Reveal How Multicellularity Enhances Drug Resistance | Romanyshyn, Oleksandra; Balazsi, Gabor | In this work we chose the multicellular clump-forming budding yeast ( Saccharomyces cerevisiae) Sigma 1278b, or TBR1 strain as the potential model of multicellular drug-resistant yeast. | Session 28: Microbiological Physics |
| 527 | Particle size dependence of 3D diffusion in live Escherichia coli cells | Valverde Mendez, Diana; Bratton, Benjamin; Sheehan, Joseph; Holt, Liam; Gitai, Zemer; Shaevitz, Joshua | We use Genetically Encoded Multimeric nanoparticles (GEMs) to probe the microrheology of the Escherichia coli cytoplasm. | Session 28: Microbiological Physics |
| 528 | Extended Keller-Segel model of chemotactic migration in heterogeneous porous media | Amchin, Daniel; Ott, Jenna; Bhattacharjee, Tapomoy; Kratz, Felix; Datta, Sujit | We show that the classic Keller-Segel model of chemotaxis can describe this behavior, but only when two revisions to the motility parameters are incorporated: (i) they are reduced in a confinement-dependent manner, and (ii) they are corrected to incorporate cell-cell collisions that are promoted by confinement. | Session 28: Microbiological Physics |
| 529 | How to Search Space using Active Filaments | Krishnamurthy, Deepak; Flaum, Eliott; Prakash, Manu | Inspired by this remarkable behavior, here we present a framework for how cells search by combining experiments using the ciliate Lacrymaria olor, and a physical model based on deformable active filaments: i.e. filaments capable of exerting active hydrodynamic stresses on the surrounding fluid. | Session 28: Microbiological Physics |
| 530 | Top-down analysis of the complexity of environmental and human-associated microbial ecosystems | Yonatan, Yogev; Amit, Guy; Bashan, Amir | Here, we introduce a computational method to approximate the effective connectance of microbial ecosystems by analyzing their assemblage-abundance relations. | Session 28: Microbiological Physics |
| 531 | Mechanisms of Diffusive Charge Transport in Redox-Active Polymer Solutions | Bello, Liliana; Sing, Charles | We use simulations and theory to show how a variety of molecular charge transport mechanisms affect diffusive motion in RAP solutions. | Session 29: Molecular and Ion Transport in Polymers |
| 532 | Li+ Ion Migration in Polymer Electrolytes: How Coordination Effects Control Li+ Transport Mechanisms | Schönhoff, Monika; Rosenwinkel, Mark; Andersson, Rassmus; Mindemark, Jonas | To shed light on the influence of the coordination properties of different polymer architectures and to identify their influence on Li ion transport, we compare PEO, poly(ε-caprolactone) (PCL), poly(trimethylene carbonate) (PTMC), and a PCL-co-PTMC random co-polymer, combined with the Lithium salt LiTFSA at varying Li +:monomer ratio r. Employing multinuclear Pulsed-Field-Gradient (PFG)-NMR diffusion, we obtain ion-specific transport information. | Session 29: Molecular and Ion Transport in Polymers |
| 533 | Understanding the Effect of Permanent Crosslinks in Dense Polymer Networks on Probe Diffusion | Sheridan, Grant; Evans, Christopher | Understanding the Effect of Permanent Crosslinks in Dense Polymer Networks on Probe Diffusion | Session 29: Molecular and Ion Transport in Polymers |
| 534 | Dissociation of Lithium Salt in Block Copolymer | Kim, Kyoungmin; Kuhn, Leah; Alabugin, Igor; Hallinan, Daniel | In this study, the interaction between lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and polystyrene (PS) – poly(ethylene oxide) (PEO) diblock copolymer was investigated using Fourier transform infrared (FTIR) spectroscopy and density functional theory (DFT) simulation. | Session 29: Molecular and Ion Transport in Polymers |
| 535 | Role of Zwitterion Addition on Ion Conduction in Polymer Electrolytes | Mei, Wenwen; Bostwick, Joshua; Hickey, Robert; Colby, Ralph | We find that addition of zwitterions to a model single-ion conducting polymer significantly increased the dielectric constant and slightly increased T g. Consequently, ionic conductivity increased despite the increase of T g. | Session 29: Molecular and Ion Transport in Polymers |
| 536 | Ion Mobilities, Transference Numbers and Inverse Haven Ratios of Polymeric Ionic Liquids | Zhang, Zidan; Wheatle, Bill; Krajniak, Jakub; Keith, Jordan; Ganesan, Venkatraghavan | In contrast to expectations, we demonstrate that the inverse Haven ratio increases with increasing degree of polymerization ( N) and then decreases at larger N. For a fixed center of mass reference frame, we demonstrate that such results arise as a consequence of the strong cation-cation correlated motions which exceed (in magnitude) the self-diffusivity of cations. | Session 29: Molecular and Ion Transport in Polymers |
| 537 | Probing ion diffusion in chemically amplified resists through experiments and atomistic simulations | Bottoms, Christopher; Terlier, Tanguy; Stein, Gila; Doxastakis, Manolis | We present a concerted experimental and computational effort to examine diffusion of an inert catalyst analogue (a cation-anion pair) in the protected and deprotected states of a model terpolymer resin. | Session 29: Molecular and Ion Transport in Polymers |
| 538 | Ion co-transport with alcohol in cation exchange membranes | Kim, Jung Min; Beckingham, Bryan | Here, we investigate the transport behavior of Nafion® 117 and PEGDA-AMPS cation exchange membranes to co-ion (formate or acetate) and alcohol (methanol and ethanol), where we observe an increase in both formate and acetate permeability in co-permeation with either methanol or ethanol. | Session 29: Molecular and Ion Transport in Polymers |
| 539 | Surface-Induced Ordering Depresses Through-Film Ionic Conductivity in Lamellar Block Copolymer Electrolytes | Coote, Jonathan; Kinsey, Thomas; Street, Dayton; Kilbey, S.; Sangoro, Joshua; Stein, Gila | This work hypothesizes that structural anisotropy is a consequence of surface-induced ordering, where preferential adsorption of one block at the electrode drives a short-range stacking of the lamellae. | Session 29: Molecular and Ion Transport in Polymers |
| 540 | Solvent Effects on the Transference Number of Dilute Polyelectrolyte Solutions | Lytle, Tyler; Yethiraj, Arun | Our work uses molecular dynamics simulations of coarse-grained polymer models to elucidate how chain length and solvent type affect the ion transference number in solution. | Session 29: Molecular and Ion Transport in Polymers |
| 541 | Understanding Gas Transport in Polymer-Grafted Nanoparticle Assemblies | Kumar, Sanat | For a given NP radius and grafting density in the dense brush regime we find that gas permeabilities display a maximum as a function of the graft chain molecular weight. | Session 29: Molecular and Ion Transport in Polymers |
| 542 | Physical aspects of cell and tissue elongation | Banavar, Samhita; Campas, Otger | In this talk, I will focus on cell and tissue elongation and highlight a common physical mechanism of elongating individual wall cells and animal embryonic tissues. | Session 30: Morphogenesis |
| 543 | Hydraulic and electric control of cell spheroids | Duclut, Charlie; Prost, Jacques; Jülicher, Frank | In this talk, we will discuss how a hydraulic or electrical perturbation, imposed for instance by a drain of micrometric diameter, can be used to perturb tissue growth. | Session 30: Morphogenesis |
| 544 | A reproducible human stem cell system reveals neural tube morphogenesis | Karzbrun, Eyal; Khankhel, Aimal; Megale, Heitor; Shraiman, Boris; Streichan, Sebastian | We perform a quantitative morphometric analysis, and discover that folding morphogenesis is driven by a combination of cell contractility and active tissue wetting. | Session 30: Morphogenesis |
| 545 | Integrating space and time in patterning of gene expression in embryogenesis via a synthetic approach | Tran, Huy; Fernandes, Gonçalo; Coppey, Mathieu; Dostatni, Nathalie; Walczak, Aleksandra | We constructed a series of synthetic ms2 reporters, where the numbers of binding sites for each TF are varied systematically. | Session 30: Morphogenesis |
| 546 | Light controlled cell-fates in embryonic development | Singh, Anand; Wu, Ping; Wieschaus, Eric; Toettcher, Jared; Gregor, Thomas | We are developing a quantitative approach to modulate TF’s input concentration and record transcriptional gene output in real-time to bring a new dimension to the study of transcriptional dynamics in a developing embryo. | Session 30: Morphogenesis |
| 547 | From super-resolution imaging to theory: cadherin clustering drives asymmetric glassy dynamics during vertebrate embryo elongation | Malmi Kakkada, Abdul; Huebner, Robert; Sarikaya, Sena; Weng, Shinuo; Thirumalai, Dave; Wallingford, John | Even as defective clustering of C-cadherin can facilitate tissue coherence in vivo, we discover that clustering of C-cadherin is crucial in the more mechanically challenging context of convergent extension. | Session 30: Morphogenesis |
| 548 | Physics-Informed Deep Learning for Characterizing Perturbed Cell Growth | Cavanagh, Henry; Endres, Robert; Lind, Rob; Mosbach, Andreas; Scalliet, Gabriel | Here, we introduce a novel framework that extends behavior analysis to nonstationary morphodynamics during early stage growth of the soybean rust pathogen, P. pachyrhizi. | Session 30: Morphogenesis |
| 549 | Modelling the dynamics of shape change in a patterned viscoelastic sheet | Krishna, Abhijeet; Modes, Carl | There is a wide-scale interest in the study of material sheets that change their 3D shape on being stimulated. | Session 30: Morphogenesis |
| 550 | The finch beak: growth, form and function | AlMosleh, Salem; Choi, Gary; Abzhanov, Arkhat; Mahadevan, L. | Guided by our morphometric analysis of finch beaks and earlier observations of the development of the zebra finch beak, we propose a minimal cellular and tissue level mechanism for beak morphogenesis that takes the form of a local geometric growth law. | Session 30: Morphogenesis |
| 551 | Reconstruct cellular dynamics from single cell data | Wang, Weikang; Poe, Dante; Ni, Ke; Xing, Jianhua | Computationally, we modified a finite temperature string method to reconstruct the reaction coordinate from the paths, and reconstruct a corresponding quasi-potential, which reveals that the EMT process resembles a barrier-less relaxation process. | Session 30: Morphogenesis |
| 552 | In vivo measurement of tissue mechanical properties in Drosophila embryos | Pham, An; Guan, Chonglin; Kiehart, Daniel; Schmidt, Christoph | Here, we introduce two experimental approaches, magnetic tweezers and glass microneedles, to probe tissue mechanical properties in Drosophila embryos peeled out of their vitelline egg shells. | Session 30: Morphogenesis |
| 553 | Morphing of growing sheets via active contractions of muscle cells | Sudhakar, Anvitha; Kosmrlj, Andrej | To capture large deformations of soft tissues we developed a theoretical and computational framework based on the finite strain theory, where the total deformation gradient tensor was decomposed into one part due to growth/active contractions and another part due to elastic deformation. | Session 30: Morphogenesis |
| 554 | Dimensionality-Reduction in the Drosophila Wing as Revealed by Landmark-Free Measurements of Phenotype | Alba, Vasyl; Carthew, James; Mani, Madhav; Carthew, Richard | We develop a mathematical approach that enables a robust description of biologically salient phenotypic variation. | Session 30: Morphogenesis |
| 555 | Patterned morphogenesis of epithelial wound detection and healing | Hutson, Shane | We present experimental and computational evidence delineating the mechanisms by which the calcium signaling patterns are established and through which cells interpret the calcium signals to drive wound repair behaviors. | Session 30: Morphogenesis |
| 556 | The Role of Environment, Material, and Regulatory Function in the Morphological Diversity of Termite Mounds | Fagundes, Tadeu; Ordonez, Juan; Yaghoobian, Neda | To explain the different but systematic shapes of termite mounds, this work develops a computational model to investigate the connection between the mound’s structural form and the mounds’ local environment, material, and regulatory functions. | Session 30: Morphogenesis |
| 557 | Collective cell mechanics of epithelial shells with organoid-like morphologies | Rozman, Jan; Krajnc, Matej; Ziherl, Primoz | Here, we propose a mechanistic theory of epithelial shells which resemble small-organoid morphologies. | Session 30: Morphogenesis |
| 558 | Cellular Fourier Transform: a new approach to analyse living tissues at multiple scales | Fruleux, Antoine; Boudaoud, Arezki | During my presentation, I will introduce the method and discuss its application to the growth of floral organs. | Session 30: Morphogenesis |
| 559 | Theory of branching morphogenesis via local interactions and global cues | Ucar, Mehmet Can; Kamenev, Dimitrii; Fachet, Dominik; Hadjab, Saida; Hannezo, Edouard | Here, we develop a theoretical framework to describe a stochastic and self-organized branching process in the presence of external guidance, based on branching and annihilating random walks in an external potential. | Session 30: Morphogenesis |
| 560 | Stability of oriented deformation in developing biological tissues | Ibrahimi, Muhamet; Merkel, Matthias | Here, we explore a scenario where the gradient of a scalar field defines active anisotropic stresses in the system. | Session 30: Morphogenesis |
| 561 | Detecting bifurcations in tissue development | Freedman, Simon; Xu, Bingxian; Goyal, Sidhartha; Mani, Madhav | Our work provides a robust mathematical framework for categorizing developmental transitions that can aid in gene network inference and help determine features of cell differentiation, such as when and why cell fate transitions are reversible or generate multiple cell types. | Session 30: Morphogenesis |
| 562 | Precision in a rush: decision making in early fly development | Desponds, Jonathan; Vergassola, Massimo; Walczak, Aleksandra | I will compare fixed-time sampling strategies to decisions made on-the-fly, which are based on updating and comparing the likelihoods of being at an anterior or a posterior location. | Session 30: Morphogenesis |
| 563 | Spontaneous strains in tissue mechanics: topologically driven morphogenesis | Duque, Carlos; Modes, Carl; Jülicher, Frank | Here, we seek to make a connection between cellular events and the physics of shape-changing materials based on the elongation and contraction of nematic elastomers. | Session 30: Morphogenesis |
| 564 | Patterned shear flows drive folding during organogenesis | Mitchell, Noah; Cislo, Dillon; Shankar, Suraj; Dogic, Zvonimir; Shraiman, Boris; Streichan, Sebastian | Here, using a combination of light-sheet microscopy, genetics, computer vision, and tissue cartography, we reconstruct the full 3D shape dynamics and identify the driving sources of the shape change by linking out-of-plane motion to the cellular flow and active contraction patterns. | Session 30: Morphogenesis |
| 565 | The role of tissue mechanics in symmetry breaking during organogenesis in the zebrafish embryo | Sanematsu, Paula; Erdemci-Tandogan, Gonca; Merkel, Matthias; Patel, Himani; Amack, Jeffrey; Manning, M Lisa | Here, we take a different approach by analyzing how mechanical drag forces on the KV generated by surrounding tailbud tissue can contribute to asymmetry. | Session 30: Morphogenesis |
| 566 | Origin of symmetry breaking underlying polarized flow during Drosophila endoderm morphogenesis | Gehrels, Emily; Chakrabortty, Bandan; Merkel, Matthias; Lecuit, Thomas | With this combination of experimental and modeling approaches, we aim to systematically unravel how organized multicellular dynamics emerge from genetic, mechanical, and geometric "information", and feedback during morphogenesis. | Session 30: Morphogenesis |
| 567 | Morphogenesis of silica microstructures in diatoms | Feofilova, Maria; Dufresne, Eric | In this work, we used confocal fluorescence microscopy to obtain high-quality 3-D images of fluorescently-labelled C. Granii diatom frustules, and precisely tracked the positions of their structural features. | Session 30: Morphogenesis |
| 568 | Mesoatomic distortions and subdomain morphology in DG and DD networks | Thomas, Edwin; Feng, Xueyan; Burke, Christopher; Reddy, Abhiram; Grason, Gregory | Mesoatomic distortions and subdomain morphology in DG and DD networks | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 569 | Atomic-scale imaging of the effect of side-chain chemistry on the crystal motifs in polypeptoid nanosheets | Seidler, Morgan; Li, Nan; Xuan, Sunting; Zuckermann, Ronald; Prendergast, David; Jiang, Xi; Balsara, Nitash | Atomic-scale imaging of the effect of side-chain chemistry on the crystal motifs in polypeptoid nanosheets | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 570 | Three-dimensional Cryogenic Electron Microscopy Imaging of Two-dimensional Polymer Crystals | Jiang, Xi; Xuan, Sunting; Li, Nan; Prendergast, David; Zuckermann, Ronald; Balsara, Nitash; Downing, Kenneth | We introduce a novel composite holey gold support that prevents cryo-crinkling and reduces beam-induced motion of two-dimensional specimens. | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 571 | Combining Advanced Experimental Methods to Characterization of Polymer Nanocomposites | Winey, Karen | We apply ion beam methods (elastic recoil detection and Rutherford backscattering) and single particle tracking methods, as well as more accessible methods such as temperature-modulated DSC and broadband dielectric spectroscopy methods, to probe the molecular weight dependence of the polymer and nanoparticles are revealed for nanoparticles of various sizes and nanoparticle-polymer interactions. | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 572 | Molecular orientation in polyamide reverse osmosis membranes revealed by polarized resonant soft x-ray scattering | Beaucage, Peter | Using polarized resonant soft x-ray scattering, a uniquely sensitive probe of molecular orientation and structure, we observe a striking degree of polarization-induced anisotropy in both commercial and model polyamide films. | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 573 | Update on resonant tender x-rays scattering user programm at the Soft Matter Interfaces beamline at NSLS II | Freychet, Guillaume; Zhernenkov, Mikhail | Update on resonant tender x-rays scattering user programm at the Soft Matter Interfaces beamline at NSLS II | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 574 | Quantification of flow-induced phase separation in polymer blends by small-angle neutron scattering | Wang, Yangyang; Wang, Weiyu; Hong, Kunlun; Liu, Yun | The methodology described in this work provides a concrete venue for quantitative studies of phase transitions of polymeric fluids under deformation and flow via small-angle scattering techniques. | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 575 | Computational Reverse Engineering Analysis of Scattering Experiments (CREASE) on Amphiphilic Block Polymer Solutions | Wessels, Michiel; Jayaraman, Arthi | In this talk we will present the extension of a recently developed Computational Reverse-Engineering Analysis for Scattering Experiments (CREASE) approach to analyze spherical, cylindrical, fibrillar, and elliptical cylinder assembled structures in amphiphilic block copolymer solutions. | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 576 | Polymer morphology measurement by Polarized Resonant Soft X-ray Scattering | DeLongchamp, Dean | I will describe our approach to polarized resonant soft X-ray scattering (P-RSoXS), which combines principles of soft X-ray spectroscopy, small-angle scattering, real-space imaging, and molecular simulation to produce a molecular scale structure measurement for soft materials and complex fluids. | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 577 | Label-free characterization of aqueous micelle nanostructure, chemistry, and dynamics via in-situ RSoXS | Collins, Brian; McAfee, Terry; Ferron, Thomas; Cordova, Isvar; Pickett, Phillip; McCormick, Charles; Wang, Cheng | Here we demonstrate a novel technique capable of such measurements based on resonant soft X-ray scattering (RSoXS), which uniquely probes organic materials using their intrinsic chemical bonds rather than laborious and disruptive labeling. | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 578 | Self-assembly of Frank-Kasper Phases in Conformationally Asymmetric Fluorinated Block Copolymers | Jeon, Seungbae; Jun, Taesuk; Jo, Seongjun; ahn, Hyungju; Lee, Byeongdu; Ryu, Du Yeol | Theoretical and experimental studies have revealed that conformational asymmetry ( ε) of the different blocks provides a key mechanism to stabilize the FK σ and A15 phases between hexagonally packed cylinder (HEX) and body centered cubic (BCC) phases in block copolymers (BCPs) self-assembly. | Session 31: Morphology Characterization: Frontier of Scattering and Microscopy |
| 579 | Atomistic Go Model to Predict the Structure of Protein Cores | Grigas, Alex | Atomistic Go Model to Predict the Structure of Protein Cores | Session 32: Native and Non-Native Protein Structure and Stability |
| 580 | Quasi-two-dimensional diffusion of interacting globular proteins | Tan, Zihan; Dhont, Jan; Calandrini, Vania; Nägele, Gerhard | The model describes globular proteins as Brownian spheres, confined to lateral motion in a planar monolayer embedded in a three-dimensional viscous fluid. | Session 32: Native and Non-Native Protein Structure and Stability |
| 581 | Dual mechanism of ionic liquid-induced protein unfolding | Lee, Peiyin | Dual mechanism of ionic liquid-induced protein unfolding | Session 32: Native and Non-Native Protein Structure and Stability |
| 582 | Investigating ‘False Positive’ Protein Decoys Based on Core Packing Features | Liu, Zhuoyi; Grigas, Alex; O’Hern, Corey | We developed a feed-forward neural network based on packing features of cores to predict how well computational models recapitulate real protein structures. | Session 32: Native and Non-Native Protein Structure and Stability |
| 583 | Binding of Proteins to Surface Plasmon Resonance Biochips Functionalized with Native and Size-Reduced Phytoglycogen Nanoparticles | van Heijst, Nicholas; Charlesworth, Kathleen; Maxwell, Aidan; Grossutti, Michael; Dutcher, John | We used infrared spectroscopy to monitor the amide bands of the bound conA molecules, confirming that conA maintained a significant portion of its native beta-sheet content and suggesting that binding of conA to phytoglycogen does not significantly reduce its bioactivity. | Session 32: Native and Non-Native Protein Structure and Stability |
| 584 | Molecular dynamics simulations of folded proteins: determining the properties of protein cores | Mei, Zhe; Grigas, Alex; Levine, Zachary; Regan, Lynne; O’Hern, Corey | In this paper, we show that three of the most commonly used MD force fields, CHARMM36M, Amber99SB-ILDN and Amber99NMR cannot accurately recapitulate the conformations of proteins solved by solution NMR. | Session 32: Native and Non-Native Protein Structure and Stability |
| 585 | Proteinaceous optical devices in squids: understanding the reflectin-lipid interaction | Altan, Irem; Fox, Dillion; Sweeney, Alison | Proteinaceous optical devices in squids: understanding the reflectin-lipid interaction | Session 32: Native and Non-Native Protein Structure and Stability |
| 586 | Time-retarded electronic friction and enhanced mass of classical nuclei innonadiabatic molecular dynamics due to self-consistent coupling to electronictime-dependent nonequilibrium Green function | Mondal, Priyanka; Nikolic, Branislav | Here we present a new scheme of ab-initio MD that self-consistently couples molecular dynamics (MD) to quantum description of electrondynamics where current induced force is calculated including all higher order terms using time-dependent nonequilibrium Green function (TDNEGF) which leads to memory effect and show that the effect of highly nonadiabatic inertia term which has not been considered in previous studies. | Session 32: Native and Non-Native Protein Structure and Stability |
| 587 | Sensing and making sense of fluctuating cellular states | Meigel, Felix; Hellwig, Lina; Contzen, Jörg; Mergenthaler, Philipp; Rulands, Steffen | Here, we show how the non-equilibrium interplay between microscopic and mesoscopic dynamics leads to a kinetic low-pass filter facilitating precise sensing of fluctuating cellular states. | Session 33: Noise and Stochasticity in Biological Networks |
| 588 | Maximizing Information from Noisy Measurements of Single-cell Gene Expression Distributions | Vo, Huy; Munsky, Brian | We propose a conceptual framework based on the Fisher Information Matrix and probability kernel together with a computational method based on the finite state projection algorithm to systematically study the impact of single-cell measurement noise on stochastic model parameter identifiability. | Session 33: Noise and Stochasticity in Biological Networks |
| 589 | The Long and Short of Templated Copying | Poulton, Jenny | This talk explores the consequences of this observation. | Session 33: Noise and Stochasticity in Biological Networks |
| 590 | Apply granger causality test to determine connections within peridodics ATP stimulated KTaR-1 cell colony | Li, Guanyu | Here we aim to understand how communication would play a role in the chemosesing process. | Session 33: Noise and Stochasticity in Biological Networks |
| 591 | Topology Control and Pruning in Intertwined Biological Flow Networks. | Kramer, Felix; Modes, Carl | We here present an advanced version of the discrete Hu-Cai model, coupling two spatial networks in 3D. | Session 33: Noise and Stochasticity in Biological Networks |
| 592 | Investigation of Allosteric Mechanism from an Evolutionary Perspective | Samanta, Riya; Muth, Calvin; Sanghvi, Neel; Beckett, Dorothy; Matysiak, Silvina | In this work, we used concepts from Network theory and applied bioinformatic tools to identify features that distinguish allosteric from non-allosteric biotin ligases. | Session 33: Noise and Stochasticity in Biological Networks |
| 593 | Can active hydrodynamic fluctuations affect barrier crossing during enzymatic catalysis? | Tripathi, Ashwani; Das, Tamoghna; Paneru, Govind; Pak, Hyuk Kyu; Tlusty, Tsvi | Here, we examine the possibility that active noise in the cell affects enzymatic catalytic rate by accelerating or decelerating the crossing of energy barriers during a reaction. | Session 33: Noise and Stochasticity in Biological Networks |
| 594 | Non-genetic heterogeneity in prostate cancer through coupled dynamics of Androgen Receptor signalling, Epithelial-Mesenchymal Transition and Notch-Delta-Jagged signalling | Singh, Divyoj; Bocci, Federico; Kulkarni, Prakash; Jolly, Mohit Kumar | Here, we investigate the coupled dynamics of feedback loops involving a) oscillations in androgen receptor (AR) signalling mediated through an intrinsically disordered protein PAGE4, b) multistability in epithelial-mesenchymal transition (EMT), and c) Notch-Delta-Jagged signalling mediated cell-cell communication, each of which can generate non-genetic heterogeneity through multistability and/or oscillations. | Session 33: Noise and Stochasticity in Biological Networks |
| 595 | RNA splicing and the renormalization group: why simple models can effectively describe complex and noisy gene networks | Vastola, John; Holmes, William | We introduce a framework for thinking about this question in the context of stochastic gene networks, and apply it to understanding RNA splicing and transcription. | Session 33: Noise and Stochasticity in Biological Networks |
| 596 | Use deep learning to infer the probability distributions for stochastic processes | Wang, Shangying; Bianco, Simone | We developed a deep learning algorithm that can predict the probability distribution of the phenotypes based on only one noisy observation for each input condition, without the prior knowledge or assumption of the probability distributions. | Session 33: Noise and Stochasticity in Biological Networks |
| 597 | Precision of Protein Thermometry | Vennettilli, Michael; Saha, Soutick; Roy, Ushasi; Mugler, Andrew | Instead, we find that precision is limited by the intrinsic copy number, turnover, and binding kinetics of temperature-sensitive proteins. | Session 33: Noise and Stochasticity in Biological Networks |
| 598 | Collective gradient sensing with limited positional information | Perez Ipina, Emiliano; Camley, Brian | Here, we apply the maximum likelihood estimation method (MLE) to study the accuracy of gradient sensing of a cluster of cells when there is limited positional information. | Session 33: Noise and Stochasticity in Biological Networks |
| 599 | Kinetic theory for structured populations: application to stochastic sizer-timer models of cell proliferation | Chou, Tom; Xia, Mingtao | Structured population models have been widely used to model cell proliferation that depends on cell age, size, and/or added size since birth. | Session 33: Noise and Stochasticity in Biological Networks |
| 600 | Disentangling intrinsic and extrinsic gene expression noise in growing cells | Lin, Jie; Amir, Ariel | In this work, we prove that the magnitude of the effective spring constant is directly related to the fraction of intrinsic noise in the total protein concentration noise. | Session 33: Noise and Stochasticity in Biological Networks |
| 601 | Unraveling the non-equilibrium dynamics of soft living matter | Broedersz, Chase | Based on a simple model, I will argue that the scaling behavior of such non-equilibrium measures can reveal physical properties of the internal driving. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 602 | Bayesian Inference for Inertial Langevin Dynamics | Ferretti, Federica; Chardès, Victor; Mora, Thierry; Walczak, Aleksandra; Giardina, Irene | We developed a novel analytical Bayesian approach to learn the parameters of such stochastic effective models from discrete finite-length trajectories. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 603 | Nonequilibrium energy transduction in stochastic strongly coupled rotary motors | Lathouwers, Emma; Lucero, Joseph Neil; Sivak, David | Using a simple model of the ingenious rotary machine FoF1-ATP synthase, we investigate the interplay between nonequilibrium driving forces, thermal fluctuations, and interactions between strongly coupled subsystems. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 604 | Using the fluctuation-response relations in biological limit-cycle oscillators to interrogate active feedback and control mechanisms | Sheth, Janaki; Bozovic, Dolores; Levine, Alex | We explore fluctuation dissipation relations in these noisy limit-cycle systems focusing primarily on the hair cells of the inner ear. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 605 | Universal thermodynamic bounds on nonequilibrium response with biochemical applications | Owen, Jeremy; Gingrich, Todd; Horowitz, Jordan | For these families, we present equalities and inequalities valid arbitrarily far from equilibrium that constrain the response of nonequilibrium steady states in terms of the strength of nonequilibrium driving. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 606 | Collision of two cellular aggregates via active vertex model and topological data analysis | Bonilla, Luis; Carpio, Ana; Trenado Yuste, Carolina | We have used an active vertex model for cells undergoing underdamped dynamics with active forces, Vicsek like alignment of cellular velocities and noise to study tumor invasion on epithelial tissue. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 607 | Improved bounds on the entropy production rate in living systems | Skinner, Dominic; Dunkel, Jorn | We demonstrate the broad applicability of this framework by providing improved bounds on the entropy production rate in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 608 | Nonlinear dependence of desynchronization effects of coordinated reset on the number of stimulation sites and frequency | Khaledi Nasab, Ali; Kromer, Justus; Tass, Peter | We study long-lasting desynchronization by coordinated reset (CR) stimulation in excitatory recurrent neuronal networks of integrate-and-fire neurons with spike-timing-dependent plasticity (STDP). | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 609 | Mean Field Theory for Generalized Cortical Branching Model | Weerawongphrom, Naruepon; Goetz, Jeremy; Williams-Garcia, Rashid; Beggs, John; Ortiz, Gerardo | To gain understanding and predict behavior of this many-body system, we develop a method to generate mean-field approximations for any given motif with or without inhibition. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 610 | The unreasonable effectiveness of cluster scaling | Matin, Sakib; Tenzin, Thomas; Klein, William; Gould, Harvey | We generalize the Fisher-Stauffer cluster scaling (from percolation theory) to study the avalanches in the nearest-neighbor stochastic Olami-Feder-Christensen (OFC) model, which is believed to be a non-equilibrium system. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 611 | A theoretical model for viscophoresis: transport in a liquid viscosity gradient | Stein, Derek; Wiener, Benjamin; Lame, Shayan | We present an explanation based on the Maxwell-Stefan (MS) theory of diffusion. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 612 | Passive colloids reveal a wet to dry crossover in active bacterial suspensions | Gokhale, Shreyas; Li, Junang; Solon, Alexandre; Gore, Jeffrey; Fakhri, Nikta | Here, by analyzing the structure and dynamics of passive colloids immersed in active suspensions of motile bacteria, we reveal the existence of two distinct regimes dominated by hydrodynamic and steric interactions respectively. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 613 | Inverse Design of Non-equilibrium Steady-States: A Large Deviation Approach | Piñeros, William; Tlusty, Tsvi | We achieve this design target from direct knowledge of the joint large deviation functional for the empirical density and flow, and a “relaxation” algorithm of the desired target states via adjustable force field parameters. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 614 | Climate variability: a manifestation of fluctuations in a nonequilibrium steady-state | Weiss, Jeffrey; Fox-Kemper, Baylor; Mandal, Dibyendu; Nelson, Arin; Zia, Royce | We propose that the phase space angular momentum and the Lévy stochastic area are useful diagnostics to intercompare climate models and to compare climate models with observations of the climate system. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 615 | Green-Kubo relations for nonequilibrium hydrodynamics transport coefficients | Chun, Hyun-Myung; Gao, Qi; Horowitz, Jordan | Here, we demonstrate that there is a class of perturbations whose response maintains the equilibrium-form of the FDT, yet remains valid arbitrarily far from equilibrium. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 616 | Parallel temperature interfaces in the Katz-Lebowitz-Spohn driven lattice gas | Mukhamadiarov, Ruslan; Priyanka, Priyanka; Tauber, Uwe | We explore a variant of the Katz-Lebowitz-Spohn (KLS) driven lattice gas in two dimensions, where the lattice is split into two regions that are coupled to heat baths with distinct temperatures. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 617 | Steady-state Entropy of Dynamical Systems Described by Intermittent Iterated Maps | Song, Yunxiang; Witten, Thomas | We use iterated phase maps to describe the dynamics of nonlinear oscillators in response to intermittent impulsive forcing. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 618 | Critical Dynamics of Anisotropic Antiferromagnets in an External Field | Nandi, Riya; Tauber, Uwe | We numerically investigate the non-equilibrium critical dynamics in three-dimensional anisotropic antiferromagnets in the presence of an external magnetic field. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 619 | Mechanism of noise-induced wave-number selection in the stabilized Kuramoto-Sivashisky equation | Saxena, Saloni; Kosterlitz, John | We revisit the question of wave-number selection in pattern-forming systems by studying the one dimensional stabilized Kuramoto-Sivashinsky equation with additive Gaussian noise. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 620 | Recovering Classical Langevin Dynamics by Coupling the System to Quantum Noise | Yao, Hong; Tauber, Uwe | We consider a general Hamiltonian system and couple it to a large heat bath consisting of an infinite number of harmonic oscillators at fixed temperature. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 621 | Stochastic charge fluctuations analyzed by factorial cumulants | Stegmann, Philipp; Kurzmann, Annika; Lochner, Pia; Kerski, Jens; Schott, Rüdiger; Ludwig, Arne; Wieck, Andreas; Lorke, Axel; Geller, Martin; Konig, Jurgen | In my talk, I will introduce an evaluation scheme based on generalized factorial cumulants [1,2] which can reveal correlations between tunneling electrons [1,2,3], a violation of detailed balance [4], hidden states and relaxation rates [5], or coherent dynamics [6]. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 622 | Modelling Spontaneous Thermal Fluctuations of Ripples in Suspended Graphene | Lasanta Becerra, Antonio; Bonilla, Luis; Thibado, Paul; Kumar, Pradeep; Singh, Surendra; Ruiz Garcia, Miguel | We present a Langevin model that captures this out-of-plane motion unique to two-dimensional materials. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 623 | Stochastic Line Integrals as Metrics of Irreversibility and Heat Transfer | Teitsworth, Stephen; Neu, John | The streamfunction provides analytical insight to the dependence of stochastic area on parameters such as the noise strength for both nonlinear and linear springs; in particular, we find distinct scaling regimes for stochastic area versus noise amplitude depending on the character of nonlinearity. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 624 | Response and flux of information in extended non-equilibrium dynamics | Vulpiani, Angelo; Baldovin, Marco; Sarra, Camilla | In order to understand the connection between the above mentioned quantities, we investigate spatially asymmetric extended systems. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 625 | A coupled two-species model for the pair contact process with diffusion | Deng, Shengfeng; Li, Wei; Tauber, Uwe | We introduce a two-species representation for the PCPD in which single particles B and particle pairs A are dynamically coupled according to the stochastic reaction processes B+B→A, A→A+B, A→0, and A→B+B, with each particle type diffusing independently. | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 626 | Thermodynamic Signalling in Underdamped Networks | Neu, John | Thermodynamic Signalling in Underdamped Networks | Session 34: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 627 | Local thermodynamics governs the formation and dissolution of protein condensates in living cells | Fritsch, Anatol; Diaz, Andres; Adame-Arana, Omar; Hoege, Carsten; Hyman, Anthony; Julicher, Frank; Weber, Christoph | To address this question, we investigate the response of P granule condensates in living cells to temperature changes as a thermodynamic perturbation. | Session 35: Non-Linear Dynamics in Biological Cells |
| 628 | Active Volume Regulation in Adhered Cells | Adar, Ram; Safran, Samuel | Our theory is based on a minimal model and describes the experimental findings in terms of measurable, mesoscale quantities. | Session 35: Non-Linear Dynamics in Biological Cells |
| 629 | Coarse-grained Modeling of Centrosome Oscillation | Young, Yuan-nan; Farhadifa, Reza; Shelley, Michael | In this talk we present theoretical modeling of centrosome oscillation due to the collective attachment/detachment of cortical force generators to astral microtubules emanating from the centrosome. | Session 35: Non-Linear Dynamics in Biological Cells |
| 630 | Computational model for cell motion on asymmetric surfaces | Herr, Corey; Aronson, Igor; Losert, Wolfgang | We have created a three-dimensional, physics-based model to describe cell motility that links a deformable boundary to an actin polarization vector field. | Session 35: Non-Linear Dynamics in Biological Cells |
| 631 | Understanding the underlying mechanisms of pattern formation and cellular aggregation | Mukhopadhyay, Debangana; De, Rumi | Here we present a model with three different cellular interactions, ie, cell adhesion via physical contact, mechanical and chemotactically driven motility to investigate the growth of collective cellular structures. | Session 35: Non-Linear Dynamics in Biological Cells |
| 632 | Modeling the dynamics of furrow ingression in Drosophila cellularization | UYSALEL, CAN; Sokac, Anna; RANGAMANI, PADMINI | In this work, we developed a quantitative biophysical model of the dynamics of furrow ingression. | Session 35: Non-Linear Dynamics in Biological Cells |
| 633 | Extreme antagonism arising from gene-environment interactions | Wytock, Thomas; Zhang, Manjing; Jinich, Adrian; Fiebig, Aretha; Crosson, Sean; Motter, Adilson | Here, we report on gene-environment (GxE) interactions involving mutations that are deleterious in a permissive environment but beneficial in a specific environment that restricts growth. | Session 35: Non-Linear Dynamics in Biological Cells |
| 634 | SiGMoiD: A superstatistical generative model for binary data | Dixit, Purushottam | Here, we address both these issues with Superstatistical Generative Model for Binary Data (SiGMoiD). | Session 35: Non-Linear Dynamics in Biological Cells |
| 635 | Loop extrusion, chromatin crosslinking, epigenetics, and the geometry, topology and mechanics of chromosomes and nuclei | Marko, John | I will discuss our work on physics-based modeling of the SMC complexes thought to be the loop-extruding elements. | Session 35: Non-Linear Dynamics in Biological Cells |
| 636 | Transport, Delivery, and Kinetics in Tubular Organelle Networks | Scott, Zubenelgenubi; Brown, Aidan; Koslover, Elena | We have developed new methods for efficient numerical simulations of diffusive network transport, for exact calculations of mean first passage times, and for analysis of dynamic experimental data such as single particle trajectories and spreading of photoactivated probes. | Session 35: Non-Linear Dynamics in Biological Cells |
| 637 | Criticality in optimal organelle biogenesis | Yu, Fang; Mukherji, Shankar | Here we propose a model of resource allocation to organelle number and size and use the tools of MINLOP to solve for optimal organelle number and size subject to the constraint of having only a limited pool of resources to build organelles from. | Session 35: Non-Linear Dynamics in Biological Cells |
| 638 | Theoretical framework for the description of transmembrane receptor cluster coalescence in cells | Spendier, Kathrin; Kenkre, Vasudev | We present an approximation method for moving boundaries or traps in reaction-diffusion processes that is applied to investigate coalescence of receptor clusters in mast cells. | Session 35: Non-Linear Dynamics in Biological Cells |
| 639 | Phase-shift and Amplitude Analysis Reveal Stages of Nanoparticle-Assisted Photothermal Annealing of Polydimethylsiloxane | Zahedian, Maryam; Dragnea, Bogdan | In this study, we show that, in conjunction with the more widespread modulation amplitude measurement, the photothermal phase provides a complementary, sensitive probe of thermally-induced changes in the local medium properties. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 640 | Improved characterization of colloidal spheres by modeling effects of spherical aberration in digital holography microscopy | Martin, Caroline; Leahy, Brian; Manoharan, Vinothan | We develop a model for spherical aberration and fit it to experimental data. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 641 | Understanding confinement effects on polymer chain conformation using Förster resonance energy transfer | Fortenberry, Alexander; Qiang, Zhe | This study aims to determine confinement effects on polymer chain conformation using Förster resonance energy transfer (FRET). | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 642 | Deactivation wavelength effect on super-resolution in 3 color lithography thin films | Gutierrez Razo, Sandra; Liaros, Nikolaos; Zeppuhar, Andrea; Petersen, John; Fourkas, John | In this work, we show the effect of optimizing the deactivation wavelength on features in thin films. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 643 | Super-resolution Interference Lithography using Photochromic Photoresists: Towards bulk volume nanopatterning | Vijayamohanan, Hari; Habib, Adela; Sundararaman, Ravishankar; Palermo, Edmund; Ullal, Chaitanya | In order to facilitate this, we develop an efficient electromagnetic (EM) perturbation theory approach that facilitates fully coupled simulations of EM and chemical kinetics to quantitatively analyze the influence of time dependent optical dynamics such as absorption, diffraction, and intensity modulation on the resist chemical kinetics. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 644 | Designable Non-linear Optics of Light-Responsive, Spiroypyran-Functionalized Hydrogels | Meeks, Amos; Mac, Rebecca; Chathanat, Simran; Aizenberg, Joanna | We demonstrate the potential of spiropyran-functionalized, light-responsive hydrogels to be a promising new platform for nonlinear optical materials. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 645 | Excitonic Wave Function Reconstruction from Near-Field Spectra Using Machine Learning Techniques | Zheng, Fulu; Nayak, Sidhartha; Gao, Xing; Eisfeld, Alexander | Here we show that from spatially resolved near field spectra it is possible to reconstruct the underlying delocalized aggregate eigenfunctions [2, 3]. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 646 | Prediction of Effective Optical Properties of Composites via Nonlocal Strong-Contrast Expansions | Torquato, Salvatore; Kim, Jaeuk | Here we derive exact expressions for the nonlocal effective dielectric constants of two-phase composites at intermediate wavelengths by using the "strong-contrast" expansion formalism. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 647 | Understanding the Working Mechanism of Vertical Organic Light Emitting Transistors | DAHAL, DRONA; Radha Krishnan, Raj Kishen; Paudel, Pushpa; Kaphle, Vikash; Lussem, Bjorn | Here, we study the operation of VOLETs experimentally and theoretically. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 648 | Visualizing and controlling polymer nanostructures through in situ optical imaging and synthesis | Wang, Muzhou | In this talk, we will present several of these studies. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 649 | Super Resolution mediated direct visualization of spatial heterogeneities in bulk PNIPAM hydrogels | Kenath, Gopal Sankar; Karanastasis, Apostolos; Yepikhin, Alexander; Ullal, Chaitanya | Here, we report on a super resolution mediated structural study of spatial heterogeneities within bulk PNIPAM hydrogels. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 650 | Resin design for deterministic control of volumetric 3d printing | Liu, Changda; Rackson, Charles; McLeod, Robert | We introduce a resin design scheme that provides deterministic control over the inhibition threshold dose in such resins. | Session 36: Optics and Photonics in Polymers and Soft Matter: Imaging, Characterization and Patterning |
| 651 | Color, structure, and rheology of a diblock bottlebrush copolymer solution | Wade, Matthew; Walsh, Dylan; Lee, Ching-Wei; Kelley, Elizabeth; Weigandt, Kathleen; Guironnet, Damien; Rogers, Simon | At the highest rates applied the solution is indigo. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 652 | Investigating the trade-off between color saturation and angle-independence in photonic glasses | Xiao, Ming; Stephenson, Anna; Hwang, Victoria; Manoharan, Vinothan | To understand why, we quantitatively analyze the trade-off between saturation and angle-dependence in photonic glasses. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 653 | Combined electric and photocontrol of selective light reflection by oblique helicoidal cholesteric doped with azobenzene derivative | Thapa, Kamal; Iadlovska, Olena; Bisoyi, Hari; Paterson, Daniel; Storey, John; Imrie, Corrie; Li, Quan; Shiyanovskii, Sergij; Lavrentovich, O | In this work, we demonstrate that a combined action of the electric field and UV irradiation could continuously tune the pitch of a Ch OH material doped with photosensitive azobenzene molecules capable of trans-cis isomerization. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 654 | Bragg diffraction of obliquely incident light at heliconical cholesteric structures | Iadlovska, Olena; Mrukiewicz, Mateusz; Shiyanovskii, Sergij; Lavrentovich, O | We develop a model of light propagation in Ch OH that explains and reproduces the observed optical effects at oblique incidence of light that might be attractive for applications such as electrically tunable band-pass filters, mirrors, low-threshold lasers, etc. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 655 | Easy to pattern, chemically resistant 1-dimensional polymer photonics | Robertson, Mark; Qiang, Zhe | Herein, we demonstrate a relatively simple and scalable approach to fabricate chemically resistant PCs from cheap commercially available materials, poly(vinylidene fluoride-co-chlorotrifluoroethylene) (PVDF-CTFE) and phenolic resin (resol), using dip-coating to tune the λ max of the PC by adjusting the substrate moving velocity. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 656 | Responsive Polyelectrolyte Multilayer Cladding for Reversibly Programmable Photonics | Sproncken, Christian; Mohammed, Mahir; Gumí-Audenis, Berta; Lazdanaité, Emilija; Stabile, Ripalta; Raz, Oded; Voets, Ilja | We present two approaches to control this shift of the device output. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 657 | Self-Assembly of Colloidal Diamond | Pine, David; He, Mingxin; Gales, Johnathon; Ducrot, Étienne; Gong, Zhe; Yi, Gi-Ra; Sacanna, Stefano | We show that by synthesizing partially compressed tetrahedral clusters with retracted sticky patches, colloidal cubic diamond can be self-assembled using patch-patch adhesion in combination with a steric interlock mechanism that selects the proper staggered bond orientation. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 658 | Waveguide Encoded Lattices (wels): slim polymer films with enhanced fields of view inspired by arthropodal compound eyes. | Benincasa, Kathryn; Saravanamuttu, Kalaichelvi; Fradin, Cecile | In this presentation, we will describe a family of 2 mm to 3 mm thick, polymer films inscribed with WELs, which – like arthropodal compound eyes – have enhanced panoramic field of view (FOV). | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 659 | Electrodynamic modeling of leafhopper brochosomes for synthetic antireflective coatings | Banerjee, Progna; Burks, Gabriel; Bialik, Sarah; Bello, Elizabeth; Alleyne, Marianne; Barrick, Jeffrey; Schroeder, Charles; Milliron, Delia | Using electrodynamic near-field modeling simulations, we study the optical properties by varying the brochosome geometry, arrangements (ordered/disordered with different packing fractions), material properties, and leafhopper species. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 660 | Chiral Liquid Crystal Lenses Confined in Microchannels | Hare, Sean; Lunsford-Poe, Beatrice; Kim, MinSu; Serra, Francesca | We have explored a weakly chiral system in which both types of defects can be present in the same material at different temperatures, and demonstrated a strategy for creating tunable lenses whose focal length can be changed with temperature. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 661 | Thermal-Responsive Second Harmonic Generation in Poly(Ethylene Oxide)/Chromophore Crystalline Films | Xu, Yifan; Zu, Rui; Martin, Rachel; Gopalan, Venkatraman; Hickey, Robert | Here, we present that films composed of poly(ethylene oxide)/ 2-chloro-4-nitroaniline (PEO/CNA) host-guest crystalline complexes exhibit stable and long-term second harmonic generation (SHG) activity, which is a result of the alignment of chromophore molecules during film crystallization. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 662 | Transient Laser Heating Enabled Nanocomposite Structures from Block Copolymers toward Photonic & Phononic Quantum Materials | Yu, Fei; Zhang, Qi; Wiesner, Ulrich | Detailed analysis of X-ray scattering data reveals symmetry reduction from cubic alternating gyroids to orthorhombic networks with D2 point group symmetry. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 663 | A Soft Photopolymer Cuboid That Computes with Binary Strings of Light | Hudson, Alexander; Ponte, Matthew; Mahmood, Fariha; Pena Ventura, Thomas; Saravanamuttu, Kalaichelvi | In this presentation, we discuss a polymer with a nonlinear optical response – namely, a light-induced increase in refractive index – and describe how this response can form the basis of computing-inspired functions. | Session 37: Optics and Photonics in Polymers and Soft Matter: Photonics |
| 664 | Science Responds and CIV: Big Data and Open Science to Combat the Pandemic | Thais, Savannah | This talk will describe the development and activities of Science Responds and in the final portion will provide a deep dive into the COVID Community Vulnerability Index project that was started within Science Responds and has since grown to an international quantitative research project. | Session 38: Physicists Responding to COVID-19 and Beyond: Science and Trajectories |
| 665 | Experiments and simulations to quantify the arrhythmic effects of Hydroxychloroquine (HCQ) and azithromycin (AZM) in the treatment of COVID19. | Fenton, Flavio | We describe numerically and then experimentally the complex, disorganized patterns of electrical activation that develop due to this bifurcation in space. | Session 38: Physicists Responding to COVID-19 and Beyond: Science and Trajectories |
| 666 | Bringing Materials Science to Bear the Covid-19 Needs | Jose-Yacaman, Miguel | In this work we will report the advances in our lab on developing SARS-CoVi-2 testing and will show that can become the golden standard for testing. | Session 38: Physicists Responding to COVID-19 and Beyond: Science and Trajectories |
| 667 | The (Un)known (Un)knowns of COVID-19 Transmission – A Fluid Dynamics Perspective | Mittal, Rajat; Meneveau, Charles; WU, WEN | Inspired by the Drake Equation that provides a framework to estimate the seemingly inestimable probability of advanced extraterrestrial life, I propose a phenomenological model for estimating the risk of airborne transmission of a respiratory infection such as COVID-19. | Session 38: Physicists Responding to COVID-19 and Beyond: Science and Trajectories |
| 668 | Epidemiological Science and How Physicists Can Contribute: The Science of Modeling Infectious Disease Outbreaks | Slayton, Rachel | We often adapt methods from the physical sciences, with compartmental models comprised of ordinary differential equations serving a central role in modeling of emerging infectious diseases. | Session 38: Physicists Responding to COVID-19 and Beyond: Science and Trajectories |
| 669 | Panel Discussion: Career trajectories and perspectives | Panel Discussion: Career trajectories and perspectives | Session 38: Physicists Responding to COVID-19 and Beyond: Science and Trajectories | |
| 670 | Crowding-induced spatial organization of gene expression in cell-sized vesicles | Chauhan, Gaurav; Norred, Elizabeth; Simpson, Michael; Abel, Steven | With a coarse-grained model of DNA plasmids and crowders, we showed that plasmids were uniformly distributed at low levels of crowding but, due to depletion interactions, became strongly adsorbed to confining surfaces at high levels of crowding. | Session 39: Physics in Synthetic Biology |
| 671 | Synthetic biological tuning of metastasis regulator reveals nonmonotonic phenotype response | Wan, Yiming; Cohen, Joseph; Farquhar, Kevin; Nest, Nicholas; smashnov, Alex; Szenk, Mariola; Balazsi, Gabor | Overall, we propose a systematic approach to quantify dose-dependent relationships between TFs and their phenotypic/regulatory functions in mammalian cells, with relevance to cancer, tissue homeostasis and development. | Session 39: Physics in Synthetic Biology |
| 672 | Monitor, categorize and manipulate label-free water-in-oil droplets in microfluidic systems | Neckernuss, Tobias; Frey, Christoph; Pfeil, Jonas; Geiger, Daniel; Platzman, Ilia; Marti, Othmar; Spatz, Joachim | We developed a novel optical device, consisting of a fast camera with integrated data processing for smart and fast algorithms enabling label-free real-time monitoring and active manipulation of passing droplets. | Session 39: Physics in Synthetic Biology |
| 673 | Improved CRISPRi gene circuit function via context-sensitive antisense RNA sequestration | Specht, David; Lambert, Guillaume | By using the binding of the catalytically-dead CRISPR protein dCas12a, we can create programmable gene circuit elements in E. coli. | Session 39: Physics in Synthetic Biology |
| 674 | Emergence of homochirality in large molecular systems | Laurent, Gabin; Lacoste, David; Gaspard, Pierre | In this work, using random matrix theory, we show that large non-equilibrium reaction networks undergo a generic and robust phase transition towards a homochiral state as a consequence of the fact that they contain a large number of chiral species. | Session 39: Physics in Synthetic Biology |
| 675 | Control of Gene Expression through Control of Plasmid Copy Number | Rouches, Miles; Lambert, Guillaume | In this work we demonstrate robust control of plasmid copy number in ColE1 plasmids in several manners – using inducible promoters and massively parallelized assays to investigate the parameters governing plasmid copy number. | Session 39: Physics in Synthetic Biology |
| 676 | Footprints in the noise: understanding gene circuit structure and function using noise spectroscopy | Simpson, Michael | This talk will describe the history of gene expression noise spectroscopy as a means to probe gene regulatory arrangements such as positive and negative autoregulation, including the positive and negative feedback loops in the HIV gene circuit. | Session 39: Physics in Synthetic Biology |
| 677 | Characterization of programmable CRISPR-based toggle switches in Escherichia coli | Xu, Yasu; Lambert, Guillaume | This work aims to provide an efficient and systematic workflow to design, assemble and fine-tune CRISPRi based genetic toggle switches from many potential constructs. | Session 39: Physics in Synthetic Biology |
| 678 | Improving CRISPR gene circuit design using Physics and Synthetic Biology | Lambert, Guillaume; Specht, David; Xu, Yasu | Using a general thermodynamic model of CRISPR-Cas binding dynamics, we unravel the complex energetic landscape of several CRISPR-Cas systems. | Session 39: Physics in Synthetic Biology |
| 679 | Synthetic Biology to Endow Novel Sensing and Reporting Functions in Plants | Stewart, C. Neal | The presentation will focus on gains to produce novel plants to detect and report environmental contaminants. | Session 39: Physics in Synthetic Biology |
| 680 | Materials Physics for Latch-Mediated Spring Actuation (LaMSA) | Crosby, Alfred | Here, we identify underlying principles of LaMSA systems, focusing on physics that define enabling structures-property relationships. | Session 40: Physics of Bio-inspired Materials |
| 681 | Mechanical Response of Bio-Inspired Suture Interface under Dynamic Loading | Nash, Richard; Li, Yaning | In this investigation, we focus on evaluate the influences of the three key design factors of sutures: the suture waviness and geometry, the number of hierarchy, and the introduction of an interphase. | Session 40: Physics of Bio-inspired Materials |
| 682 | Folding of flexible colloidal polymers into colloidal clusters | McMullen, Angus; Brujic, Jasna | Borrowing a concept from biology, here we reduce the dimensionality of the problem by folding 1-D colloidomer chains into compact architectures. | Session 40: Physics of Bio-inspired Materials |
| 683 | Counting the optical cost of disorder in biological photonic systems | Vukusic, Pete | In this presentation, we review biological structurally coloured systems that, in particular, present ordered, quasi-ordered or disordered photonic structures. | Session 40: Physics of Bio-inspired Materials |
| 684 | Biomimetic structural color through arrested phase separation | Sicher, Alba; Menzel, Andreas; Feofilova, Maria; Style, Robert; Rossi, René; Dufresne, Eric | Here, we attempt to scale this process down to the optical scale through polymerization-induced phase separation in a 0.1 GPa-scale network. | Session 40: Physics of Bio-inspired Materials |
| 685 | The role of material architecture to achieve functional hierarchy in the cuticle of the flower beetle, Torynorrhina flammea | Jia, Zian; Fernandes, Matheus; Deng, Zhifei; Yang, Ting; zhang, qiuting; Yin, Jie; Lee, Jae-Hwang; Han, Lin; Weaver, James; Bertoldi, Katia; Aizenberg, Joanna; Kolle, Mathias; Vukusic, Pete; Li, Ling | In this study, we address these challenges based on the cuticle of the flower beetle, Torynorrhina flammea. | Session 40: Physics of Bio-inspired Materials |
| 686 | Continuous, autonomous sub-surface cargo shuttling | Russell, Thomas; Xie, Ganhua; Li, Pei; Gu, Pei-Yang; Helms, Brett; Ashby, Paul; jiang, lei | Inspired by these systems found in nature, we demonstrate autonomous, aqueous-based synthetic systems that overcome the meniscus barrier and shuttle underwater cargo beneath the water surface to and from a landing site and a targeted drop-off site. | Session 40: Physics of Bio-inspired Materials |
| 687 | Hybrid Surface Designs with Passive Anti-Frosting Capabilities | Machado, Christian; Park, Kyoo-Chul (Ken) | Here, we devise an engineered surface to focus a majority of frost formation on millimetric-sized features, inspired by typical leaf structures, while creating a planar region that is thermodynamically preferred to prevent frost. | Session 40: Physics of Bio-inspired Materials |
| 688 | Understanding the multifunctional design of glass skeleton of Euplectella Aspergillum sponge | Chen, Hongshun; Jia, Zian; Li, Ling | With quantitative structural measurements, we construct a biomimetic model to conduct computational study on the mechanics of different cylindrical lattices under different loadings. | Session 40: Physics of Bio-inspired Materials |
| 689 | Bioinspired materials with self-adaptable mechanical properties | Kang, Sung | Inspired by bone mineralization, we report a material system that triggers mineral formation from ionic solutions on scaffolds upon mechanical loadings so that it can self-adapt to mechanical loadings. | Session 40: Physics of Bio-inspired Materials |
| 690 | Growth and roughening of biofilms | Bravo, Pablo; Ng, Siu; Hammer, Brian; Yunker, Peter | Using high-resolution interferometry we study the evolution of surface growth and fluctuations of Vibrio cholerae strains with different rates of EPS production. | Session 41: Physics of Biofilms |
| 691 | Flow-induced symmetry breaking in growing bacterial biofilms | Pearce, Philip; Song, Boya; Skinner, Dominic; Mok, Rachel; Hartmann, Raimo; Singh, Praveen; Jeckel, Hannah; Oishi, Jeff; Drescher, Knut; Dunkel, Jorn | Here, we combine highly time-resolved single-cell live imaging with 3D multi-scale modeling to investigate the mechanisms by which flow affects the dynamics of all individual cells in growing biofilms. | Session 41: Physics of Biofilms |
| 692 | Biomechanical feedback during confined biofilm growth revealed by single-cell resolution imaging | zhang, qiuting; Yan, Jing; Li, Jian; Cohen, Tal; Lu, Haoran; nijjer, japinder | In this presentation, we will integrate single-cell live imaging, finite element modeling, mechanics theories, and mutagenesis to investigate how Vibrio cholerae biofilms grow inside agarose gels. | Session 41: Physics of Biofilms |
| 693 | Physical determinants of bacterial biofilm architecture development | Jeckel, Hannah; Díaz-Pascual, Francisco; Skinner, Dominic; Song, Boya; Jiménez Siebert, Eva; Dunkel, Jorn; Drescher, Knut | In this study we set out to determine which distinct properties of a bacterial species or strains account for the differences between the structure of biofilm microcolonies. | Session 41: Physics of Biofilms |
| 694 | Control of biofilm growth through substrate mechanics | Asp, Merrill; Patteson, Alison | Here, we report the use of synthetic polyacrylamide hydrogels with tunable stiffness and controllable pore size to assess the effects of substrate mechanics on biofilm development. | Session 41: Physics of Biofilms |
| 695 | Growth Characteristics of Pseudomonas Biofilms in Different Types of Gels | Chen, Zilei; Eccles, Mara; Gordon, Vernita | In a current study, we make use of data left from previous researches to observe bacterial attachment to a different kind of gel, the poly(ethylene glycol) diacrylate (PEGDA) hydrogels, to compare to the agar-based gel experiments. | Session 41: Physics of Biofilms |
| 696 | Biofilms deform soft surfaces | Cont, Alice; Rossy, Tamara; Persat, Alexandre | Here, we show that biofilms of the pathogens Vibrio cholerae and Pseudomonas aeruginosa can induce large deformations of soft synthetic hydrogels. | Session 41: Physics of Biofilms |
| 697 | Interfacial Dynamics in Bacterial Growth Patterns | McCalla, Scott; von Brecht, James; Wilking, James | In this talk we will discuss nonlocal pattern forming mechanisms in the context of bacterial colony formation with an emphasis on arrested fronts. | Session 41: Physics of Biofilms |
| 698 | Role of physical interactions in early stages of biofilm formations | Pokhrel, Aawaz; Yunker, Peter | Here we develop a three dimensional agent based model of biofilm formation to investigate the role of physical and biological interactions in biofilm formation. | Session 41: Physics of Biofilms |
| 699 | Revealing biomechanical feedback during biofilm growth with single-cell resolution imaging and modeling | Yan, Jing | In this talk, I will discuss about our recent progress in single-cell imaging and characterization tools to study the morphological evolution of biofilms grown under confinement in the model organism Vibrio cholerae, the agent causing the cholera pandemic. | Session 41: Physics of Biofilms |
| 700 | To Biofilm or Not To Biofilm: A Competition Between Accumulation and Dispersal | Ott, Jenna; Amchin, Daniel; Chiu, Selena; Bhattacharjee, Tapomoy; Datta, Sujit | In some cases, biofilms serve a positive purpose, such as improving health or remediating polluted water; in other cases, they negatively impact our lives, such as by causing infection or fouling equipment. | Session 41: Physics of Biofilms |
| 701 | Watching Gut Microbes Swim, Stick, and Survive | Parthasarathy, Raghuveer | I will describe this approach and experiments that have revealed how bacteria can manipulate intestinal mechanics, how antibiotics can cause collapses in gut populations by altering bacterial community morphology, and how the host immune system might sense bacterial activity. | Session 41: Physics of Biofilms |
| 702 | Emergent robustness of bacterial quorum sensing in fluid flow | Pearce, Philip; Dalwadi, Mohit | Here, we develop and apply a general theory that identifies the conditions required for QS activation in fluid flow by linking cell- and population-level genetic and physical processes. | Session 41: Physics of Biofilms |
| 703 | Simulating biofilm initiation and growth in porous media flow | Lohrmann, Christoph; Lee, Miru; Holm, Christian | We present a bacterial model based on coupling single cells to a surrounding flow. | Session 41: Physics of Biofilms |
| 704 | Experimental Method Development and Analysis of Pseudomonas aeruginosa Surface Attachment | Eccles, Mara; Chen, Zilei; Gordon, Vernita | This study analyzes growth patterns and collection methods to recommend methods for measuring attachment and surface conditions to minimize bacterial growth. | Session 41: Physics of Biofilms |
| 705 | Positive feedback between type IV pili activity and mechanosensation commits P. aeruginosa to surface associated behaviors | Talà, Lorenzo; Kühn, Marco; Negrete, Jose; Pierrat, Xavier; Vos, Iscia; Al-Mayyah, Zainebe; Inclan, Yuki; Patino, Ramiro; Engel, Joanne; Persat, Alexandre | Here we show that Chp activation by TFP provides a positive feedback on its activity. | Session 41: Physics of Biofilms |
| 706 | Phage-bacteria dynamics in spatially structured bacterial communities | Selvakumar, Hemaa; Dominguez-Mirazo, Marian; Thomas, Jacob; Diggle, Stephen; Weitz, Joshua; Curtis, Jennifer | In this study, we investigate the density-dependent dynamics arising from interactions between P. aeruginosa and phage. | Session 41: Physics of Biofilms |
| 707 | Diversity loss as a function of colony morphology | Golden, Alexander; Korolev, Kirill | We study a stochastic model for microbial colony morphology that includes nutrient dynamics and a growth instability, and observe how different colony morphologies affect genetic drift. | Session 41: Physics of Biofilms |
| 708 | Bacterial mechanosensing of substrate stiffness during biofilm initiation: a tale of two steps (and two sensors) | Wang, Liyun; Wong, Yu-Chern (” chad”);=”” blacutt,=”” jacob;=”” gordon,=”” vernita”=” | We use ultrathin and thick hydrogels coated on glass coverslips to create stiff and soft composite materials, respectively, with the same surface chemistry. | Session 41: Physics of Biofilms |
| 709 | Making biofilms easier to eat: a story of blood, bacteria, and bulk mechanics | Wells, Marilyn; Gordon, Vernita | Understanding how the production of particular polymers contributes to the bulk mechanics of a biofilm could lead to developing new methods of compromising the matrix structure and rendering the biofilm more susceptible to antibiotic treatment and/or clearance by the immune system. | Session 41: Physics of Biofilms |
| 710 | Drug effects on Enterococcus faecalis biofilms: growth, topology, and population dynamics | Guardiola Flores, Keanu; Wood, Kevin | In this talk, I will discuss our ongoing work to understand how antibiotics shape, and are reshaped by, the spatial architecture of bacterial biofilms at the single-cell level. | Session 41: Physics of Biofilms |
| 711 | Can bacteria in a biofilm sense and respond to mechanical inputs? | Niese, Brandon; Gordon, Vernita | Recent work, from our group and others, has shown that bacteria can sense and respond to mechanical cues when they are in the single-cell state. | Session 41: Physics of Biofilms |
| 712 | Self-organization of bacteria in confined interstitial biofilms | Nijjer, Japinder; Li, Changhao; Zhang, Sulin; Yan, Jing | Using Vibrio Cholerae as a model biofilm former, we examine the growth of biofilms confined at the interface of a glass and gel surface. | Session 41: Physics of Biofilms |
| 713 | A low dose of cell-wall targeting antibiotic can promote aggregation of Escherichia coli bacteria | Tavaddod, Sharareh; Dawson, Angela; Allen, Rosalind | To study how low-dose antibiotic can promote aggregation and biofilm formation, we developed an experimental assay where E. coli bacteria form aggregates in a shaken suspension upon exposure to a low dose of cell-wall targeting antibiotic. | Session 41: Physics of Biofilms |
| 714 | Mechanical behavior of a migrating cell monolayer. | Delanoe-Ayari, Helene | We observe spontaneous velocity waves, or induce a heterogeneous cell flow around an obstacle to observe cell shape changes and neighbor rearrangements. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 715 | Rigidity sensing regulates epithelial monolayer integrity | LIN, Shaozhen; Sonam, Surabhi; Balasubramaniam, Lakshmi; Prost, Jacques; Rupprecht, Jean-François; Mège, René-Marc; Ladoux, Benoît | To decipher the physical mechanism of hole opening both at the cell and tissue levels, we design a cell-based computational framework (called vertex model) whereby we evaluate two possible models where holes may either form along junctions experiencing high tensile normal stresses (model 1) or along junctions of fast shear strain (model 2). | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 716 | Clustering and ordering in cell assemblies with generic asymmetric aligning interactions | Bertrand, Thibault; d’Alessandro, Joseph; Maitra, Ananyo; Mège, René-Marc; Ladoux, Benoît; Voituriez, Raphaël | We build the corresponding active hydrodynamic theory and show that such asymmetric aligning interaction generically destroys large scale clustering and ordering. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 717 | Boundary conditions determine emergence and dynamics of density patterns in microbial suspensions | Drewes, Nicole; Fragkopoulos, Alexandros; Baeumchen, Oliver | We showed that dense suspensions of motile Chlamydomonas reinhardtii cells aggregate in 2D confinement in response to a reduction of the light intensity. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 718 | Deciphering how forces pull the nucleus during confined cell motility. | Davidson, Patricia; Amiri, Sirine; Sykes, Cécile | We thus reveal one gear of the “mechanostransduction” chain between the cytoskeleton and the nucleoskeleton. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 719 | Collective migration of cells in confinement – contact following and contact inhibition of locomotion | Zadeh, Pedrom; Camley, Brian | We build a model for CIL and CFL within the phase-field approach, which treats cells as continuously deformable objects. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 720 | Collective chemotaxis in a vertex model for confluent clusters | Lawson-Keister, Elizabeth; Manning, M Lisa | Therefore, we construct a 2D Voronoi model for a confluent tissue that incorporates feedback between individual cell properties and a biochemical signaling gradient. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 721 | A Mechano-chemical cell cycle for growing cell colonies | Li, Jintao; Schnyder, Simon; Turner, Matthew; Yamamoto, Ryoichi | We develop a simplified model of the cell cycle, the fundamental regulatory network controlling growth and division, and couple this to physical stress. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 722 | Fluctuations can induce local nematic order and extensile stress in motile cell monolayers | Vafa, Farzan; Bowick, Mark; Shraiman, Boris; Marchetti, M. Cristina | Our work shows that activity can drive either extensile or contractile stresses in tissue, depending on the relative strength of the contractility of the cortical cytoskeleton and tractions by cells on the extracellular matrix. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 723 | Hydrodynamic self-assembly of living chiral crystals | Higinbotham, Hugh; Han, Tzer; Mietke, Alexander; Chen, Yuchao; Foster, Peter; Gokhale, Shreyas; Dunkel, Jorn; Fakhri, Nikta | Here, we report on the formation of chiral crystals of starfish embryos which undergo autonomous order-disorder transitions. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 724 | Active wrinkling in viscoelastic thin sheets | Sknepnek, Rastko; Matoz Fernandez, Daniel; Stanley-Wall, Nicola; Davidson, Fordyce | In this talk, we will show that a viscoelastic thin sheet driven out of equilibrium by active structural remodeling (e.g., fast growth) develops a wide variety of shapes as a result of a competition between viscous relaxation and activity. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 725 | Unravelling the photoreceptor underlying light-switchable adhesion of Chlamydomonas by micropipette force measurements | Girot, Antoine; Catalan, Rodrigo; Vargas, Luiza; Kelterborn, Simon; Hegemann, Peter; Baeumchen, Oliver | In this presentation, we focus on the adhesion of the biflagellated unicellular model organism Chlamydomonas reinhardtii. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 726 | Motility-induced buckling and glassy dynamics regulate 3D transitions in bacterial colonies | Takatori, Sho; Mandadapu, Kranthi | In this talk, we explore the mechanisms behind the 2D-to-3D transition of motile Pseudomonas aeruginosa colonies. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 727 | Intrinsic Rhythms in a Giant Single-Celled Organism and the Interplay with Time-Dependent Drive, Explored via Self-Organized Macroscopic Waves | Afik, Eldad; Liu, Tony; Meyerowitz, Elliot | We explore the system under non-circadian periods, its relaxation times — analogous to jet lag recovery, and the limits at which the system no longer follows the period of the external drive. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 728 | Nonequilibrium polarity-induced chemotaxis: emergent Galilean symmetry and exact scaling exponents | Mahdisoltani, Saeed; Ben Alì Zinati, Riccardo; Duclut, Charlie; Gambassi, Andrea; Golestanian, Ramin | Here we propose a novel mechanism for such interactions, in the context of chemotaxis, which originates from the polarity of the particles and generalizes the well-known Keller-Segel interaction term. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 729 | The role of eDNA in the formation of biofilm streamers | Savorana, Giovanni; Vitale, Alessandra; Eberl, Leo; Stocker, Roman; Rusconi, Roberto; Secchi, Eleonora | Here, we show that a laminar flow of a diluted suspension of Pseudomonas aeruginosa PA14 around a pillar can trigger the formation of suspended filamentous biofilm structures known as streamers and that extracellular DNA (eDNA) plays a fundamental structural role in streamer formation. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 730 | Genome-scale simulations of Escherichia coli colony morphologies and genetic demixing | Dukovski, Ilija; Golden, Alexander; Segrè, Daniel; Korolev, Kirill | Here, we study how environmental factors and metabolic strategies affect morphology and genetic diversity via simulations in COMETS (Computation Of Microbial Ecosystems in Time and Space). | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 731 | Tubulation and dispersion of oil by growth of marine bacteria on oil droplets | Hickl, Vincent; Juarez, Gabriel | Here, we describe experimental observations on the emergence of tubular structures arising from the growth of rod-shaped bacteria at the interface of oil droplets in water. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 732 | Chemotactic smoothing of bacterial populations | Bhattacharjee, Tapomoy; Amchin, Daniel; Alert, Ricard; Ott, Jenna; Datta, Sujit | Here, we describe a previously undocumented mechanism by which bacterial populations regulate their morphology: via self-generated chemotaxis, biased motion in response to a self-generated nutrient gradient. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 733 | Light-regulated cell aggregation in confinement | Fragkopoulos, Alexandros; Vachier, Jeremy; Zwicker, David; Wilczek, Michael; Mazza, Marco; Baeumchen, Oliver | We demonstrate that under confinement this adaptation in a suspension of soil-dwelling Chlamydomonas reinhardtii cells leads to a spontaneous separation into regions of high and low cell densities. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 734 | Density phase transition of spatially confined bacteria | Karita, Yuya; Hallatschek, Oskar | In this study, we culture fly-gut-derived Acetobacter indonesiensis cells in microfluidics, and find three distinct density states sharply depending on the chamber depth. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 735 | Trail following in bacteria | Copenhagen, Katherine; Shaevitz, Joshua | We study the motion of individual M. xanthus cells as they create and follow along trails. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 736 | Growth and characteristic layering of Myxococcus xanthus active nematic droplets | Yang, Cassidy; Shaevitz, Joshua | We find that these aggregates break symmetry and are often elongated in shape with distinctively non-uniform contact angles. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 737 | Bacteria growth and self-organization at liquid interfaces can buckle and deform oil droplets | Juarez, Gabriel | Here we present experimental work where we use microfluidics and time-lapse microscopy to examine the growth of rod-shaped bacteria on stationary oil droplets with maximum diameters ranging from 10 to 200 micrometers. | Session 42: Physics of Biological Active Matter: Cell Colonies |
| 738 | From topological defects to fruiting bodies in bacterial colonies | Alert, Ricard | In this talk, I will show that, in each layer, the rod-shaped M. xanthus cells are densely packed, aligned with neighboring cells, and motile. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 739 | Dynamic coacervation of a DNA Liquid | Abraham, Gabrielle; Chaderjian, Aria; Nguyen, Dan; Saleh, Omar | We aim to mimic this dynamic, self-regulating system using a model DNA liquid system that is transformed by RNA produced from in vitro transcription. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 740 | A theoretical framework for active chiral filaments | Plochocka, Aleksandra; Fuerthauer, Sebastian; Shelley, Michael | Here, we develop a framework for coarse graining chiral filament-filament interactions to obtain an active gel theory for living chiral materials. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 741 | Controlling membrane-less organelles via chemical reactions | Kirschbaum, Jan; Zwicker, David | We investigate how fuel-driven chemical reactions influence the properties of those organelles when the droplet material can switch between a phase separating and a soluble form. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 742 | A data-driven statistical field theory of active matter | Borzou, Ahmad; Schwarz, J. M. | To begin to illuminate the underlying principles, I will present a data-driven statistical field theory for active matter—a leading candidate for quantifying living systems. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 743 | Kinetics of light-switchable surface association of C. reinhardtii populations | Catalan, Rodrigo; Fragkopoulos, Alexandros; Kelterborn, Simon; Hegemann, Peter; Baeumchen, Oliver | We observe that both processes exhibit a lag response relative to the time at which blue- or red-light conditions are set and we model this feature using time-delayed Langmuir kinetics. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 744 | Comparison of different approaches to single-molecule imaging of enhanced enzyme diffusion | Xu, Mengqi; Rogers, W. Benjamin; Ahmed, Wylie; Ross, Jennifer | Using this newly-designed lipid-coated/glycerol chamber, we compare two different analysis approaches for SPT: the mean-squared displacement (MSD) analysis and the jump-length analysis. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 745 | Layered Liquids: A complex tensor theory of simple smectics | Paget, Jack; Shendruk, Tyler | In this work, we take inspiration from the nematic tensor order parameter and derive a novel mathematical description for confined smectic liquid crystals, characterised by a smectic complex tensor order parameter, E. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 746 | Active carpets drive non-equilibrium transport and feature self-cleaning properties | Guzman-Lastra, Francisca; Löwen, Hartmut; Mathijssen, Arnold | Here, we derive the enhanced diffusivity as a function of distance from an active carpet and, following Schnitzer’s telegraph model, we cast these results into generalised Fick’s laws. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 747 | Role of Active Trafficking Dynamics on the Shape and Morphogenesis of Subcellular Compartments | Rautu, Alex; Rao, Madan | We develop a general theory which allows us to study the dynamical interplay of such active processes of fusion and fission with the membrane morphology as well as the hydrodynamics of the ambient fluid. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 748 | Dynamic Mode Structure of Bacterial Turbulence | Martin, Olivia; Henshaw, Richard; Guasto, Jeffrey | Here, we extend the use of modal decomposition to study the dynamical flow structure of this model active matter system. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 749 | Stochastic Spatial Modeling of Attachment and Detachment Processes in Molecular Motor-Cargo Systems | Kramer, Peter; Choudhary, Abhishek; Huang, Yushen | We describe an analytical framework to characterize motor attachment or reattachment times to microtubules in a parallel architecture as a function of the physical and geometric properties of the motor, the cargo to which it is attached, and possibly a second motor attached to the same cargo and a microtubule. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 750 | Photoisomerization-induced wrinkling and leakage in azobenzene-based photoswitchable solid lipid bilayer membranes | Manafirad, Arash; Oville, Christopher; Dinsmore, Anthony | Over a broad range of, we found phase separation into solid DPPC domains and azo-PC enriched domains. | Session 43: Physics of Biological Active Matter: Liquids and Model Systems |
| 751 | Diffusion Tensor Imaging (DTI) Based Drug Diffusion – Population Model in a Solid Tumor | kara, erdi; Rahman, Aminur; Aulisa, Eugenio; Ghosh, Souparno | In this work, we study the effect of drug distribution on tumor cell death when the drug is internally injected in the tumorous tissue. | Session 44: Physics of Cancer |
| 752 | Distinct Roles of Tumor-Associated Mutations in Collective Cell Migration | Lee, Rachel; Vitolo, Michele; Losert, Wolfgang; Martin, Stuart | Multiple studies suggest that cell groups are more likely to form clinically dangerous metastatic tumors. | Session 44: Physics of Cancer |
| 753 | Spatial Distribution of Immune Cells in Tumors | Wortman, Juliana; He, Ting-Fang; Solomon, Shawn; Zhang, Robert; Rosario, Anthony; Wang, Roger; Tu, Travis; Schmolze, Daniel; Yuan, Yuan; Yost, Susan; Li, Xuefei; Levine, Herbert; Atwal, Gurinder; Lee, Peter; Yu, Clare | We describe various techniques we have developed to explore the question of whether the spatial distribution rather than just the density of immune cells in the tumor is important in forecasting whether cancer recurs. | Session 44: Physics of Cancer |
| 754 | EMT-induced cell mechanical changes enhance mitotic rounding strength | Hosseini, Kamran; Taubenberger, Anna; Werner, Carsten; Fischer-Friedrich, Elisabeth | Here, we show that epithelial mesenchymal transition (EMT), a hallmark of cancer progression and metastasis, gives rise to cell-mechanical changes in breast epithelial cells. | Session 44: Physics of Cancer |
| 755 | Quantifying ECM micromechanical remodeling by an invading tumor | Naylor, Austin; McIntyre, David; Sun, Bo | We find that the tumor can introduce strong mechanical anisotropy as well as stiffen the ECM. | Session 44: Physics of Cancer |
| 756 | Mean-field interactions between living cells in linear and nonlinear elastic matrices | Sirote, Chaviva; Shokef, Yair | We consider two simple effective geometries for the spatial arrangement of cells, with spherical and with cylindrical symmetries, and model the presence of neighboring cells by imposing zero-displacement at some distance from the cell, which represents the surface of symmetry between neighboring cells. | Session 44: Physics of Cancer |
| 757 | Spatial variation in cell volume within proliferating tumorigenic cell clusters is amplified by gap-junction-mediated ion flow | McEvoy, Eoin; Han, Yulong; Guo, Ming; Shenoy, Vivek | In this work, we propose a mechano-osmotic model to investigate the evolution of volume dynamics within multicellular systems. | Session 44: Physics of Cancer |
| 758 | Mechanical adaptation of metastatic cancer cells during organ colonization in vivo | Tanner, Kandice | Specifically, this study aims to identify unique mechanical drivers of extravasation in the brain that could be targeted to inhibit brain metastasis in breast cancer patients. | Session 44: Physics of Cancer |
| 759 | Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer | Chauhan, Lakshya; Ram, Uday; Hari, Kishore; Jolly, Mohit Kumar | Here, we investigate a regulatory network underlying phenotypic heterogeneity in small cell lung cancer, a devastating disease with no molecular targeted therapy, and abysmal prognosis. | Session 44: Physics of Cancer |
| 760 | Tumor spheroid chemotaxis in epidermal growth factor gradients revealed by a 3D microfluidic platform | Suh, Young Joon; Pandey, Mrinal; Segall, Jeffrey; Wu, MingMing | We found that EGF gradients promoted tumor cells to detach from the spheroid core, and the position of the tumor spheroid core showed a mild chemotactic response towards the EGF gradients. | Session 44: Physics of Cancer |
| 761 | Understanding the crosstalk between mechanical and chemical guidance in 3d cell migration | Esfahani, Pedram; Sun, Bo | To quantitively analyze the strength of their crosstalks, we develop a u-fluidics device to control the strength of chemo- as well as mechno- cues by aligning ECM fibers. | Session 44: Physics of Cancer |
| 762 | Collective T cell Migration within a 3D printed Immunotherapy Model | Morley, Cameron; Angelini, Thomas | In order to systematically study the interactions of these two cell populations, we employ a method of 3D bioprinting into a bed of jammed microgels where we have control over the spatial relationship between the two cell types. | Session 44: Physics of Cancer |
| 763 | Game Theory Cancer Models of Cancer Cell-Stromal Cell Dynamics using Interacting Particle Systems | Sun, Yusha; Zheng, Yinan; Torga, Gonzalo; Pienta, Kenneth; Austin, Robert | We describe an evolutionary game theory model that has been used to predict the population dynamics of interacting cancer and stromal cells. | Session 44: Physics of Cancer |
| 764 | Tension-dependent Myosin Dynamics on Contractile Actomyosin Structures | Chou, Wen-hung; Kovar, David; Gardel, Margaret | In this work, we assess myosin turnover dynamics on stress fibers with fluorescence recovery after photobleaching (FRAP) experiments. | Session 45: Physics of Cytoskeleton Across Scales |
| 765 | Investigating AGT-DNA covalent and non-covalent interactions in methyl-induced DNA damage repair | Koirala, Rajendra; Pokhrel, Rudramani; Baral, Prabin; Tiwari, Purushottam; Chapagain, Prem; Adhikari, Narayan | Our analysis shows that residues THR95, TYR114, and SER151 in AGT consistently form hydrogen bonding with THY9, THY23, and methylated GUA7 (or repaired GUA7) in DNA suggesting the importance of these residues/nucleotides in the AGT-DNA complex formation. | Session 45: Physics of Cytoskeleton Across Scales |
| 766 | Force and Power Generation by Contractile Actomyosin Gels | Flommersfeld, Johannes; Brückner, David; Jia, Haiyang; Schwille, Petra; Broedersz, Chase | Here, we introduce a novel experimental system which couples reconstituted actomyosin networks to 3D-printed elastic scaffolds, enabling a dynamic quantification of the generated forces. | Session 45: Physics of Cytoskeleton Across Scales |
| 767 | Dissecting cytoquakes in the actomyosin cortex using super-resolved micropost arrays | Sivarajan, Shankar; Shi, Yu; Xiang, Katherine; Crocker, John; Reich, Daniel | We present detailed analysis of the dynamics and size distributions of these cortical "cytoquake" phenomena, via subnanometer particle tracking with poly(dimethylsiloxane) micropost array detectors. | Session 45: Physics of Cytoskeleton Across Scales |
| 768 | Elasticity from entanglements in branched actin | Lenz, Martin; Bouzid, Mehdi; Valencia Gallardo, Cesar; Foffi, Giuseppe; Heuvingh, Julien; du Roure, Olivia | To understand the microscopic underpinnings of their response, we show using high-sensitivity micromanipulation experiments, numerical simulations and theory that unlike usual crosslinked networks, branched actin is dominated by the proliferation of interfilament contacts under compression. | Session 45: Physics of Cytoskeleton Across Scales |
| 769 | Discrete mechanical model of lamellipodial actin networks | Rutkowski, David; Vavylonis, Dimitrios | We developed a filament-level computational model of an actin network undergoing retrograde flow simulated via 3d Brownian dynamics. | Session 45: Physics of Cytoskeleton Across Scales |
| 770 | Exploring the impact of Arp2/3 concentration on actomyosin dynamics | Li, Chengxuan; Liman, James; Eliaz, Yossi; Cheung, Margaret | We have implemented graph theory to quantify the higher-order organization inside actomyosin networks, powerful to visualize the hierarchy of the complex networks as well as to extract unprecedented insights on the dynamics of actomyosin networks that can be validated experimentally. | Session 45: Physics of Cytoskeleton Across Scales |
| 771 | Regulation of actin turnover by myosin activity and network architecture | Scheff, Danielle; Gardel, Margaret | Here, we investigate the ability of myosin activity and actin architecture to control turnover. | Session 45: Physics of Cytoskeleton Across Scales |
| 772 | Dynamic actin waves in primary rat cortical astrocytes sense environmental cues | O’Neill, Kate; Saracino, Emanuela; Barile, Barbara; Mennona, Nicholas; Pathak, Spandan; Mola, Maria Grazia; Nicchia, Grazia Paola; Benfenati, Valentina; Losert, Wolfgang | We propose that actin dynamics are a local manifestation of astrocytes’ global homeostatic response to changes in the extracellular microenvironment. | Session 45: Physics of Cytoskeleton Across Scales |
| 773 | Model of dendritic actin network with distributed turnover and structural remodeling | Holz, Danielle; Hall, Aaron; Vavylonis, Dimitrios | We thus propose a unified mechanism that fits a diverse set of basic lamellipodia phenomenology. | Session 45: Physics of Cytoskeleton Across Scales |
| 774 | The dual role of calcium/calmodulin-dependent kinase II in transducing calcium signals and reorganizing actomyosin networks | Cheung, Margaret | The observation made by a team of collaborators using an integrated approach of experiments, theory, and computation provides a simple mechanism by which the structural dynamics of CaMKII establishes a link between calcium signaling and the morphological plasticity of dendritic spines. | Session 45: Physics of Cytoskeleton Across Scales |
| 775 | Quantifying mechano-chemical coupling between RhoA and the actomyosin cortex in vivo | Tekant, Melis; Choi, Gary; Hastewell, Alasdair; Bacanu, Alexandru; Dunkel, Jorn; Fakhri, Nikta | This method provides a novel approach to probe the local coupling between biochemistry and mechanics. | Session 45: Physics of Cytoskeleton Across Scales |
| 776 | Reconstituting an active cytoskeleton in a droplet | Zhao, Jianguo; Duclut, Charlie; Golipour, Rahil; Pham, An; Golshaei, Behzad; Guan, Chonglin; Harden, James; Jülicher, Frank; Schmidt, Christoph | We constructed a hydrodynamic model of a contracting network with turn-over that can explain the measured actin velocity and density profiles and the resulting stress field, that we probe by local UV laser cutting and magnetic beads. | Session 45: Physics of Cytoskeleton Across Scales |
| 777 | Spatial optimization of transport and capture processes in extended cellular regions | Mogre, Saurabh; Koslover, Elena | We model this diffusive capture process and show that a dispersed microtubule tip arrangement can minimize capture time. | Session 45: Physics of Cytoskeleton Across Scales |
| 778 | Surface fluidity of membrane-bound cargoes enhance their ability to navigate roadblocks | Sarpangala, Niranjan; Gopinathan, Ajay | To explore the mechanisms available for cargoes to get past such roadblocks, we developed a Brownian dynamics simulation of membrane-bound cargo transport by teams of kinesin motors along microtubules that are populated with different kinds of roadblocks. | Session 45: Physics of Cytoskeleton Across Scales |
| 779 | Rare convulsive movements observed in simulations of motorized actin networks with the Arp2/3 complex | Liman, James; Bueno, Carlos; Eliaz, Yossi; Waxham, Neal; Wolynes, Peter; Levine, Herbert; Cheung, Margaret | In this work, we simulate the reorganizations of motorized actin networks with and without the actin-related protein 2/3 (Arp2/3) complex. | Session 45: Physics of Cytoskeleton Across Scales |
| 780 | Modulation of Kinesin’s Load-Bearing Capacity by Force Geometry and the Microtubule Track | Pyrpassopoulos, Serapion; Shuman, Henry; Ostap, Michael | In this study, we found that the effect of opposing forces on the kinesin-microtubule attachment duration depends strongly on experimental assay geometry. | Session 45: Physics of Cytoskeleton Across Scales |
| 781 | Effect of Cargo-Motor Dissociation on transport properties of molecular motor ensemble: A Semi-Analytical Approach | Shrivastava, Rachit; Rai, Ashim; Salapaka, Murti; Sivaramakrishnan, Sivaraj | We hypothesize that the cargo-motor dissociation rate significantly impacts cargo transport by ensembles of molecular motor. | Session 45: Physics of Cytoskeleton Across Scales |
| 782 | Tuning cargo run length via fractional change in kinesin number | Wilson, John; Zaragoza, Arturo; Xu, Jing | Toward this goal, here we employed Monte Carlo simulations to examine the run length of cargos carried by 1-2 motors. | Session 45: Physics of Cytoskeleton Across Scales |
| 783 | Modeling mechanical-force transmission and interactions of myosin motors in the disordered cytoskeleton network | Kumar, Abhinav; Quint, David; Dasbiswas, Kinjal | In future, we will extend our model to describe the force-dependent remodeling dynamics of the actomyosin structures of the cytoskeleton. | Session 45: Physics of Cytoskeleton Across Scales |
| 784 | FRAGMENTATION OF LIPOSOMES BY HYDROPHOBICALLY-MODIFIED POLYPEPTOIDS: ELUCIDATING THE ROLE OF MOLECULAR CHARACTERISTICS | Yu, Tianyi; Omarova, Marzhana; John, Vijay; Zhang, Donghui | In this work, hydrophobically modified polypeptoids (HMPs) have been designed and investigated as facially amphiphiles to fragment liposome to form stable HMP-lipid complexes or nanodiscs. | Session 45: Physics of Cytoskeleton Across Scales |
| 785 | Cholesterol in cargo membrane amplifies inhibitory effect of MAP tau on kinesin-1 | Xu, Jing; Li, Qiaochu; Wilson, John; Ferrare, James; Qiu, Weihong; Vershinin, Michael; King, Stephen; Neuman, Keir; Silver, Jonathan | Here we combine advances in membrane biophysics with established single-molecule optical-trapping assays to characterize the transport of membrane-enclosed cargos in vitro. | Session 45: Physics of Cytoskeleton Across Scales |
| 786 | Intracellular Transport on Dynamic Actin Networks | Ali, Imtiaz; Gopinathan, Ajay | We use a stochastic simulation model that accounts for both active transport along filaments as well as passive diffusion and incorporates the dynamics of the explicitly represented actin network. | Session 45: Physics of Cytoskeleton Across Scales |
| 787 | Motor guidance by long-range communication through the microtubule highway | Wijeratne, Sithara; Fiorenza, Shane; Subramanian, Radhika; Betterton, Meredith | Here we report that microtubules can physically couple motor movement in the absence of short-range interactions. | Session 45: Physics of Cytoskeleton Across Scales |
| 788 | Actin and microtubule crosslinkers roles in mobility and co-localization of filaments in a composite cytoskeletal network | Farhadi, Leila; Rust, Michael; Das, Moumita; Robertson-Anderson, Rae; Ross, Jennifer | Here, we use fluorescent microscopy, fluctuations, and correlation analysis to explore the effect of the actin and microtubule crosslinkers in the cytoskeletal composite network. | Session 45: Physics of Cytoskeleton Across Scales |
| 789 | Polymorphism of tubulin assemblies | Garcia-Aguilar, Ireth; Zwaan, Steven; Giomi, Luca | By modelling tubulin aggregates as continuous elastic materials, we investigate how spontaneous curvature and anisotropic elastic properties influence the resulting equilibrium shape. | Session 45: Physics of Cytoskeleton Across Scales |
| 790 | Optical Tweezers Microrheology of Active Co-entangled Actin-Microtubule Networks | Sheung, Janet; Achiriloaie, Daisy; Lee, Gloria; Peddireddy, Karthik; Robertson-Anderson, Rae | To address this gap, we perform nonlinear optical tweezers microrheology measurements on active actin-microtubule networks driven by the molecular motor myosin II. | Session 45: Physics of Cytoskeleton Across Scales |
| 791 | Tuning Dynamics of Myosin-Driven Actin-Microtubule Networks | Lee, Gloria; leech, gregor; Currie, Christopher; Rust, Michael; Das, Moumita; Ross, Jennifer; McGorty, Ryan; Robertson-Anderson, Rae | Here, we create active composite networks of actin and microtubules that exhibit contractile dynamics driven by myosin II. | Session 45: Physics of Cytoskeleton Across Scales |
| 792 | Microtubule motor protein dynein mediates the collapse of the mitotic spindle following ablation in fission yeast S. pombe | Zareiesfandabadi, Parsa; Elting, Mary | In this work, we find that previously hypothesized viscoelastic relaxation of the nucleus cannot fully explain spindle shortening in response to laser ablation. | Session 45: Physics of Cytoskeleton Across Scales |
| 793 | Principles of spindle size regulation and scaling | Farhadifar, Reza; Yu, Che-Hang; Fabig, Gunar; Wu, Hai-Yin; Stein, David; Müller-Reichert, Thomas; Needleman, Daniel; Shelley, Michael | We used a combination of quantitative microscopy and biophysical perturbations to establish the importance of a balance of cortical pulling forces in the regulation of spindle length and dynamics. | Session 45: Physics of Cytoskeleton Across Scales |
| 794 | A Strong Non-equilibrium Bound for Sorting of Crosslinkers on Growing Biopolymers | Qiu, Yuqing; Nguyen, Michael; Freedman, Simon; Hocky, Glen; Dinner, Aaron; Vaikuntanathan, Suriyanarayanan | Here we use the framework of stochastic thermodynamics to investigate how the actin polymerization rates tune the sorting of actin binding proteins(ABPs) in a growing actin bundle. | Session 45: Physics of Cytoskeleton Across Scales |
| 795 | Breaking down microtubule severing motors: A computational study of lower order katanin oligomers | Macke, Amanda; Varikoti, Rohith Anand; Dima, Ruxandra | We use the combination of structural, kinetic, and Machine Learning approaches to shed light on the stability of lower order oligomers, and the influence of the nucleotide and the substrate on the networks of interactions responsible for the dynamic stability of oligomers. | Session 45: Physics of Cytoskeleton Across Scales |
| 796 | Vimentin Intermediate Filaments Stabilize Dynamic Microtubules by Direct Interactions | Lorenz, Charlotta; Schaedel, Laura; Schepers, Anna; Klumpp, Stefan; Köster, Sarah | Here, we study the interaction between vimentin IFs and MTs in a minimal in vitro system and show that MTs are stabilized against depolymerization by the IFs. | Session 45: Physics of Cytoskeleton Across Scales |
| 797 | Centering of kinetochores is promoted by length-dependent pulling forces exerted by bridging microtubules | Bosilj, Agneza; Tolić, Iva; Pavin, Nenad | In conclusion, we propose that antiparallel overlaps exert length-dependent forces on kinetochores to navigate their positioning in the center of the metaphase plate. | Session 45: Physics of Cytoskeleton Across Scales |
| 798 | Relating energy dissipation to effective interactions and structure formation in the cytoskeleton | Lamtyugina, Alexandra; Qiu, Yuqing; Vaikuntanathan, Suriyanarayanan | Here we aim to find the metrics that govern the formation and stability of structures in the cytoskeleton. | Session 45: Physics of Cytoskeleton Across Scales |
| 799 | Experimental Measurement of Three-Body Interactions of Lipid Membrane-Deforming Colloidal Spheres | Azadbakht, Ali; Doherty, Rachel; Kraft, Daniela | Here, we use this setup to investigate the many-body interactions that arise from three membrane-deforming spheres on a GUV. | Session 45: Physics of Cytoskeleton Across Scales |
| 800 | Actomyosin-driven mechanics of starfish oocytes | Foster, Peter; Fakhri, Nikta | As a step towards addressing this, we here consider the actomyosin-driven surface contraction wave of meiotic starfish oocytes. | Session 45: Physics of Cytoskeleton Across Scales |
| 801 | Mechanisms of actin force production in clathrin-mediated endocytosis revealed by integrating computational modeling with in situ cryo-electron tomography | Akamatsu, Matthew; Serwas, Daniel; Moayed, Amir; Vasan, Ritvik; Vegesna, Karthik; Hill, Jennifer; Schoneberg, Johannes; Davies, Karen; RANGAMANI, PADMINI; Drubin, David | We previously used an experimentally constrained mathematical model to find that a minimal endocytic actin network can self-organize, bend, and produce sufficient force at sites of CME for pit internalization (Akamatsu et al., eLife 2020). | Session 45: Physics of Cytoskeleton Across Scales |
| 802 | Direct measurements of interactions between intermediate filaments | Schepers, Anna; Lorenz, Charlotta; Nietmann, Peter; Janshoff, Andreas; Klumpp, Stefan; Köster, Sarah | Direct measurements of interactions between intermediate filaments | Session 45: Physics of Cytoskeleton Across Scales |
| 803 | Cytoskeletal heavy tails | Camley, Brian; Swartz, Daniel | We present a simple model that naturally creates heavy power-law tails in cytoskeletal displacements. | Session 45: Physics of Cytoskeleton Across Scales |
| 804 | Nonequilibrium simulation of cytoskeletal proteins: assembly, bundling and gelation. | Sorichetti, Valerio; Lenz, Martin | We show that this simple model leads to a very rich range of different behaviors, giving rise to filaments, bundles, and complex bundle/filament networks depending on the thermodynamic parameters considered. | Session 45: Physics of Cytoskeleton Across Scales |
| 805 | Studying in vitro the effect of actin dynamics on membrane tubes | Allard, Antoine; Campillo, Clément; Sykes, Cécile | To address this issue, I use in vitro reconstituted systems with a minimal number of compounds to control the growth of a branched actin sleeve at the surface of preformed tubes. | Session 45: Physics of Cytoskeleton Across Scales |
| 806 | Generic stress rectification in nonlinear elastic materials | Benoist, Félix; Saggiorato, Guglielmo; Lenz, Martin | Here we show that rectification is a more general effect, present in any nonlinear elastic material regardless of the geometry of the applied forces, which results in contraction or expansion depending on the material’s nonlinearities. | Session 45: Physics of Cytoskeleton Across Scales |
| 807 | Coarse-grained simulations of actin polymerization | Hall, Aaron; Horan, Brandon; Vavylonis, Dimitrios | We used such models to reproduce the polymerization of actin monomers to the barbed and pointed ends of actin filaments, the binding of profilin to actin, and the delivery of profilin-actin to the barbed end through flexible disordered regions of actin filament regulators. | Session 45: Physics of Cytoskeleton Across Scales |
| 808 | Nonlinear Viscoelasticity of Semiflexible Polymer Networks | Chen, Sihan; Markovich, Tomer; MacKintosh, Frederick | In this talk, we present an analytical framework for the viscoelasticity of semiflexible polymer networks. | Session 45: Physics of Cytoskeleton Across Scales |
| 809 | Structural actin analysis in primary rat cortical astrocytes predicts culturing nanotopography | Mennona, Nicholas; Barile, Barbara; O’Neill, Kate; Saracino, Emanuela; Pathak, Spandan; Mola, Maria Grazia; Nicchia, Grazia Paola; Benfenati, Valentina; Losert, Wolfgang | We propose that additional co-culture experiments (neurons cultured with astrocytes) will reveal similar disparities at this actin level and may predict astrocytic modulation of neuronal activity. | Session 45: Physics of Cytoskeleton Across Scales |
| 810 | A design framework for highly crosslinked cytoskeletal networks | Fuerthauer, Sebastian; Needleman, Daniel; Shelley, Michael | I will present how this theory is constructed, and discuss its implications for cytoskeletal networks in vitro and in vivo, highlighting how it has helped to quantitatively understand motor driven microtubule fluxes in a system made from XCTK2 motors and stabilized microtubules, and how it resolved long-standing puzzles about the motion of microtubules in spindles. | Session 45: Physics of Cytoskeleton Across Scales |
| 811 | Non-equilibrium fluctuations in cells report on driving forces and organelle mechanics | Nishi, Kengo; Raja, Sufi; Pham, An; MacKintosh, Frederick; Schmidt, Christoph | We present the theory describing the non-equilibrium dynamics of a probe filament embedded in the cytoplasm and show how the method can be applied in HeLa cells. | Session 45: Physics of Cytoskeleton Across Scales |
| 812 | Unified free energy landscapes of non-disulfide-bonded μ conotoxins differ in population depending on folding pathway | Mansbach, R | In this article, we employ the composite diffusion map approach to study their unified folding landscape with unconnected disulfides. | Session 45: Physics of Cytoskeleton Across Scales |
| 813 | Escape of cargo from morphological traps in cytoskeletal networks | Kogan, Oleg; Randell, Brooke; Sarpangala, Niranjan; Gopinathan, Ajay | To calculate the mean time for this escape, we constructed a one-dimensional model that consists of two layers: the advective layer (AL) – representing filaments, and a diffusive layer (DL) – representing the cytoplasm. | Session 45: Physics of Cytoskeleton Across Scales |
| 814 | Effects of External Electric Field on the Thermodynamic Properties of Microtubules During Dynamic Instability | WILLY ANISET, NGANFO | Abstract We investigate the dynamics of microtubules (MTs) under the influence of the electric field using the Ising model. | Session 45: Physics of Cytoskeleton Across Scales |
| 815 | Lagrangian structure and stretching in bacterial turbulence | Henshaw, Richard; Guasto, Jeffrey | In this work, we use Lagrangian analysis techniques to study the chaotic flow fields generated by “bacterial turbulence” in dense suspensions of a model bacterium ( Bacillus subtilis). | Session 45: Physics of Cytoskeleton Across Scales |
| 816 | Distinct connectivity states in actomyosin networks described using the Flory-Stockmayer theory. | Bueno, Carlos; Liman, James; Schafer, Nicholas; Cheung, Margaret; Wolynes, Peter | In this work we model the actomyosin networks using the Flory-Stockmayer theory to describe the conditions under which connectivity percolation occurs. | Session 45: Physics of Cytoskeleton Across Scales |
| 817 | Length fluctuations of long cell protrusions: statistics of passage times, random & extreme excursions | Patra, Swayamshree; Chowdhury, Debashish | Using the generic stochastic models of length control of long cell protrusions and exploiting the techniques of level crossings developed for random excursions of stochastic processes, we have derived analytical expressions of (a) passage times for hitting various thresholds, (b) sojourn times of random excursions beyond the threshold and (c) the extreme lengths attained during the lifetime of these protrusions. | Session 45: Physics of Cytoskeleton Across Scales |
| 818 | Buckling transition for filamentous bundles under constant strain | Morrison, Greg | Using a mean field approach, I identify a critical strain at which buckling will occur for a single filament. | Session 45: Physics of Cytoskeleton Across Scales |
| 819 | Mechanical adaptation via non-equilibrium binding kinetics in the cell cytoskeleton | Tabatabai, Alan; Seara, Daniel; Tibbs, Joseph; Yadav, Vikrant; Murrell, Michael | We show that active catch bonds induce a macroscopic fluid-solid transition, where the extent of broken detailed balance and distinct time-reversal symmetries characterize each material phase. | Session 45: Physics of Cytoskeleton Across Scales |
| 820 | Insights from Graph Theory on the Morphologies of Actomyosin Networks with Multilinkers | Eliaz, Yossi; Nedelec, Francios; Morrison, Greg; Levine, Herbert; Cheung, Margaret | We investigated the role of multivalent actin-binding proteins (ABPs) in reorganizing actin filaments into higher order complex networks via a computer model of semiflexible filaments. | Session 45: Physics of Cytoskeleton Across Scales |
| 821 | Confined filaments in soft vesicles- the case of sickle red blood cells. | Behera, Arabinda; Kumar, Gaurav; Sain, Anirban | Here, we focus on sickle-shaped RBC, which form due to the abnormal growth of semi-rigid hemoglobin (HbS) fibers confined in RBC. | Session 45: Physics of Cytoskeleton Across Scales |
| 822 | Beller Lectureship (2021): Organizing Principles of Mitochondria, from Fission to RNA Granules | Manley, Suliana | We use super-resolution microscopy and fluorescent sensors of physiological and biophysical states to understand how mitochondrial division and transcription are physically regulated and organized. | Session 45: Physics of Cytoskeleton Across Scales |
| 823 | Programmable phase behavior in biopolymer solutions | Jacobs, William | Here we describe a theoretical model of phase separation in which components may be shared among multiple condensates. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 824 | Elastic frustration in self assembling system leads to fiber formation | Le Roy, Hugo; Terzi, Mert; Lenz, Martin | We try to understand this tendency that a wide variety of protein exhibit using a very general mechanism. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 825 | Modeling Multiparticle Complexes in Fock Space | Rousseau, Rebecca J; Kinney, Justin | We approach this challenge by describing an operator formalism for classical multi-particle complexes. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 826 | Protein Aggregation in vivo: Stochasticity and the Method of Second Stochastization | Shen, Jia-Liang; Tsai, Min-Yeh; Schafer, Nicholas; Wolynes, Peter | To explore the mechanistic details of the stochastic aggregation process more efficiently, we explore a new approach to stochastic aggregation kinetics based on accompanying noise in averaged equations based on mathematical moment closure schemes. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 827 | Condensate rheology affects the irreversible formation of fibrils | Pönisch, Wolfram; Michaels, Thomas; Weber, Christoph | To address this question, we present a kinetic theory of fibril aggregation in the presence of phase-separated condensates and account for condensate rheology by a mobility that depends on the aggregate size. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 828 | The role of complementary shape in protein dimerization | Gao, Fengyi; Glaser, Jens; Glotzer, Sharon | Using molecular simulation, we investigated the binding of 50 protein dimers with atomic-level resolution of rigid molecular shape and a generic entropic depletion interaction to isolate the role of shape in the assembly of these dimers, and compared the assembled configurations with known native structures. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 829 | Mechanobiology of stator remodeling in the bacterial flagellar motor | Wadhwa, Navish; Tu, Yuhai; Berg, Howard | We built a model that captures the observed dynamics and provides insight into the underlying molecular interactions. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 830 | Active and stochastic triggering of protein self-assembly in cells | FU, YIBEN; Guo, Sikao; Johnson, Margaret | Using kinetic and reaction-diffusion modeling, we show how the stoichiometry of the assembly components, which can be effectively controlled via enzymatic reactions (which turn on and off interactions), can control the kinetics and success of clathrin assembly. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 831 | Observables for seperating droplets and binding-site clusers in foci | Heltberg, Mathias | In this work we outline possible observables to differentiate between the two existing models based on tracking of single molecules. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 832 | Physical Principles for Assemblies in Protein-complexes | Gasic, Andrei; Sarkar, Atrayee; Cheung, Margaret | Here, we utilized the tools of statistical inference and modeling from experimental data dealing with the average abundances of various protein species. | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 833 | Hierarchically Organized Structure of Electrospun Nanofibers from Computationally Designed Peptide Bundlemers | Kim, Kyunghee; Kloxin, Christopher; Saven, Jeffery; Pochan, Darrin | Hierarchically Organized Structure of Electrospun Nanofibers from Computationally Designed Peptide Bundlemers | Session 46: Physics of Emergent Protein-Complex Assemblies |
| 834 | Strategies transcription factors use to gain access to nucleosomal DNA | Poirier, Michael | Strategies transcription factors use to gain access to nucleosomal DNA | Session 47: Physics of Genome Organization |
| 835 | Three-dimensional modeling dynamics of nuclear organization | Laghmach, Rabia; Di Pierro, Michele; Potoyan, Davit | Here, we present a multiphasic liquid model of nucleus to study the 3D chromatin organization dynamics. | Session 47: Physics of Genome Organization |
| 836 | Decoding DNA Barcodes using a Double-Nanopore System | Seth, Swarnadeep; Vuong, An; Reisner, Walter; Dunbar, William; Bhattacharya, Aniket | We propose alternative method to rectify this which we believe is relevant for experiments. | Session 47: Physics of Genome Organization |
| 837 | Mechanical Control of Transcriptional Elongation by DNA Supercoiling | Tripathi, Shubham; Brahmachari, Sumitabha; Onuchic, Jose; Levine, Herbert | Here, we describe a theoretical model that couples RNAP motion and DNA torsional response, and use the model to predict the RNAP velocity on stretched and / or twisted DNA. | Session 47: Physics of Genome Organization |
| 838 | Dynamic nuclear structure emerges from chromatin crosslinks and motors | Liu, Kuang; Patteson, Alison; Banigan, Edward; Schwarz, J | To identify the physical mechanisms, we develop a model of an active, crosslinked Rouse chain bound to a polymeric shell. | Session 47: Physics of Genome Organization |
| 839 | Aberrant CTCF binding facilitates phase-separated transcriptional condensate formation in cancer | Wang, Zhenjia; Zang, Chongzhi | Using an integrative data science approach, we systematically analyzed hundreds of CTCF ChIP-seq datasets and other genomic big data across different human tissues and cancer samples and identified cancer-specific patterns of gained and lost CTCF binding in several cancer types. | Session 47: Physics of Genome Organization |
| 840 | Piercing Mechanism of Biological Nano-injection Machines | Maghsoodi, Ameneh; Perkins, Noel | We propose a dynamic model of contractile phages to elucidate how they work in real-time. | Session 47: Physics of Genome Organization |
| 841 | Molecular switch control of nucleic-acid processing machines | Chemla, Yann | In this talk, I will discuss our work developing new single-molecule methods and integrating them with computational approaches to provide unprecedented access into the mechanisms of these molecular machines. | Session 47: Physics of Genome Organization |
| 842 | Inference of emergent spatio-temporal processes in single-cell genomics | Olmeda, Fabrizio; Lohoff, Tim; Clark, Stephen; Benson, Laura; Krueger, Felix; Reik, Wolf; Rulands, Steffen | We capture these findings in a mechanistic model of de-novo methylation. | Session 47: Physics of Genome Organization |
| 843 | Malleable DNA knot translocation in single-digit nanopores | Sharma, Rajesh; Agrawal, Ishita; Dai, Liang; Doyle, Patrick; Garaj, Slaven | Here, using solid-state nanopores, we study the translocation dynamics of knots in 48.5 kbp long lambda DNA molecules in a new regime of nanoscale confinement, large driving forces applied over short timescales. | Session 47: Physics of Genome Organization |
| 844 | THE EFFECT OF GENOME SIZE ON THE STRUCTURE OF VIRAL SHELLS | Panahandeh, Sanaz; Li, Siyu; Zandi, Roya | We develop a model to investigate the impact of genome size on the structure of capsids. | Session 47: Physics of Genome Organization |
| 845 | Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales | Messelink, Joris; van Teeseling, Muriel; Janssen, Jacqueline; Thanbichler, Martin; Broedersz, Chase | We develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi-C experiments on the model organism Caulobacter crescentus. | Session 47: Physics of Genome Organization |
| 846 | Structural and Dynamical Signatures of Local DNA Damage in Live Cells | Eaton, Jonah; Zidovska, Alexandra | We investigate the interphase chromatin dynamics in human cells in response to local damage, DNA double strand breaks (DSBs), by monitoring the DSB dynamics and the compaction of the surrounding chromatin in live cells. | Session 47: Physics of Genome Organization |
| 847 | Mapping the organization of Esherichia Coli Chromosome in a HI-C integrated model | Mondal, Jagannath; Wasim, Abdul; Gupta, Ankit | In the seminar we will present a model where we combine a beads-on-a-spring polymer-based framework with recently reported high-resolution Hi-C data of E. coli chromosome to develop a comprehensive model of E. coli chromosome at 5 kilo base-pair resolution. | Session 47: Physics of Genome Organization |
| 848 | The influence of transcription in nucleosome positioning | Jiang, Zhongling; Zhang, Bin | Through numerical simulations, we investigated the influence of DNA sequence specificity, transcription factor binding, enzyme remodeling, and Pol II elongation in nucleosome positioning across species near the transcription start site (TSS). | Session 47: Physics of Genome Organization |
| 849 | Theoretical study of chromatin organization at the mesoscale | Adame-Arana, Omar; Bajpai, Gaurav; Safran, Samuel | Motivated by these findings, we provide analytical insight using two complementary approaches. | Session 47: Physics of Genome Organization |
| 850 | Exploring coupled epigenetic and genetic switches with variational methods | Sood, Amogh; Zhang, Bin | In this work, we introduce a minimal kinetic model for gene regulation that accounts for the impact of histone modifications on protein production by a self-activating gene. | Session 47: Physics of Genome Organization |
| 851 | Plasticity of genome structure and organization governed by the differential activity of SMC complexes | Brahmachari, Sumitabha; Contessoto, Vinicius; Di Pierro, Michele; Onuchic, Jose | Here, we adopt an energy-landscape-based polymer model of chromosomes that features SMC-driven linear compaction as an externally controllable degree of freedom. | Session 47: Physics of Genome Organization |
| 852 | Homolog locus pairing is a transient, diffusion-mediated process in meiotic prophase | Beltran, Bruno; Newman, Trent; Burgess, Sean; Spakowitz, Andrew | We develop a theory for Rouse polymers with “homologous” linkages, and show that the plateau behavior is consistent with a handful of randomly-spaced linkages per chromosome forming over the course of meiosis. | Session 47: Physics of Genome Organization |
| 853 | Chromatin Structure and Activity Modifies Dynamics and Interactions | Forte, Giada; Brackley, Chris; Gilbert, Nick; Marenduzzo, Davide | In this talk I will discuss the HiP-HoP model to predict the mobility of the Pax6 locus in mouse cell lines with different expression states. | Session 47: Physics of Genome Organization |
| 854 | Fibration symmetries uncover the building blocks of biological networks | Leifer, Ian; Morone, Flaviano; Makse, Hernan | We found that genetic networks exhibit fibration symmetry, which have never been observed in physical systems. | Session 47: Physics of Genome Organization |
| 855 | On the Border of Order: Chromosomal Organization in Space and Time | Dudko, Olga | We show how concepts from statistical physics help reveal the physical principles by which cells solve this first-passage problem with astonishing efficiency. | Session 47: Physics of Genome Organization |
| 856 | Centromeres and Telomeres as Rheological Probes of the Human Nucleus | Clavijo, Alexis; Ionov, Steven; Zidovska, Alexandra | In this work, we investigate dynamics of specific genomic loci, centromeres and telomeres, the centers and ends of the linear interphase chromosomes, respectively, in the context of their local rheological environment. | Session 47: Physics of Genome Organization |
| 857 | Noninvasive Measurement of Interphase Chromatin Rheology In Vivo | Eshghi, Iraj; Eaton, Jonah; Zidovska, Alexandra | Recently, we developed an injection-free noninvasive approach to study chromatin rheology using nuclear organelles as native probes [2]. | Session 47: Physics of Genome Organization |
| 858 | Synchronization on the random graph with non-linear interaction: application to breathing. | Slepukhin, Valentin; Ashhad, Sufyan; Feldman, Jack; Levine, Alex | We consider a system of leaky integrate-and-fire neurons interacting through a lognormal distribution of synaptic weights on random, directed graphs. | Session 48: Physics of Neural Systems |
| 859 | Stimulus information in collective response of tree networks of excitable elements | Chauhan, Kanishk; Khaledi-Nasab, Ali; Tass, Peter; Neiman, Alexander | We show that in the strong coupling limit, the MI is determined by the number of nodes and leaves. | Session 48: Physics of Neural Systems |
| 860 | Information tradeoffs in receptor arrays | Holmes, Caroline; Bialek, William | We explore this tradeoff between bits of sensory information and bits of positional information. | Session 48: Physics of Neural Systems |
| 861 | Controlling phase-locked functional connectivity states with local perturbations to multi-regional brain circuits | Papadopoulos, Evangelia; Battaglia, Demian; Bassett, Danielle | Past work has proposed multistable phase-locking as a way for fixed networks to yield multiple functional states, without the need to rewire anatomical links. | Session 48: Physics of Neural Systems |
| 862 | Stimulation-induced long-lasting desynchronization of plastic neuronal networks | Kromer, Justus; Tass, Peter | We present a Random Reset stimulation protocol that specifically targets synaptic connections. | Session 48: Physics of Neural Systems |
| 863 | Decoding locomotion from population neural activity in moving C. elegans | Hallinen, Kelsey; Dempsey, Ross; Scholz, Monika; Yu, Xinwei; Linder, Ashley; Randi, Francesco; Sharma, Anuj; Shaevitz, Joshua; Leifer, Andrew | We investigate neural representations of locomotion by recording calcium activity from the majority of neurons in the compact brain of the nematode C. elegans as it crawls freely. | Session 48: Physics of Neural Systems |
| 864 | Experimental Evidence of Quasicriticality in the Brain | Fosque, Leandro; Williams-Garcia, Rashid; Ortiz, Gerardo; Beggs, John | We address this problem using the organizing principle of quasicriticality, developed as a framework for cortical dynamics. | Session 48: Physics of Neural Systems |
| 865 | Scaling Theory in Axons and Dendrites | Desai-Chowdhry, Paheli; Brummer, Alex; Savage, Van | Here, we explore the possibility of extending this theoretical framework to analyze structural properties of neurons, aiming to understand the relationship between neuron structure and function. | Session 48: Physics of Neural Systems |
| 866 | Predictive capacity of a dynamical system | Krishnamurthy, Kamesh; Bialek, William; Frishman, Anna; Chen, Xiaowen | Here we propose an alternative explanation based on Prediction — i.e. larger N allows us to better predict the entire future state of the environment from the current internal state. | Session 48: Physics of Neural Systems |
| 867 | Associative memory by generalized holography | Bergmann, Ernest; Fowler, W | Associative memory by generalized holography | Session 48: Physics of Neural Systems |
| 868 | Conservation of underlying stereotypy in olfaction. | Alus, Or; Magnasco, Marcelo; Wachowiak, Matt | Given data of mice glomeruli responses to a large number of chemicals we show conservation across animals of the underlying activity and therefore of the encoding transformation carried out by the receptors. | Session 48: Physics of Neural Systems |
| 869 | Impact of Sodium Channel Distribution in the Axon Initial Segment on the Initiation and Backpropagation of Action Potentials | Barlow, Benjamin; Joos, Bela; Longtin, Andre | We propose an intuitive explanation: the cell becomes more excitable —including backpropagation— when the Na v distribution places more low-threshold channels closer to the site of stimulation. | Session 48: Physics of Neural Systems |
| 870 | Automatic Neuron Correspondence Prediction In C.elegans With Deep Learning | Yu, Xinwei; Creamer, Matthew; Leifer, Andrew | We present a deep learning method based on the transformer architecture for finding neural correspondence and apply it to the brain of C. elegans. | Session 48: Physics of Neural Systems |
| 871 | A mathematical model of reward-mediated learning in drug addiction | Maestrini, Davide; D’Orsogna, Maria; Chou, Tom | We propose a mathematical model combining the so-called opponent process theory (OPT) and the reward prediction error (RPE) in the context of drug addiction. | Session 48: Physics of Neural Systems |
| 872 | Statistical Motor Biomarkers Characterizing age-dependence in Neurodevelopmental Disorders | Doctor, Khoshrav; Wu, Di; Phadnis, Aditya; Nurnberger, John; Plawecki, Martin; Jose, Jorge | We broadened our previous studies of subjects with Autism Spectrum Disorder (ASD), to subjects with Attention Deficit Hyperactivity Disorder (ADHD), Comorbid ASD and ADHD. | Session 48: Physics of Neural Systems |
| 873 | Reaction-diffusion modeling of neurotransmitter processing at a high frequency synapse | Alkhammash, Elham; L’Heureux, Ivan; Morris, Catherine; Joos, Bela | Assuming periodic release of ACh into the cylindrical synaptic gap, we solve numerically a one dimensional reaction-diffusion model at 200Hz and 500Hz. | Session 48: Physics of Neural Systems |
| 874 | Generalized ORGaNICs: Towards a Unifying Framework for Neural Dynamics | Rawat, Shivang; Heeger, David; Martiniani, Stefano | Here, we derive a generalized class of ORGaNICs, enabling us to broaden the range of cognitive and perceptual phenomena that can be recapitulated by this framework under realistic biophysical constraints. | Session 48: Physics of Neural Systems |
| 875 | Quantal slowing in coupled rhythmogenic neural networks: Applications to breathing | Womack, Taylor | We examine this phenomenon using leaky integrate-and-fire neuron models of both central pattern generators with synaptic coupling between them. | Session 48: Physics of Neural Systems |
| 876 | Local homeostatic regulation of the spectral radius of echo-state networks | Schubert, Fabian; Gros, Claudius | We demonstrate the effectiveness of the new adaption rule by applying it to echo-state networks and testing their task performance under a time-delayed XOR operation on random binary input sequences. | Session 48: Physics of Neural Systems |
| 877 | Nonequilibrium Green’s functions for functional connectivity in the brain | Randi, Francesco; Leifer, Andrew | In this talk, I will show how nonequilibrium Green’s functions can be used to describe the time-dependent functional connectivity of a continuous-variable network of neurons. | Session 48: Physics of Neural Systems |
| 878 | Biological learning of local motion detectors | Tesileanu, Tiberiu; Genkin, Alexander; Chklovskii, Dmitri | Here we provide a normative model to explain why more distant connections are not used. | Session 48: Physics of Neural Systems |
| 879 | Using Neural Networks for Dual Dimensionality Reduction | Abdelaleem, Eslam; Nemenman, Ilya | Here we develop a deep learning based method for performing a dual dimensionality reduction: compressing two multidimensional variables while maximizing the correlation between their compressed description. | Session 48: Physics of Neural Systems |
| 880 | Crystallinity characterization of white matter in the human brain | Teich, Erin; Cieslak, Matthew; Giesbrecht, Barry; Vettel, Jean; Grafton, Scott; Satterthwaite, Theodore; Bassett, Danielle | Here, we address these issues by introducing tools from materials science for the characterization of white matter microstructure. | Session 48: Physics of Neural Systems |
| 881 | Hysteresis in Models of Neuronal Dynamics | Weis, Cheyne; Fruchart, Michel; Galda, Alexey; Hanai, Ryo; Littlewood, Peter; Vitelli, Vincenzo | The Wilson-Cowan model has described a variety of different statistical behaviors in neocortical dynamics. | Session 48: Physics of Neural Systems |
| 882 | A phenomenological model explains critical periods in learning | Sederberg, Audrey; Nemenman, Ilya | Building on the Langevin dynamics formulation of this model for the dynamics of Bayesian learning, we develop a general approach to find conditions under which critical periods naturally appear as a result of Bayes-optimal learning. | Session 48: Physics of Neural Systems |
| 883 | Ensembling Diverse Neural Networks for Improved Protein Contact Prediction | Billings, Wendy; Della Corte, Dennis | We propose that the deep learning practice of ensembling has the potential to improve protein contact prediction by combining the outputs of discrete neural networks. | Session 48: Physics of Neural Systems |
| 884 | Dynamically learning neural interactions that improve information | Tchernookov, Martin; Singh, Vijay | To demonstrate a possible unsupervised search mechanism, we develop a model of orientation-selective neurons where the interactions between the neurons are learned dynamically from the responses to external stimuli. | Session 48: Physics of Neural Systems |
| 885 | Computational Enzyme Design: Progress and Obstacles | Young, Naomi | This talk draws from this review to discuss the significant developments of computational enzyme design within the last five years and unique solutions to long-standing issues. | Session 49: Physics of Proteins |
| 886 | Non-Equilibrium Dynamics of a Pump Protein Measured with Multidimensional Single-Molecule Spectroscopy | King, John; talele, saurabh | Here, we study the dynamics of bacteriorhodopsin during its light-activated, multi-step catalytic cycle that results in vectorial H+ transport across a membrane. | Session 49: Physics of Proteins |
| 887 | Probing Local Structures of an Intrinsically Disordered Protein Through Single-Molecule Force Stretching Experiments | Truong, Hoang; Morgan, Ian; Saleh, Omar | Overall, we show complex elastic behaviors that reveal local structures in an IDP, and we demonstrate a framework to study the conformations of IDPs through force stretching experiments. | Session 49: Physics of Proteins |
| 888 | Protein Dynamics from Distance Predictions | Jarrett, Austin; Morris, Connor; Della Corte, Dennis | Many of these methods use machine learning techniques to generate inter-residue distance predictions. | Session 49: Physics of Proteins |
| 889 | Network inference for analyzing protein dynamics | Liu, Jenny; Keten, Sinan; Amaral, Luis A | We apply this inverse approach to two adhesion proteins, FimH and Siglec-8, to identify networks that are distinct from correlation networks and instead resemble a contact map. | Session 49: Physics of Proteins |
| 890 | Computation of exit times for potential landscapes in CRISPR binding | Rigas, Pete | In this work, an IVP associated with a stochastically driven oscillator for the exit time will be presented, from which exit times for varying potential landscapes are obtained. | Session 49: Physics of Proteins |
| 891 | The folding of a metamorphic protein | Wallin, Stefan; Seifi, Bahman | We used a hybrid sequence-structure based all-atom model to simulate the folding and fold switching of the C-terminal domain (CTD) of the bacterial transcription factor RfaH, a prototypical metamorphic protein. | Session 49: Physics of Proteins |
| 892 | Sequence-dependent mechanics of collagen proteins reflect their structural and functional organization | Al-Shaer, Alaa; Lyons, Aaron; Ishikawa, Yoshihiro; Hudson, Billy; Boudko, Sergei; Forde, Nancy | Here, we combine position-dependent flexibility analysis with single-molecule imaging by atomic force microscopy (AFM), and find that collagens exhibit variable flexibility along their backbones. | Session 49: Physics of Proteins |
| 893 | Time-resolved Infrared Structural Biology of Proteins: Bringing New Light to Protein Structural Dynamics and Function | Xie, Aihua | Time-resolved Infrared Structural Biology of Proteins: Bringing New Light to Protein Structural Dynamics and Function | Session 49: Physics of Proteins |
| 894 | Universality in activated barrier crossing | Adhikari, Sudeep; Beach, Kevin | We identify universal behavior of the barrier crossing process and demonstrate that data collapse onto a universal curve can be achieved for simulated data over a wide variety of energy landscapes having barriers of different height and shape. | Session 49: Physics of Proteins |
| 895 | Molecular Dynamics Investigations of Inward-facing and Outward-facing Isomerization of PfMATE | Hossen, Md Lokman; Bhattarai, Nisha; Gerstman, Bernard; Chapagain, Prem | To investigate this process, we performed molecular dynamics simulations of different systems of inward- and outward-facing PfMATE in the native archaeal lipid bilayer. | Session 49: Physics of Proteins |
| 896 | A local probe for evolutionary conformational changes of proteins | Das, Tamoghna; Tlusty, Tsvi | Here, we employ a purely geometric, nonlinear measure of local conformational changes and study its statistics. | Session 49: Physics of Proteins |
| 897 | Tug-of-war in motor proteins and the emergence of Levy walk | Moon, Kyungsun; Moon, Hyungseok | We have theoretically studied a random walk model based on majority rule. | Session 49: Physics of Proteins |
| 898 | Towards integrative structural biology of proteins at ultra-high resolution | Hoff, Wouter; Matsuo, Junpei; Kikukawa, Takashi; Fujisawa, Tomotsumi; Unno, Masashi; Xie, Aihua | Here we propose to use integrative structural biology to obtain insights at very high structural resolution. | Session 49: Physics of Proteins |
| 899 | Probing Dynamics of Hemeproteins in Solution by the High Sensitivity Dielectric Terahertz Spectroscopy | Doan, Luan; Seay, Sarah; Nguyen, Vinh | Probing Dynamics of Hemeproteins in Solution by the High Sensitivity Dielectric Terahertz Spectroscopy | Session 49: Physics of Proteins |
| 900 | Investigation of Electrical Conductance in Immobilized Zebrafish Cryptochrome (zfCRY4) Protein | Nguyen, Anh; Partch, Carrie; Lederman, David | In the past decades, several studies have shown that many animals, especially migratory birds, have an ability to detect and utilize the Earth’s magnetic field information to navigate their way during migration. | Session 49: Physics of Proteins |
| 901 | Computational Studies of Asymmetric Conformational Dynamics of AAA+ Machines Involved in Protein Disaggregation | Dayananda, Ashan; Dima, Ruxandra; Stan, George | To study the allosteric regulation and asymmetric conformational dynamics of this machine, we performed all-atom molecular dynamics simulations of two different conformational states (“ring” and “spiral”) of ClpB in nucleotide and/or substrate-bound or apo configurations. | Session 49: Physics of Proteins |
| 902 | A Comparison of the Slow Dynamics in the Protein Ubiquitin Predicted by the LE4PD, PCA, and tICA from a Long Equilibrium Molecular Dynamics Simulation | Beyerle, Eric; Guenza, Marina | Here, we connect the slow dynamics predicted by the LE4PD to that predicted by principal component analysis (PCA) and time-lagged component analysis (tICA). | Session 49: Physics of Proteins |
| 903 | Combining Consensus and Ensemble Docking Methods Improves Molecular Docking | Morris, Connor; Stark, Brenden; Della Corte, Dennis | We present a combined consensus and ensemble docking protocol to further improve docking predictions. | Session 49: Physics of Proteins |
| 904 | TBD | Nussinov, Ruth | TBD | Session 49: Physics of Proteins |
| 905 | Binding mechanism of SARS-CoV-2 spike protein with human ACE2 receptor | Koirala, Rajendra; Thapa, Bidhya; Khanal, Shyam; Powrel, Jhulan; Adhikari, Rajendra; Adhikari, Narayan | In the present work, we have studied the dynamical behaviour of the complex by analyzing the molecular dynamics (MD) trajectories.The major interacting residues of SARS-CoV-2CTD and hACE2 have been identified by analyzing the nonbonded interactions such as hydrogen bondings, salt bridges, hydrophobic interactions, van der Waals interactions etc. | Session 49: Physics of Proteins |
| 906 | Flow sensing in the bacterial flagellar motor of E. Coli | Sinjab, Faris; Krasnopeeva, Ekaterina; Rosko, Jerko; Pilizota, Teuta | We are characterising this response by varying the flow speed and adjusting the availability of torque-generating stator proteins, and modifying some recent biophysical models to explore possible shear flow sensing mechanisms. | Session 49: Physics of Proteins |
| 907 | Coarse-grained model of dielectric geometry-modified screened electrostatic protein-protein interactions | Dickie, Joshua; Ross, David; Hamilton, John; Wahle, Christopher; Thurston, George | To refine a coarse-grained model of protein interactions, we seek to conveniently represent how dielectric interface geometry and charge placement affect screened aqueous electrostatic interactions. | Session 49: Physics of Proteins |
| 908 | van der Waals Forces in Biomolecular Systems: from Solvation to Long-range Interaction Mechanisms | Stoehr, Martin; Gori, Matteo; Kurian, Philip; Tkatchenko, Alexandre | Here, we investigate the electronic response properties and vdW interaction in biomolecular systems within a quantum-mechanical many-body treatment. | Session 49: Physics of Proteins |
| 909 | Electron transport through single proteins, peptides and amino acids | Romero-Muñiz, Carlos; Ortega, María; Vilhena, Jose Guilherme; Diéz-Pérez, Ismael; Perez, Ruben; Cuevas, Juan Carlos; Zotti, Linda Angela | In particular, the blue-copper azurin extracted from Pseudomonas aeruginosa has been the subject of many experimental studies, although the exact transport mechanism is still under debate. | Session 49: Physics of Proteins |
| 910 | Multi-Scale Computational Study on SARS-CoV and SARS-CoV-2 | Xie, Yixin; Li, Lin | Key residues that are involved in salt bridges and hydrogen bonds are identified in this study, which may help the future drug design against COVID-19. | Session 49: Physics of Proteins |
| 911 | Building blocks of protein structure – physics meets biology | Skrbic, Tatjana; Banavar, Jayanth; Giacometti, Achille; Maritan, Amos; Rose, George | We use this as a guiding principle to derive the geometry of the building blocks of protein structures – alpha helices and strands assembled into beta-sheets – with no adjustable parameters, no amino acid sequence information, and no chemistry. | Session 49: Physics of Proteins |
| 912 | In-silico epitope prediction against the Lassa virus glycoprotein | Baral, Prabin; Pavadai, Elumalai; Gerstman, Bernard; Chapagain, Prem | Using various molecular computational tools, we have identified LASV GP major histocompatibility complex (MHC) class I and II T cell epitopes. | Session 49: Physics of Proteins |
| 913 | Computational biomimetic-inspired modifications on the reaction and geometry of the FeNi Hydrogenase active site | McGreal, Meghan; Goodpaster, Jason | We performed a KS-DFT study of the catalytic cycle of FeNi Hydrogenase. | Session 49: Physics of Proteins |
| 914 | A protein that remembers its past: Glassy behavior in an intrinsically disordered protein | Morgan, Ian; Rahamim, Gil; Beck, Roy; Saleh, Omar | We present a mechanism by which conformational heterogeneity creates a rich mechanical response in single polymers. | Session 49: Physics of Proteins |
| 915 | Glycine Shows Preference for Polyproline II Indicating Greater Role for Amino Acid Backbone | Andrews, Brian; Zhang, Shuting; Schweitzer-Stenner, Reinhard; Urbanc, Brigita | In this work, triglycine (GGG), which is intrinsically disordered due to its short length, is simulated using three commonly used Molecular Dynamic (MD) force fields. | Session 49: Physics of Proteins |
| 916 | Visualizing Amino Acid Substitutions in Physicochemical Space for Machine Learning | Nemzer, Louis | This work can be applied to machine learning algorithms to better understand the underlying mechanisms behind these hereditary conditions. | Session 49: Physics of Proteins |
| 917 | Did proteins evolve structural asymmetry for faster co-translational folding? | McBride, John; Tlusty, Tsvi | To explore this question, we analyze 16,200 structures from the protein data bank (PDB). | Session 49: Physics of Proteins |
| 918 | Endogenous metabolite modulates protein-protein interactions in Escherichia coli | Gupta, Rachit; Chawla, Ravi; Perdomo, Nicolas; Rhee, Kathy; Lele, Pushkar | In this work, we studied the influence of indole on the functioning of a large, multimeric protein complex-the flagellar motor-in E. coli. | Session 49: Physics of Proteins |
| 919 | Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence | Smith, Douglas; Mo, Youbin; Keller, Nick; Deltoro, Damian; Ananthaswamy, Neeti; Harvey, Stephen; Rao, Venigalla | To more generally test sequence dependence, we conducted correlation analyses across pairs of events. | Session 49: Physics of Proteins |
| 920 | Allosteric communications between protein domains via linker and substrate modulate the function | SARKAR, SUSANTA | We calculated the distance between the two locations from the single molecule Forster Resonance Energy Transfer (smFRET) between the two dyes, measured using a Total Internal Reflection Fluorescence (TIRF) microscope. | Session 49: Physics of Proteins |
| 921 | Langevin Equations for Macromolecules in Body-Fixed Frames | Hall, Jesse | We present a Langevin equation for systems of interacting particles, based on a previous approach to Langevin mode analysis, in the canonical coordinates of an arbitrary body-fixed frame that accounts for these frame effects and couplings. | Session 49: Physics of Proteins |
| 922 | A mass spectrometer for single-molecule protein sequencing | Drachman, Nicholas; Stein, Derek | Here we report the development of a new mass spectrometry technique featuring a nanocapillary ion source capable of emitting single amino acid ions directly into high vacuum from aqueous solution, sidestepping the drawbacks of conventional electrospray. | Session 49: Physics of Proteins |
| 923 | Measuring the flow-mediated transport velocity of lipid-anchored proteins in supported lipid bilayers | Ratajczak, Amanda; Miller, Ethan; Rivera, Xaymara; Honerkamp-Smith, Aurelia | Here, we use microfluids and fluorescence microscopy to monitor the dynamics of membrane reorganization under an applied flow in order to investigate the underlying biophysics of flow responses. | Session 49: Physics of Proteins |
| 924 | Markerless tracking of an entire insect colony | Bozek, Katarzyna; Hebert, Laetitia; Portugal, Yoann; Stephens, Greg | We present a method for the markerless tracking of nearly all individuals in a colony of honey bees Apis mellifera. | Session 50: Physics of Social Interactions |
| 925 | Voronoi analysis of laboratory midge swarms | Feng, Yenchia; Yang, Patricia; Ouellette, Nicholas | By constructing Voronoi tessellations of swarms, we demonstrate that we can divide them into distinct concentric layers. | Session 50: Physics of Social Interactions |
| 926 | Specialization and plasticity in a primitively social insect | Patalano, Solenn; Alsina, Adolfo; Rulands, Steffen; Reik, Wolf | Here we use primitive societies of Polistes wasps as a model system where we experimentally perturb the social structure by removing the queen and follow the re-establishment of the social steady state over time. | Session 50: Physics of Social Interactions |
| 927 | Black soldier larvae actively modify packing density under ramping airflows | Ko, Hungtang; Shishkov, Olga; Aydin, Enes; Hu, David; Goldman, Daniel | In a fluidized bed (9.5 cm in diameter) of active granular media consisting of 300 and 600 g of black soldier fly larvae, we observe no hysteresis in a fluidization/defluidization cycle, while dead (freshly frozen) larvae behave like inert granular media. | Session 50: Physics of Social Interactions |
| 928 | Modeling collective dynamics of aquatic worm blobs | Nguyen, Chantal; Ozkan-Aydin, Yasemin; Bhamla, Saad; Peleg, Orit | We demonstrate how a blob is able to collectively traverse temperature gradients via the coupling between the active motion and the environment. | Session 50: Physics of Social Interactions |
| 929 | Critical density in collective escape waves in fish | Poel, Winnie; Daniels, Bryan; Sosna, Matthew; Twomey, Colin; Couzin, Iain; Romanczuk, Pawel | We find that even though dynamical range and sensitivity are maximized at the critical point, the fish schools remain subcritical, which we attribute to a trade-off between false and true positives. | Session 50: Physics of Social Interactions |
| 930 | Early social context alters paired interactions in the bumblebee Bombus impatiens | McKenzie-Smith, Grace; Wang, Z. Yan; Cho, Hyo Jin; Pereira, Talmo; Kocher, Sarah; Shaevitz, Joshua | In this study we investigate whether this period is also an important part of social development by quantifying the effects of social isolation on adult behavior. | Session 50: Physics of Social Interactions |
| 931 | Collective problem solving by social insects | Mahadevan, Lakshminarayanan | Motivated by observations in the field and in the lab, I will describe our attempts to understand how insects build and use active architectures to regulate their micro-environment in such contexts as termite mound morphogenesis and physiology, and active ventilation, mechanical stabilization and thermoregulation in bee clusters. | Session 50: Physics of Social Interactions |
| 932 | De Gennes’s "Ant is A Labyrinth" problem confronted by real ants | feinerman, ofer; Gelblum, Aviram; Fonio, Ehud; Rodeh, Yoav; Korman, Amos | To set a scale on the navigational efficiency of the ants ,we mapped their motion onto the ‘Ant-in-a-Labyrinth’ framework which studies physical transport through disordered media. | Session 50: Physics of Social Interactions |
| 933 | Analysis of the internal structure of honeybee swarms with x-ray CT | Shishkov, Olga; Nave, Gary; Peleg, Orit | We use x-ray computed tomography to investigate how honey bees structure their arrangement within the swarm such that the load on each bee is bearable, the bees do not fall down, and the swarm can adapt to the changing environment. | Session 50: Physics of Social Interactions |
| 934 | Collective Aggregation via Directed Pheromone Signaling in Honeybee Swarms | Nguyen, Dieu My; Iuzzolino, Michael; Mankel, Aaron; Bozek, Katarzyna; Stephens, Greg; Peleg, Orit | We combine a novel behavioral assay with computer vision for bee detection and scenting recognition to track the swarming dynamics. | Session 50: Physics of Social Interactions |
| 935 | Group size effects in jackdaw flocks | Yang, Patricia; Feng, Yenchia; Mclvor, Guillam; Thornton, Alex; Ouellette, Nicholas | We will describe the structure and dynamics of more than 100 transit flocks of jackdaws, a highly social corvid species, measured in the field. | Session 50: Physics of Social Interactions |
| 936 | Quantifying the pairwise fighting behavior of zebrafish in 3D | O’Shaughnessy, Liam; Izawa, Tatsuo; Shaevitz, Joshua; Stephens, Greg | We study fighting behavior in pairs of male zebrafish imaged at high spatiotemporal resolution in 3D. | Session 50: Physics of Social Interactions |
| 937 | Information spread enhanced by criticality in high-responsive groups of fish | Gómez Nava, Luis Alberto; Lange, Robert; Klamser, Pascal; Sprekeler, Henning; Romanczuk, Pawel | We study high-density giant schools of fish (sulphur mollies; up to 3000 fish/m2) which in their natural habitat (sulphuric ponds/streams) are mostly confined to the surface. | Session 50: Physics of Social Interactions |
| 938 | Mean Field Trajectories in a Spin Model for Decision Making on the Move | Gorbonos, Dan; Couzin, Iain; Gov, Nir | A model of collective decision making regarding direction of travel was introduced as an extension of the Ising model where the spin-spin interaction is interpreted as a social force. | Session 50: Physics of Social Interactions |
| 939 | Vocal communication as cooperative sensing for navigation | Zhang, Yisi; Ghazanfar, Asif | In both the laboratory and field studies, changes in acoustic features of affiliative vocalizations exhibit a consistent relationship with physical distance from conspecifics: longer distances induce louder calls. | Session 50: Physics of Social Interactions |
| 940 | The Emergence of a Collective Threshold in the Response of Colonies of Clonal Raider Ants to Temperature Perturbations | Gal, Asaf; Kronauer, Daniel | Here we study this emergence in the clonal raider ant ( Ooceraea biroi), a model system that provides convenient and precise control over the properties of the colony. | Session 50: Physics of Social Interactions |
| 941 | A model of collective behavior based purely on vision | Bastien, Renaud; Romanczuk, Pawel | Our work suggests a different approach for the development of purely vision-based autonomous swarm robotic systems and formulates a mathematical framework for exploration of perception-based interactions and how they differ from physical ones. | Session 50: Physics of Social Interactions |
| 942 | Social cognition— shaped by Social Complexity or Coercion? A test with socially complex fish | Cummings, Molly | Our research enables us to identify the social factors that contribute to the development of adult behavior, cognitive abilities, and the forces that shape the circuitry of the vertebrate brain. | Session 50: Physics of Social Interactions |
| 943 | A pipeline for robustly measuring social behavior using deep learning | Agezo, Sena; Borie, Amelie; Kacsoh, Dori; Young, Larry; Liu, Robert; Berman, Gordon | To improve the tracking of animals within social contexts, where the animals are in close proximity for long periods of time, we implemented a pipeline that combines multiple deep-learning-based tracking methods to obtain detailed and high-accuracy postural trajectories of multiple animals. | Session 50: Physics of Social Interactions |
| 944 | Evolutionary spatial games with mean-field interactions | Antonov, Dmitriy; Burovski, Evgeni; Shchur, Lev | We introduce a mean-field term to an evolutionary spatial game model. | Session 50: Physics of Social Interactions |
| 945 | Yeasts collectively extend the limits of habitable temperatures | Laman Trip, Diederik; Youk, Hyun | We show that budding yeasts, despite being single-celled organisms, collectively combat rising temperatures [1]. | Session 50: Physics of Social Interactions |
| 946 | Early warning signals in motion inference | Hart, Yuval; Vaziri Pashkam, Maryam; Mahadevan, Lakshminarayanan | We show that the transition to action has the hallmark of a critical transition that is accompanied by early warning signals. | Session 50: Physics of Social Interactions |
| 947 | Synchronization of Coupled Kuramoto Oscillators under Resource Constraints | Kroma-Wiley, Keith; Mucha, Peter; Bassett, Danielle | A fundamental understanding of synchronized behavior in multi-agent systems can be acquired by studying analytically tractable Kuramoto models. | Session 50: Physics of Social Interactions |
| 948 | Information Propagation and Synchrony in Firefly Natural Swarms | Sarfati, Raphael; Peleg, Orit | Despite casual descriptions of collective flashing and hasty analogies with models of coupled oscillators, careful observations and quantitative analysis suggest that the underlying mechanisms of synchrony are complex and remain poorly understood. | Session 50: Physics of Social Interactions |
| 949 | Ecological significance of imperfectly synchronized collective behaviors | Martinez Garcia, Ricardo; Rossine, Fernando; Sgro, Allyson; Gregor, Thomas; Tarnita, Corina | We propose that Dictyostelium loners—cells that do not join the multicellular life stage— arise from a dynamic population-partitioning process, the result of each cell making a stochastic, signal-based decision. | Session 50: Physics of Social Interactions |
| 950 | Universal scaling laws of interaction time distribution in honeybee and human social networks | Choi, Sang Hyun; Rao, Vikyath; Gernat, Tim; Hamilton, Adam; Robinson, Gene; Goldenfeld, Nigel | We report high-throughput automated measurements of trophallaxis and face-to-face event durations of honeybees. | Session 50: Physics of Social Interactions |
| 951 | An Adaptive Voter Model in Heterogeneous Environments | Chu, Olivia; Wiedermann, Marc; Donges, Jonathan | In this work, we explore the effects that such heterogeneous preferences have on the dynamics of the adaptive voter model. | Session 50: Physics of Social Interactions |
| 952 | Catalyzing Collaborations: A Model for the Dynamics of Team Formation at Conferences | Zajdela, Emma; Abrams, Daniel; Wiener, Richard; Feig, Andrew | In this work, I present a dynamical model for predicting the formation of scientific collaborations at conferences, inspired by the process of catalysis. | Session 50: Physics of Social Interactions |
| 953 | Accurate Density-Functional Fluctuation Theory (DFFT) approach to forecasting ethnic composition of neighborhoods. | Barron, Boris; Kinkhabwala, Yunus; Hall, Matthew; Cohen, Itai; Arias, Tomas | Here, we demonstrate the power of Density-Functional Fluctuation Theory (DFFT) to address challenges (1) and (2) to produce novel forecasts of neighborhood-level composition changes. | Session 50: Physics of Social Interactions |
| 954 | Opinion dynamics under antagonistic influences | Bhat, Deepak | We study the opinion dynamics of a generalized voter model in which N voters are additionally influenced by two antagonistic news sources. | Session 50: Physics of Social Interactions |
| 955 | Understanding mate choice signal-receiver dynamics using a phase space embedding approach | Etheredge, Robert; Stephens, Greg; Jordan, Alex | Here we use high-resolution descriptions of animal movement to build a principled basis for investigating courtship signaling dynamics in guppies. | Session 50: Physics of Social Interactions |
| 956 | Psychophysics of Musical Rhythms and the Riddle of Swing | Geisel, Theo; Nelias, Corentin; Datseris, George | Can we clarify the controversial role of microtiming deviations for the swing feel? | Session 50: Physics of Social Interactions |
| 957 | Phase Behavior of Polymer-Grafted Nanoparticles | Frischknecht, Amalie; Koski, Jason; Santos, Andrew | We use theoretically-informed Langevin dynamics (TILD) simulations to determine the structure of polymer brushes on single grafted NPs and to calculate equilibrium phase diagrams in solution. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 958 | The Bulk Phase Behavior of Ternary Mixtures of Polymers and Two Good Solvents | Zhang, Xiangyu; Zong, Jing; Meng, Dong | In this study, we combine the self-consistent field (SCF) calculations and the Gibbs-ensemble simulations that employ identical models to determine the binodal curves of ternary mixtures of polymers and two good solvents. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 959 | Shear-Sensitive Chain Extension of Poly(ethylene oxide) by Aluminate Ions During Concrete Curing | Hoagland, David; Srivastava, Satyam; Fink, Zachary; Russell, Thomas; Burns, Elizabeth | We hypothesize weak, attractive ion-mediated chain-chain interactions, and in particular, a weak coupling between hydroxyl end groups (at just one PEO chain end) disrupted by the shearing during intrinsic viscosity measurements. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 960 | Helical Persistence Length of Poly-L-Lysine | Wilcox, Kathryn; Dingle, Marlee; Morozova, Svetlana | In order to understand the role of α-helical flexibility in protein function, we investigate the helical and electrostatic contributions to the persistence length ( l p) of poly-L-lysine (PLL) independently by inducing a coil-helix transition by changing the pH, and probing the electrostatic effects by changing the solution ionic strength. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 961 | Kinetics of xanthan in denaturation and renaturation process in dilute aqueous NaCl solution | Tomofuji, Yu; Terao, Ken; Matsuo, Koichi | Our research suggests that the slow deformation and rapid recovery of ordered structure of the main chain may contribute to maintain the functionality derived from the polymer conformation. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 962 | Ion jacket regulates flexible biopolymer conformation in salt mixtures | Innes-Gold, Sarah; Jacobson, David; Pincus, Philip; Stevens, Mark; Saleh, Omar | We use single-molecule magnetic tweezers to measure three biological PEs in various salt mixtures. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 963 | Characterizing Synthetic Random Heteropolymers through Simulation | Hilburg, Shayna; Xu, Ting; Alexander-Katz, Alfredo | Here, we present the impact of composition, molecular weight, and solvent environment on a single-chain methacrylate-based synthetic heteropolymer system. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 964 | Decoupling conjugated polymer’s backbone and sidechain conformation by selective deuteration and neutron scattering | Cao, Zhiqiang; Li, Zhaofan; Zhang, Song; Galuska, Luke; Li, Tianyu; Do, Changwoo; Xia, Wenjie; Hong, Kunlun; Gu, Xiaodan | We obtained the form factor of P3ATs’ backbone, sidechains, and cross scattering term by deconvoluting their respective scattering signals. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 965 | Designing Bottlebrush Additives with Polyfluoropolyether (PFPE) Sidechains: Focus on Bottlebrush Architecture and Effects of Solvent Quality | Tu, Sidong; Choudhury, Chandan; Wei, Liying; Luzinov, Igor; Kuksenok, Olga | We develop a coarse-grained model of this amphiphilic bottlebrush using dissipative particle dynamics (DPD) approach and validate our model with respect to the prior molecular dynamics simulations and experimental studies. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 966 | Coarse-grained Simulations of Poly (ethylene oxide) Linear Chains and Catenanes in dilute solutions | Chen, Jiuke; qian, kun; Tsige, Mesfin | Here, we report Molecular dynamics (MD) simulation results on the structural and dynamical properties of PEO linear chains and catenanes in dilute solutions. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 967 | Entropy Driven Assemblies in Dilute Solution | Xu, Ting | I will describe a recent studies showing that chemical diversity and complexity can enhance system miscibility such that entropy-driven phase behavior can be realized in composites. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 968 | Structure-property relationships of branched polyethylene in dilute solution | Ivancic, Robert; Thompson, Chase; Orski, Sara; Audus, Debra | Here, we perform molecular dynamics simulations using an experimentally inspired potential to study the structure-property relationships of branched polyethylene in the dilute regime. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 969 | Nitroxide Radical Polymer-Solvent Interactions and Solubility Parameter Determination | Easley, Alexandra; Vukin, Lillian; Flouda, Paraskevi; Howard, Dylan; Pena, Jose; Lutkenhaus, Jodie | In this talk, the Hildebrand and Hansen solubility parameters of poly(2,2,6,6-tetramethylpiperidinyloxy-4-yl methacrylate) (PTMA) and oxidized PTMA (PTMA+) will be discussed from both experimental and group contribution methods. | Session 51: Polymer Structure Formation and Dynamics in Solution: Chain Conformations and Phase Separation |
| 970 | Formation and Equilibration of Block Copolymer Micelle in Ionic Liquids via Co-solvent Method | Chen, Liwen; Early, Julia; Lodge, Timothy | In this work, 1,2-polybutadiene- b-poly(ethylene oxide) (PB-PEO) was first dissolved in a mixture of the PEO-selective ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide and a neutral solvent dichloromethane. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 971 | Criteria governing rod formation vs. wormlike micelle growth in self-assembled polymers | McCauley, Patrick; Patel, Kush; Kumar, Satish; Calabrese, Michelle | This research sheds light on the fundamental role of poloxamer subunit and solution conditions on assembly and growth processes, providing a comprehensive dataset for validating thermodynamic models. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 972 | Self-assembly of Amphiphilic Bottlebrush Bock Copolymers in Solution | Pan, Tianyuan; Patel, Bijal; Walsh, Dylan; Dutta, Sarit; Guironnet, Damien; Diao, Ying; Sing, Charles | Using this new model, we perform non-dilute Molecular Dynamics simulations of bottlebrush block copolymer solution assembly. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 973 | Solution Self-Assembly of Coil-Crystalline Diblock Copolypeptoids: The Effects of Linear and Branched N-Alkyl Substituents | Jiang, Naisheng; Kang, Liying; Chao, Albert; Zhang, Meng; Yu, Tianyi; Wang, Jun; John, Vijay; Li, Ruipeng; Fukuto, Masafumi; Zhang, Donghui | Solution Self-Assembly of Coil-Crystalline Diblock Copolypeptoids: The Effects of Linear and Branched N-Alkyl Substituents | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 974 | Computational Reverse-Engineering Analysis for Scattering Experiments (CREASE) on the Self-Assembly of Amphiphilic Polymer-peptide Conjugates | Ye, Ziyu; Jayaraman, Arthi | Taking in scattering intensity profiles and polymer chemistries as inputs, CREASE combines genetic algorithm and molecular reconstruction simulations to determine the peptide amphiphile bilayer composition, vesicle dimensions (e.g. core diameter, layer thicknesses) and molecular level packing within the nanostructure. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 975 | Equilibration and Dynamics in Block Copolymer Micelles | Lodge, Timothy | We will describe measurements using dynamic light scattering, small-angle X-ray scattering, and liquid-phase TEM to follow the fragmentation process in detail. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 976 | Self-Growing Polymer Gels with Tunable Swelling Properties | Chatterjee, Rayan; Biswas, Santidan; Yashin, Victor; Balazs, Anna | To this end, we present a minimalistic theoretical model of two types of self-growing polymer gels, one comprising of an interpenetrating network (IPN) of two parent-chains, and the other one consisting of a random copolymer network (RCN), with the copolymers being formed by an inter-chain exchange between the IPN units. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 977 | Salt Dependent Structure in Methylcellulose Fibrillar Gels | Liberman, Lucy; Schmidt, Peter; Coughlin, McKenzie; Matatyaho, Asia; Davidovich, Irina; Edmund, Jerrick; Ertem, S. Piril; Morozova, Svetlana; Talmon, Yeshayahu; Bates, Frank; Lodge, Timothy | We propose two different mechanisms of fibril diameter reduction with the addition of salt. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 978 | The role of hydrogen bonding and chain configuration in magnetically-induced ordering of block copolymer systems | Kresge, Grace; Calabrese, Michelle | We recently discovered anomalous field-induced phase transitions in industrially-relevant BCP solutions (20-30 wt%) using weak magnetic fields (B > 0.5 T), which can be used to control their self-assembly and long-range ordering. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 979 | Effect of poly(N-isopropylacrylamide) grafting on the temperature dependent properties of methylcellulose solutions | Coughlin, McKenzie; Edmund, Jerrick; Bates, Frank; Lodge, Timothy | In this study, we present the effect of PNIPAm on the chain conformation and fiber formation of MC. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 980 | Free Energy Profile for Chain Expulsion from a Diblock Copolymer Micelle | Seeger, Sarah; Dorfman, Kevin; Lodge, Timothy | We utilize umbrella sampling to probe the full free energy profile of expulsion of a single chain from a diblock copolymer micelle in solvent. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 981 | Structure and dynamics of polymeric hybrid physical-covalent assemblies of computationally designed peptidic bundlemers | Sinha, Nairiti; Shi, Yi; Jensen, Grethe; Pochan, Darrin | Structure and dynamics of polymeric hybrid physical-covalent assemblies of computationally designed peptidic bundlemers | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 982 | The Cosolvent Effects on Micellization of Diblock Copolymers in a Selective Solvent | Zong, Jing; Zhang, Xiangyu; Meng, Dong | In this study, the Field-Accelerated Monte Carlo simulation and the self-consistent field calculations are employed in the grand canonical ensemble to examine the influence of adding a mutual solvent (a good solvent for both polymer blocks) on the DBC micelles formed in a selective solvent. | Session 52: Polymer Structure Formation and Dynamics in Solution: Structure and Assembly |
| 983 | Explaining the mechanical properties of hygroscopic bacterial spores using water nanoconfinement | Harrellson, Steven; DeLay, Michael; Chen, Xi; Cavusoglu, Ahmet Hamdi; Sahin, Ozgur | Here we show the coupling of the mechanical properties and water nanoconfinement in Bacillus Subtilis spores can be understood by using a simple statistical mechanical model. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 984 | Adaptable hydrogels for organoid culture | Heilshorn, Sarah | Here we present the design of a family of double-network hydrogels that undergo two stages of crosslinking: the first stage uses reversibly dynamic covalent chemistry bonds, while the second stage reinforces the hydrogel through thermal-induced polymer aggregation. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 985 | Polymer field theory applied to Liquid Crystal Elastomers | Khandagale, Pratik; Majidi, Carmel; Dayal, Kaushik | In the many-chain setting, we use statistical field theory to account for inter-segment interaction using an excluded volume approach. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 986 | Computational Study of Mechanochemical Activation in Nanostructured Triblock Copolymers | Huo, Zijian; Laaser, Jennifer; Statt, Antonia | In this work, we use molecular dynamics simulations to investigate mechanical activation in ABA triblock copolymers. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 987 | Computational Study of the AC Susceptibility of Isolated Magnetic Nanoparticles in a Polymer Suspension | Kreissl, Patrick; Holm, Christian; Weeber, Rudolf | We present a computational study of isolated magnetic nanoparticles in a polymer suspension, considering only hydrodynamic and excluded volume interactions. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 988 | A Kinetic Monte Carlo algorithm for swelling drug delivery systems | Ignacio, Maxime; Slater, Gary | In this talk, we present this algorithm and test it for systems where one can derive an analytical solution, namely a core/shell structures and a swelling system in the adiabatic regime. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 989 | Microion-Driven Free Swelling of Cylindrical Ionic Microgels | Alziyadi, Mohammed; Denton, Alan | Combining electrostatic and gel osmotic pressures, the latter modeled using Flory-Rehner theory, we explore the dependence of swelling on charge density and salt concentration. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 990 | Chemical controlled tangential growth leads to autonomous shell morphology | Li, Siyu; Matoz Fernandez, Daniel; Olvera De La Cruz, Monica | In this work, we study the autonomous shell dynamics undergoing a periodically reduction-oxidation reaction and build a general model to simulate the chemical reaction and the shell elasticity simultaneously. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 991 | Polymer Dispersity Affects Conformation of Brushes Grafted on Nanoparticles | Li, Tzu-Han; Yadav, Vivek; Conrad, Jacinta; Robertson, Megan | Here, we show that the effect of dispersity on the conformational pH-response of polyelectrolyte brushes depends on the molecular weight. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 992 | Exploration of the ordered morphologies of thermo- and photo-responsive LCOT block copolymer systems | Seitzinger, Claire; Lodge, Timothy | By incorporating small amounts of the photoactive molecule azobenzene into the polymer sidegroups, we have identified a system that exhibits both thermo- and photo-responsive behavior. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 993 | A biocompatible hydrogel pH sensor to measure tumor acidosis | Kiridena, Sachindra; Wijayaratna, Uthpala; Arifuzzaman, MD; Anker, Jeffrey | We developed a chemically responsive polyacrylic acid-based injectable hydrogel sensor to noninvasively measure local pH in a tumor location biopsied and used for diagnosis using plain radiography. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 994 | Monitoring prosthetic hip infections using a synovial fluid pH sensor | Wijayaratna, Uthpala; Kiridena, Sachindra; Arifuzzaman, MD; Anker, Jeffrey | We developed a hydrogel-based synovial fluid pH sensor which can be attached to prosthetic hips for early detection and monitoring of hip infections using plain radiography. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 995 | Magnetically triggered heating in poly acrylic acid stabilized magnetic nanoemulsions: influence of surfactant conformation on global heating efficiency | Ranoo, Surojit; Lahiri, Barid; Philip, John | Magnetically triggered heating in poly acrylic acid stabilized magnetic nanoemulsions: influence of surfactant conformation on global heating efficiency | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 996 | Ferroelasticity in magnetorheological elastomers | Rambausek, Matthias; Danas, Kostas | Our contribution is inspired by experimental observations and highlights a third avenue to potential applications that is based on the physics that emerge from microstructural multistability of very soft MREs: ferroelasticity. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 997 | Light and Magnetic Control of Hydrogel Robots | Yuan, Hang; Li, Chuang; Aggarwal, Aaveg; Lau, Garrett; Stupp, Samuel; Olvera De La Cruz, Monica | We report here on the design of hydrogels containing aligned ferromagnetic nanowires dispersed in a polymer network that change shape in response to light and experience torques in rotating magnetic fields. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 998 | Controlled tough responsive tissue adhesion | Li, Jianyu | This talk will present design strategies and material systems to achieve controlled tough responsive tissue adhesion. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 999 | Using Reactive Dissipative Particle Dynamics to Understand Local Shape Manipulation of Polymer Vesicles | Zhu, Qinyu; Scott, Timothy; Tree, Douglas | To better understand the possible mechanisms of local morphological changes in a popular protocell system, the block copolymer vesicle, we developed a reaction-diffusion model that combines Dissipative Particle Dynamics (DPD) and the Split Reactive Brownian Dynamics algorithm (SRBD), which is capable of modeling the dynamics of polymer solution as they undergo chemical reactions. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 1000 | Stretchable wavy structures on dielectric elastomeric substrates | Ghosh, Abhishek; Basu, Sumit | The efficiency of the system(within the failure bounds) and the extent up to which the mechanical instability can be harnessed in this system, under an applied electric field, is studied in this work. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 1001 | A Methodology for Calibrating Mechanophore Activation Intensity to Applied Stress | Rencheck, Mitchell; Mackey, Brandon; Chang, Chia-Chih; Sangid, Michael; Davis, Chelsea | To date, semi-quantitative studies have shown that the fluorescent intensity increases with applied force, but systematic calibration of the MP response to local stresses remains a current challenge. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 1002 | Controlling phase behavior of diamagnetic, low viscosity polymer solutions using low intensity magnetic fields | Suresh, Karthika; Calabrese, Michelle | Assembling materials via this mechanism provides a new approach to develop BCP materials with long-range order using low-intensity magnetic fields. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 1003 | Magnetoelastic actuation of superparamagnetic nanoparticle membranes | Esposito, Edward; Jackson, Grayson; Jaeger, Heinrich | We find that an applied magnetic field can induce large, micron-scale deflections of the membranes, which we track in 3D with high-resolution confocal microscopy. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 1004 | Room Temperature Photochemical Actuation of A Semi-Crystalline Poly(azobenzene) | Zhou, Hantao; Kuenstler, Alexa; Hayward, Ryan | We have shown the ability to reversibly destroy and restore semi-crystalline order by photo isomerization of azobenzene powered by UV and visible light, respectively. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 1005 | Light activated folding of hydrogel sheets into origami inspired 3D structures | Aggarwal, Aaveg; Olvera De La Cruz, Monica | To this end, we report our theoretical work on the light induced deformations in spiropyran based hydrogel systems and the design of self-folding origami structures using this photo-active material. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 1006 | Eliciting diverse self-regulated actuation pathways from a compositionally uniform liquid crystalline elastomer microstructure | Li, Shucong; Lerch, Michael; Martens, Reese; Deng, Bolei; Waters, James; Yao, Yuxing; Bertoldi, Katia; Aizenberg, Michael; Balazs, Anna; Aizenberg, Joanna | Here, we report a conceptually new approach to reconfigurable microactuators: by employing directional stimuli on a single high-aspect-ratio micropost fabricated from compositionally uniform materials (a photoresponsive liquid crystalline elastomer) with tilted directionality, we elicit reversible, multimodal deformations including light-seeking, light-avoiding, clockwise and counterclockwise twisting. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 1007 | Programmable Photothermal Actuators Using Donor Acceptor Stenhouse Adducts Photoswitches | Lee, Jaejun; Sroda, Miranda; Stricker, Friedrich; Read de Alaniz, Javier; Valentine, Megan | We introduce a novel approach for programmable actuation using negatively photochromic molecular photoswitches, termed donor-acceptor Stenhouse adducts (DASAs), capable of generating programmed mechanical energy using photochemically programmed logic. | Session 53: Responsive Polymers, Soft Materials, and Hybrids |
| 1008 | Imaging the spatiotemporal heterogeneities of gelling nanoemulsions | Hsiao, Lilian; Smith, Kristine | We use a colloidal gel system of nanoemulsion droplets of poly(dimethylsiloxane) suspended in a continuous phase, comprised of a liquid precursor that contains poly(ethylene glycol diacrylate). | Session 54: Rheology of Gels |
| 1009 | Shear-induced memory effect in boehmite gels | Sudreau, Iana; Manneville, Sebastien; Divoux, Thibaut; Servel, Marion | To understand the mechanisms by which the shear modifies the gel’s structure after flow cessation, we study the rheological properties of a boehmite gel depending on the value of the preshear rate. | Session 54: Rheology of Gels |
| 1010 | Connecting the viscoelastic response of nanosheet gels to the elastic properties of the particles | Barwich, Sebastian; Mobius, Matthias | We present a new analytical model that explains this behaviour and connects the bulk response to the elastic properties of single nanosheets and their size. | Session 54: Rheology of Gels |
| 1011 | Phase Behavior and Mechanics of Bridging Gels with pH-Tunable Attractions | Conrad, Jacinta; Gallegos, Mariah; Soetrisno, Diego; Park, Nayoung | We study the phase behavior and mechanics of a colloid-polymer model system with bridging attractions, in which the strength of the polymer adsorption can be tuned through the pH of the system. | Session 54: Rheology of Gels |
| 1012 | Two modes of cluster dynamics govern the viscoelasticity of colloidal gels | Cho, Jae Hyung; Bischofberger, Irmgard | We study the thermal fluctuations of the clusters using differential dynamic microscopy by decomposing them into two modes of dynamics, and link them to the macroscopic viscoelasticity via rheometry. | Session 54: Rheology of Gels |
| 1013 | Polymer microgels containing nanodiamonds: pH-dependent component interactions and rheology | Jani, Pallav; Farias, Barbara; Khan, Saad | Here, we investigate the pH-dependent interactions of microgels with carboxylated nanodiamonds (NDs), a relatively novel carbonaceous material, using rheology. | Session 54: Rheology of Gels |
| 1014 | Microstructure and viscoelasticity of thermoreversible gels composed of anisotropic particles with short-range interactions | SUMAN, KHUSHBOO; Lee, Haesoo; Murphy, Ryan; Wagner, Norman | To quantify these effects, we study the temperature-induced state change of a colloidal anisotropic model system of octadecyl-coated silica rods with dimensions 30 – 300 nm, also termed as adhesive hard rods (AHR). | Session 54: Rheology of Gels |
| 1015 | Isolating the yield stress in thixotropic fibrillar gels | Poling-Skutvik, Ryan; Osuji, Chinedum | Here we propose a rheological strategy to quantify the yield stress in thixotropic materials. | Session 54: Rheology of Gels |
| 1016 | Study of lifetime of bonds and microstrucure of attractive gels at intermediate volume fractions | Nabizadeh, Mohammad; Jamali, Safa | By continuously tracking bonds, we present an analysis of their life and death mechanism. | Session 54: Rheology of Gels |
| 1017 | Interplay between structure and mechanical performances of multi-component colloidal gels. | Bouzid, Mehdi; Ferreiro Cordova, Claudia; Del Gado, Emanuela; Foffi, Giuseppe | We present a detailed numerical study of composite colloidal gels obtained by arrested phase separation. | Session 54: Rheology of Gels |
| 1018 | Linear viscoelastic spectra of soft particulate gels: master curve and physical origin of the fractal constitutive behavior | Bantawa, Minaspi; Keshavarz, Bavand; Geri, Michela; Bouzid, Mehdi; Divoux, Thibaut; McKinley, Gareth; Del Gado, Emanuela | We investigate the connection between the load-bearing network structure in soft particulate gels and their linear viscoelastic spectrum in a 3-D microscopic numerical model, using large scale simulations with Optimally Windowed Chirp (OWCh) signals. | Session 54: Rheology of Gels |
| 1019 | The microstructure and rheology of a model, thermoreversible nanoparticle gel under steady shear and large amplitude oscillatory shear (LAOS) | Kim, Jung Min; Eberle, Aaron; Gurnon, A Kate; Porcar, Lionel; Wagner, Norman | The microstructure-rheology relationship for a model, thermoreversible nanoparticle gel is investigated using a new technique of time-resolved neutron scattering under steady and time-resolved large amplitude oscillatory shear (LAOS) flows. | Session 54: Rheology of Gels |
| 1020 | Direct confocal imaging of fracture precursors in casein gel | SINGH, Akash; Tateno, Michio; Simon, Gilles; Vanel, Loic; leocmach, Mathieu | For this, we have designed our own setup which is based on the principle of measuring the deflection of a cantilever. | Session 54: Rheology of Gels |
| 1021 | Electrically Programmable Micro-scale Morphing Robots Based on Mechanical Metamaterials | Liu, Qingkun; Wang, Wei; Sinhmar, Himani; Cortese, Alejandro; Griniasty, Itay; Reynolds, Michael; Taghavi, Milad; Apsel, Alyssa; Kress-Gazit, Hadas; McEuen, Paul; Cohen, Itai | Here, we show that such electrically actuated auxetic metamaterials can be utilized to design micro-scale robots. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1022 | Origami-inspired, high energy-density, low-voltage voice coil actuators for autonomous micro-robotic applications | Eligar, Sagar Shashikant; Hari Prasad, Hari Krishna; Jayaram, Kaushik | Preliminary modeling and experimental results show that our prototype (1.4cm in dimension), using a 3.175mm cubical N52 magnet produces about 50 times its body weight as static Lorenz force on a 41AWG, 46-turn, 4.75 mm diameter tightly wound coil with a constant input current of 0.1 A. Using impedance control, we propose to demonstrate various single-legged high-frequency hopping behaviors. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1023 | Robust Control for Robots via Minimal-Information Policies | Pacelli, Vincent; Majumdar, Anirudha | This study investigates a fundamental trade-off between a robot’s state information usage and optimal decision making. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1024 | Hierarchical control in sea star inspired locomotion | Heydari, Sina; Po, Theodora; McHenry, Matthew; Kanso, Eva | We developed mathematical models of the biomechanics of the tube feet and the sea star body. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1025 | Rock-and-Walk Manipulation: Robotic Object Transport through Passive Dynamic and Quasistatic Manipulation | Nazir, Syed; Xu, Pu; Seo, Jungwon | We present a novel robotic manipulation capability for transporting an object on the ground in a dynamic and nonprehensile manner. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1026 | Wing opening and leg flailing together facilitates strenuous self-righting on the ground | Othayoth Mullankandy, Ratan Sadanand; Li, Chen | Here, we studied whether simultaneous wing opening and leg flailing is beneficial. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1027 | Bio-inspired mask filters with breathing resistance control | Yuk, Jisoo; Frohlich, Karl; Connor, Robert; Basu, Saikat; Chamorro, Leonardo; Jung, Sunghwan | In this study, we proposed a 3D tortuous mask filter inspired by animal’s nasal cavity. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1028 | From Particles to Parts: Building Artificial Life from Soft Multifunctional Materials | Kramer-Bottiglio, Rebecca | During this talk, I will present recent work toward particulate and fibrous composites that address distributed sensing, variable stiffness properties, and variable trajectory motions inspired by these capabilities in animals. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1029 | Independent Control of Microrobots using Q-learning framework | Aslam, Zain; Beaver, Logan; Malikopoulos, Andreas; Das, Sambeeta | In this talk, we present the first foundational step towards realizing this objective by developing a Q-learning-based controller which approximately optimizes the trajectories of the microrobots through rewards and discounts while avoiding obstacles, such as randomly dispersed micro-objects, or already formed microstructures. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1030 | Interfacial pumping inspired by snails | Pandey, Anupam; Sequeira, Yohan; Wang, Emily; Yuk, Jisoo; Lee, Sungyon; Takagi, Daisuke; Jung, Sunghwan | We observe that floating particles far away are sucked into the robotic snail. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1031 | Characterizing The Marangoni effect in NASA STDCE-1 experiments | sequeira, yohan; Jung, Sunghwan | We utilize multiple Particle Image Velocimetry and Particle Tracking Velocimetry methods to extract the flow field form NASA STDCE-1 videos and compare the experimental data to the numerical results of the flow-field. | Session 55: Robophysics: Robotics Meets Physics: Actuation, Control, Design |
| 1032 | Attractoring-based locomotion | Sándor, Bulcsú; Nowak, Michael; Gros, Claudius | To illustrate these control schemes, we present a simple model of an actuator controlled by a rate encoding neuron with internal adaption and with inputs representing self-coupling, respectively delayed proprioceptive feedback. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1033 | Force-chain evolution in granular packings under a razor-clam inspired penetration | Huang, Sichuan; Tao, Junliang | Here we investigate how the shell opening facilitates the soil burrowing of razor clams using a clam-inspired penetrator and photoelasticity. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1034 | Better Stair Climbing By Using Symmetry | Bishop, Arun; Revzen, Shai | Instead, we construct a solution based on understanding of the problem’s symmetries. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1035 | Morphological compliance enables robot locomotion through cluttered terrain | Kabutz, Heiko; Jayaram, Kaushik | We propose to extend this idea by hypothesizing that soft bodied animals and robots could employ an alternate yet equally effective strategy relying on their distributed body compliance to squeeze through cluttered obstacles. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1036 | Testing whether potential energy landscape can predict stochastic obstacle traversal | Zheng, Bokun; Xuan, Qihan; Li, Chen | Our recent study established a quasi-static potential energy landscape approach to locomotor transitions (Othayoth, Thoms, Li, 2020, PNAS). | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1037 | A potential energy landscape based dynamic model of locomotion in complex 3-D terrain | Xuan, Qihan; Li, Chen | Because it is challenging to calculate torques of conservative forces from energy landscape gradient using Euler angles, we used virtual rotation to calculate them. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1038 | A robophysical model to study physical sensing of obstacles in legged traversal of complex 3-D terrain | Wang, Yaqing; Othayoth Mullankandy, Ratan Sadanand; Li, Chen | To study this, we developed a robophysical model with actuated flexible head and abdomen and underactuated body pitch and roll control which mimicked the effect of leg motions. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1039 | Landing Energy Management | Gart, Sean; Kessens, Chad; Pusey, Jason; Nicholson, John; Koditschek, Daniel | In this study, we investigate the role of leg springs and dampers, body orientation, and geometry on landing energy management. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1040 | Simple untethered flagellated robot in fluids and granular media | Du, Yayun; Miller, Andrew; Khalid Jawed, Mohammad | We report a simple untethered flagellated robot that can swim in both granular media and fluids at low Reynolds number. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1041 | Parapodia inspired soft appendages enable robot propulsion in granular media | Chopra, Shivam; Jadhav, Saurabh; Tolley, Michael; Gravish, Nick | We present experimental results where the appendage is oscillated in a controlled granular environment and show that propulsion is highly dependent on the bending stiffness, increasing with the increase in stiffness until it reaches a maximum value and then starts decreasing. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1042 | Bioinspired Embodied Control of Locomotion in Complex Environments | Full, Robert | In turn, robophysics approach to biological locomotion can inspire the design of novel robots and applied mathematics. | Session 56: Robophysics: Robotics Meets Physics: Complex Environment |
| 1043 | Biomimetic navigation of complex environments | Vergassola, Massimo | Biomimetic navigation of complex environments | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1044 | Excitable spring-wing dynamics 1: Common dynamics and transitions between synchronous and asynchronous insect flight. | Gau, Jeffrey; Lynch, James; Gravish, Nick; Sponberg, Simon | To address how discrete oscillatory behavior emerges from a continuum of actuator properties, we combined the two types of actuation with a resonant spring-wing mechanics model. | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1045 | Excitable Spring-Wing Dynamics 2: Synchronous and asynchronous regimes of actuation in robophysical spring-wing systems | Lynch, James; Gau, Jeffrey; Sponberg, Simon; Gravish, Nick | In this talk, we detail the construction and implementation of a self-excited spring-wing model based on measurements of insect muscle response. | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1046 | Excitable spring-wing dynamics 3: The dynamics of asynchronous actuation and emergent spring-wing oscillations | Gravish, Nick; Lynch, James; Gau, Jeffrey; Sponberg, Simon | Overall in this talk we will establish the rules of dSA oscillations in a model system of asynchronous spring-wing systems. | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1047 | Insect-like flying robots | Jafferis, Noah; Wood, Robert | In this talk we will describe several advances for the Harvard “RoboBee” platform (an 80-mg flapping-wing vehicle) over the past five years that are bringing this goal closer to reality, including non-linear resonance modeling, multi-wing designs, and scaling analysis. | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1048 | Active vision improves sensory acquisition and coordinates motor control in insect flight | Cellini, Benjamin; Mongeau, Jean-Michel | We studied how flying fruit flies overcome these challenges by actively controlling their head to shape the visual inputs that are sensed by the eyes. | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1049 | Two DOF underactuated swimming robot with high maneuverability and passive adaptability | Liu, Bangyuan; Hammond III, Frank | Upon that premise, we designed a bioinspired two DOF soft swimming robot with high maneuverability and passive adaptability to obstacles. | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1050 | Unique ‘figure-of-8’ swimming style provides a new idea for robot design: rotation is important for swimming. | Jin, Bowen; Luo, Haoxiang; Ding, Yang | We use a 3D model combining with computational fluid dynamics to study the kinematics and dynamics of larval locomotion and found that larva not only moves forward but also rotates its body around the center of mass. | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1051 | Minimal robophysical model for multi-flagellate propulsion | Diaz, Kelimar; Robinson, Tommie; Ozkan-Aydin, Yasemin; Goldman, Daniel; Wan, Kirsty | Here to test if these performance differences are a sole function of the diverse gaits (appendage coordination patterns) employed by different species, we developed a macroscopic robophysical model (four appendages, body length of 3.9 cm) with the capability to self-propel in a viscous fluid (mineral oil, 1,000 cSt). | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1052 | Electrically actuated artificial cilia for microfluidic applications | Wang, Wei; Liu, Qingkun; Reynolds, Micheael; Miskin, Marc; McEuen, Paul; Cohen, Itai | Here, we present a new platform for fabricating artificial cilia that uses surface electrochemical actuators made of nm thin Platinum films. | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1053 | Effect of kinematics and physical properties of caudal fin on performance of a robotic fish | Nayak, Anshul; Pendar, Hodjat | In this work, we built a Robo-physical model to study the effect of various physical, geometrical, and kinematic parameters of fin on performance. | Session 57: Robophysics: Robotics Meets Physics: Flight & Swimming |
| 1054 | Calibration Challenges for Measuring Multi-Legged Ground Contact Forces | Wu, Ziyou; Revzen, Shai | We present the force-torque sensing framework used in our robot and the present challenging calibration problems that arise. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1055 | Leveraging Aerodynamic Drag for Tails in Legged Robot Locomotion | Norby, Joseph; Li, Jun Yang; Selby, Cameron; Patel, Amir; Johnson, Aaron | We present a model of the dynamics induced by aerodynamic drag and from this derive a metric that allows for direct comparison between aerodynamic and inertial tails. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1056 | Towards an Insect Inspired Segmented Robot Leg for Passive Deflection Over Steps | Lathrop, Emily; Tolley, Michael; Gravish, Nick | Inspired by the multi-segmented architecture of insect legs, we have developed a 3D printed segmented robot leg that allows a walking robot to passively deflect over obstacles in the swing phase and bear weight during the stance phase. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1057 | Arachnids as systems for robophysical study | Spagna, Joseph | We suggest that for these varied arachnid adaptations, robotic systems can be used to better test- and possibly optimize- key mechanisms of these systems and their analogs. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1058 | A Motion Planning Framework for Dynamic Monopedal Locomotion on Deformable Terrain | Lynch, Daniel; Lynch, Kevin; Umbanhowar, Paul | We apply our framework to the task of finding period-1 hopping gaits for a monopedal robot. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1059 | Optimizing Contact Area and Joint Stiffness of a Passive Foot-Ankle Exoskeleton for Locomotion on Deformable Terrain | Gosyne, Jonathan; Sawicki, Gregory | We modelled an exoskeletal device with variable ankle stiffness and foot contact area coupled to a Hill-Type model representing the calf-Achilles tendon MT. During fixed frequency locomotion cycles, we found terrain-specific exoskeleton parameters that eliminated the P met penalty incurred during locomotion on sand vs. solid ground. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1060 | An insect-scale robot reveals the effects of different body dynamics regimes during open-loop running in feature-laden terrain. | SCHIEBEL, PERRIN; Cerbone, Henry; Wood, Robert | We used the quadrupedal Harvard Ambulatory MicroRobot to study trot and pronk gaits at vertical and pitch/roll body resonances and above resonance. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1061 | Reactive velocity control reduces the energetic cost of transport for a direct-drive robot on granular media | Roberts, Sonia; Koditschek, Daniel | The simulations used a bulk-behavior model of the forces exerted by granular media in response to intrusion. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1062 | Collective transport in an entangled robotic worm blob | Ozkan-Aydin, Yasemin; Bhamla, Saad; Goldman, Daniel | Here, we develop a robophysical model of the collective dynamics of physically entangled collectives, worm blobs, where thousands of centimeter-long aquatic worms knot their bodies to form large-scale aggregates capable of surviving extended desiccation, mechanical impacts and directed locomotion under temperature gradients. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1063 | Toward a Simple Model for Friction Dominated Multi-legged Locomotion | Zhao, Dan; Revzen, Shai | We have previously shown that multi-legged animals and robots almost inevitably slip a great deal, and that an alternative, non-Coulomb friction anzats provided promising simulation results with far less complexity. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1064 | Enhancing Legged Robot navigation of Rough Terrain via Use of a Tail | Soto, Daniel; Goldman, Daniel | Here we take a different approach, augmenting the emergent high-performance capabilities of a compliant-legged robot with a simple controllable tail. | Session 58: Robophysics: Robotics Meets Physics: Legged locomotion |
| 1065 | Efficient sliding locomotion for two- and three-link bodies | Alben, Silas; Puritz, Connor | We study the possibility of efficient intermittent (inertia-based) locomotion for two-link bodies that open and close periodically in time. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1066 | Terrestrial limbless gait selection through friction modulation | Zhang, Xiaotian; Naughton, Noel; Parthasarathy, Tejaswin; Gazzola, Mattia | This simple perspective provides new understanding of how snakes and other limbless creatures may exploit their compliant body and naturally occurring substrate features to achieve adaptivity, control and gait selection. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1067 | Nematode omega turns improve reorientation in a limbless robot | Wang, Tianyu; Chong, Baxi; Diaz, Kelimar; Whitman, Julian; Lu, Hang; Goldman, Daniel; Choset, Howie | We use geometric mechanics tools to model the superposition of two traveling waves to generate effective body rotation while avoiding self-collision, and generate a scheme to reorient the robot to arbitrary angles via modulation of joint angle amplitudes. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1068 | A new robophysical model for limbless locomotion reveals the importance of passive dynamics in obstacle navigation. | Maisonneuve, Marine; SCHIEBEL, PERRIN; Diaz, Kelimar; Goldman, Daniel | To discover principles by which passive body buckling can simplify control in complex terrain, we developed a robot (8 joints, 45 cm long) that models biological muscle morphology and head-to-tail propagating wave activation patterns. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1069 | Reconstruction of Backbone Curves for 3-D Locomotion of Limbless Robots | Wang, Tianyu; Lin, Bo; Chong, Baxi; Whitman, Julian; Travers, Matthew; Goldman, Daniel; Choset, Howie; Blekherman, Greg | Here we propose a method for snake robots to reconstruct desired backbone curves by solving a polynomial optimization problem that exploits the robot’s geometric structure. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1070 | A sensorized robot to study physical interaction in limbless locomotion in complex 3-D terrain | Ramesh, Divya; Fu, Qiyuan; Wang, Kaiwen; Othayoth Mullankandy, Ratan Sadanand; Li, Chen | We aim to understand how snakes sense and control physical interaction with the obstacles to generate effective locomotion. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1071 | Nonlocal control of active agents on a deformable substrate | Gynai, Hussain; Li, Shengkai; Ozkan-Aydin, Yasemin; Tarr, Steven; Aydin, Enes; Laguna, Pablo; Goldman, Daniel | In an effort to construct a robophysical analog gravity system, we previously studied the dynamics of a 200-gram differential wheeled vehicle driving on a deformable spandex membrane (d=2.4m) with a static central depression (Li et al., 2019). | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1072 | Optimizing the Locomotion of a Robotic Active Matter System of Smarticles | Taylor, Annalisa; Berrueta, Thomas; Murphey, Todd | We consider the locomotive properties of an active matter system of shape-changing robots. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1073 | Synchronized swimming: collisions drive gait compatibility in undulatory robots | Zhou, Wei; Dezha-Peralta, Jaquelin; Hao, Zhuonan; Gravish, Nick | In this presentation we demonstrate how groups of simple bio-inspired robots that move through lateral body undulation and interact only through contact forces can collectively locomote in close proximity. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1074 | Emergent cooperation in ant-like robots | Giardina, Fabio; Prasath, S Ganga; Mandal, Souvik; Murthy, Venkatesh; Mahadevan, L. | We present simple behavioral rules that lead to emerging cooperation in our robotic platform and will show how these insights can inform us on the internal processes that drive collective construction in biological systems. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1075 | When the mob sees the light – distributed learning of phototaxis without local gradients using robot morphology | Ben Zion, Matan Yah; Mirhosseini, Yoones; Bredeche, Nicolas; Dauchot, Olivier | We show that a completely decentralized population of kilobots can collectively find a successful phototactic strategy even in the total absence of a local gradient-field. | Session 59: Robophysics: Robotics Meets Physics: Limless & Collective Locomotion |
| 1076 | Decision making behaviors in a brainless organism (Physarum polycephalum) can emerge from self-organized physical interactions within a single cell. | Haque, Abid; Graham, Jason; Edwards, Andrew; Ray, Subash; Garnier, Simon | In this study, we use a brainless unicellular protist Physarum polycephalum (slime mold) to examine the mechanisms it employs to “choose” one food source over another. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1077 | Cooperatively enhanced reactivity and "stabilitaxis" of dissociating oligomeric proteins | Agudo-Canalejo, Jaime; Illien, Pierre; Golestanian, Ramin | By studying the generic spatial transport properties of such proteins, we investigate here whether their ability to reversibly associate and dissociate may confer them a functional advantage with respect to non-dissociating proteins [1]. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1078 | Uni- and bidirectional forcing in Dictyostelium discoideum streaming | Bull, Abby; Mosher, Molly; Hourwitz, Matt; Fourkas, John; Losert, Wolfgang | Here we investigate the combination of chemical and topographic guidance cues. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1079 | Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue | Sahu, Preeti; Schwarz, J; Manning, M Lisa | To uncover the underlying physical mechanisms driving these geometric features, we develop two simple toy models that identify an energy competition between bulk cell shapes and two-tissue interface area. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1080 | The Physical Basis of Curvaure Sensing by Septins | Shi, Wenzheng; Cannon, Kevin; Gladfelter, Amy; Nazockdast, Ehssan | Here we use a combination of biophysical modeling and simulations, single molecule imaging and scanning electron microscopy to study the interplay between membrane’s curvature and the different processes involved in septin assembly, including septins’ membrane association/dissociation, diffusion and polymerization rates. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1081 | Unraveling cytoplasmic streaming using a coarse-grained model of microtubule hydrodynamics | Stein, David; De Canio, Gabriele; Lauga, Eric; Goldstein, Raymond; Shelley, Michael | Using a coarse-grained model for the hydrodynamics of ordered fibers, we show that sufficiently dense microtubule arrays, forced only by molecular motors transporting cargo, undergo a "swirling transition" that is fundamentally different than the buckling transition which leads to the flapping motion of isolated filaments. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1082 | Chimeras as a way to model anatomical reentry in cardiac models | Welsh, Andrea; Fenton, Flavio | We present an extension to a FHN system with purely local coupling that models waves and unresponsive cells and explore the rich dynamics that result. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1083 | Irwin Oppenheim Award (2021): Design of conditions for self-replication | Sarkar, Sumantra | In this talk, I shall report progress in addressing this need. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1084 | Self-organization in composite biopolymer liquid crystals | Weirich, Kimberly | Here, we discuss composite biological liquid crystals, formed form filaments mixed with biological polymers of different rigidities. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1085 | How motors shape their roads: self-organisation in dynamic filament networks | Striebel, Moritz; Brauns, Fridtjof; Frey, Erwin | Here we propose a microscopic model for the interplay between the spatial microtubule network architecture and molecular motors that control filament length by catalysing their depolymerization. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1086 | Interacting associative memory networks as a model for tissue self-organization | Smart, Matthew; Zilman, Anton | To capture cell-cell interactions we propose to model interacting cells using a lattice of interacting Hopfield networks. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1087 | Designing the Morphology of Separated Phases in Multicomponent Liquid Mixtures | Kosmrlj, Andrej; Mao, Sheng; Chakraverti-Wuerthwein, Milena; Gaudio, Hunter | To address this issue, we developed novel algorithms for constructing phase diagrams and for predicting the morphology of separated phases. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1088 | Soft nanotubes confining adhensive elastic nanoparticles | Wu, Zeming | The aim of this work is to theoretically analyze the interaction between soft nanotubes with various membrane tension and confined nanoparticles with different bending rigidities, and covering the cases of a single particle and multiple particles of spatial periodicity. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1089 | Dielectrophoresis characterization of Neuroblastoma cells | Rikhtehgaran, Samaneh; Mosavati, Babak; Wille, Luc; Wei, Jianning; Du, E | This work presents a dielectrophoresis-based method for a label-free noninvasive characterization of neuroblastoma cells. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1090 | Synchronization and noise in arrays of hydrodynamically coupled cilia | Solovev, Anton | Past research proposed hydrodynamic coupling as a mechanism of synchronization, yet if such synchronization is stable in the presence of noise (corresponding to active fluctuations of cilia beating) has been addressed only for n=2 cilia [2], while the question of multi-stable synchronization in cilia carpets ( n>>1) remains open. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1091 | Sensing Cell Shape at the Micron Scale with Reaction-Diffusion | Singh, Amit; Camley, Brian | We simulate wave-pinning on a curved surface and show that high-activity domains migrate to peaks and troughs of the surface. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1092 | Nanofluidic Device for Measuring the Surface Charge of Extracellular Vesicles via a Tunable Electrostatic Landscape | Isaac Hosseini, Seyed Imman; Liu, Zezhou; Reisner, Walter; Mahshid, Sara | Here, we propose a nanofluidic device to perform simultaneous size and charge measurement of EVs. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1093 | Delay-induced transitions in swarmalator clusters | Blum, Nicholas; O’Keeffee, Kevin; Kogan, Oleg | We investigate the role of delay in the collective dynamics of swarmalators introduced recently by O’Keeffe, Hong, and Strogatz. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1094 | Numerical simulation of dielectrophoretic behavior of neuroblastoma cells | Mosavati, Babak; Rikhtehgaran, Samaneh; Du, E; Wei, Jianning | This work presents a numerical simulation of neuroblastoma cell DEP using the finite element method. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1095 | Inducing Integer Charge Topological Defects in Cell Monolayers | Endresen, Kirsten; Kim, MinSu; Serra, Francesca | We identify two different cell configurations near topological defects with azimuthal symmetry, where cells are able to change not only their alignment, but also their shape. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1096 | The roles of patchy attractions and Brownian motion in fundamental biological processes in a model cell | Hofmann, Jennifer; Zia, Roseanna | Here, we present our results investigating the structure and dynamics of these coarse-grained systems, probing the inseparable connection between colloidal-scale transport and biological function. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1097 | Physics-based modeling of whole-cell function: colloidal fundamentals to life-essential processes | Zia, Roseanna; Endy, Drew; Maheshwari, Akshay; Gonzalez Gonzalez, Emma del Carmen; Sunol, Alp | We showed that Brownian motion is essential but insufficient to recover experimentally measured elongation rates; we proposed other colloidal physics mechanisms that close the gap. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1098 | Physical scaling of size and shape in an early diverging animal | Vyas, Pranav; Bull, Matthew; Li, Hongquan; Prakash, Manu | We utilize high-throughput scanning microscopy to collect long term temporal datasets on the growth trajectories of individual organisms to identify scaling laws governing measurable changes in shape metrics with size. | Session 60: Self-Organization in Biological Systems: Subcellular to Tissue Scales |
| 1099 | Advanced Dielectric Polymeric Materials with Rational Design of Nano-Morphologies | Chen, Xin; Zhang, Qiyan; Zhang, Tian; Zhang, Qiming | In this talk, we will present several strategies to modify the nanostructures for developing polymer dielectrics with outstanding performance. | Session 61: Structure and Dynamics of Charged Polymers |
| 1100 | The nanostructure and ion dynamics of novel hydrocarbon ionene AEMs via scattering and simulation | Schibli, Eric; Holdcroft, Steven; Frisken, Barbara | We have investigated a promising series of fully aromatic hydrocarbon ionene anion-exchange membranes (AEMs) utilizing a combination of X-ray scattering and molecular dynamics simulations to elucidate the morphology of these materials and have utilized molecular dynamics to investigate the role of cation and polymer architecture in ion transport dynamics. | Session 61: Structure and Dynamics of Charged Polymers |
| 1101 | Charging Dynamics and Structure of Ionic Liquids in Nanoporous Supercapacitors | Breitsprecher, Konrad; Holm, Christian; Kondrat, Svyatoslav | Charging Dynamics and Structure of Ionic Liquids in Nanoporous Supercapacitors | Session 61: Structure and Dynamics of Charged Polymers |
| 1102 | Intra-chain electrostatic correlations govern charge regulation of weakly dissociating polyelectrolytes | Ghasemi, Mohsen; Larson, Ronald | Here, we develop a detailed model that combines an acid-base equilibrium with a random phase approximation (RPA) of electrostatic correlations for a solution containing weak polyacids. | Session 61: Structure and Dynamics of Charged Polymers |
| 1103 | Field Theory Description of Polyelectrolyte-Surfactant Coacervate Phase Behavior | Madinya, Jason; Sing, Charles | In this work we present a field theoretic calculation(1) for modeling phase separation in charged polymer and surfactant solutions, where we treat micelle surface sites as permanent sites interacting with polymer density fields. | Session 61: Structure and Dynamics of Charged Polymers |
| 1104 | Effect of Added Salt on Disordered Poly(ethylene oxide)-Block-Poly(methyl methacrylate) Copolymer Electrolytes | Shah, Neel; Dadashi-Silab, Sajjad; Galluzzo, Michael; Chakraborty, Saheli; Loo, Whitney; Matyjaszewski, Krzysztof; Balsara, Nitash | We studied the effect of salt addition on a diblock copolymer system with a negative Flory-Huggins interaction parameter, χ, indicative of attractive interactions between the two blocks. | Session 61: Structure and Dynamics of Charged Polymers |
| 1105 | Conformation and aggregation of polyelectrolyte in poor solvents | Duan, Chao; Wang, Rui | Here, we develop a theory by systematically including the electrostatic interactions into the self-consistent field theory for polymers to study the single-chain conformation and multi-chain aggregation of PE in poor solvents. | Session 61: Structure and Dynamics of Charged Polymers |
| 1106 | A computational approach to characterize gating in ion channels | Guardiani, Carlo; Costa, Flavio; Giacomello, Alberto | Since this process occurs on a timescale not reachable by MD simulations, we employed Targeted MD, a technique that imposing a bias on RMSD, steers the molecule between fixed end states. | Session 61: Structure and Dynamics of Charged Polymers |
| 1107 | Controlling the Properties of Ion Containing Polymers, Hydrogels and Membranes | Olvera De La Cruz, Monica | Here we explore the physical properties, including structure, ion transport and reconfigurability of ion-containing polymers, gels and membranes in bulk and confinement for ionic devices utilization. | Session 61: Structure and Dynamics of Charged Polymers |
| 1108 | Self Assembly of Block Copolymers in Ionic-liquid Cured Epoxy | Liu, Deborah; Krogstad, Daniel | In this work, the ability of ionic liquids to act as both a structure directing and curing agent in epoxy/block copolymer (BCP) blends is discussed. | Session 61: Structure and Dynamics of Charged Polymers |
| 1109 | Effect of Cluster Cohesion on Dynamics of Ionic Polymers in Solutions: MD Simulations Studies | Kosgallana, Chathurika; Grest, Gary; Perahia, Dvora | We find that the dynamics of the polymer that is constrained on the length scale of the ionic cluster in toluene is enhanced as tiny quantities of ethanol are added. | Session 61: Structure and Dynamics of Charged Polymers |
| 1110 | A Coarse-grained Approach to Understanding the Behavior of Polyelectrolyte Solutions | Kaur, Supreet; Yethiraj, Arun | We present a coarse-grained approach to modeling polyelectrolyte solutions, with a goal of studying large systems with adequate chemical detail, including explicit solvent. | Session 61: Structure and Dynamics of Charged Polymers |
| 1111 | Polyelectrolyte gels in salt solutions: a computational study | Wang, Zilu; Jacobs, Michael; Dobrynin, Andrey | To understand the factors influencing the PG swelling, we performed coarse-grained molecular dynamics simulations of PGs in salt solutions. | Session 61: Structure and Dynamics of Charged Polymers |
| 1112 | A purely Lamarckian ‘evolution’ permits survival of a bacterium to a lethal stressor | Lee, Jessica; Riazi, Siavash; Nemati, Shahla; Bazurto, Jannell; Vasdekis, Andreas; Ridenhour, Benjamin; Remien, Christopher; Marx, Christopher | We tend to appreciate microbes for their simplicity and predictability: a population of genetically identical cells inhabiting a uniform environment is expected to behave in a uniform way. | Session 62: The Many Dimensions of Evolution |
| 1113 | Evolutionary dynamics in large microbial communities | Good, Benjamin | In this talk, I will describe our recent efforts to address this question using data from the human gut microbiome. | Session 62: The Many Dimensions of Evolution |
| 1114 | Attack of the Clones: What Causes Population Structure in Bacteria and How Can We Use It? | Hanage, William | We have recently shown, using the pneumococcus as a model organism, that we can explain which clones are present in a community with a simple model of negative frequency dependent selection operating on a subset of the genome: namely the accessory genome of loci not present in all isolates of the species. | Session 62: The Many Dimensions of Evolution |
| 1115 | Microbial interactions across time and space | Koskella, Britt | In this talk I discuss the relative importance of interactions among bacteria and phage viruses, between bacterial strains and species within a microbiome, and between a host and its symbionts to emphasize the role of evolution and coevolution in shaping diversity across scales. | Session 62: The Many Dimensions of Evolution |
| 1116 | The ecology and evolution of collective behaior | Gordon, Deborah | There are more than 14K species of ants in every habitat on Earth, using diverse stochastic algorithms, producing different feedback regimes, in different environments. | Session 62: The Many Dimensions of Evolution |
| 1117 | Diblock Copolymer Melts of Linear Chains, Rings and Trefoil Knots in Lamellar Morphology: A Molecular Dynamics Simulations Study | Carrillo, Jan-Michael; Kumar, Rajeev; Sumpter, Bobby | We present results of coarse-grained molecular dynamics simulations of phase separating diblock copolymer melts having different chain topologies. | Session 63: Topological Effects in Soft Matter |
| 1118 | Topological Tuning of Polymer and DNA Dynamics | Michieletto, Davide | In this talk, I will discuss how subtle architecture-specific topological interactions called “threadings” can be identified using persistence homology [1] and present numerical evidence of how they can drive the onset of a "topological glass" in systems of ring polymers [2,3]. | Session 63: Topological Effects in Soft Matter |
| 1119 | Nonlinear Dynamics of Nonconcatenated Entangled Ring Polymers | Rubinstein, Michael; Parisi, Daniele; Costanzo, Salvatore; Jeong, Youncheol; Ahn, Junyoung; Chang, Taihyun; Vlassopoulos, Dimitris; Halverson, Jonathan; Kremer, Kurt; Ge, Ting; Grest, Gary; Srinin, Watee; Grosberg, Alexander | We develop a shear slit model explaining many subtle details of observed conformations and dynamics as well as the chain length-dependent behavior of viscosity in the non-universal regime at large shear rates. | Session 63: Topological Effects in Soft Matter |
| 1120 | Free Energy of a Knotted Polymer Confined to Narrow Cylindrical and Conical Channels | Polson, James; Hastie, Cameron | For cylindrical confinement, we examine polymers with a single knot of topology 3 1, 4 1, or 5 1, as well as unknotted polymers that are capable of forming S-loops. | Session 63: Topological Effects in Soft Matter |
| 1121 | The many faces of topological defects in smectic liquid crystals | Monderkamp, Paul; Wittmann, Rene; Smallenburg, Frank; Loewen, Hartmut | As previous work has largely focused on understanding the topological defects in nematic liquid crystals, our goal is to quantify the topological features of smectic states in confinement. | Session 63: Topological Effects in Soft Matter |
| 1122 | Topological entanglement of polymers and viscoelasticity | Panagiotou, Eleni | In this talk we will see how rigorous measures of topological complexity from Knot Theory can be applied to quantify polymer entanglement. | Session 63: Topological Effects in Soft Matter |
| 1123 | Predicting Degeneracy and Topological Properties in 2D Phononic Band Diagrams | Dethe, Tejas; Sarkar, Siddhartha; Marincic, Matevz; Zhilkina, Polina; Kosmrlj, Andrej | We can draw analogies between band diagrams in phononic crystals that describe wave propagation and electronic band diagrams using the well-established tools in hard condensed matter theory. | Session 63: Topological Effects in Soft Matter |
| 1124 | Topological-Order Beyond 2D U(1) Systems: A Novel Perspective on Solidification and Curvature in Crystals and Glassy Solids | Gorham, Caroline | We suggest that the existence of glassy solids is an artifact of quaternion orientational order parameter undergoing a phase transition in the quaternion plane (4D/3D+1t). | Session 63: Topological Effects in Soft Matter |
| 1125 | When Do Polyelectrolytes Entangle? | Jacobs, Michael; Dobrynin, Andrey | Here, we develop an approach based on a scaling relationship between solution correlation length ξ≈lgν/B and number of monomers per correlation blob g for polymers with monomer projection length l. Numerical coeffiecients B are obtained from plateaus of normalized specific viscosity ηsp(c)cα/N as a function of monomer concentration c with degree of polymerization N. Exponent α=1/(1-3ν) describes the concentration dependence of the number of monomers per correlation blob, g∼c α. | Session 63: Topological Effects in Soft Matter |
| 1126 | Disentangling the Dynamics of Prime Knots | Park, Hyo Jung; Mahadevan, Lakshminarayanan; Lappala, Anna | With the help of Molecular Dynamics simulations, we build a framework to analyze correlated motions in prime knots modeled as polymer chains, and study how these motions relate to their local structural properties. | Session 63: Topological Effects in Soft Matter |
| 1127 | Discovering Topological Invariants in Inhomogeneous Polymeric Systems | Kumar, Rajeev | In this talk, I will present our work related to understanding topological invariants in melts of linear and ring polymers. | Session 63: Topological Effects in Soft Matter |
| 1128 | Three-dimensional imaging of force-generating molecular networks inside of cells using cryo-electron tomography | Hylton, Ryan; Grillo, Michael; Swulius, Matthew | In this presentation, I will briefly overview the protein components that make and regulate these cytoskeletal networks, and talk about how my lab is using live-cell imaging and cryo-electron tomography to study these molecules in the context of neuronal outgrowth. | Session 64: Visualizing the Physics Behind Cell Biology through Cryo-Electron Tomography |
| 1129 | Opening a new window into the cell with super-resolution imaging and in situ cryo-electron tomography | Freyberg, Zachary | We have integrated these approaches with in situ cryo- electron tomography (cryo-ET), and cryo-correlative light and electron microscopy (cryo-CLEM) to visualize the endoplasmic reticulum (ER) and its relationships with other intracellular organelles in near-native states. | Session 64: Visualizing the Physics Behind Cell Biology through Cryo-Electron Tomography |
| 1130 | In-cell structural dissection of the type IVa pilus machine by cryo-electron tomography | Chang, Yi-Wei | In this presentation, I will use the bacterial type IVa pilus machine as an example to demonstrate how such cryoET analysis has helped us understand the mechanism of this dynamic molecular grappling hook for bacterial cell motility. | Session 64: Visualizing the Physics Behind Cell Biology through Cryo-Electron Tomography |
| 1131 | Visualizing mitochondrial division machinery in situ | Grotjahn, Danielle; Mageswaran, Shrawan; Jensen, Grant | By mapping out the precise interactions of these components relative to mitochondrial membranes, our work describes the complete ultrastructural architecture of the mitochondrial fission machinery required for membrane constriction, and establishes cellular tomography as a valuable approach for studying snapshots of mitochondrial dynamics in situ. | Session 64: Visualizing the Physics Behind Cell Biology through Cryo-Electron Tomography |
| 1132 | Automatic Analysis of Cryo-Electron Tomography Using Computer Vision and Machine Learning | Min, Xu | We developed and adapted a suite of computer vision and machine learning methods for such analysis. | Session 64: Visualizing the Physics Behind Cell Biology through Cryo-Electron Tomography |