Highlights of Biological Physics (DBIO) Talks @ APS 2020 March Meeting
American Physics Society (APS) March meeting is one of the largest physics meetings in the world. In 2020, the meeting was canceled due to concerns over the rapid spread of 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 | Dipolar Extensile Dynamics in Microtubule-Based 2D Active Nematics | Lemma, Linnea; Dogic, Zvonimir | Theories describe 2D active nematics in terms of liquid crystals, hydrodynamics and chaotic fluids. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 2 | Design of active nematic systems with controllable defect dynamics and flows | Zhang, Rui; Mozaffari, Ali; De Pablo, Juan | In this talk, I will summarize our recent progress in active nematics research, with an emphasis on the interplay between molecular interactions, elasticity, and hydrodynamic forces. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 3 | Control of bacterial dynamics by splay and bend in nematic vortices | Koizumi, Runa; Turiv, Taras; Genkin, Mikhail; Lastowski, Robert; Yu, Hao; Chaganava, Irakli; Wei, Qihuo; Aronson, Igor; Lavrentovich, Oleg | We explore the effect of splay and bend of the director field on the individual and collective behavior of motile Bacilli subtilis. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 4 | Spatiotemporal Optimal Control of an Extensile Active Nematic Suspension | Norton, Michael; Grover, Piyush; Baskaran, Aparna; Hagan, Michael; Fraden, Seth | Towards developing experimental methods for controlling these dynamics, we consider an optimal control problem which seeks to find the spatiotemporal pattern of active stress strength required to drive the system towards a desired director field configuration. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 5 | Self propelling nematic microcapsules | Maass, Corinna; Hokmabad, Babak Vajdi; Baldwin, Kyle; Bahr, Christian | Building on an established active emulsion platform, we have developed a new approach to the problem of encapsulation by using nematic active double emulsions, where a solubilization mechanism induces activity and the molecular nematicity provides stability. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 6 | The Dynamics of Active Nematic Defects on The Sphere Surface | Zhang, Yiheng; Deserno, Markus; Tu, Zhanchun | Here we study the active counterpart of such a system, in which a self-driven directional motion of the individual nematogens creates a large-scale flow that drives the system out of equilibrium. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 7 | Emergent dynamics of large scale collective rotations in 2D active nematic | Quint, David; Chapman, Dali; Gross, Steven; Beller, Daniel; Gopinathan, Ajay; Xu, Jing | Motivated by recent work on active nematics we employ here a microtubule and kinesin motor gliding assay system to examine dynamic collective order in 2D. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 8 | Defect dynamics of 3D active nematic turbulence | Kos, Ziga; Binysh, Jack; Copar, Simon; Aplinc, Jure; Zumer, Slobodan; Alexander, Gareth; Ravnik, Miha | Our work aims to provide insight into 3D active turbulence from the perspective of the topology of the emergent 3D defects and their self-induced dynamics. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 9 | Topological Defects in Cell Monolayers Guided by Topography | Endresen, Kirsten; Kim, MinSu; Serra, Francesca | We survey multiple cell types (EpH-4 and 3T6) to characterize their alignment, density, and dynamics near defects of various topological charges, and define LC parameters such as defect core sizes and elastic constants. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 10 | Clustering, jamming, and topological defects in growing bacterial colonies at liquid interfaces | Langeslay, Blake; Juarez, Gabriel | Here, we present experimental results on growing colonies of rod-shaped bacteria confined in two dimensions by adsorption at an oil-water interface. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 11 | Topological defects drive layer formation in bacteria colonies | Copenhagen, Katherine; Alert, Ricard; Wingreen, Ned; Shaevitz, Joshua | By measuring cell flows, we find an influx of cells towards positive defects and an outflux away from negative defects. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 12 | Pulsating air bubbles can swim in anisotropic fluids | Kim, Sung-Jo; Um, Eujin; Jeong, Joonwoo | Here we explore the swimming of a spherical bubble with a periodic change in its radius. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 13 | Defect Ordering and Patterning in Active Nematics | Shankar, Suraj; Marchetti, M Cristina | By focusing on defects as the relevant excitations, we develop a hydrodynamic theory of active defects incorporating both defect motility and active torques that align defect orientations. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 14 | Ordering and Correlations of Active Nematic Defects in 2D Flat Space | Nambisan, Jyothishraj; Pearce, Daniel; Ellis, Perry; Giomi, Luca; Fernandez-Nieves, Alberto | One of the aims of our work is to address the orientation of defects in curved geometries. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 15 | Defect order in active nematics | Chen, Zhitao; Bowick, Mark; Marchetti, M Cristina | In this talk, we will discuss the interplay between elastic and active torques, active flows and frictional dissipation in controlling defect patterns in these active liquid crystals. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 16 | Dynamical Behavior of Defects in Circularly Patterned Active Nematics | Mozaffari, Ali; Zhang, Rui; Sokolov, Andrey; Snezhko, Alexey; De Pablo, Juan | We show that by patterning the activity by imposing active stresses in circular domains near the center of confinement, it is possible to regulate the motion of defects. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 17 | Photo-Patterning DNA Structures with Topological Defects and Arbitrary Patterns through Multiple Length Scales | Peng, Chenhui; Jiang, Jinghua; Dhakal, Netra | In this work, we demonstrate that the orientational order of DNA molecules can be precisely controlled by using photo-patterning technique. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 18 | Cells as liquid crystals, and what happens when they can’t align | Endresen, Kirsten; Kim, MinSu; Serra, Francesca | Our goal is to connect biological properties of cells to the LC properties of the monolayers that the cells can form. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 19 | Quantifying orientational interactions among defects in active nematics | Pokawanvit, Supavit; You, Zhihong; Marchetti, M Cristina; Bowick, Mark | Specifically, we demonstrate that the polar +1/2 defects interact via torques that tend to align the defect polarization with the elastic force they experience from other defects, as in previously studied models of flocking. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 20 | Effect of active enzyme diffusion on mesoscale particles | Rouhvand, Bahar; Ross, Jennifer | Prior work has used bacteria or colloidal active matter to serve as active baths that can turn rotors or be rectified. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 21 | Collective trapping of flocking particles by asymmetric obstacles | Aragones, Juan; Martinez, Raul; Alarcon, Francisco; Valeriani, Chantal | In this talk, I will show that flocking particles which follow the Vicsek model aligning rules experience a collective trapping in the presence of a wall of funnels made of chevrons, concentrating at the opposite side of a wall of funnels than run-and-tumbling particles. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 22 | Polar flocking of active clusters | Dommersnes, Paul; Fossum, Jon Otto | Here we report on a system of electro-propelled rolling granular beads with tuneable interactions. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 23 | Flocking and clustering of self-propelled disks with active reorientation | Zheng, Ting; Chen, Lu; Tu, Zhanchun; Cheng, Xiang; Xu, Xinliang | In this talk we present a numerical investigation of self-propelled disks that integrates a behavior of active reorientation in analogy to collision avoidance in animal herds. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 24 | Active folding and coiling in vivo | Mitchell, Noah; Cislo, Dillon; Shankar, Suraj; Dogic, Zvonimir; Shraiman, Boris; Streichan, Sebastian | We present a quantitative account of the dynamics of folding and coiling of the midgut that links cellular motion and deformation to the macroscopic shape change of the organ. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 25 | Dynamical self-consistent field-theory for active nematic liquid crystals: Nematic order and spatio-temporal structure in surface colonies of rod-like bacteria | Lee, Drake; Wickham, Robert | We present a dynamical self-consistent field theory for interacting, self-propelled rods that we use to study fascinating time-dependent, inhomogeneous structures observed in surface colonies of twitching Pseudomonas aeruginosa bacteria. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 26 | Growth and dynamics of active nematic droplets of Myxococcus xanthus bacteria | Yang, Cassidy; Shaevitz, Joshua | Unlike passive fluids that form axisymmetric spherical cap-shaped droplets, we find that these aggregates break symmetry and are often elongated in shape with non-uniform contact angles. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 27 | Solid-liquid transitions of deformable active particles | Loewe, Benjamin; Chiang, Michael; Marenduzzo, Davide; Marchetti, M Cristina | To describe such situations, we have developed a multi-phase field model where cells are characterized by multiple scalar fields, and interact through steric repulsion. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 28 | Uncovering the dynamic precursors to motor-driven contraction of active gels | Alvarado, José | Here we investigate the microscopic dynamics of reconstituted actin–myosin networks using real-space video microscopy and Fourier-space dynamic light scattering. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 29 | Microscopic simulations of a 3D active nematic composed of semiflexible polymers | Peterson, Matthew; Hagan, Michael; Baskaran, Aparna | Here, we will use particle-based simulations to better understand the dynamical properties of dry active nematics in 3D, both in bulk and under confinement. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 30 | The structure and dynamics of microtubule bundles mediated by motor proteins | Lemma, Bezia; Lemma, Linnea; Fuerthauer, Sebastian; Shelley, Michael; Dogic, Zvonimir; Needleman, Daniel | We can measure the geometric structure of these MT-based bundles using small-angle x-ray scattering and determine the polar structure of these materials by taking advantage of their chiral crystal lattice which produces constructive interference of second harmonic signal between polar-aligned MTs. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 31 | Microscopic to mesoscopic: what can modular molecular motors teach us about the nature of active stress? | Redford, Steven; Ruijgrok, Paul; Colen, Jonathan; Zemsky, Sasha; Vitelli, Vincenzo; Bryant, Zev; Dinner, Aaron; Gardel, Margaret | Coarse-grained hydrodynamic theories have proven invaluable to our understanding of active nematic liquid crystals. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 32 | 2D Patterns of Active Stress ascribe 3D Deformations of Driven Actomyosin Networks | Yadav, Vikrant; Kim, Taeyoon; De La Cruz, Enrique; Murrell, Michael | To understand this relation, we design an invitro actomyosin network with tunable mechanical stiffness and activity. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 33 | Confinement effects on the phase behavior of collagen-like semiflexible polymers | Spencer, Russell; Ha, Bae-Yeun | In this talk, we discuss the phase behavior of collagen-like semi-flexible polymers in the presence or absence of confinement, focusing on isotropic, nematic and cholesteric phases. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 34 | Shape study of Spindle-like microtubule tactoids using experiment and computation | Sahu, Sumon; Herbst, Lena; Quinn, Ryan; Ross, Jennifer | We explored the phase space of this organization by varying initial conditions like filament number, orientation, and length as well as crosslinker number, binding dynamics. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 35 | Shear-induced gelation of self-yielding active networks | Gagnon, David; Dessi, Claudia; Dogic, Zvonimir; Blair, Daniel | In this talk, I will describe how microscopic dynamics modify the macroscopic mechanical properties of extensile microtubule networks. | Session 1: Active Matter and Liquid Crystals in Biological Systems |
| 36 | Clogging and Depinning of Active Matter Systems in Disordered Media | Reichhardt, Cynthia | We numerically examine the transport of active run-and-tumble particles with steric particle-particle interactions driven with a drift force over random disordered landscapes comprised of fixed obstacles. | Session 2: Active Matter in Complex Environments |
| 37 | Flocking through disorder | Chardac, Amélie; Shankar, Suraj; Marchetti, M Cristina; Bartolo, Denis | I will present a series of quantitative experiments that elucidate the existence of a novel state of active matter that supports orientational order (through a sparse rivers network) but no net transport. | Session 2: Active Matter in Complex Environments |
| 38 | Enhanced bacterial motility in colloidal media | Kamdar, Shashank; Francis, Lorraine; Cheng, Xiang | Using confocal microscopy, we image the motion of fluorescent-labeled bacteria and implement an in-house tracking algorithm to obtain the speeds of bacteria. | Session 2: Active Matter in Complex Environments |
| 39 | Theoretical Framework to Describe Traveling Waves of Bacteria in Porous Media | Amchin, Daniel; Bhattacharjee, Tapomoy; Kratz, Felix; Ott, Jenna; Datta, Sujit | To address this gap in knowledge, we use confocal microscopy to directly track bacteria deep inside transparent porous media. | Session 2: Active Matter in Complex Environments |
| 40 | The role of diversity for collective bacterial migration through diverse environments | Mattingly, Henry; Emonet, Thierry | We recently showed that diverse cells can travel together in the expanding front by sorting themselves by chemotactic ability, which compensates for their differences by matching ability to the local chemotactic signal (Fu, Kato et al. | Session 2: Active Matter in Complex Environments |
| 41 | Light-Sensing Microbes in Complex Geometries: Surface Adhesion, Gliding Motility and Self-Organization | Fragkopoulos, Alexandros; Till, Sebastian; Raum, Sebastian; Catalan, Rodrigo; Baeumchen, Oliver | Based on cell tracking and statistical analysis, we study the surface adsorption and gliding motility of light-sensing microbes and demonstrate how surface gliding, in conjunction with cell-cell interactions, may control the emergence of microbial self-organization in confinement. | Session 2: Active Matter in Complex Environments |
| 42 | Active Brownian filaments: deviations from blob scaling theory and dynamics inside cavities | Das, Shibananda; Cacciuto, Angelo | Via a numerical study we establish how the standard blob scaling theory representations of a polymer breaks down when dealing with active polymers under confinement. | Session 2: Active Matter in Complex Environments |
| 43 | Fitness of cell colonies to navigate obstacles | Li, Bo; Yu, Sun-Min; Cho, Yoon-Kyoung; Granick, Steve | Stretched leader cells trigger acceleration of the whole group; the resulting velocity difference, in turn, reinforces stretching of the leaders and establishes positive feedback between cell morphology and mechanical strength, as we confirm by direct visualization of F-actin expression, cadherin localization, and the shapes of cells and their nuclei. | Session 2: Active Matter in Complex Environments |
| 44 | Anomalous size-dependence of bacterial diffusion in a micropillar array | Chopra, Pooja; Quint, David; Gopinathan, Ajay; Liu, Bin | We develop an agent-based model that purely relies on the geometry of the micropillars, bacteria and residency time. | Session 2: Active Matter in Complex Environments |
| 45 | Colloidal random-walkers for probing anomalous diffusion in heterogeneous micro-environments | Karani, Hamid Reza; Kokot, Gašper; Vlahovska, Petia | Building on our recently developed tunable colloidal random walker, we combine microfluidics experiments with theory to characterize and quantify the degree of anomalous diffusion. | Session 2: Active Matter in Complex Environments |
| 46 | Transport properties of circle microswimmers in heterogeneous media | Chepizhko, Oleksandr; Franosch, Thomas | Here, we investigate a model for a single circle swimmer exploring a two-dimensional disordered array of impenetrable obstacles. | Session 2: Active Matter in Complex Environments |
| 47 | Escape of a Nanoparticle from Cavities in a Porous Matrix | Wu, Haichao; Greydanus, Benjamin; Schwartz, Daniel | Here, we used a three-dimensional (3D) tracking method to explicitly visualize the process of passive Brownian nanoparticle and self-propelled Janus particle diffusion within periodic porous nanostructures. | Session 2: Active Matter in Complex Environments |
| 48 | The Physics of Cold Active Matter: on how time-independent disorder affects the motion of self-propelled particles | Peruani, Fernando | Despite this, most experimental and theoretical efforts have focused on homogeneous media and the impact of environmental heterogeneities on individual and collective properties of active systems has remained, up to recently, unexplored. | Session 2: Active Matter in Complex Environments |
| 49 | The motion of active colloids and their induced flow field at fluid interfaces | Molaei, Mehdi; Chisholm, Nicholas; Deng, Jiayi; Yao, Tianyi; Crocker, John; Stebe, Kathleen | We consider an ideal flat "clean" interface characterized solely by a uniform interfacial tension. | Session 2: Active Matter in Complex Environments |
| 50 | Hydrodynamic attraction of bacteria to gas and liquid interfaces | Ahmadzadegan, Adib; WANG, Shiyan; Vlachos, Pavlos; Ardekani, Arezoo | We develop a new theory based on Brownian dynamics including hydrodynamics and short-range physio-chemical interactions between bacteria and surfactant-laden interfaces and explain our experimental findings. | Session 2: Active Matter in Complex Environments |
| 51 | Non-Markovian active droplets | IZZET, Adrien; Zakine, Ruben; Vanden-Eijnden, Eric; Brujic, Jasna | Here we show that the trajectories of larger droplets display complex non-Markovian behaviors, such as self-interacting dynamics, that require a more complicated model than rotational diffusion. | Session 2: Active Matter in Complex Environments |
| 52 | Stigmergy in active furrowers | Imaran, MD; Prabhakar, Ranganathan; Chelakkot, Raghunath; Inamdar, Mandar | We attempt to explain our observations through a coarse-grained, but general, model of stigmergy. | Session 2: Active Matter in Complex Environments |
| 53 | Slip and distance effects on the self-propulsion of catalytic microswimmers close to a wall | Ketzetzi, Stefania; de Graaf, Joost; Doherty, Rachel; Kraft, Daniela | In this talk, we will present quantitative measurements of the effect of the substrate on the velocity of Pt-coated model microswimmers. | Session 2: Active Matter in Complex Environments |
| 54 | Measuring chaotic advection in a biological active nematic in viscous environments | Tan, Amanda; Mitchell, Kevin; Hirst, Linda | We investigate how the external changes from viscosity affect various quantitative parameters from chaotic advection theory, such as local fluid stretching rates within the network and topological entropy calculated from defect braiding. | Session 2: Active Matter in Complex Environments |
| 55 | Hydrodynamic interactions between passive colloids in an active bacterial bath | Gokhale, Shreyas; Li, Junang; Solon, Alexandre; Gore, Jeffrey; Fakhri, Nikta | By quantifying spatial velocity correlations and the short time pair diffusivity tensor for colloids, we show that bacterial motion leads to partial screening of long-ranged hydrodynamic interactions. | Session 2: Active Matter in Complex Environments |
| 56 | Self-organization of swimmers drives long-range fluid transport in bacterial colonies | Haoran, Xu; Dauparas, Justas; Das, Debasish; Lauga, Eric; Wu, Yilin | Here, we show that motile cells in sessile colonies of peritrichously flagellated bacteria can self-organize into two adjacent, centimeter-scale motile rings surrounding the entire colony. | Session 2: Active Matter in Complex Environments |
| 57 | Linear instability and nonlinear dynamics of droplets and layers of active fluid | Stein, David; Young, Yuan-nan; Shelley, Michael | In this work we focus on the effects of surface tension on the stability and nonlinear dynamics in droplets and layers of active fluid. | Session 2: Active Matter in Complex Environments |
| 58 | Swimming of active drops in confinements with external flows | Dey, Ranabir; Buness, Carola M.; Jin, Chenyu; Maass, Corinna | We feel that understanding such swimming behaviour of active matter will make significant contribution towards better comprehension of certain important biological phenomena. | Session 2: Active Matter in Complex Environments |
| 59 | Examining collective mechanical properties of fish schools using projected light fields | Puckett, James; Pokhrel, Aawaz | Models have shown that simple local interactions between individuals gives rise to the emergent self-organized macroscopic states such as flocks, swarms, or schools. | Session 2: Active Matter in Complex Environments |
| 60 | Spatial-temporal organization of bacterial suspensions under confinement | Aronson, Igor | We present experimental and theoretical studies on the expansion of highly concentrated bacterial droplets into an ambient bacteria-free fluid. | Session 2: Active Matter in Complex Environments |
| 61 | Trapping of microswimmers in vortex flows | Berman, Simon; Mitchell, Kevin | We propose heteroclinic bifurcations between swimming fixed points as a general mechanism for the creation of stable swimmer trajectories. | Session 2: Active Matter in Complex Environments |
| 62 | Sensorimotor processing and navigation in confined microswimmers | Bentley, Samuel; Anagnostidis, Vasileios; Gielen, Fabrice; Wan, Kirsty | We present a novel microfluidic platform which allowed us for the first time to monitor and analyse algal cell motility over hours, and even developmental timescales. | Session 2: Active Matter in Complex Environments |
| 63 | Topographical guidance of highly-motile cells using cell-sized features | Wondergem, Joeri; Schakenraad, Koen; Witzel, Patrick; Mytiliniou, Maria; Holcman, David; Heinrich, Doris | Here, we focused on a larger scale, and studied the influence of cell-sized obstacles on highly-motile, persistent cell migration. | Session 2: Active Matter in Complex Environments |
| 64 | Quenching active matter using light: Light mediated motility in swarming Serratia marcescens | Gopinath, Arvind; Yang, Junyi; Patteson, Alison; Arratia, Paulo | Complementing our experimental results, we propose and analyze a minimal Brownian dynamics model to study the escape of bacteria from the exposed region before they are completely immobilized and trapped. | Session 2: Active Matter in Complex Environments |
| 65 | Submerged micro-strucutures generate a soft boundary effect on active nematic flows | Khaladj, Dimitrius; Tan, Amanda; Hirst, Linda | We study the behavior of an active nematic microtubule system confined by submerged complex geometries. | Session 2: Active Matter in Complex Environments |
| 66 | Lattices by design: exploring long-ranged interactions with gradient sensing droplets | Molina, Anton; Prakash, Manu; Kumar, Shailabh | Here, we develop exotic lattice systems that exploit the tools of photolithography to fabricate arbitrary patterns of hydrophobic boundaries, enabling us to experimentally manipulate the geometry in which long-ranged degrees of freedom interact. | Session 2: Active Matter in Complex Environments |
| 67 | Arresting Active Spinning Particle Coarsening in Passive Media via Actuation Protocols | Steimel, Joshua; Tollefsen, Ryan; Alexander-Katz, Alfredo | We present a novel approach which allows the control of coarsening behavior and resultant characteristic domain size via modulation of the activity actuation protocol. | Session 2: Active Matter in Complex Environments |
| 68 | Flocking Transition in a Self-propelled Particle Model Using Experimental Motility Conditions | Lyles, Jelani; Yanka, Paul; Tung, Chih Kuan; Sussman, Daniel; Manning, M. Lisa | Flocking transition has been studied using self-propelled particle models for decades. | Session 2: Active Matter in Complex Environments |
| 69 | Re-entrant self pumping in confined active fluids | Varghese, Minu; Baskaran, Arvind; Hagan, Michael; Baskaran, Aparna | In this talk, I will discuss the origin of this phenomenon using an active hydrodynamic theory. | Session 2: Active Matter in Complex Environments |
| 70 | Tunable self-organization of swimming magnetic bacterial suspensions | Wijesinghe, Hiran; Pierce, Christopher; Mumper, Eric; Lower, Brian; Lower, Steven; Sooryakumar, Ratnasingham | We present population-level self-organization in a flagellated magnetic bacterial suspension of Magnetospirillum magneticum (AMB-1) that is amenable to experimental control using programmable fields. | Session 2: Active Matter in Complex Environments |
| 71 | Dynamics of 2D Active Nematics Confined in an Annulus | Joshi, Chaitanya; Zarei, Zahra; Norton, Michael; Fraden, Seth; Baskaran, Aparna; Hagan, Michael | In this talk, we will discuss a theoretical and computational study of 2D active nematics confined to an annulus. | Session 2: Active Matter in Complex Environments |
| 72 | Self-organization of bacterial active matter in space and time | Liu, Song; Wu, Yilin | Here we found that tuning the rheological properties of bacterial active fluids enables large-scale spatial and temporal self-organization. | Session 2: Active Matter in Complex Environments |
| 73 | Nonequilibrium phases in mixtures of active and passive particles | Li, Junang; Gokhale, Shreyas; Solon, Alexandre; Gore, Jeffrey; Fakhri, Nikta | Here, we map the computational phase diagram of a binary mixture of active and passive particles as a function of orientational interactions and Peclet number and observe new emergent behavior of dynamical clustering and a polar band of active particles. | Session 2: Active Matter in Complex Environments |
| 74 | Tuning the self-organization of confined active particles by the steepness of the trap | Rana, Shubhashis; Samsuzzaman, Md.; Saha, Arnab | We consider the collective dynamics of self-propelling particles in two dimensions. | Session 2: Active Matter in Complex Environments |
| 75 | Active matters: broken symmetries and response | Dal Cengio, Sara; Levis, Demian; Pagonabarraga, Ignacio | We address the question of how interacting active systems in a non-equilibrium steady-state respond to an external perturbation. | Session 2: Active Matter in Complex Environments |
| 76 | Spontaneous symmetry breaking induced unidirectional rotation of a chain-grafted colloidal particle in the active bath | TIAN, WENDE | Here we show, by simulations, that a chain-grafted disk-like colloidal particle can rotate unidirectionally and hence output work when immersed in a thin film of active particle suspension. | Session 2: Active Matter in Complex Environments |
| 77 | Temperature dependence of microtubule-based active fluid | Bate, Teagan; Jarvis, Edward; Varney, Megan; Wu, Kun-Ta | This temperature-dependent speed was reported to follow the Arrhenius Law. | Session 2: Active Matter in Complex Environments |
| 78 | Elasticity mediated attraction between active polar particles | Gupta, Rahul; Kant, Raushan; Soni, Harsh; Sood, Ajay; Ramaswamy, Sriram | We present a theory for this active attraction based on the forcing imposed by the motile rods on the crystalline medium of beads, and the action of the medium on the rod orientation. | Session 2: Active Matter in Complex Environments |
| 79 | Light-regulated swimming motility induces cell aggregation in confinement | Fragkopoulos, Alexandros; Vachier, Jérémy; Frey, Johannes; Le Menn, Flora-Maud; Wilczek, Michael; Mazza, Marco; Baeumchen, Oliver | We observe that a suspension of freely swimming C hlamydomonas reinhardtii cells, a unicellular soil-dwelling microalgae and a model organism of puller-type microswimmers, forms such large-scale aggregations under confinement in specific light conditions. | Session 2: Active Matter in Complex Environments |
| 80 | Undulatory intruder dynamics in water-saturated granular beds | Kudrolli, Arshad; Huynh, Trinh | We will report an investigation of active intruder dynamics through complex media with {\texit Lumbriculus variegatus} moving through water saturated granular beds which are refractive index matched to enable observation of their motion inside the bed. | Session 2: Active Matter in Complex Environments |
| 81 | Pressure of bacterial suspensions on confining walls and freely moving chains | Ma, Xiaolei; Guo, Shuo; Xu, Xinliang; Cheng, Xiang | In particular, mechanical pressure, a state variable in equilibrium systems, shows a nontrivial dependence on system boundary as well as specific measurement methods. | Session 2: Active Matter in Complex Environments |
| 82 | Active surfers on a vibrating bath: self-propulsion and interactions | Oza, Anand; Ho, Ian; Pucci, Giuseppe; Harris, Daniel | We present a combined experimental and theoretical investigation of a newly discovered active matter system consisting of objects floating on a vertically vibrating fluid bath. | Session 2: Active Matter in Complex Environments |
| 83 | Nutrient depletion thresholds in 3D printed cell assemblies | Morley, Cameron; Angelini, Thomas | In this talk, we will describe experiments that test the 200 micron rule in which we 3D print controlled distributions of hepatocytes into 3D culture medium made from jammed granular microgels. | Session 2: Active Matter in Complex Environments |
| 84 | Control of Active Nematics through Friction | Thijssen, Kristian; Metselaar, Luuk; Shendruk, Tyler; Doostmohammadi, Amin; Yeomans, Julia | Our work demonstrates novel methods to control active matter without the introduction of invasive solid bounding walls. | Session 2: Active Matter in Complex Environments |
| 85 | Inertial effects on trapped active matter | Sandoval-Espinoza, Mario; Gutierrez, Lorenzo | Here, we analytically find the effect of inertia on the mean-square displacement and mean-square speed of a system of inertial active Brownian particles subject to a weak and a strong harmonic trap. | Session 2: Active Matter in Complex Environments |
| 86 | Wiggling arthropods induce flow in granular materials | Kendall, Melia; Chen, Shih-Yuan; Daniels, Karen | Just as heating a viscous fluid causes its viscosity to drop, we observe that the introduction of active particles into a passive granular material can increase its flowability. | Session 2: Active Matter in Complex Environments |
| 87 | Uncovering the dynamical structure of behavioral repertoires | Pinkoviezky, Itai; Berman, Gordon | In this talk, we take a different approach, fitting dynamical models to long behavioral sequences from fruit flies and other species. | Session 3: Animal Behavior |
| 88 | Collective bumblebee foraging in a controlled stochastic environment | Hofmann, David; Roman, Ahmed; McDermott, Donna; Brosi, Berry; Nemenman, Ilya | In this study, an entire colony of tagged bees is kept in the foraging chamber for 4-6 days. | Session 3: Animal Behavior |
| 89 | A Low-Cost Modular Camera System for 3D Pose Estimation in the Field | Wolf, Scott; Ayroles, Julien; Shaevitz, Joshua | To fill this gap, we developed a low-cost, modular camera platform to generate 3D imaging data compatible with contemporary pose estimation techniques. We initially generated datasets from three camera modules that allow for 3D pose estimation in a large outdoor area of over 600m 2 and demonstrate its use in an open field experiment at the Mpala Research Centre and Wildlife Foundation in Nanyuki, Kenya. | Session 3: Animal Behavior |
| 90 | Bridging time scales in C. elegans behavior through transfer operators | Costa, Antonio; Jordan, David; Stephens, Greg | We introduce a principled method to simultaneously reconstruct and partition the dynamical state-space, which we use to approximate the Perron-Frobenius operator. | Session 3: Animal Behavior |
| 91 | Inferring behavioral homologies from dynamical models | Overman, Katherine; Pinkoviezky, Itai; Berman, Gordon | By fitting dynamical models to these transitions, we can reproduce the summary statistics of our dataset, including long timescale dynamics and hierarchical structure. | Session 3: Animal Behavior |
| 92 | Long timescale dynamics in freely behaving rats | Jain, Kanishk; Menichini, Elena; Muzzu, Tomaso; Macke, Jakob; Saleem, Aman; Berman, Gordon | Using these postural time series’ we create a low-dimensional behavioral state space using unsupervised methods that characterizes stereotypic behavioral bouts. | Session 3: Animal Behavior |
| 93 | Measuring and modeling the dynamics of the thermal memory 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 3: Animal Behavior |
| 94 | Multi-animal pose tracking using deep neural networks | Pereira, Talmo; Ravindranath, Shruthi; Tabris, Nathaniel; Li, Junyu; Murthy, Mala; Shaevitz, Joshua | Here we present a new framework we term SLEAP (Social LEAP Estimates Animal Poses) that can explicitly model the relationship between body parts, enabling accurate multi-animal pose estimation. | Session 3: Animal Behavior |
| 95 | Phenotype to Function: Predicting drug mode of action from behavioural fingerprints | McDermott-Rouse, Adam; Minga, Eleni; Brown, Andre | Therefore, an important problem in developing new compounds to combat the rise of anthelmintic resistance is determining their mode of action. | Session 3: Animal Behavior |
| 96 | Probing the neural substrates of movement generation across the rodent behavioral repertoire | Marshall, Jesse; Aldarondo, Diego; Dunn, Timothy; Wang, William; Berman, Gordon; Olveczky, Bence | To extend the range of behaviors and contexts that can be studied, we developed a new behavioral monitoring system, CAPTURE, that combines motion capture and deep learning to track the 3D movements of twenty points on a freely behaving rat’s trunk and appendages, continuously over week-long timescales. | Session 3: Animal Behavior |
| 97 | Speed selection and sampling strategies for terrestrial trail tracking | Reddy, Gautam; Vergassola, Massimo; Shraiman, Boris | Our work provides a general framework for trail tracking and testable hypotheses on the algorithms that animals use to follow trails. | Session 3: Animal Behavior |
| 98 | Specialization of control strategies in terrestrial slithering snakes. | Schiebel, Perrin; Lin, Bo; Hubbard, Alex; Chen, Lillian; Blekherman, Greg; Goldman, Daniel | We hypothesized that the generalists instead controlled reaction forces and tested this using a simplified terrain, a single force-sensitive post on whiteboard. | Session 3: Animal Behavior |
| 99 | Proceed with caution: dynamics of novelty-directed risk assessment behavior in mice | Yamamura, Yoriko; Wickens, Jeffery | We ask whether 1) a feed-forward model can predict retreat timings from preceding trajectories of approach, and 2) including feedback from risk to snout velocity explains the asymmetrical dynamics of "risk assessment". | Session 3: Animal Behavior |
| 100 | Transitions between stochastic and oscillatory active sensing in pulse-type 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 3: Animal Behavior |
| 101 | Steering and turning control of C. elegans | Diaz, Kelimar; Chong, Baxi; Wang, Tianyu; Bates, Kathleen; Ding, Jimmy; Sartoretti, Guillaume; Lu, Hang; Choset, Howie; Goldman, Daniel | To search for steering control principles in undulatory locomotion, we studied C. elegans traversing both agar and liquid buffer. | Session 3: Animal Behavior |
| 102 | Flow due to chirality in suspensions of magnetotactic bacteria | Cebers, Andrejs | As a particular example that is simple enough for analysis we consider a layer of magnetotactic bacteria suspension with thickness h and width 2d above a solid wall. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 103 | Active depinning of bacterial droplets due to gravity | Shankar Kotian, Harshitha; Abdulla, Amith; K. N., Hithysini; Singh, Varsha; Varma, Manoj | Contrary to this belief, we present experimental evidence that motility of the individual bacteria and the stiffness of the agar dominates the de-pinning dynamics to an extent that de-pinning can happen even in mutant strains incapable of producing surfactants. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 104 | Optimal Geometry of Perfusion in Flow Networks | Gavrilchenko, Tatyana; Katifori, Eleni | Motivated by this system, we study networks where flow is laden with nutrients able to diffuse out of the vessels and into the surrounding faces. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 105 | Confined Diffusion of a Colloidal Particle Between Two Parallel Walls: Quantifying Diffusing Diffusivity | Slater, Gary; Ignacio, Maxime; Qiao, Le | Instead of using the Kurtosis as a measure of the non-ideality of the diffusion motion, we introduce a new empirical fitting function with a tunable exponent and a critical time scale. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 106 | Fluid flow dynamics in networks of compliant vessels | Fancher, Sean; Katifori, Eleni | Here, we develop a theoretical model of pulsatile flow using compliant vessels that interact with the flow and are capable of storing material and elastic energy. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 107 | Optimization of solute dissemination in complex flow networks | Gounaris, Georgios; Ruiz Garcia, Miguel; Katifori, Eleni | We propose a local adaptation rule for the vessel radii that is able to equalize perfusion, while minimizing energy dissipation to circulate the flow and a cost constraint. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 108 | Probing in-mouth texture perception with a biomimetic tongue | Prevost, Alexis; Thomazo, Jean-Baptiste; Contreras Pastenes, Javier; Pipe, Christopher; Le Révérend, Benjamin; Wandersman, Elie | To probe the behavior under physiological flow conditions, deflections of model papillae are measured using a novel fluorescent imaging technique enabling sub-micrometer resolution of the displacements. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 109 | Towards a synthetic post-translational protein oscillator | Kimchi, Ofer; Goodrich, Carl; Curatolo, Agnese; Courbet, Alexis; Woodall, Nick; Zorine, Dmitri; Baker, David; Brenner, Michael | We will describe the systems, the intuition behind them, and their dependence on the (few) kinetic parameters. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 110 | Protein recruitment through indirect mechanochemical interactions | Goychuk, Andriy; Mohite, Atul; Frey, Erwin | We suggest a generic feedback mechanism that explains how cooperativity can directly arise from mechanochemical coupling between the membrane and proteins. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 111 | Modelling the Ear with Electronic Oscillators: The Wien Bridge Oscillator as a Physical Analogue for the Hair Cell | Fleming, Courtney; Tagg, Randall; Asadi-Zeydabadi, Masoud | We will introduce our theoretical model for nonlinearity and resonance within the Wien bridge oscillator based on experimental results, and discuss parallels between the dynamics of the Wien bridge oscillator and the dynamics of the hair cell. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 112 | Bulk-surface coupling reconciles Min-protein pattern formation in vitro and in vivo | Brauns, Fridtjof; Pawlik, Grzegorz; Halatek, Jacob; Kerssemakers, Jacob; Frey, Erwin; Dekker, Cees | Here, we combine experiments and theory to show that this variety of patterns originates from distinct pattern-forming mechanisms (oscillation modes) that operate at different ratios of cytosolic volume to membrane surface area. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 113 | Low dimensional structures in cardiac alternans | Velasco Perez, Hector; Fenton, Flavio | Here, we will focus on the study of traveling waves with alternans, that is, the change in the action potential wave length and/or amplitude in time. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 114 | Acoustic Coupling between Active Oscillators Allows for their Synchronization and Explains Identical-Frequency Sounds Emitted from the Two Ears | O Maoileidigh, Daibhid; Roongthumskul, Yuttana; Hudspeth, AJ | We record SOAEs simultaneously from the two ears of the tokay gecko and find several synchronized SOAEs. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 115 | Patterns make patterns: how hierarchical self-organization couples cell shape to biochemical dynamics | Tan, Tzer Han; Wigbers, Manon; Brauns, Fridtjof; Swartz, Zachary; Frey, Erwin; Fakhri, Nikta | By combining experiments in starfish oocytes with mathematical modelling, we find that cell shape information encoded in a cytosolic gradient can be decoded by a bistable front of a RhoA regulator. | Session 4: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
| 116 | Areca Sheath: A Bio-Degradable Alternative for Synthetic Materials in the Food Industry | Mohanty, Debapriya Pinaki; Viswanathan, Koushik; Udupa, Anirudh; Chandra, Anil; Chandrasekar, Srinivasan | In this study, we report on the results of an investigation of their formability. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 117 | Polycarbonate Mold Copying Technique to Fabricate Microengineered Devices for Biophysical Studies | Sonmez, Utku; LeDuc, Philip | Here, we report a novel microfabrication technique that we have developed for benchtop fabrication of microengineered devices outside the cleanroom so that they can be cheaply fabricated with high throughput. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 118 | The Design and Modeling of Adsorption Based Filters and the Bioremediation of Heavy Metal Contaminated Water | McCarthy, Chris | I will discuss kinetic models of adsorption, as well as our mathematical models of such filters. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 119 | Reciprocal Control of Hierarchical DNA Origami-Nanoparticle Assemblies | Johnson, Joshua; Dehankar, Abhilasha; Winter, Jessica; Castro, Carlos | We present an actuation scheme utilizing NPs as control elements enabling rapid and reversible thermal actuation of DNA origami and higher order assemblies. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 120 | Fiber fluorescence photo thermometry during magnetic heating reveals directional alignment of suspended nanoparticles | Munshi, Rahul; He, Muye; Rubio-Castellanos, Idoia; Sethi, Komal; Liu, Junting; Pralle, Arnd | We developed highly sensitive camera-based fiber fluorescence photometry to measure temperature changes of magnetically heated nanoparticles. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 121 | Landscapes, nonlinearity, and optimality of ion transport in sub-nanoscale pores | Sahu, Subin; Elenewski, Justin; Rohmann, Christoph; Zwolak, Michael | We demonstrate how this works in a synthetic selectivity filter and discuss how to probe this system, which will help to experimentally quantify optimal transport conditions and will give the foundation for a robust understanding of more complex biological pores. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 122 | Potentiometric Detection of Single Protein Molecules in Solution by Nanoimpact Method | Pandey, Popular; He, Jin | In this presentation, I will demonstrate a facile potentiometric method of detecting protein at the single-molecule level in solution based on the nanoimpact events of proteins at the nanoelectrode, which is further supported by molecular dynamics (MD) simulation. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 123 | Drops: A bio-inspired tool to structure materials | Amstad, Esther | Inspired by nature, we use emulsion drops as building blocks of macroscopic granular hydrogels with well-defined micrometer-scale structures and locally varying compositions. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 124 | On the interaction of molecular rotors with lipid nanodroplets | Ziolek, Robert; Cornell, Bethan; Smith, Paul; Steinmark, I. Emilie; Suhling, Klaus; Lorenz, Christian | In this presentation, I will present the results of several large-scale classical molecular dynamics simulations in which we investigate the molecular scale interactions of a molecular rotor, BODIPY-C12, with lipid droplets. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 125 | Design of bio-inspired surface topographies via polymer bilayer wrinkling superposition | Pellegrino, Luca; Khodaparast, Sepideh; Cabral, Joao | Here, we investigate the formation of analogous 2D wrinkling patterns in artificial soft materials, built as a superposition of single frequency features. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 126 | Near-IR Absorbing Quantum Dots Designed to Kill Multidrug-Resistant Pathogens | Levy, Max; Bertram, John; Eller, Kristen; ding, yuchen; Chatterjee, Anushree; Nagpal, Prashant | We show that low doses of QDs can kill pathogens without harming human cells. | Session 5: Biomaterials: Nano and Bioinspired materials |
| 127 | The avian eggshell: evolution and engineering of a tough, lightweight biological material | Stoddard, Mary; Deng, Zhifei; Jia, Zi’an; Li, Ling; Weaver, James | 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 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 128 | Misorientation and enhanced hardness in tooth enamel | Stifler, Cayla; Sun, Chang-Yu; Beniash, Elia; Gilbert, Pupa | We used PIC (polarization-dependent imaging contrast) 3,4 mapping at the calcium L-edge 5 to reveal the crystal orientations within rods in mammalian enamel and in bundles in fish enameloid. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 129 | Crystallographic Parameters Of Rod And Interrod Enamel Crystallites Differ Systematically | Free, Robert; DeRocher, Karen; Stock, Stuart; Joester, Derk | Our objective was to test the hypothesis that crystallographic features of two microstructural features of ename, rod and interod enamel, differ as a consquence of their developmental origin. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 130 | Characterization of a Novel Antimicrobial Agent for Endodontic Applications | Zhu, Aris; Wolberg, Jeffrey; Koosha, Farzad; Etwaru, Karena; Rafailovich, Miriam | This study characterizes the antimicrobial properties, cytotoxicity, and differentiation potential of CASA for dental pulp stem cells (DPSCs). | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 131 | Evolutionary patterns in skeletal biomineralization | Porter, Susannah; Moore, John; Riedman, Leigh Anne | We have identified >80 acquisitions of mineralized skeletons in eukaryotes along with their time of first appearance and their mineralogy, and have found several interesting patterns. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 132 | Biomineralization by particle attachment in early animals | Gilbert, Pupa; Porter, Susannah; Sun, Chang-Yu; Xiao, Shuhai; Gibson, Brandt; Shenkar, Noa; Knoll, Andrew | The convergent evolution of biomineral CPA may have been dictated by the same thermodynamics and kinetics as we observe today. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 133 | 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, 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 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 134 | Building with melanin: Low complexity Glycera jaw protein is master of multitasking | Waite, J Herbert | Building with melanin: Low complexity Glycera jaw protein is master of multitasking | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 135 | Memory and learning in biomolecular soft materials | Collier, Charles; Najem, Joseph; Williams, Stan; Taylor, Graham; Schuman, Catherine; Belianinov, Alex; Doughty, Benjamin; Weiss, Ryan; Hasan, Md Sakib; Rose, Garrett; Sarles, Stephen | We are integrating lipid and polymer bilayer membranes with micro- and nanofabrication to develop fundamentally new types of neuromorphic elements that have the composition (biomolecules), structure (biomembranes), and switching mechanism (voltage-sensitive ion channels) of real biological synapses, and operate at lower power than the current state-of-the-art. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 136 | Formation temperature of biomaterials through geologic time | Bergmann, Kristin; Goldberg, Sam; Anderson, Noah; Jost, Adam; Gilbert, Pupa; Myers, Corinne | Formation temperature of biomaterials through geologic time | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 137 | Nano-optical characterization of photosynthetic bacteria-2D material coupled system | Ambardar, Sharad; Frey, Zachary; Voronine, Dmitri | We use conventional far-field (FF) photoluminescence (PL) and near-field (NF) tip-enhanced photoluminescence (TEPL) to investigate the bio-sensing applications of TMD materials by depositing photosynthetic cyanobacteria on MoS 2-WS 2 heterostructure grown on SiO 2/Si substrate. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 138 | African Elephant Sensing Capabilities through Skin and Hair | Schulz, Andrew; Boyle, Colin; Higgins, Claire; Hu, David | In this study, we dissect an African elephant trunk and perform histology and measurement of the mechanical properties of the skin. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 139 | The role of residual stresses in biomineral morphogenesis revealed by 3D dark-field x-ray microscopy | Schöppler, Vanessa; Zlotnikov, Igor | In this work, we employed the recently developed technique—dark-field x-ray microscopy—to study the relationship between residual stresses and crystallographic properties of biogenic calcite in the prismatic ultrastructure in the bivalves Pinna nobilis and Pinctada nigra in 3D. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 140 | Effect of Sea Water pH on the Maturation of Marine Mussel Plaques | Bernstein, Justin; Filippidi, Emmanouela; Waite, J Herbert; Valentine, Megan | Here, we examine the effects of seawater pH on the time evolution of the internal microstructures in Mytilus californianus plaques. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 141 | Mechanics and Adhesive Performance of Mussels on Roughness- and Geometry- controlled 3D printed Substrates | Kwon, Younghoon; Bernstein, Justin; Valentine, Megan; Cohen, Noy | Using 3D printing, sandblasting, and laser texturing we created substrates with differing surface treatments and introduced these to mussels, which in turn adhered to the engineered surfaces via plaque-thread byssal structures. | Session 6: Biomaterials: Paleo and Modern Structure and Function in Animals |
| 142 | Filament Nucleation Tunes Mechanical Memory in Active Polymer Networks | Yadav, Vikrant; Banerjee, Deb; Tabatabai, Alan; Kovar, David; Kim, Taeyoon; Banerjee, Shiladitya; Murrell, Michael | We find that nucleation of F-actin mediates the accumulation and dissipation of polymerization-induced F-actin bending energy. | Session 7: Biomaterials: Tissue-Scale Physics |
| 143 | Bioinspired materials with self-adaptable mechanical behaviors | Orrego, Santiago; Chen, Zhezhi; Krekora, Urszula; Hou, Decheng; Jeon, Seung-Yeol; Pittman, Matthew; Montoya, Carolina; Chen, Yun; Kang, Sung | To overcome the issue, we have investigated synthetic materials inspired by bone that trigger mineral syntheses from ionic solutions on scaffolds upon mechanical loadings so that they can self-adapt to mechanical loadings. | Session 7: Biomaterials: Tissue-Scale Physics |
| 144 | The continuum of allosteric behavior in mechanical networks | Rocks, Jason; Liu, Andrea; Katifori, Eleni | We apply this analysis to a collection of proteins, allowing us to identify potential sets of residues that are important for facilitating allosteric communication between different binding sites. | Session 7: Biomaterials: Tissue-Scale Physics |
| 145 | A microfluidic model of periarterial spaces in the glymphatic system | Quirk, Keelin; Nordstrom, Kerstin; Kelley, Douglas | We have designed microfluidic devices to serve as two-dimensional models of periarterial spaces. | Session 7: Biomaterials: Tissue-Scale Physics |
| 146 | Ultrafast Finger Snap is Mediated by a Frictional Skin Latch | Acharya, Raghav; Challita, Elio; Bhamla, Saad | We find that the mechanics of the snap are strongly mediated by human skin friction, which acts as a latch to generate rapid motion. | Session 7: Biomaterials: Tissue-Scale Physics |
| 147 | Unveiling Interfacial Properties of Surfactant Assemblies Mimicking Healthy and Diseased States in Lung Membranes | Porras-Gomez, Marilyn; Leal, Cecilia | We performed structural and mechanical characterization by GISAXS, AFM and Fast Force Mapping on lipid-based mimicking pulmonary membranes in healthy and diseased states. | Session 7: Biomaterials: Tissue-Scale Physics |
| 148 | Hybrid active matter: particles and cellular aggregates | Brochard-Wyart, Francoise | We investigate the collective migration of cell on adhesive substrates, using 3D cellular aggregates as a model system. | Session 7: Biomaterials: Tissue-Scale Physics |
| 149 | The role of heterogeneous environments and docetaxel gradients in the emergence of polyploid, mesenchymal and resistant prostate cancer cells. | Austin, Robert | In this work, we use a micro-fabricated “evolution accelerator” environment to create a complex heterogeneous yet controllable in-vitro environment with a spatially-varying drug concentration. | Session 7: Biomaterials: Tissue-Scale Physics |
| 150 | Predicting Pericellular Matrix Structure from Simple Models of Hyaluronan Secretion | Scrimgeour, Jan | I present a simple kinetic model that allows an examination of the secretion process. | Session 7: Biomaterials: Tissue-Scale Physics |
| 151 | Electrical detection of Hachimoji nucleobases via a nanopore device incorporated in a graphene/h-BN heterostructure | Sivaraman, Ganesh; de Souza, Fabio; Fyta, Maria; Scheicher, Ralph; Scopel, Wanderla; Amorim, Rodrigo | Hence in this talk, we propose a computational study based on density functional theory and non-equilibrium Green’s function formalism, to unravel the electrical read-out of synthetic and natural nucleobases. | Session 7: Biomaterials: Tissue-Scale Physics |
| 152 | Modeling the rheology of dense biological tissues | Huang, Junxiang; Bi, Dapeng | In this work, we use a minimal vertex-based model to investigate the rheology of confluent epithelial tissues. | Session 7: Biomaterials: Tissue-Scale Physics |
| 153 | Autonomous synthesis and assembly of a ribosomal subunit on a chip | Levy, Michael; Falkovich, Reuven; Daube, Shirley; Bar-Ziv, Roy | Autonomous synthesis and assembly of a ribosomal subunit on a chip | Session 8: Biopolymers: Nucleic Acids and Structural |
| 154 | The formation of filopodia bridge and intercellular nanotube : A Critical rule of torque and restorative force. | Lee, O-chul; Chang, Minhyeok; Oh, Jaeho; Lee, Jong-Bong; Jeon, Jae-Hyung | In this study, we quantitatively investigate the conformation, stability, and dynamics of the filopodia in comparison with the experiment by using the Langevin dynamics simulation. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 155 | A novel coarse-grained energy functions for RNA folding | ZHANG, DONG; Chen, Shi-Jie | We recently developed a novel approach to extract RNA coarse-grained energy functions from the structural database. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 156 | Non-ergodic transport and conformational dynamics of DNA in biomimetic cytoskeleton networks | Garamella, Jonathan; aguirre, gina; Regan, Kathryn; McGorty, Ryan; Robertson-Anderson, Rae | Here, we use single-molecule conformational tracking (SMCT) to elucidate the transport properties and conformational dynamics of linear and relaxed circular (ring) DNA in in vitro composite networks of actin and microtubules with variable types of crosslinking. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 157 | Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures | Bundschuh, Ralf; Shatoff, Elan | Here, we use a modified version of the Vienna RNA folding package and PAR-CLIP data for HuR (ELAVL1) in humans to characterize the genome-wide effect of single nucleotide polymorphisms on HuR binding and show that they can have a many-fold effect on the affinity of HuR binding to RNA transcripts from tens of bases away. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 158 | COARSE-GRAINED MODELING OF DNA PLECTONEME FORMATION IN THE PRESENCE OF BASE-PAIR MISMATCHES | Desai, Parth Rakesh; Das, Siddhartha; Neuman, Keir | We develop a simulation framework using the oxDNA model to study the effect of mismatches on both positively and negatively supercoiled DNA. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 159 | A quantitative model of temperature actuated DNA origami nanocaliper constructs | Crocker, Kyle; Johnson, Joshua; Castro, Carlos; Bundschuh, Ralf | We develop a physical model of this system that uses partition function analysis of the interaction between the nanocaliper and nanoparticle to predict the probability that the nanocaliper is open at a given temperature. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 160 | A dynamic model of DNA Supercoiling | Wan, Biao; Yu, Jin; Xu, Xinliang | Based on this time separation, we developed a new model where the fast mechanical balancing dynamics are coarse grained. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 161 | Real-Time Tracking and Quantification of Transposible Element Activity | Kaur, Davneet; Lee, Gloria; Sherer, Nicholas; Urriola, Elliot; Kim, Hneil; Xue, Chi; Martini, K. Michael; Goldenfeld, Nigel; Kuhlman, Thomas | We show that we can obtain a deeper understanding of the roles of TEs and their individual proteins through our analysis. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 162 | Simulating the Polarization Effects of Gas-Phase Nucleic Acids | Myers, Christopher; Chen, Alan | In the work presented here, we explore the dynamical properties an appropriately tuned electrostatic force field for gas phase nucleic acids should replicate. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 163 | Existence of the B-Form DNA helix in nanoDNA liquid crystals and its variation due to aggregate assembly | Smith, Gregory; Fraccia, Tommaso; Zhernenkov, Mikhail; Bellini, Tommaso; Clark, Noel | We show using diffraction of a synchrotron X-ray microbeam that liquid crystalline aggregates of 12mer nanoDNA, such as the Drew-Dickerson Dodecamer (DD), demonstrate a B-form DNA double helix with a comparable degree of order to that seen in longer DNA, such as the calf-thymus DNA used by Rosalind Franklin to produce the historic Photo 51. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 164 | Constructing Out-of-plane Auxetic Response in Paper | Verma, Prateek; Griffin, Anselm; Shofner, Meisha | In this research, we apply our understanding of this mechanism to construct auxetic paper handsheets. | Session 8: Biopolymers: Nucleic Acids and Structural |
| 165 | What do 21st century biology students need to know and be able to do? The view from biology education research | Smith, Michelle | In this talk, I will explore what transformed biology education looks like and discuss connections with the skills learned in undergraduate physics classrooms. | Session 9: Bringing Together Biology, Medicine, and Physics in Education |
| 166 | Transform and Thrive: Large-Scale Change in Introductory Physics for the Life Sciences | McNeil, Laurie | I will describe how we accomplished this transformation, the benefits (and difficulties) it affords, and offer advice to departments contemplating a similar reformation. | Session 9: Bringing Together Biology, Medicine, and Physics in Education |
| 167 | Pre-health students may not know what physics is. | Sweeney, Alison | This talk discusses my experience and possible insights from reforming a traditional pre-health physics course, to teach the conceptual core of physics to students completely inexperienced with physics. | Session 9: Bringing Together Biology, Medicine, and Physics in Education |
| 168 | The Purpose of Homework Problems is Insight, Not Numbers: Crafting Exercises for an Intermediate Biological Physics Class | Roth, Bradley | I will use examples from courses in Biological Physics and Medical Physics to illustrate this idea. | Session 9: Bringing Together Biology, Medicine, and Physics in Education |
| 169 | Essential data science instruction for biophysicists | Bois, Justin | In this talk, I will discuss what I view as essential data science principles we should teach students. | Session 9: Bringing Together Biology, Medicine, and Physics in Education |
| 170 | A Path to the Exascale for Atomistic Simulations with Improved Accuracy, Length and Time Scales | Wood, Mitchell; Thompson, Aidan; Plimpton, Steven; Niklasson, Anders; Perez, Danny | This talk will overview the U.S. Department of Energy* EXAALT (EXascale Atomistics for Accuracy, Length and Time) project and our efforts to provide software tools for MD that not only scale efficiently to huge atom counts, but also enable efficient MD simulations for smaller systems too. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 171 | Accelerating Quantum Molecular Dynamics simulations: Can GPUs really help? | Fattebert, Jean-Luc; Negre, Christian; Mohd-Yusof, Jamal; Adedoyin, Toks; Osei-Kuffuor, Daniel; Mniszewski, Susan | In this talk we will present some software library solutions in development to facilitate porting electronic structure codes to new architectures, as well as parallel strategies and algorithms that can help speed up time-to-solution in real applications. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 172 | Multibillion Atom Molecular Dynamics Simulations of Cellular Membranes | Trebesch, Noah; Tajkhorshid, Emad | To take advantage of this opportunity, we have developed xMAS (E xperimentally-Derived Membranes of Arbitrary Shape) Builder, software designed to turn low resolution EM-based structures of cellular membranes into atomistic models that are suitable for MD. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 173 | Unveiling the structural properties of HIV-1 vesicle from atomistic molecular dynamics simulations | Gonzalez, Fabio; Reddy, Tyler; Perilla, Juan | Here, exploiting the advances of molecular modeling, we present the first insights towards the construction of an all-atomistic model of the HIV-1 mature and immature virion. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 174 | Molecular Understanding of Membranes for the Water-Energy Nexus in the Exascale Realm | Perahia, Dvora; Grest, Gary | Here we will present molecular dynamics simulation results that depict the structured motion and transport in polymeric membranes that consists of units, or blocks, with different chemical structures, tailored into a macromolecule with targeted roles. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 175 | Multi-GPU parallelization of Deep Potential Molecular Dynamics for high-performance computing | Lu, Denghui; Jia, Weile; Chen, Mohan; Wang, Han; Zhang, Linfeng | In this work, we develop the multi-GPU parallelization for DeePMD-kit [3], an implementation of DPMD, and optimize the workflows when the package interfaces with LAMMPS and TensorFlow. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 176 | Scalable Frameworks for Reinforcement Learning for Control of Self-Assembling Materials and for Chemistry Design | Welch, Paul; Sweeney, Christine; Schram, Malachi; Ward, Logan | The ExaLearn Exascale Computing Project has developed scalable frameworks for reinforcement learning (RL) to create policies to control scientific processes such as the self-assembly of block copolymers and chemical design. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 177 | Exascale-ready neural network interatomic potentials with CabanaMD | Reeve, Sam; Desai, Saaketh; Belak, James | In the drive towards exascale computing, new hardware and software technologies are enabling more complex, accurate, and expensive models, but only with rethinking of algorithms, communication patterns, and data layouts. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 178 | DOE Software Center for Non-perturbative Studies of Functional Materials Under Non-equilibrium Conditions (NPNEQ) | Ogitsu, Tadashi; Andrade, Xavier; Correa, Alfredo; Tan, Liang; Prendergast, David; Pemmaraju, Sri Chaitanya Das; Lindenberg, Aaron | In this presentation, we will introduce the software center, NPNEQ, where the open-source real-time time-dependent density-functional-theory (RT-TDDFT) code is being developed. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 179 | Towards fast and accurate exascale density functional theory calculations using DFT-FE — a massively parallel real-space code using adaptive finite-element discretization | Das, Sambit; Motamarri, Phani; Gavini, Vikram | In this talk, we present a significant advance in the state-of-the-art for accurate DFT calculations -via- the development of DFT-FE, that has enabled fast, scalable and accurate large-scale DFT calculations on material systems with tens of thousands of electrons. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 180 | Massively-Parallel Real-Time TDDFT Simulations of Electronic Stopping in Solvated DNA under Proton Irradiation | Yost, Dillon; Yao, Yi; Shepard, Chris; Kanai, Yosuke | We discuss massively-parallel real-time, time-dependent density functional theory (RT-TDDFT) simulations for investigating electronic stopping in DNA solvated in water. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 181 | Spatiotemporal Mapping of Polymer Dynamics | Ma, Jihong; Carrillo, Jan-Michael; Sumpter, Bobby; Wang, Yangyang | In this talk, we demonstrate a novel approach to resolve the fine spatiotemporal features of entangled polymer dynamics, by leveraging the computational resources at the Oak Ridge Leadership Computing Facility. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 182 | Towards adaptive exascale workflows for simulating long timescales | Ossyra, John; Sedova, Ada; Smith, Jeremy | We present a highly scalable workflow software, AdaptiveMD, that implements a massively parallel adaptive-sampling algorithm to build a Markov-state model of long-timescale biomolecular kinetics. | Session 10: Building the Bridge to Exascale: Applications and Opportunities for Materials, Chemistry, and Biology |
| 183 | “Cellular Stokesian Dynamics”: a computational model for biological cells | Zia, Roseanna; Endy, Drew; Maheshwari, Akshay; Gonzalez Gonzalez, Emma del Carmen; Sunol, Alp | I will discuss our physics-based computational model of a biological cell, where biomolecules and their interactions are physically represented, individually and explicitly. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 184 | 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 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 185 | The structure of tubular organelle networks can accelerate diffusive transport and kinetics | Brown, Aidan; Koslover, Elena | We describe how the structure of these tubular network organelles controls diffusive search times and kinetic rates, using both analytical calculation and computational simulation of diffusive first-passage times on organelle structures extracted from yeast and mammalian cells. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 186 | Elucidating mechanics of vascular regression in Botryllus schlosseri using image analysis | Madhu, Roopa; Rodriguez, Delany; Guzik, Claudia; Singh, Shambhavi; Tomaso, Anthony; Valentine, Megan; Loerke, Dinah | We examined epithelial tube remodeling in vivo using a novel model system: Botryllus schlosseri vasculature. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 187 | Vesicle formation processes on the Golgi significantly altered by overexpression – Duel FRAP investigation | Sager, Garrett; Sztul, Elizabeth; Kawai, Ryoichi | Specifically, we are investigating two proteins that are vital during initial vesicle formation on the Golgi (GBF1 and Arf1). | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 188 | Probing force balance in the S. pombe mitotic spindle by laser ablation | Zareiesfandabadi, Parsa; Elting, Mary | We find that spindle pole bodies collapse toward each other following ablation, but that spindle geometry is often rescued, allowing spindles to resume elongation. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 189 | 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 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 190 | Modeling cells as pressurized elastic shells | Golshaei, Behzad; Rezvani, Samaneh; Albarran, Octavio; Schmidt, Christoph | To interpret micro-mechanical optical trapping experiments with suspended rounded eukaryotic cells, we developed finite element simulations and modeled cells as pressurized elastic shells. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 191 | Probing the mechanical integrity of the mammalian k-fiber in live cells by laser ablation and speckle microscopy | Begley, Marcus; Davis, Elizabeth; Ohi, Ryoma; Elting, Mary | Probing the mechanical integrity of the mammalian k-fiber in live cells by laser ablation and speckle microscopy | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 192 | 3D particle diffusion in Escherichia coli cells. | Valverde Mendez, Diana; Bratton, Benjamin; Sheehan, Joseph; Gitai, Zemer; Shaevitz, Joshua | We use Genetically Encoded Multimeric nanoparticles (GEMs) to probe the microrheology of the Escherichia coli cytoplasm. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 193 | Opto-genetic control of gene regulation in living fly embryos | Singh, Anand; Wu, Ping; Wieschaus, Eric; Toettcher, Jared; Gregor, Thomas | In order to construct causal relationships in the programs underlying gene regulatory networks and transcription, we developed a light-inducible system to directly interfere with these programs and to quantitatively measure the cellular response in living fly embryos. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 194 | NMR and small-angle neutron scattering examination of dynamics and structure in a polymer-colloid model system directed at understanding macromolecular crowding in cells | PALIT, SWOMITRA; He, Lilin; Hamilton, William; Yethiraj, Arun; Yethiraj, Anand | In this work [1], we study long-time self diffusion (using pulsed-gradient NMR) and size (via small-angle neutron scattering) of a linear polymer, polyethylene glycol (PEG, radius of gyration $R_g$, and a more compact crowder (polysucrose, radius $R_c$) of varying size ratio $R_g/R_c$. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 195 | Analysis and simulations of Bcl10 self-assembly and degradation in activated T cells | Campanello, Leonard; Traver, Maria; Schaefer, Brian; Losert, Wolfgang | Here, we will provide insights into Bcl10 filament formation and degradation via image analysis and Monte Carlo simulations. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 196 | Investigating the eukaryotic CO2-fixing phase-separated organelle, the pyrenoid | He, Guanhua; He, Shan; Jonikas, Martin; Wingreen, Ned | We use microscale thermophoresis (MST) to determine the dissociation constant (Kd) of EPYC1-Rubisco binding. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 197 | Dynamics of Self-Organized Organelle Transport in a Developing Macroscopic Single-Celled Organism | Afik, Eldad; Meyerowitz, Elliot | In this work we seek to establish a framework to study the dynamics of homeostasis and its stability. | Session 11: Cellular Biophysics: structure, mechanics, and dynamics |
| 198 | Spontaneous Appearance of Chiral Structures from Lyotropic Liquid Crystals in Confinement | Srinivasarao, Mohan; Nayani, Karthik; Chang, Rui; Fu, Jinxin; Park, Jung O | In this talk, I intend to discuss the appearance of chiral structures from a class of liquid crystals, the so-called lyotropic liquid crystals. | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 199 | Threading the Spindle: A Geometric Study of Chiral Liquid Crystal Polymer Microparticles | Ansell, Helen; Kim, Dae Seok; Kamien, Randall; Katifori, Eleni; Lopez-Leon, Teresa | In this study we investigate the swelling behavior of chiral twisted spindle-shaped polymer microparticles, which are formed due to the anisotropic contraction of spherical bipolar polymer liquid crystalline microparticles during deswelling. | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 200 | Chiral nematic liquid crystals in cylinders: Layering transition and conservation of layer structure | Eun, Jonghee; Kim, Sung-Jo; Jeong, Joonwoo | Chiral nematic liquid crystals in cylinders: Layering transition and conservation of layer structure | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 201 | Truth about the origin of twist – a circular argument | Matsumoto, Elisabetta; Dastan, Alireza; Cleaver, Doug | We examine emergent twist by applying both simulation and molecular theory to chromonic amphiphiles. | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 202 | Thermoresponsive Colloidal Chains Collapse to Form Helices | Biswas, Bipul; Fayis, KP; Bhat, Suresh; Kumaraswamy, Guruswamy | Here, we demonstrate that these chains exhibit thermally-induced reversible transitions. | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 203 | Skyrmion formation and organization on a shell | Palacio-Betancur, Viviana; Durey, Guillaume; Cohen, Alexander; Sadati, Monirosadat; López León, Teresa; Hernandez-Ortiz, Juan; De Pablo, Juan | Beyond confinement in a channel, here, we consider the effect of curvature by confining a ChLC in spherical shells. | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 204 | Peculiar Phase Morphologies from Twisting of Self-Assembled Ribbons in Chiral Block Copolymers | Yang, Kai-Chieh; Ho, Rong-Ming | Peculiar Phase Morphologies from Twisting of Self-Assembled Ribbons in Chiral Block Copolymers | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 205 | Folding of chiral colloidal membranes | Sharma, Prerna; Saikia, Lachit; Khanra, Ayantika; Dogic, Zvonimir | Folding of chiral colloidal membranes | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 206 | Self-assembly of chiral networks in achiral block copolymer systems using coarse-grained simulations | Buchanan, Natalie; Browka, Krysia; Ketcham, Lianna; Le, Hillary; Padmanabhan, Poornima | In this talk, we investigate the self-assembly of model achiral block copolymers into alternating gyroid morphologies using coarse-grained molecular simulation. | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 207 | Amino Acids as RNA-Folding Chaperones: Single Molecule Experiments Reveal Chiral Sensitivity | Nicholson, David; Nesbitt, David | The kinetic and thermodynamic features of this chiral interaction are presented, and with the help of all-atom molecular dynamics simulations, we propose a mechanistic interpretation of these results based on nonspecific arginine-RNA interactions. | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 208 | Insensitivity of Sterically-Defined Helical Chain Conformation to Solvent Quality in Dilute Solution | Yu, Beihang; Danielsen, Scott; Yang, Kai-Chieh; Ho, Rong-Ming; Walker, Lynn; Segalman, Rachel | Insensitivity of Sterically-Defined Helical Chain Conformation to Solvent Quality in Dilute Solution | Session 12: Chirality in Polymers and Soft Matter: From Molecular to Hierarchical Scales |
| 209 | Comparison of different approaches to single particle tracking of enzymes displaying enhanced diffusion | Xu, Mengqi; Ross, Jennifer | We found that while the overall mobility of enzyme is improved by 2-3 folds at saturated substrate concentration, the mode of diffusion remains Brownian. | Session 13: Composite Active Materials |
| 210 | Vortices, space-time braids and loops in the membrane of a living cell. | Liu, Jinghui; Miller, Pearson; Dunkel, Jörn; Fakhri, Nikta | Here, we show a defect-mediated turbulence underlies the complex wave propagation patterns of Rho-GTP signaling proteins on the membrane of starfish oocytes. | Session 13: Composite Active Materials |
| 211 | Creation and evolution of defects in composite biopolymer nematics | Weirich, Kimberly; Zhang, Rui; De Pablo, Juan | Here we present a composite structured liquid formed from biopolymers of distinct rigidities, actin and DNA. | Session 13: Composite Active Materials |
| 212 | Microtubule based composite active matter | Dogic, Zvonimir | Microtubule based composite active matter | Session 13: Composite Active Materials |
| 213 | Information and motility exchange in collectives of active particles | Paoluzzi, Matteo; Leoni, Marco; Marchetti, M Cristina | In a minimal model of information exchange, we have studied numerically run-and-tumble runners with an additional two-state internal variable that specifies their motile or nonmotile state. | Session 13: Composite Active Materials |
| 214 | Corralling Active Brownian Particles With "Active Billiard" Particles | Nilles, Alexandra; Pervan, Ana; Berrueta, Thomas; Murphey, Todd | We will present extensions of this theoretical approach to statistical models of our example active matter system, with a focus on developing strategies for control. | Session 13: Composite Active Materials |
| 215 | Spontaneous demixing of mixed active-passive suspensions. | Polin, Marco; Williams, Steven; Jeanneret, Raphaël | We show that this can be used to induce the system to de-mix spontaneously. | Session 13: Composite Active Materials |
| 216 | Unifying descriptions of phase separation in multi-component driven, steady-state systems. | Watson, Garrett; Luijten, Erik | Combined experimental and computational work has shown that a nonequilibrium driven system of Janus particles exhibits phase behavior that is accurately described by the standard Ising model. | Session 13: Composite Active Materials |
| 217 | Phase Diagram of a 2D system of Granular Self-propelled Particles | Shen, Zhejun; Menon, Narayanan | We report experiments on the phase behaviour of granular squares as a function of number density and activity. | Session 13: Composite Active Materials |
| 218 | Irreversibility in biological active matter | Fakhri, Nikta | In this talk, I will address the question: why measure dissipation in such nonequilibrium systems? | Session 13: Composite Active Materials |
| 219 | Synthetic Biology: Physical Biology by Design | Collins, James | In this talk, we highlight recent efforts to create synthetic gene networks and programmable cells, and discuss a variety of synthetic biology applications in biotechnology and biomedicine. | Session 14: Delbruck Prize Session |
| 220 | Physical principles from evolutionary synthetic biology | Balazsi, Gabor | I will present examples of how evolving synthetic gene circuits can provide deeper understanding of evolutionary processes, specifically of gene networks mediating the adaptation of cell populations. | Session 14: Delbruck Prize Session |
| 221 | Synthetic Biology: Building to learn so that we might learn to build | Hasty, Jeff | This talk will be anchored by my quest to build genetic oscillators in cells, with a particular focus on the utility of mathematical modeling in determining general design principles. | Session 14: Delbruck Prize Session |
| 222 | Context dependence of biological circuits: Predictive models and engineering solutions | Del Vecchio, Domitilla | I will introduce a general engineering framework, grounded on control theoretic concepts, that can serve as a basis for creating devices that mitigate context-dependence. | Session 14: Delbruck Prize Session |
| 223 | Universality in Cardiac Dynamics | Glass, Leon | Application of these concepts provides a physical perspective to the classification of cardiac arrhythmias by cardiologists. | Session 14: Delbruck Prize Session |
| 224 | Control and characterization of thin film formation by electrospray deposition techniques | Toth, Kristof; Doerk, Gregory; Yager, Kevin; Osuji, Chinedum | We describe a simple feedback control for visual analysis of various electrospray modes and their corresponding film formation. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 225 | Morphological Control of Multifunctional Melting Gel Coatings via Electrospray Deposition | Gamboa, Arielle Marie; Lei, Lin; Mercado, James; Guzman, Jennifer; Klein, Lisa; Jitianu, Andrei; Singer, Jonathan | Morphological Control of Multifunctional Melting Gel Coatings via Electrospray Deposition | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 226 | Using Multiplexed Electrosprays to Manipulate Fluids and (Soft) Materials | Gomez, Alessandro | Using fluid mechanics and electrostatics, we a) developed criteria for compact multiplexing to increase flow rate drastically, b) microfabricated systems with high packing densities (1.1 104 sources/cm2), 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: Electrohydrodynamics |
| 227 | Self-Limiting Electrospray Deposition for the Surface Modification of Additively Manufactured Parts | Kovacevich, Dylan; Lei, Lin; Han, Daehoon; Kuznetsova, Christianna; Kooi, Steven; Lee, Howon; Singer, Jonathan | Having demonstrated three-dimensional coating with film thickness in the range of 1-50 µm on a variety of conductive objects, in this study we employed model substrates and finite element method simulations to quantitatively study the technique’s limits with regard to geometry and scale. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 228 | The Role of Surface Charging in Electrospray Printing of Thin Films | Zhu, Yaqun; Chiarot, Paul | We report on the use of electrospray printing to create thin continuous multiscale films from nanoparticle aggregates. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 229 | Effect of Processing Conditions on the Formation and Microstructure of Electrospray Printed Polymer Films | Kingsley, Bryce; Chiarot, Paul | We report on the use of electrospray to print thin films of polytetrafluoroethylene (PTFE) on silicon substrates. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 230 | Electrospray deposition of nanowire forests through spinodal gellation | Lei, Lin; Nachtigal, Catherine; Chen, Shensheng; Moy, Tyler; Yong, Xin; Singer, Jonathan | Such a morphology has yet to be observed experimentally, which we propose is the result of spatially-varying viscosity in sprayed droplets. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 231 | Modelling Nanowire Formation in Electrospray Deposition of Polymeric Droplets | Chen, Shensheng; Yong, Xin | We conducted computer simulations to uncover the physics underpinning the morphological evolution of a highly charged polymeric droplets in ESD. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 232 | Influence of ionic conductivity on unconfined melt electrospinning of thermoplastics | Sheoran, Neelam; Boland, Brenton; Shabani, Elnaz; Gorga, Russell; Bochinski, Jason; Clarke, Laura | I will report ionic conductivity measurements obtained using broad-band impedance spectroscopy for two different grades of commercial linear low-density polyethylene with varying viscosities as a function of melt temperature and additive concentration. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 233 | Unconfined melt electrospinning from molten polymer experiencing an electric discharge to manipulate ion density and ionic conductivity | Boland, Brenton; Sheoran, Neelam; Clarke, Laura; Bochinski, Jason | We utilize an unconfined geometry where jets spontaneously form and organize on the edge of a melt-covered plate under the influence of the applied electrospinning electric field. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 234 | Liquid Selection for Electrohydrodynamic Capillary Thermal Switches | Ma, Tianxing; Dsouza, Darrel; Ryerson, Kyrsten McKenzie; Signorelli, Matthew; Zhao, Yang; Osuji, Chinedum; Singer, Jonathan | The deformation of sessile droplets and capillary bridging in a parallel-plate capacitor under DC field has been the subject of several scientific studies. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 235 | Dielectric modulation of two-dimensional dipolar materials | Wang, Ziwei; Luijten, Erik | We demonstrate that in dipolar films, a prototypical system for pattern formation, patterns can be induced by dielectric effects alone [1]. | Session 15: Electrostatic Manipulation of Fluids and Soft Matter: Electrohydrodynamics |
| 236 | Precision measurement of tribocharging in acoustically levitated sub-millimeter grains | Kline, Adam; Lim, Melody; Jaeger, Heinrich | In this talk, we present a new experimental method [1], extending a prior approach [2] based on acoustic levitation, which allows us to controllably and repeatedly collide two sub-millimeter grains head-on and measure the evolution of their electric charges. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 237 | Tuning friction and slip at solid-nanoparticle suspension interfaces by electric fields. | Seed, Caitlin; Acharya, Biplav; Brenner, Donald; Smirnov, Alex; Krim, Jacqueline | We report an experimental Quartz Crystal Microbalance (QCM) study of tuning interfacial friction and slip lengths for aqueous suspensions of ceramic (Al 2O 3, TiO 2 and SiO 2) nanoparticles on planar platinum surfaces by external electric fields. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 238 | Particle assembly using confined electro-hydrodynamics: Driven versus active assembly | Fossum, Jon Otto; Dommersnes, Paul | We give examples of driven colloidal shell assembly on drop interfaces by application of DC-electrohydrodynamics and dielectrophoresis, using standard leaky dielectric carrier fluids for non-polarisable and/or polarizable colloids. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 239 | Electrostatic patterns from peeling tape | Reiter, Mary; VanDusen-Gross, Matthew; Shinbrot, Troy | In this talk, we discuss new and surprising aspects of triboelectric charging associated with tape peeling including entirely different charge patterns on formerly adjoining surfaces. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 240 | Sublattice Melting in Binary Superionic Colloidal Crystals | Lin, Yange; Olvera De La Cruz, Monica | Sublattice Melting in Binary Superionic Colloidal Crystals | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 241 | Band-collision gel electrophoresis (BCGE) for visualizing molecular and colloidal interactions | Bikos, Dimitri; Mason, Thomas | Band-collision gel electrophoresis (BCGE) for visualizing molecular and colloidal interactions | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 242 | Controlling surfactant self-assembly in dodecane via applied potential | Vuorte, Maisa; Lokka, Aapo; Sammalkorpi, Maria | Here, we present a molecular modelling study of the aggregation of dioctyl sodium sulfosuccinate (AOT) surfactant in apolar dodecane solvent under applied potential. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 243 | Dumbbell model for the simulation of polyelectrolytes in combination of flow and electric fields | Setaro, Angelo; Underhill, Patrick | To gain insight to the underlying phenomena, we used a combination of theoretical calculations and Brownian Dynamics simulations in order to understand the mechanism of migration and why it results in a non-monotonic trend. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 244 | Electrostatically Stabilized Microphase Separation in Polyelectrolyte Blends: Analogy to Nuclear "Pasta" Phases | Rumyantsev, Artem; De Pablo, Juan | We develop the weak segregation theory of microphase separation in stoichiometric blends of oppositely and weakly charged polyelectrolytes, which would be immiscible in the absence of charged units. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 245 | Determination of diffusion constant of antimicrobial peptide nisin interacting with Langmuir monolayers of DPPC and DPPG molecules | Pasha, Imran; Kumar, Bharat | We present a method of determining the diffusion constant of peptides interacting with lipid films. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 246 | Capture and Translocation of a Rod-like dsDNA by a Nanopore:~A Lattice Boltzmann Simulation Study | Qiao, Le; Holm, Christian; Szuttor, Kai; Slater, Gary | In this talk, we investigate this problem further using a coarse-grained (CG) model of a charged double-stranded DNA where the hydrodynamic interactions are added by coupling the CG DNA with a lattice-Boltzmann fluid via a raspberry approach. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 247 | Nontrivial effects of dielectric mismatch on the conformational behavior of confined polyelectrolytes | Nguyen, Trung; Olvera De La Cruz, Monica | We investigate the conformational behavior of a highly charged polyelectrolyte confined in a spherical cavity where the media inside and outside the cavity have different dielectric constants. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 248 | Interaction of highly charged rigid polymer in monovalent salt | Li, Yaohua; Jimenez-Angeles, Felipe; Olvera De La Cruz, Monica | Using an empirical ion potential that reproduces pair correlations from all atom molecular dynamics (MD) simulations, we study ion distributions and DNA-DNA interactions by coarse-grained MD simulations with explicit salt ions. | Session 16: Electrostatic Manipulation of Fluids and Soft Matter: Self-Assembly |
| 249 | Dynamics and self-organization of active surfaces | Julicher, Frank | I will present a minimal model of the mechano-chemical self-organization of the cell cortex that is based on a hydrodynamic theory of curved active surfaces and that can capture the emergence of shapes. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 250 | Microtubule Motility on Fixed and Diffusive Motor Proteins | Memarian, Fereshteh; Lopes, Joseph; Hirst, Linda | Here we investigate motor-based transportation and behavior of MTs. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 251 | Modeling of the collective motion of microtubules with mobile kinesin motors. | Athani, Madhuvanthi; Memarian, Fereshteh; Hirst, Linda; Beller, Daniel | We use Brownian Dynamics simulations to model the collective motions of microtubules with explicit consideration of the concentration of the motors. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 252 | Multi-functional crystalline frameworks self-assembled from amphiphilic DNA nanostructures. | Brady, Ryan; Brooks, Nicholas; Cicuta, Pietro; Di Michele, Lorenzo | I will discuss a novel class of amphiphilic DNA building blocks dubbed “C-stars” that combine Watson-Crick base pairing and hydrophobic forces to self-assemble into 3D single crystals [1-3]. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 253 | Controlled membrane remodeling by DNA origami nanorods: Experiments targeting the design principles for membrane-based materials | Zuraw, Sarah; Dinsmore, Anthony; Siavashpouri, Mahsa; Dogic, Zvonimir; Gerling, Thomas; Dietz, Hendrik | Inspired by this system, we use DNA origami nanorods to illuminate the role of particle shape and adhesion on membrane reconfiguration. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 254 | A coarse-grained model for lipid bilayer formation, fusion, and its hydrodynamics | Young, Yuan-nan; Fu, Szu-Pei; Ryham, Rolf | In this paper a theoretical model for long-range, hydrophobic attraction between amphiphilic particles is developed to quantify the macroscopic assembly and mechanics of a lipid bilayer membrane in solvents. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 255 | Phase separation and domain registry in giant multilamellar vesicles prepared with biologically-relevant lipid compositions. | Steer, Dylan; Leal, Cecilia | Here we report on the macroscopic arrangement of phase-separated domains in multilamellar forms with biologically-relevant compositions. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 256 | Clustering dynamics of collectively migrating malignant lymphocytes | Golnaraghi, Farnaz; Quint, David; Gov, Nir; Gopinathan, Ajay | We aim to quantify cell cluster shape dynamics and chemotactic efficiency as a function of cellular parameters such as, cell-cell adhesion and alignment, contact inhibition and chemotactic response. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 257 | Imaging the emergence of bacterial turbulence using light-powered E. coli | Peng, Yi; Liu, Zhengyang; Cheng, Xiang | We investigate the emergence of the collective motion of Escherichia coli suspensions and explore the kinetic pathway towards bacterial turbulence. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 258 | Activity-induced phase transitions in confined bacterial suspensions | Ghosh, Dipanjan; Liu, Zhengyang; Cheng, Xiang | Here, we study the emergence of collective order in confined suspensions of genetically engineered Escherichia coli, whose propulsion speed can be controlled via intensity of light. Our study provides an experimental benchmark for understanding the role of complex interplays between hydrodynamic and steric interactions responsible for the emergence of ordered phases in confined active systems. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 259 | Comparing sperm collective swimming with flocking transition | Oduor, Allan; Bililign, Yishak; Sussman, Daniel; Cheong, Soon Hon; Suarez, Susan; Manning, M. Lisa; Tung, Chih-Kuan | Analyzing these flocks, we found the decay of the orientation correlation function to be linear on a log-log plot. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 260 | Correlations in suspensions of microswimmers | Morozov, Alexander | Here, we present a novel kinetic theory that predicts the existence of strong correlations even below the transition to collective motion. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 261 | Collective migration of bacteria in disordered media | Bhattacharjee, Tapomoy; Amchin, Daniel; Kratz, Felix; Ott, Jenna; Datta, Sujit | Here, we use direct visualization and 3D bioprinting to investigate how this behavior manifests in multicellular communities in porous media. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 262 | Collective behavior of platelets in blood clotting | Sun, Yueyi; Myers, David; Lam, Wilbur; Alexeev, Alexander | With experimental insights, we develop a mesoscale computational approach based on dissipative particle dynamics to examine the biophysics of clot contraction. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 263 | Living oil-water interfaces: Buckling of droplets by cell growth at finite liquid interfaces | Juarez, Gabriel | Here, through microfluidic experiments and time-lapse microscopy, we demonstrate that the colonization of oil droplets by the growth and division of rod-shaped bacteria depends strongly on the droplet diameter, or the interfacial curvature. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 264 | A trace amount of surfactants enable diffusiophoretic swimming of bacteria | Doan, Viet Sang; Saingam, Prakit; Yan, Tao; Shin, Sangwoo | We show that even a trace amount of ionic surfactants, down to a single ppm level, can impact the bacteria diffusiophoresis by boosting the surface charge of the cells. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 265 | Bridging Scales to Model Emergent Collective Oscillations in Social Amoeba | Huyan, Chuqiao; Golden, Alexander; Zhu, Xinwen; Mehta, Pankaj; Sgro, Allyson | We compared each model to published experimental findings about how amoeba cells modulate internal cAMP dynamics in response to external changes in cAMP. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 266 | Pattern engineering of living bacterial colonies using meniscus-driven fluidic channels | Kantsler, Vasily; Ontañón-McDonald, Elena; Kuey, Cansu; Ghanshyam, Manjari J; Roffin, Maria; Asally, Munehiro | Here we present controlled meniscus-driven fluidics, MeniFluidics; an easily implementable technique for patterning living bacterial populations. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 267 | Control of patterning in human pluripotent stem cell colonies via a Turing system with reactive boundaries | McMaster, Benjamin; Kaul, Himanshu; Aguilar-Hidalgo, Daniel; Zandstra, Peter | This work presents a general framework for self-organized pattern formation that explain observed patterns in hPSC colonies, leading to a design-based specification of collective cell behavior. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 268 | Cellular integration of physical and biochemical damage signals in the generation of tissue-level wound responses | Stevens, Aaron; Tasneem, Kazi; OConnor, James; Hutson, Shane; Page-McCaw, Andrea | We have developed a computational model to test the plausibility of multiple hypothesized mechanisms driving these calcium signals and to further understand the underlying biology. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 269 | Dorsal closure in numbers: quantification of epithelial cell oscillations using machine learning | Haertter, Daniel; Rhodes, Dante; Crawford, Janice; Kiehart, Daniel; Schmidt, Christoph | We present a novel analysis pipeline, based on a convolutional neural network (machine learning), that allows an automated and robust segmentation of large numbers of video recordings. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 270 | Signatures of tissue surface tension in 3D models with two tissue types | Sahu, Preeti; Schwarz, J; Manning, M. Lisa | To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D model for confluent tissues. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 271 | Defect Driven Morphogenesis: Active Cell Division Generates Four-Fold Order | Cislo, Dillon; Qin, Haodong; Bowick, Mark; Streichan, Sebastian | We present a quantitative profile of exotic non-equilibrium pattern formation in the crustacean Parhyale hawaiensis. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 272 | Quantifying mechanics in non-confluent tissues using an extended vertex model | Lawson-Keister, Elizabeth; Parker, Amanda; Schwarz, Jennifer; Manning, M. Lisa | Vertex models for tissues have correctly predicted cell shapes and fluid-solid transitions in confluent epithelial monolayers where there are no gaps between cells and negligible curvature along cell-cell boundaries. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 273 | The branched architecture of the airway is physically shaped by the extracellular matrix and contractile airway smooth muscle during lung development | Spurlin, James; Zhang, Rawlison; Nelson, Celeste | Using comparative embryology, we have found several novel mechanisms of how airway branches are physically shaped. | Session 17: Emergent Collective Dynamics in Biology: from Microbes to Organs |
| 274 | Resource-rich environments can reduce stability and diversity in microbial communities by strengthening interspecies interactions | Ratzke, Christoph; Barrere, Juliene; Gore, Jeffrey | Here we show in microbial ecosystems in the lab that the concentrations of available nutrients can set the strength of interactions between bacteria. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 275 | Niche-Neutral Transition in a Lotka-Volterra Model of Diverse Ecosystems | Wu, Jim; Schwab, David; Mehta, Pankaj | In this work, we draw a bridge between these two opposing theories. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 276 | Competition-driven strategies for controlling multistable microbial communities | Dubinkina, Veronika; Goyal, Akshit; Fridman, Yulia; Pandey, Parth; Maslov, Sergei | Here, we propose two strategies to control multistable microbial communities: that of controlling the colonization order in which species are introduced into a community, and that of controlling the supply of nutrients to a community. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 277 | Long-range patterns of activity shaped by signaling interactions within bacterial communities | Boedicker, James; Silva, Kalinga Pavan; Yusufaly, Tahir | Our work explored how signaling interactions between multiple cell types shape global patterns of gene expression. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 278 | Ecological interactions constrain the coexistence of generalists and specialists during coevolution in microbial communities | Goyal, Akshit | Here, we propose and study a minimal model of a co-evolving microbial community shaped by ecological interactions. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 279 | Criticality on topologically disordered systems and the Harris criterion | Barghathi, Hatem; Vojta, Thomas | We recently introduced [1] a modified stability criterion, (d+1)ν>2, for systems in which the presence of topological constraints suppresses disorder fluctuations, resulting in a violation of the usual Harris criterion. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 280 | The Emergence of Spatial Patterns in Tree Yield: A New Model for the Masting Phenomenon | Esmaeili, Shadisadat; Hastings, Alan; Abbott, Karen; Machta, Jonathan; Nareddy, Vahini Reddy | In this talk, we introduce a new model to emulate the observed spatial patterns and study the effects of local coupling and external forces on the dynamics of the system. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 281 | Binary Decisions of Large Cliques of Evidence Accumulators | Karamched, Bhargav; Kilpatrick, Zachary; Josic, Kresimir; Stickler, Megan; Ott, Will; Lindner, Benjamin | We consider cliques of N evidence accumulators making a binary decision based on noisy observations. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 282 | Identifying Suspicious Users and Products to Predict New Opinions | Chung, Sukhwan | In this work, a solution to those issues is suggested using the Rev2 algorithm (developed by S. Kumar, et al) and the principle of maximum entropy. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 283 | Optimal evidence accumulation on social networks | Karamched, Bhargav; Stolarczyk, Simon; Josic, Kresimir; Kilpatrick, Zachary | Here we derive network models of rational agents who accumulate private measurements and observe decisions of their neighbors to choose between two options. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 284 | Sensitivity of collective outcomes identifies pivotal components | Lee, Edward; Katz, Daniel; Bommarito, Michael; Ginsparg, Paul | Using the information geometry of minimal models from statistical physics, we develop a general approach for identifying key "pivotal" components on which aggregate statistics depend most sensitively. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 285 | Community optimization and ruggedness of ecological landscapes | B. George, Ashish; Korolev, Kirill | We show that consumer-resource models with and without cross-feeding have unique steady states that depend only on the presence or absence of species in the community. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 286 | History-dependent tradeoffs in changing environments | Tikhonov, Mikhail | Using a simple model, I will show that this feedback can lead to counterintuitive consequences in the context of multiple or changing environments: specifically, a direct exposure to some environment of interest will, in general, no longer be the most effective way of achieving highest fitness in it. | Session 18: Evolutionary and Ecological Dynamics: Communities and Networks |
| 287 | Evolutionary dynamics of immune repertoires | Mora, Thierry | In this talk I will discuss how the diversity of receptors is generated and how it evolves and self-organises over time to protect us efficiently. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 288 | Evolutionary regain of lost network function | Kheir Gouda, Mirna; Manhart, Michael; Balazsi, Gabor | To test the reversibility of evolutionary breakdown, we use a synthetic gene circuit (PF) integrated into yeast cells. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 289 | Measuring mutations with droplet microfluidics | Hennessey-Wesen, Mike; Guet, Calin; Hof, Bjoern | We use a droplet-based, microfluidic platform to make real-time measurements of point mutations in bacteria under various conditions with high precision. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 290 | The Evolutionary Dynamics of Incubation Periods | Ottino-Loffler, Bertrand; Scott, Jacob; Strogatz, Steven | Here, we propose an explanation based on evolutionary dynamics on graphs. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 291 | Evolution of systems with power-law memory: Do we have to die? | Edelman, Mark | 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 19: Evolutionary and Ecological Dynamics: Evolution |
| 292 | Spatial Expansions and Serial Bottlenecks Produce Different Topologies of Genealogical Trees | Birzu, Gabriel; Hallatschek, Oskar; Korolev, Kirill | Here, we show that range expansions can produce extremely different topologies of genealogical trees, which are very sensitive to the growth dynamics at the front. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 293 | Early Multicellular Organisms Co-opt Cell-Level Characteristics into Group-Level Properties via the Principle of Maximum Entropy | Day, Thomas; Yanni, David; Jacobeen, Shane; Yunker, Peter | Here we demonstrate that lab-evolved simple multicellular groups with permanent intercellular bonds follow the principle of maximum entropy. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 294 | Evolution of microbial growth traits under serial dilution | Lin, Jie; Manhart, Michael; Amir, Ariel | We find that the fixation probability of a beneficial mutation depends on a linear combination of its growth rate and lag time relative to its immediate ancestor, even under clonal interference. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 295 | Physical constraints on epistasis | Husain, Kabir; Murugan, Arvind | Here, we demonstrate that the physical dynamics of a biological system can generically constrain epistasis. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 296 | Emergence of heritability of higher-level traits in a major transition | Burnetti, Anthony; Zamani Dahaj, Seyed Alireza; Herron, Matthew; Ratcliff, William | Using the ‘snowflake yeast’ model system of early multicellularity, we investigated the biophysical basis of emergent multicellular traits. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 297 | Lineage Branching During Recovery from Simulated Mass Extinction | King, Dawn; Hanke, Tyler; Bahar, Sonya | Here, we use methods from coalescent theory to show that population lineages undergo a structural change near the extinction-survival transition, with a sharp divergence in the time to most recent common ancestor (TMRCA). | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 298 | Evolution of Macroscopic size in nascent multicellular organism | Zamani Dahaj, Seyed Alireza; Bozdag, Gonensin; Day, Thomas; Ratcliff, William; Yunker, Peter | In this work we show how small changes at the cell level trait lead to emergent properties in the microscopic level and helped to overcome tremendous mechanical constraints on their size. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 299 | Evolution of hardwired behavioral strategies through competitive population dynamics | Liang, Tong; Brinkman, Braden | Here we develop mechanistic evolutionary models to investigate whether normative principles can predict the most evolutionarily advantageous strategies. | Session 19: Evolutionary and Ecological Dynamics: Evolution |
| 300 | The price of a shortcut | Shou, Wenying | I will also experiment with a different presentation style where scientific work is described through story-telling. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 301 | Long-term Nutrient Cycling in a Materially Closed Ecosystem | de Jesús Astacio, Luis; Li, Zeqian; PRABHAKARA, KAUMUDI; Kuehn, Seppe | To address this question, we present a new method for making precision measurements of carbon cycling in CES using low-cost piezoresistive pressure sensors. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 302 | Growth and form control population dynamics of cellular aggregates | Golden, Alexander; Korolev, Kirill | To understand how growth morphology influences evolutionary dynamics, we have developed a numerical model of two-dimensional colonies in which microbes grow by consuming a diffusible nutrient and have a density-dependent motility. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 303 | 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 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 304 | Dynamics of prey-predator: effect of cooperative interaction and inertial forces | Chakraborty, Dipanjan; De, Rumi | We present a simple theoretical model to investigate the effect of cooperative interactions on the survival chances of a prey group while chased by a predator. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 305 | Representing spatially extended ecological oscillators by kinetic Ising models with memory | Nareddy, Vahini Reddy; Machta, Jonathan; Abbott, Karen; Esmaeili, Shadisadat; Hastings, Alan | In this talk we will discuss the question of accurately representing a system of coupled, noisy two-cycle oscillators by an Ising model. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 306 | Ocean currents promote rare species diversity in protists | Villa Martin, Paula; Bucek, Ales; Bourguignon, Tom; Pigolotti, Simone | We introduce a spatially explicit coalescence model able to reconstruct species ancestry and diversity in the presence of currents. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 307 | Spatial segregation as a necessity for beneficial gene loss in cross-feeding bacterial communities: a kinetic perspective on the Black Queen Hypothesis | Di Salvo, Mario; Setayeshgar, Sima; McKinlay, James | We explore the emergence of mutualistic cross-feeding in bacterial cocultures in the context of the BQH. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 308 | Localization transitions in age-structured populations | Nozoe, Takashi; Kussell, Edo | We discuss age-structured population models that exhibit a range of collective phenomena including phase transitions and population-level oscillations. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 309 | Formation of Phage Lysis Patterns and Implications on Co-Propagation of Phages and Motile Host Bacteria | Chen, Jing | Here, we combine an experimental approach and mathematical modeling to explore how phages and their motile host bacteria coexist and co-propagate. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 310 | Spatial competition of toxin-secreting strains of yeast | Giometto, Andrea; Murray, Andrew; Nelson, David | Theoretical models of well-mixed population genetics with antagonistic interactions predict that a stronger competitor can invade a weaker one only if its initial population is larger than a critical inoculum size. | Session 20: Evolutionary and Ecological Dynamics: Population Ecology |
| 311 | Elementary contractile unit and collective motor behavior | Prost, Jacques | In particular I will show how a symmetry breaking transition, emergent feature of a large number of molecular motor collection, underpins a number of biological functions such as muscle oscillations. | Session 21: Frontiers in Actomyosin Stress Sensing and the Dynamics of the Cytoskeleton |
| 312 | Dissecting fat-tailed fluctuations in the cytoskeleton with active micropost arrays | Reich, Daniel | Using active micropost array detectors containing magnetic actuators, we have characterized the mechanics and fluctuations of cells’ actomyosin cortex and stress fiber networks in detail. | Session 21: Frontiers in Actomyosin Stress Sensing and the Dynamics of the Cytoskeleton |
| 313 | How immune cells respond to physical cues – the role of cytoskeletal dynamics | Upadhyaya, Arpita | We have used single molecule imaging to examine BCR movement and machine learning techniques to relate receptor trajectories to their signaling states. | Session 21: Frontiers in Actomyosin Stress Sensing and the Dynamics of the Cytoskeleton |
| 314 | Cells in microgels: 3D printed microtissues and three-dimensional cell migration | Bhattacharjee, Tapomoy; Angelini, Thomas | Instead, we have developed a 3D growth medium from the jammed system of granular polyelectrolyte microgels that allows for 3D culture of cells. | Session 21: Frontiers in Actomyosin Stress Sensing and the Dynamics of the Cytoskeleton |
| 315 | Solving the equilibrium dynamics of particle systems in infinite dimensions | Manacorda, Alessandro; Zamponi, Francesco; Schehr, Grégory | In the last years, a general framework to study the dynamics of particle systems in infinite dimensions has been developed. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 316 | Investigating Hydrogen Glass Dynamics in Amorphous Germanium and Amorphous Silicon-Germanium Alloys | Knauber, Brenda; EslamiSaray, Mohammad Ali; Kakalios, James | A set of hydrogenated amorphous silicon-germanium alloys are studied to investigate the transition in the noise statistics and conductivity relaxation as the alloy fraction changes. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 317 | Towards a Unifying Scaling Theory of Rigidity Transitions | Jafarpour, Farshid; Ridout, Sean; Liu, Andrea | We study a spring-network model that exhibits both types of transitions and provide a unifying perspective based on a scaling ansatz for the rigidity transition in this model. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 318 | Soft glassy dynamics and rheology: A damped soft-sphere model | Thirumalaiswamy, Amruthesh; Riggleman, Robert; Crocker, John | In this work, we extend our previous study by performing bubble dynamics simulations with damped, non-inertial bubbles evolving similar to ripening observed in foams. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 319 | Crystallization Instability in Glass-Forming Mixtures | Royall, Paddy; Ingebrigsten, Trond; Dyre, Jeppe; Schroder, Thomas | Here we use GPU simulations to reveal a general nucleation mechanism in mixtures. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 320 | Cells on spheres: glassy dynamics of vertex models in curved space | Sussman, Daniel | The analogy between cellular monolayers and aggregates on the one hand and jammed solids or colloidal glasses on the other has provided a powerful framework for probing questions of rigidity, motilitiy, and collective excitations in dense biological tissues. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 321 | Anticipating Challenges of Propensity Measurements in Colloidal Systems | Donofrio, Cordell; Weeks, Eric | We introduce polydispersity by splitting the population of each of the binary components into its own binary where half are increased in size and the other half are decreased in size by the same percentage. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 322 | Glassy behavior and memory effects in the elastic response of a disordered protein | Morgan, Ian; Avinery, Ram; Beck, Roy; Saleh, Omar | We use a single-molecule stretching technique, magnetic tweezers, to force a disordered polyprotein out of equilibrium, and observe the relaxation of its end-to-end extension. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 323 | Crystallization properties of amorphous and supercooled liquid antimony | Mazzarello, Riccardo; Ronneberger, Ider; Chen, Yuhan; Zhang, Wei | In this talk, we investigate the structural and crystallization properties of amorphous and supercooled liquid models of pure and alloyed antimony by ab initio molecular dynamics. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 324 | Jammed solids held together with pins: The effect of pin geometry on structure and mechanical response | Graves, Amy; Packer, Liam; Jenike, Brian; Liloia, Ari; Ridout, Sean | Here, we address unanswered questions on the geometrical role that a scaffolding of fixed particles, or "pins", plays in structure and dynamical response of jammed, soft bi- or polydisperse particles. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 325 | Boundary and Interface Modes in Periodically Triangulated Origami | McInerney, James; Chen, Bryan; Theran, Louis; Santangelo, Christian; Rocklin, Zeb | Here, we investigate the linear modes of triangulated origami, for which the number of constraints matches the number of degrees of freedom, i.e. mechanical criticality. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 326 | High Throughput Mechanical Quantification of Glassy Thin Films using Additively Manufactured Elastomeric Lattices | Vaia, Richard; Auguste, Anesia; Schantz, Allen; Gillman, Andrew; Tibbits, Andrew; Buskohl, Philip | In this work, we will discuss a high throughput concept to measure the elastic moduli, plasticity and failure strain of thin polymer films. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 327 | Classical E&M with a twist: A geometric Hall effect without magnetic field | Schade, Nicholas; Schuster, David; Nagel, Sidney | We demonstrate a fundamentally novel use of geometry to create transverse potentials along curved paths without any magnetic field. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 328 | Rigidity Transitions in Flexible Polymer Networks | Little, Justin; Bruinsma, Robijn | We show that networks of flexible polymers in good solvent described by the Edward’s Hamiltonian undergo first-order rigidity transitions as the excluded volume interaction is increased. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 329 | Biological Regulatory Networks are Minimally Frustrated | Tripathi, Shubham; Kessler, David; Levine, Herbert | Here, using a Boolean modeling framework to compare the dynamical behavior of five real biological networks to that of random networks with similar topological features, we show that biological networks possess sets of stables states that are minimally frustrated. | Session 22: Glassy Dynamics: From Simple Models to Biological Tissues |
| 330 | Universality of biochemical feedback and its application to immune cells | Erez, Amir; Byrd, Tommy A.; Vogel, Robert M; Altan-Bonnet, Gregoire; Mugler, Andrew | We consider a coarse-grained view of this cascade, its output and response to inhibition, and propose a theory which maps the stochastic dynamics to thermodynamic state variables. | Session 23: Immune Sensing and Response |
| 331 | Optimal non-equilibrium decision making to store immune memory | Schnaack, Oskar; Nourmohammad, Armita | To do so, we have developed a theoretical framework, where memory storage is a non-equilibrium decision-making process between an adaptive exploration to mount a specific response and exploitation of existing yet suboptimal memory that can be utilized immediately to suppress an infection. | Session 23: Immune Sensing and Response |
| 332 | Visualizing and controlling immune response to gut microbes | Schlomann, Brandon; Wiles, Travis; Wall, Elena; Guillemin, Karen; Parthasarathy, Raghuveer | I will present work that investigates interactions between immune cells and resident gut bacteria through live imaging of naturally transparent, larval zebrafish. | Session 23: Immune Sensing and Response |
| 333 | Durable Control of Macrophage Polarizations with Backpacks | Shields, Wyatt; Evans, Michael; Wang, Lily; Mitragotri, Samir | In this talk, I will present a class of particles, referred to as “backpacks”, that can regulate the phenotype of adoptively transferred macrophages in vivo. | Session 23: Immune Sensing and Response |
| 334 | Inference and adaptation in innate immunity | Qin, Yawei; Mace, Emily; Barton, John | We describe a quantitative model of the regulation of nonspecific activation that is grounded in Bayesian inference. | Session 23: Immune Sensing and Response |
| 335 | A mathematical model of aging in the immune system | Jones, Eric; Sheng, Jiming; Wang, Shenshen; Carlson, Jean | In this study we develop a mathematical model of the immune system that couples the innate and adaptive components of the immune system, allowing investigation of the mutual modulation of the innate and adaptive immune branches over time. | Session 23: Immune Sensing and Response |
| 336 | 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 23: Immune Sensing and Response |
| 337 | Aging in the immune system is a loss of balance | Sheng, Jiming; Jones, Eric; Carlson, Jean; Wang, Shenshen | In this talk, I introduce a mathematical model of immune response that integrates the innate and adaptive components, which enables studies of their mutual modulation over an individual’s lifetime. | Session 23: Immune Sensing and Response |
| 338 | Influenza virus geometry shapes the immune response against it | Amitai, Assaf; Sangesland, Maya; Lingwood, Daniel; Chakraborty, Arup | Using mice experiments, in-silico models of designed immunogens (nanoparticles) and of antibody development against flu, we study how a targeted response against conserved stem residues can be elicited. | Session 23: Immune Sensing and Response |
| 339 | Spurious higher-order correlations from non-linearities in a receptor-ligand model | Zhu, Richard; Murugan, Arvind | We study a simple receptor-ligand model and demonstrate that spurious higher-order interactions can arise from simpler interactions combined with non-linearities not accounted for. | Session 23: Immune Sensing and Response |
| 340 | 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 23: Immune Sensing and Response |
| 341 | What can and can’t Machine Learning do for Physics? | Mehta, Pankaj | What can and can’t Machine Learning do for Physics? | Session 24: Inference, Information, and Learning in Biophysics: |
| 342 | Coarse scale representation of spiking neural networks: from dynamics to backpropagation through spikes | Yanguas-Gil, Angel | In this work we have explored the development of coarse scale representations of leaky integrate and fire neurons that operate at this timescale. | Session 24: Inference, Information, and Learning in Biophysics: |
| 343 | Towards a grammar of probabilistic models for large biological networks | Fleig, Philipp; Nemenman, Ilya | Here we present first steps of an approach to overcome this obstacle. | Session 24: Inference, Information, and Learning in Biophysics: |
| 344 | Different noise assumptions yield qualitatively different landscapes and transition paths in gene regulation models | Vastola, John; Holmes, William | Building on earlier work that analyzed one and two gene toy models, we present results on how noise assumptions affect landscapes and transition paths in models of the epithelial-to-mesenchymal transition (EMT) and early T cell development. | Session 24: Inference, Information, and Learning in Biophysics: |
| 345 | Stochastic Modelling of Dynein Motors on a One-Dimensional Lattice: Dynamics and Stationary State | Nandi, Riya; ., Priyanka | Inspired by the dynamics of dyneins, we have developed a model of an exclusion process on a one-dimensional lattice, where the motors can move in the forward direction up to four steps depending on the load attached to it. | Session 24: Inference, Information, and Learning in Biophysics: |
| 346 | Limits to biochemical signalling in a changing environment as an inference problem | Mora, Thierry; Nemenman, Ilya | Here, we calculate a new bound to concentration sensing of a changing concentration by mapping the problem onto a field theory through Bayesian inference, which we solve using a Gaussian approximation. | Session 24: Inference, Information, and Learning in Biophysics: |
| 347 | Human information processing in complex networks | Lynn, Christopher; Papadopoulos, Evangelia; Kahn, Ari; Bassett, Danielle | Here we develop an analytical framework to study the information generated by a system as perceived by a human observer. | Session 24: Inference, Information, and Learning in Biophysics: |
| 348 | Information tradeoffs in sensing and sampling | Holmes, Caroline; Bialek, William | We explore this tradeoff, asking about the maximum entropy of the sampling lattice that is consistent with gathering a certain amount of information from a Gaussian random signal; bits of sensory information are traded against bits of positional information. | Session 24: Inference, Information, and Learning in Biophysics: |
| 349 | Optical reservoir computing with tumor spheroids | Pierangeli, Davide; Palmieri, Valentina; Marcucci, Giulia; Moriconi, Chiara; Perini, Giordano; De Spirito, Marco; Papi, Massimiliano; Conti, Claudio | We demonstrate a random optical network realized by tumor spheroids. | Session 24: Inference, Information, and Learning in Biophysics: |
| 350 | Stochastic Force Inference | Ronceray, Pierre; Frishman, Anna | We propose a principled framework, Stochastic Force Inference, for the inverse problem of Brownian dynamics: reconstruct spatially dependent force and diffusion fields from individual trajectories. | Session 24: Inference, Information, and Learning in Biophysics: |
| 351 | Predicting the future from the past in visual object motion: optimal representations of mixed stochastic/deterministic trajectories | Sachdeva, Vedant; Walczak, Aleksandra; Mora, Thierry; Palmer, Stephanie | Here, we propose that the encoding scheme used by such biological systems can be predicted by the information bottleneck method. | Session 24: Inference, Information, and Learning in Biophysics: |
| 352 | Quantifying success and failure in simple models of large neural populations | Meshulam, Leenoy; Gauthier, Jeffrey; Brody, Carlos; Tank, David; Bialek, William | In statistical physics we routinely study models for collective behaviors that are simpler than the underlying microscopic mechanisms. | Session 24: Inference, Information, and Learning in Biophysics: |
| 353 | Quantifying temporal information accumulation for biochemical signaling dynamics | Tang, Ying; Adelaja, Adewunmi; Ye, Xiaofeng; Deeds, Eric; Wollman, Roy; Hoffmann, Alexander | We find that a type of stochastic process can be used to represent the signaling activities that show a high degree of cell-to-cell variability. | Session 24: Inference, Information, and Learning in Biophysics: |
| 354 | The strange case of Dr Jekyll and Mr Hyde: The two faces of singular models. | Wiggins, Paul | In this talk, we will explore the phenomenology of learning from two physical perspectives: First, we explore the correspondence between statistical physics and statistics and demonstrate that there is equivalence between predictive performance and heat capacity, which gives new physical insight into why learning has universal scaling as well as explaining how and why these universal rules fail in the context of singular models. | Session 24: Inference, Information, and Learning in Biophysics: |
| 355 | Learning dynamical information from static protein and sequencing data | Pearce, Philip; Woodhouse, Francis; Forrow, Aden; Kelly, Ashley; Kusumaatmaja, Halim; Dunkel, Jorn | Here, we introduce a flexible and robust numerical framework to infer Markovian transition networks directly from time-independent data sampled from stationary equilibrium distributions. | Session 24: Inference, Information, and Learning in Biophysics: |
| 356 | Associative Memory of Structured Knowledge | Steinberg, Julia; Sompolinsky, Haim | We model each knowledge structure as a set of binary relations between events and cues (cues may represent e.g., temporal order, spatial location, role in semantic structure). | Session 24: Inference, Information, and Learning in Biophysics: |
| 357 | Can model reduction replace expert intuition for modeling complex biological systems? | Petrie, Cody; Bjork, Dane; Transtrum, Mark | We report on a comparative study of model reduction of the Wnt signaling pathway, comparing automatic methods with expert intuition. | Session 24: Inference, Information, and Learning in Biophysics: |
| 358 | Limits on the suppression of molecular fluctuations and oscillation dephasing in stochastic reaction networks | Yan, Jiawei; Paulsson, Johan | Here we aim to identify general principles in stochastic reaction networks that apply regardless of parameters and the form of rate functions. | Session 24: Inference, Information, and Learning in Biophysics: |
| 359 | Kalman-like Self-Tuned Sensitivity in Biophysical Sensing | Husain, Kabir; Pittayakanchit, Weerapat; Pattanayak, Gopal; Rust, Michael; Murugan, Arvind | Here, we argue that living cells can navigate these conflicting demands by dynamically tuning their environmental sensitivity. | Session 24: Inference, Information, and Learning in Biophysics: |
| 360 | Searching for the Relevant Properties of Binary Datasets: Is your Model Truly Pairwise? | De Mulatier, Clelia; Mazza, Paolo; Marsili, Matteo | Information theory provides a quantitative method to select the best of potential explanations for data, by optimizing the balance between goodness-of-fit and simplicity. | Session 24: Inference, Information, and Learning in Biophysics: |
| 361 | Information efficiency of bacterial chemotaxis | Mattingly, Henry; Kamino, Keita; Zhang, Xiaowei; Machta, Benjamin; Emonet, Thierry | We show that climbing a gradient with drift speed vD requires an information rate of at least I φ→ M = 12 Dr ( vD/ v0) 2 (1- TB), where Dr is the rate of rotational diffusion, v0 is the run speed, and TB is the fraction of time the cell is tumbling. | Session 24: Inference, Information, and Learning in Biophysics: |
| 362 | Decision-making at a T-junction by gradient-sensing agents | Gandhi, Tanvi; Huang, Jinzi; Aubret, Antoine; Li, Desmond; Ramananarivo, Sophie; Vergassola, Massimo; Palacci, Jeremie | In our study, we investigate the navigation of inert particles in a network that has multiple junctions. | Session 24: Inference, Information, and Learning in Biophysics: |
| 363 | Trading bits in the readout of positional information | Bauer, Marianne; Bialek, William; Gregor, Thomas; Petkova, Mariela; Wieschaus, Eric | We show that to capture ~90% of the available information, we need more bits than intuitively biologically reasonable. | Session 24: Inference, Information, and Learning in Biophysics: |
| 364 | Single-Molecule Conductance and Conformational Analysis with Engineered Nano-Junctions for Nucleic Acid Sequencing | Korshoj, Lee; Afsari, Sepideh; Chatterjee, Anushree; Nagpal, Prashant | We address these issues by engineering nano-junctions for conductance measurements on conformationally constrained single nucleotides within electrostatically bound DNA molecules on a self-assembled cysteamine monolayer. | Session 24: Inference, Information, and Learning in Biophysics: |
| 365 | 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 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 366 | Protein-Corona-by-Design in 2D: A Molecular Dynamics study to Decode Bio-Nano Interactions for Quality-by-Design Nanomedicines | Al-Badri, Mohamed Ali; al-Jamal, Khuloud; Lorenz, Christian | Here we investigate the interaction of graphitic materials with an array of proteins with all-atom molecular dynamics simulations and perform analytical modelling ito identify safe and toxic protein corona profiles in 2D that could pave the way for future quality by design 2D/3D nanomedicines & better clinical translation. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 367 | Single-Molecule Characterization of Nanoparticle Bioconjugates using Microwell Array Analysis | Abdul-Moqueet, Mohammad; Tovias, Leeana; Mayer, Kathryn | A need for characterizing these nanoparticle bioconjugates at the single-particle level using optical methods is needed. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 368 | Single-Molecule Kinetics of Taq Polymerase up to 94 °C | Turvey, Mackenzie; Lee, Wonbae; Taulbee, Jeffrey; Lau, Calvin; Gabriel, Kristin; Vargas, Rebecca; Weiss, Gregory; Collins, Philip | Our electronic biosensor approach provides direct access to single-nucleotide incorporation activity [2] from room temperature up to 94 °C. For example, the incorporation rate of a single Taq molecule was monitored from 1 bp/s at 22 °C to greater than 100 bp/s at 72 °C, the typical PCR operating temperature. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 369 | Monitoring Antipsychotic Drug Effects on Stimulated Dopamine Release Using Carbon Nanotube Transistors with Nafion-Radical Hybrid Films | Park, Inkyoung; Pham Ba, Viet Anh; Cho, Dong-guk; Hong, Seunghun | In this work, carbon nanotube field-effect transistors with floating electrodes were functionalized with nafion films containing 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS●) radicals to build selective biosensors for the dopamine detection. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 370 | Synthesis and toxicity of bio-templated fluorescent metal nanoclusters in human Neuro-2a cells | Karna, Shashi; Perry, Karima; Kumar, Raj; Gupta, Raj | Here we present the synthesis of Au and Fe nanoclusters synthesized in vitro using human neuro-2a cells. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 371 | Protein Aggregation Characterization by Nanopore technology | Li, Jiali | In this talk, we report our study on characterizing protein aggregation with a solid-state nanopore device, together with AFM and DLS techniques. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 372 | Active and stable palladium nano-thin-film structure development for rapid and direct biomolecules conjugation and sensing | Chang, Chia-Ching; Chang, Chia-Yu; Huang, Yun-Tzu; Chen, Wei | In this study, a PET substrate has been selected for metal atoms absorption and a stable and active Pd nano-thin-film (NTF) surface has been developed. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 373 | Spontaneous ssDNA Stretching on Graphene and Hexagonal Boron Nitride In-plane Heterostructures | Luan, Binquan | Given the significance of ssDNA stretching in genome analysis, here a novel ssDNA stretching platform is proposed: two dimensional in-plane heterostructure comprising graphene and hexagonal boron nitride (h-BN), and I show that ssDNA can be stretched on a h-BN nanostripe sandwiched between two adjacent graphene domains ("nanochannel”). | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 374 | Block Optical DNA Sequencing with Plasmonic Substrates for Rapid Biomarker Diagnostics | Korshoj, Lee; Prabhune, Ameya Gajanan; Nagpal, Prashant | In a push for improved precision diagnostics, we describe an optical sequencing platform that uses surface-enhanced Raman spectroscopy (SERS) measurements from plasmonic nanostructured surfaces and nanoparticles for label-free determination of nucleobase content in DNA k-mer blocks. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 375 | Dynamics of DNA in periodic temperature gradient field created by plasmonic heating | Shimada, Ryoko; Watanabe, Hiroshi | In this work, we utilized the plasmonic heating from periodic silver (Ag) domains under emission of blue light (400 – 440 nm) to create the periodic temperature gradient (with a large amplitude of ~ 0.5 K/um), thereby attempting to observe the Soret effect on DNA molecules mixed in polyethylene glycol (PEG) solutions. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 376 | Tunneling Spectroscopy on Engineered Surfaces for RNA Nucleotide and Structural Label Identification | Korshoj, Lee; Abel Jr., Gary; Chatterjee, Anushree; Nagpal, Prashant | We present a method for identification of RNA nucleotides and structural labels for mapping of single RNA molecules. | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 377 | Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox | Shi, Guang; Thirumalai, Dave | Here, we show that the FISH-Hi-C paradox can be resolved using a theory based on a Generalized Rouse Model for Chromosomes (GRMC). | Session 25: Interrogating Biomolecules with Synthetic Nanostructures |
| 378 | Machine Learning and Data in Polymer Physics Research – Interpretation of Experiments, Model Development, and Enhanced Sampling | De Pablo, Juan | In the second I will present models of biological systems – DNA and chromatin – that use machine learning to integrate experimental and computational information form a wide range of sources, and explain how the resulting information can be used to address important questions in epigenetics. | Session 26: Machine Learning and Data in Polymer Physics |
| 379 | Neural Network Accelerated Self-Consistent Field Theory | Huang, Hejin; Gadelrab, Karim; Alexander-Katz, Alfredo | In this work, we train a neural network (NN) to predict the evolving field during SCFT free energy minimization. | Session 26: Machine Learning and Data in Polymer Physics |
| 380 | Neural network for phase diagrams of polymer-containing liquid mixtures | Nakamura, Issei | In this talk, we discuss our new hidden layer that is constructed through coarse-grained mean-field theory and the scaling laws in polymer physics. | Session 26: Machine Learning and Data in Polymer Physics |
| 381 | Predicting the glass transition behaviors of polymers via integration of molecular simulations, theory, and machine learning | Xia, Wenjie; Alesadi, Amirhadi | In this work, we develop an innovative framework by integrating cheminformatics and coarse-grained molecular dynamics (MD) simulations to predict the glass transition temperature of diverse sets of hundred polymers. | Session 26: Machine Learning and Data in Polymer Physics |
| 382 | Extracting molecular mechanisms of shear-thinning of liquids at high strain rates using machine learning | Jadhao, Vikram; Kadupitiya, JCS | This talk explores the use of machine learning to probe the molecular origins of this rheological transition. | Session 26: Machine Learning and Data in Polymer Physics |
| 383 | 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 26: Machine Learning and Data in Polymer Physics |
| 384 | Developing Databases for Polymer Informatics | Tchoua, Roselyne; Hong, Zhi; Audus, Debra; Patel, Shrayesh; Ward, Logan; Chard, Kyle; De Pablo, Juan; Foster, Ian | In an effort to overcome this barrier, we developed pipelines to harness the vast quantities of valuable experimental polymer data trapped in the literature. In our first effort, we developed the largest Flory-Huggins chi parameter database using crowdsourcing and found that the burden to review papers could be lessened by training a classifier to identify promising articles. | Session 26: Machine Learning and Data in Polymer Physics |
| 385 | Data Science and Machine Learning for polymer films and beyond | Ushizima, Daniela; Noack, Marcus; Hexemer, Alexander | As a powerful example of how machine learning (ML) algorithms can streamline discovery from experimental data, scientists at the LBNL Advanced Light Source have employed Convolutional Neural Networks (CNN) [1, 2] to enable lattice structure classification using diffraction patterns, and Gaussian process regression to construct surrogate models and error functions based on the limited experimental data. | Session 26: Machine Learning and Data in Polymer Physics |
| 386 | Parameter Estimation for Spatio-Temporal Models using Bayesian Optimisation and Gaussian Processes | Clarke, Nigel; Cabral, Joao; Wilkinson, Richard; Ward, Wil; Pont, Sebastian | Instead of a computationally expensive grid-based search for the minimum loss, we adopt a Bayesian optimisation approach placing a Gaussian process over the loss, representing the function as an infinite-dimensional normal distribution that can be used to estimate it over its entire input space, with quantified uncertainty. | Session 26: Machine Learning and Data in Polymer Physics |
| 387 | Evolutionary couplings detect side-chain interactions in protein structures | Hockenberry, Adam; Wilke, Claus | We use both simulations and empirical analyses to highlight that purely backbone-based definitions of true residue–residue contacts may underestimate the accuracy of evolutionary coupling algorithms by as much as 40% and that a commonly used reference point (Cβ atoms) underestimates the accuracy by 10–15%. | Session 26: Machine Learning and Data in Polymer Physics |
| 388 | Tracking Accelerated Aging of Cross-Linked Polyethylene Pipes by Applying Machine Learning Concepts to Infrared Spectra | Hiles, Melanie; D’Amico, Joseph; Morling, Benjamin; Abbasi, Fatemeh; Grossutti, Michael; Dutcher, John | Infrared (IR) microscopy combines the chemical specificity of IR spectroscopy with the high spatial resolution of light microscopy, and we have used this technique to track variations in the degree of crystallinity and additive concentration across the wall thickness of PEX pipes. | Session 26: Machine Learning and Data in Polymer Physics |
| 389 | Protein condensates as aging Maxwell fluids | Jawerth, Louise | Here, we present our efforts to quantify these new materials as they age in vitro. | Session 27: Macromolecular Phase Separation in Biology |
| 390 | Surface Fluctuations and Coalescence of Nucleolar Droplets in the Human Cell Nucleus | Caragine, Christina; Haley, Shannon; Zidovska, Alexandra | Our study presents a noninvasive approach, using natural probes to investigate material properties of the cell as well as to understand the physical interactions between nucleoli and chromatin solution [1,3]. | Session 27: Macromolecular Phase Separation in Biology |
| 391 | Phase separation in the nucleus is limited by chromatin mechanics | Zhang, Yaojun; Lee, Daniel; Meir, Yigal; Brangwynne, Cliff; Wingreen, Ned | Here, we combine coarse-grained molecular dynamics simulations and theory of liquid-liquid phase separation to show that mechanical interactions with chromatin can constrain the size of droplets in the nucleus. | Session 27: Macromolecular Phase Separation in Biology |
| 392 | Subdiffusive Dynamics of Optogenetic Droplets Report on Local Chromatin Mechanics | Lee, Daniel; Shimobayashi, Shunsuke; Chang, Yi-Che; Strom, Amy; Wingreen, Ned; Brangwynne, Cliff | Here, we show that droplet growth dynamics are directly inhibited by chromatin. | Session 27: Macromolecular Phase Separation in Biology |
| 393 | Converting Stochastic Assembly into an Assembly Line: Non-Equilibrium Droplet Dynamics Assists Ribosome Formation | Harmon, Tyler; Julicher, Frank | We show numerically and analytically that the binding of specific rProteins to rRNA can be localized within a well-defined radial shell inside the nucleolus instead of being homogeneously distributed. | Session 27: Macromolecular Phase Separation in Biology |
| 394 | Reentrant Liquid Condensation of Ribonucleoprotein–RNA Complexes | Raju, Muralikrishna; Laghmach, Rabia; Potoyan, Davit | Using an archetypal disordered RNP, fused in sarcoma (FUS), here we employ atomistic simulations to study how RNA, a primary component of RNP granules, can modulate the phase behavior of RNPs by controlling both droplet assembly and dissolution. | Session 27: Macromolecular Phase Separation in Biology |
| 395 | Size selection of phase-separated liquid droplets in strain-stiffening elastic networks | Mao, Sheng; Haataja, Mikko; Kosmrlj, Andrej | Motivated by these observations, we developed a model to investigate the coupling between the separating liquid mixture and the elastic network. | Session 27: Macromolecular Phase Separation in Biology |
| 396 | A hydrodynamic instability drives TPX2 protein droplet formation on microtubules and leads to branching microtubule nucleation | Setru, Sagar; Gouveia, Bernardo; Alfaro-Aco, Raymundo; King, Matthew; Stone, Howard; Shaevitz, Joshua; Petry, Sabine | Using atomic force microscopy, fluorescence imaging, electron microscopy, and hydrodynamic theory, we show that the dynamics of liquid TPX2 are crucial for nucleating branched microtubules. | Session 27: Macromolecular Phase Separation in Biology |
| 397 | Motif Sequences and Intracellular Phase Separation | Weiner, Benjamin; Meir, Yigal; Wingreen, Ned | We propose a statistical physics model of IDPs to elucidate the relationship between motif sequence, the phase boundary, and the partitioning of proteins between phases. | Session 27: Macromolecular Phase Separation in Biology |
| 398 | Coupling signaling cascades to membrane criticality | Schaffner, Taylor; Machta, Benjamin | In order to create a theory that explains the interplay between signaling cascades and membrane criticality, here we present a model and Monte-Carlo simulation framework for proteins coupled to their surrounding lipid membrane using a 2D Ising model. | Session 27: Macromolecular Phase Separation in Biology |
| 399 | Wetting of Critical Membranes by Protein Droplets | Rouches, Mason; Veatch, Sarah; Machta, Benjamin | Here, we consider the underlying thermodynamics of this interaction, constructing a minimal Landau theory describing the wetting of protein droplets to a near-critical membrane. | Session 27: Macromolecular Phase Separation in Biology |
| 400 | Probing the Dynamics of Optically Induced Protein Droplets with Single-Walled Carbon Nanotubes | Higinbotham, Hugh; Coupe, Sebastian; Jung, Yoon; Fakhri, Nikta | Here, we use single-walled carbon nanotubes (SWNTs), which fluoresce in the near infrared and are photostable, to probe the local environment of optically induced protein droplets in vivo. | Session 27: Macromolecular Phase Separation in Biology |
| 401 | Measuring protein concentrations in biomolecular condensates via quantitative phase microscopy | McCall, Patrick; Kim, Kyoohyun; Wang, Jie; Fritsch, Anatol; Poznyakovskiy, Andrey; Diederich, Benedict; Kreysing, Moritz; Heintzmann, Rainer; Guck, Jochen; Alberti, Simon; Brugués, Jan; Hyman, Anthony | To address these, we use quantitative phase microscopy and optical diffraction tomography to measure the refractive index of model condensates, from which the protein concentration may be inferred. | Session 27: Macromolecular Phase Separation in Biology |
| 402 | Pollen cell walls form from modulated phases | Radja, Asja; Sweeney, Alison; Lavrentovich, Maxim | We formulated a Landau-Ginzburg free energy description of this process in which we treat the primexine concentration as a scalar field coupled to the cell membrane and calculated the equilibrium states. | Session 27: Macromolecular Phase Separation in Biology |
| 403 | Designing morphology of separated phases in multicomponent liquid mixtures | Chakraverti-Wuerthwein, Milena; Mao, Sheng; Gaudio, Hunter; Haataja, Mikko; Kosmrlj, Andrej | We developed a novel method based on graphs that enabled us to enumerate all topologically distinct morphologies of separated phases. | Session 27: Macromolecular Phase Separation in Biology |
| 404 | Microscopic Model of a Biological Condensate | Htun, Swan; Chou, Han-Yi; Sarthak, Kumar; Aksimentiev, Aleksei | Using existing structural and biochemical information, we constructed a coarse-grained model of the FUS protein. | Session 27: Macromolecular Phase Separation in Biology |
| 405 | Microstructure in biological phase transition | Bhandari, Kamal; Schmit, Jeremy | Since the condensed phase has a low density, we propose that molecules are highly aligned to form zipper structures. | Session 27: Macromolecular Phase Separation in Biology |
| 406 | Experimental determination of binodal compositions of protein and peptide solutions | Filippidi, Emmanouela; Julicher, Frank; Hyman, Anthony | We will present quantitative measurements of both branches of the binodal curves of the phase diagrams obtained via quantitative phase imaging microscopy for the protein FUS and simpler peptide sequences. | Session 27: Macromolecular Phase Separation in Biology |
| 407 | Spinodal Dynamics in Non-Equilibrium Compression of Two Self-Avoiding Polymer Chains | Zeng, Lili; Seyboldt, Rabea; Liu, Zezhou; Capaldi, Xavier; Khorshid, Ahmed; Francois, Paul; Provatas, Nikolas; Reisner, Walter | We interpret this phenomenon as a spinodal decomposition of the two polymers and rationalize it using a model based on a 1D convective Cahn-Hilliard equation, a classic model describing spinodal decomposition in driven binary systems. | Session 27: Macromolecular Phase Separation in Biology |
| 408 | Relating chemical and physical properties controlling oligonucleotide polyelectrolyte complex phase separation | Marras, Alexander; Vieregg, Jeffrey; Lueckheide, Michael; Tirrell, Matthew | Here, we present an investigation of the impact of physical and chemical properties of each polyelectrolyte on complex and micelle assembly. | Session 27: Macromolecular Phase Separation in Biology |
| 409 | Entropic localization of plasmids in nanofluidic compartments | Liu, Zezhou; Capaldi, Xavier; Zeng, Lili; Lamothe, Rodrigo; Reisner, Walter | Here, we present a nanofluidic device with compartments simulating the confinement induced by a cell membrane. | Session 27: Macromolecular Phase Separation in Biology |
| 410 | Computational Insights into Phase Separation of Multivalent Polymers | Zumbro, Emiko; Alexander-Katz, Alfredo | In this work we compare phase separation of multivalent polymers through non-specific Van der Waals interactions to phase separation through specific reactive-binding interactions. | Session 27: Macromolecular Phase Separation in Biology |
| 411 | Stable drops: the Gibbs-Thomson condition and drop dynamics | Rutenberg, Andrew; Cameron, Samuel | This talk addresses three questions for systems with small stable droplets: how does the Gibbs-Thomson condition generalize, how does Lifshitz-Slyozov-Wagner dynamics generalize, and how much of this should apply when stable drops arise from non-equilibrium processes? | Session 27: Macromolecular Phase Separation in Biology |
| 412 | Simulation Informed Thermodynamic Model for Polyampholyte Self-Coacervation with Heterogeneous Charge Distribution | Madinya, Jason; Sing, Charles | In this work we present a coarse-grained simulation model to resolve phase separation in polyampholytes with any arbitrary charge sequence. | Session 27: Macromolecular Phase Separation in Biology |
| 413 | Nematic transition and liquid-liquid phase separation in semiflexible polymers – nanoparticle mixtures | Roy, Supriya; Chen, Yeng-Long | In the present study, we used GPU-accelerated Langevin dynamics simulation to explore how polymer-NP interaction affect the isotropic-nematic (I-N) transition and microstructural modifications of a matrix of semi-flexible polymers with persistence length P=20 and contour length L=25. | Session 27: Macromolecular Phase Separation in Biology |
| 414 | Valence and Patterning of Aromatic Residues Determine the Phase Behavior of Disordered Prion-Like Domains | Holehouse, Alex; Martin, Erik; Peran, Ivan; Pappu, Rohit; Mittag, Tanja | Here, we use multipronged biophysical approaches that integrates across simulation, experiment, and theory to address this question and uncover the physical principles underlying how an archetypal PLD derived from hnRNPA1 avoids aggregation in favor of LLPS. | Session 27: Macromolecular Phase Separation in Biology |
| 415 | A Random Heteropolymer Model of Protein Aggregation | Falk, Martin; Triandafillou, Catherine; Murugan, Arvind | In this context, the phenomenon of protein aggregation is a particularly appealing subject of study. | Session 27: Macromolecular Phase Separation in Biology |
| 416 | Actin(g) on phase separation | Wiegand, Tina; Hyman, Anthony; Grill, Stephan | Our aim is to recapitulate the complex spectrum of kinetic behaviors observed for actomyosin in vivo. | Session 27: Macromolecular Phase Separation in Biology |
| 417 | Elasticity dominated small molecule migration in polymer mixtures and gels | Chakrabarti, Buddhapriya; Mukherjee, Biswaroop | We report a simultaneous phase separation and surface migration phenomena in oligomer-polymer and oligomer-gel systems following a temperature quench. | Session 27: Macromolecular Phase Separation in Biology |
| 418 | Looped liquid-liquid coexistence in protein crystallization | Glaser, Jens; Glotzer, Sharon | Here we report liquid-liquid phase separation (LLPS) with a highly asymmetric coexistence region in a computational model of rubredoxin with real molecular shape. | Session 27: Macromolecular Phase Separation in Biology |
| 419 | Intermolecular association of the variable domain of dynamin related protein 1 in crowding conditions suggests a role in dynamin assembly | Harden, James; Posey, Ammon; Bagheri, Mehran; Harwig, Megan; Kennedy, Nolan W.; Hilser, Vincent; Hill, R. Blake | This talk focuses on the behaviour of isolated VD from Drp1 isoform 1. | Session 27: Macromolecular Phase Separation in Biology |
| 420 | Model for intrinsically disordered proteins with a strong dependence of liquid-liquid phase separation on sequence | Statt, Antonia; Casademunt, Helena; Brangwynne, Cliff; Panagiotopoulos, Athanassios | In this talk, we present the phase separation behavior of different sequences of a coarse-grained model for intrinsically disordered proteins and show that they exhibit a surprisingly rich phase behavior. | Session 27: Macromolecular Phase Separation in Biology |
| 421 | Quantitative droplet FRAP based on physical principles | Hubatsch, Lars; Jawerth, Louise; Hyman, Anthony; Weber, Christoph | This results in the following improvements: we can (i) distinguish the time scales of exchange through the droplet interface (set by bulk diffusion and boundary kinetics) from diffusion inside the droplet, (ii) quantify the impact of the interface (iii) provide improved measurements for several biologically important proteins, and (iv) use our analysis framework to explore several multi-component scenarios. | Session 27: Macromolecular Phase Separation in Biology |
| 422 | Probing ATPase Dependent Physical Properties of Biological Condensates | Coupe, Sebastian; Jung, Yoon; Fakhri, Nikta | In studying how this model condensate system responds to base-pairing RNAs, ATP, and accessory proteins we will shed light on principles underlying energetic regulation of condensate fluidity. | Session 27: Macromolecular Phase Separation in Biology |
| 423 | The robust bioinformatic analysis of the protein sequences with phase behavior | Badaczewska-Dawid, Aleksandra Elzbieta; Potoyan, Davit | The long-term goal of our research is the creation of a publically accessible database that would be used by both experimentalists for designing controlled mutations and for computationally-oriented scientists for developing new modeling tools. | Session 27: Macromolecular Phase Separation in Biology |
| 424 | Effects of protein charge and charge patterning on complex coacervation for enzymatic microreactors | Zervoudis, Nicholas; Obermeyer, Allie | Effects of protein charge and charge patterning on complex coacervation for enzymatic microreactors | Session 27: Macromolecular Phase Separation in Biology |
| 425 | The role of a hidden ordered domain in controlling the material properties of RNA-protein condensates | Seim, Ian; Klotsa, Daphne; Gladfelter, Amy | By mutating specific residues in the CC, we demonstrate a range of material states in vitro, characterized by kinetic mean-field modeling of condensate formation. | Session 27: Macromolecular Phase Separation in Biology |
| 426 | The nematic feedback between cancer cells and the extracellular matrix | Sun, Bo | In this talk I will first discuss quantitative measurements of cellular response to 3D contact guidance cues, which are inevitiblly noisy and spatially heterogeneous. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 427 | Mechanical regulation of shape deformation by matrix viscoelasticity in breast tissues | Elosegui-Artola, Alberto; Gupta, Anupam; Mahadevan, L; Mooney, David | In this study, we are further looking into the role of such mechanical properties in inducing the malignant phenotype in normal mammary epithelium MCF10A cell line. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 428 | Why do rigid tumors contain soft cancer cells? | Fuhs, Thomas; Wetzel, Franziska; Fritsch, Anatol; Bi, Dapeng; Stange, Roland; Pawlizak, Steve; Kiessling, Tobias; Morawetz, Erik; Grosser, Steffen; Sauer, Frank; Lippoldt, Jürgen; Renner, Fred; Friebe, Sabrina; Zink, Mareike; Horn, Lars-Christian; Aktas, Bahriye; Bendrat, Klaus; Oktay, Maja; Niendorf, Axel; Condeelis, John; Höckel, Michael; Marchetti, M Cristina; Manning, M. Lisa; Kaes, Josef | We investigate primary samples from patients with mammary and cervical carcinomas on multiple length scales from tissue level down to single cells. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 429 | A tug of war between cell-cell and cell-ECM interaction during tumor invasion | Huang, Yu Ling; Dey, Sumit; Shiau, Carina; Wu, Cindy; Ma, Yujie; Segall, Jeffrey; Wu, MingMing | In this talk, we will present a newly developed 3D tumor model in which tumor spheroids were embedded within collagen matrix, and tumor cell dynamics are subsequently imaged and analyzed. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 430 | Understanding the crosstalk between mechanical and chemical guidance in 3D cell migration | Esfahani, Pedram; Eddy, Christopher; Kim, Jihan; Wong, Ryan; Sun, Bo | In our continuing work, we will develop a mathematical model to recapitulate our experimental observations and fully characterize the cell response to coupled chemical and mechanical cues. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 431 | The role of tissue biophysics in organ selectivity in metastasis | Tanner, Kandice | Here I discuss using optical tweezer based active microrheology to measure the mechanical cues that may influence disseminated tumor cells in different organ microenvironments. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 432 | Distinct Roles of Tumor-Associated Mutations in Collective Cell Migration | Lee, Rachel; Vitolo, Michele; Losert, Wolfgang; Martin, Stuart | By using cells with controlled mutations, we show that Ras activation and PTEN deletion lead to opposing effects on collective migration, despite both mutations being frequently found in patient tumors. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 433 | Precision of flow sensing by self-communicating cells | Vennettilli, Michael; Fancher, Sean; Hilgert, Nicholas; Mugler, Andrew | Here we derive the precision of flow sensing for two ubiquitous mechanisms: absorption of the chemical and binding/unbinding to surface receptors. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 434 | Classification of healthy and cancerous cells using optical rheology and machine learning | Morawetz, Erik; Tschodu, Dimitrij; Kaes, Josef | We use the high throughput of the OS to perform machine learning based discrimination of individual cells with a breast cancer model. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 435 | Modeling biophysical tumor-stroma interactions in 3D co-cultures of pancreatic cancer cells and pancreatic stellate cells | Struth, Eric; Celli, Jonathan | Going forward, we are leveraging this system to model and study drug delivery through fibrotic PDAC stroma and evaluate stromal depletion therapies. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 436 | 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 28: Mechanics of Cells and Tissues Across Scales |
| 437 | Force generation and self-organization in mitosis | Betterton, Meredith | This talk will discuss how force is generated by motors, crosslinkers, and chromosomes over time during mitosis to correctly assemble the spindle. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 438 | Intrinsic time-scales of active forces control the dynamics of soft living matter | Gradziuk, Grzegorz; Torregrosa Cortés, Gabriel; Broedersz, Chase | Living cells are crowded with active agents which consume energy and perform work on their surrounding environment, constantly keeping the system out of thermodynamic equilibrium. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 439 | Mechanical properties of intermediate filament networks under compression | Carroll, Bobby; Gandikota, Mahesh Chandrasekhar; Elbalasy, Iman; Schnauss, Joerg; Kas, Josef; Schwarz, Jennifer; Patteson, Alison | Here, we study the mechanical response of reconstituted polymer networks comprised of the intermediate filament proteins vimentin and keratin using a parallel-plate rheometer. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 440 | Cytoskeletal Regulation of Three-Dimensional Epithelial Cell Shape | 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 epithelial cells regulate shape and volume. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 441 | Physical limits to sensing material properties | Beroz, Farzan; Zhou, Di; Mao, Xiaoming; Lubensky, David | In this talk, I will present the limits to the precision of such constitutional sensing for sensors embedded in disordered media. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 442 | Cell shape as a window into cell state | Prasad, Ashok | Using these we show that quantifiers of cell shape and cytoskeletal texture can be used to discriminate between different cell states. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 443 | The Morphodynamics of 3D Migrating Cancer Cells | Eddy, Christopher; Wong, Ryan; Sun, Bo | Here, we physically characterize morphodynamics (the temporal fluctuations of cell shape) rather than real-space migration alone. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 444 | Switching between optimum substrate rigidity and focal adhesion reinforcement at the cell leading edge | De, Partho Sakha; De, Rumi | We have developed a theoretical model for the dynamics at the leading edge of a cell placed on a viscoelastic substrate, involving a pair of coupled reaction-diffusion equations. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 445 | Mechanics of endocytosis under large osmotic pressure | Ma, Rui; Berro, Julien | In this talk, I will discuss membrane deformations powered by a point force under the condition of high pressure and low tension, which is rarely studied but directly relevant for endocytosis in yeast cells with a cell wall. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 446 | Plasticity in vertex model of epithelial tissues | Popovic, Marko; Druelle, Valentin; Wyart, Matthieu | Motivated by this question in this work we study plastic properties of vertex model of epithelial tissues, in which mechanical properties of cells are prescribed and emerging tissue mechanics is obtained from their collective behaviour. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 447 | Loops versus lines and the compression stiffening of cells | Gandikota, Mahesh Chandrasekhar; Pogoda, Katarzyna; van Oosten, Anne; Engstrom, Tyler; Patteson, Alison; Janmey, Paul; Schwarz, Jennifer | We find for the fiber network with area-conserving loops model that the stress-strain curves are sensitive to the packing fraction and size distribution of the area-conserving loops, thereby creating a mechanical fingerprint across different cell types. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 448 | Vimentin intermediate filament biomechanics in 3D cell motility | Patteson, Alison | We propose a minimal model in which a perinuclear vimentin cage constricts along with the nucleus during motility through confining spaces, providing mechanical resistance against large strains that can damage the structural integrity of cells and their nuclei. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 449 | Confined cell migration – a dynamical systems perspective | Brückner, David; Fink, Alexandra; Schmitt, Matthew; Arlt, Nicolas; Rädler, Joachim; Broedersz, Chase | To provide such a framework, we employ a data-driven approach to infer the dynamics of cell movement, morphology and interactions of cells confined in two-state micropatterns. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 450 | Finite element simulation of a cell entering a pipette: Effects of large deformation and frictional contact | Sun, Xiaohao; Wang, Ke; Wu, HengAn; Chen, Jian; Long, Rong | Here we present a simulation approach that can continuously update the boundary condition according to the contact status as the cell enters the channel, thus enabling more accurate description of the pressure and frictional conditions. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 451 | Modeling the effect of vimentin on confined cell motility. | Gupta, Sarthak; Patteson, Alison; Schwarz, Jennifer | We have developed a biophysical model for a cell moving through various confined geometries based on Brownian dynamics. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 452 | Regulation of nuclear architecture, mechanics, and nucleocytoplasmic shuttling of epigenetic factors by cell geometric constraints | Alisafaei, Farid; Jokhun, Doorgesh Sharma; Shivashankar, GV; Shenoy, Vivek | To elucidate the physical mechanisms involved in this regulation, we developed an active 3D chemomechanical model to describe the three-way feedback between the adhesions, the cytoskeleton, and the nucleus. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 453 | Effective pressure in a dense cell monolayer and collective cell migration | Khain, Evgeniy | For a non-uniform system, I will consider the cell shift due to the gradient of the effective pressure and examine its effect on the average cell area profiles. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 454 | Effects of cell-cell adhesion on collective migration of multicellular clusters | Roy, Ushasi; Mugler, Andrew | We develop both a minimal framework based on the lattice gas model of statistical physics, as well as a more realistic framework based on the cellular Potts model. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 455 | Plasticity of cell migration resulting from mechanochemical coupling | Ghabache, Elisabeth; Cao, Yuansheng; Rappel, Wouter-Jan | We find that a sufficient decrease of the protrusion force can destabilize keratocyte-like cells, resulting in cells that employ amoeboid-like migration. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 456 | Collective Cell Migration in Wound Healing | Vazquez, Kelly; Notbohm, Jacob | Collective Cell Migration in Wound Healing | Session 28: Mechanics of Cells and Tissues Across Scales |
| 457 | Traction dynamics in collective cell migration | Saraswathibhatla, Aashrith | Recent theoretical models have emphasized cell motility force as a key driver of collective cell migration. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 458 | How does extracellular matrix rigidity affect the fluidity of an embedded spheroid? | Parker, Amanda; Marchetti, M Cristina; Manning, M. Lisa; Schwarz, J | Using a computational model, we explore how a simple mechanical interaction between a spheroid and its ECM promotes changes in the spheroid’s rigidity, morphology and the shapes of its constituent cells, as well as the ECM’s rigidity and structure. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 459 | Self-organized vasculogenesis in 3D printed mixed cell populations | Ellison, Sarah; Angelini, Thomas | Preliminary data and analysis will be presented. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 460 | Interrogating collagen mechanics at the single-molecule level | Forde, Nancy | I’ll describe what we have learned about collagen’s flexibility and stress response, how local sequence context matters, and how our work resolves some of the many contentious findings regarding collagen’s mechanics. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 461 | Mechanical response of the vitreous gel in our eyes: Results from an inhomogeneous two-fluid model | Lwin, Pancy; Franklin, Scott; Thurston, George; Ross, David; Das, Moumita | We study rheological properties of this gel by simulating it as a two-fluid model made of an inhomogeneous polymer network interacting with a fluid. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 462 | Kinetics of Cell Adhesion Through Biomimetic Glycocalyx | Jing, Yu; Cohen, Shlomi; Faubel, Jessica; Curtis, Jennifer | We introduce a biomimetic glycocalyx platform to investigate the kinetics of cell adhesion in the presence of sugar-rich interfaces. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 463 | Length regulation of epithelial cell junctions | Staddon, Michael; Cavanaugh, Kate; Munro, Edwin; Gardel, Margaret; Banerjee, Shiladitya | We propose a new theory for epithelial tissue mechanics that highlights two essential properties of intercellular junctions. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 464 | Fast Confined Dynamics in Lipid Bilayers | Gupta, Sudipta | We have investigated the molecular dynamics of complex phospholipid membranes in their fluid phases by neutron spin echo spectroscopy. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 465 | In vitro characterization and numerical simulations of red blood cell transmigration through splenic inter-endothelial slits | Garcia de Herreros, Antoni; Lu, Huijie; Peng, Zhangli; Del Alamo, Juan | To study the mechanics of RBC splenic filtration, we designed and characterized a family of microfluidic devices where a suspension of human RBCs flows through an array of channels of controlled length (L), width (W) and height (H). | Session 28: Mechanics of Cells and Tissues Across Scales |
| 466 | Nucleation and Formation of a Primary Clot in Insect Blood Probed by Magnetic Rotational Spectroscopy | Kornev, Konstantin; Aprelev, Pavel; Adler, Peter; Brasovs, Artis | Using larvae of Manduca sexta, we discovered that clot nucleation is a two-step process whereby cell aggregation is the time-limiting step followed by rigidification of the aggregate. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 467 | Microfluidic platform for label-free viability cell sorting | Chrit, Fatima Ezahra; Raj, Abhishek; Stone, Nick; Sulchek, Todd; Alexeev, Alexander | We propose a biophysical approach for cell viability sensing, enumeration, and purification that is label-free and continuous. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 468 | Simultaneous Measurement of Electrical and Mechanical Properties of Biological Cells Using a Tuning Fork-Coupled Conductive Probe | Schiller, Mark; Ivanov, Alexandra; Maci, Megi; Pontrelli, Eva; Merlo, Juan; Connolly, Timothy; Naughton, Michael | We have devised a conductive tip tuning fork probe, which is intended to simultaneously measure mechanical properties and membrane potential of a cell. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 469 | Brain Mechanics Drive Cavitation and Fracture Response | Dougan, Carey; Galarza, Sualyneth; Barney, Christopher; zheng, yue; Cai, Shengqiang; Crosby, Alfred; Peyton, Shelly | By understanding the strain rate deformation of specific areas of the brain, we aim to gain further insight into how cavitation-related events lead to irreversible damage. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 470 | Rheological properties of cellular aggregates formed by pilus mediated interactions | Kuan, Hui-Shun; Julicher, Frank; Zaburdaev, Vasily | Motivated by colonies of Neisseria gonorrhoeae bacteria, we develop a continuum theory to study cellular aggregates formed by attractive pulis mediated intercellular interactions. | Session 28: Mechanics of Cells and Tissues Across Scales |
| 471 | Optical tweezer application with Autofocusing Airy-Bessel beams | Liang, Yi; Xiang, Yinxiao; Shi, Fan | We proposed a new autofocusing beams named autofocusing Airy-Bessel beams (AABB). | Session 28: Mechanics of Cells and Tissues Across Scales |
| 472 | Controlled neighbor exchanges drive intermittency and cell streaming in epithelial tissues | Das, Amit; Bi, Dapeng | Here we introduce this important biological constraint in a vertex-based model as an intrinsic single-cell property and study how this rate-limiting process affects the mechanics and collective behavior of cells in a tissue. | Session 29: Mechanics of cells and tissues across scales |
| 473 | Mechanical Instabilities in Growing Biological Systems: Wrinkling and Branching | Kosmrlj, Andrej | In this talk I will focus on mechanical instabilities that cause the wrinkling of Vibrio cholerae bacterial biofilms and branching in developing lungs. | Session 29: Mechanics of cells and tissues across scales |
| 474 | Quasi-realistic modelling of expanding epithelial cell monolayer | Deng, Youyuan; Levine, Herbert | We propose a quasi-realistic model for this phenomenon. | Session 29: Mechanics of cells and tissues across scales |
| 475 | Symmetry breaking and axis formation in Hydra | Collins, Eva-Maria | In my talk, I will present our recent work that answers some of these questions. | Session 29: Mechanics of cells and tissues across scales |
| 476 | Configurations and dynamics of membrane-bound elastic filaments | Lough, Wilson | We discuss the mechanics of surface-bound filaments and present a collection of analytical and numerical results. | Session 29: Mechanics of cells and tissues across scales |
| 477 | Bacteria sense and respond to the mechanics of the surface to which they attach | Gordon, Vernita; Wang, Liyun; Blacutt, Jacob | Here, we examine the relationship between substrate stiffness, mechanical deformation of the bacterial cell, accumulation of bacteria on the surface, and dynamics of an intracellular signal that control biofilms development. | Session 29: Mechanics of cells and tissues across scales |
| 478 | Mechanical impacts of complex topology on epithelial cells | Yu, Sun-Min; Li, Bo; Amblard, francois; Granick, Steve; Cho, Yoon-Kyoung | In the current study, we found that strong mechanical impacts of complex topology on the epithelial system. | Session 29: Mechanics of cells and tissues across scales |
| 479 | Three-dimensional Packing of Curved Epithelia: Biology and Topology meet Physics | Gómez-Gálvez, Pedro; Vicente Munuera, Pablo; Anbari, Samira; Escudero, Luis M; Buceta Fernandez, Javier | Here we address this problem using a combination of experiments, mathematical analyses, computer simulations, and biophysical approaches. | Session 29: Mechanics of cells and tissues across scales |
| 480 | Topological analysis of multicellular structures | Skinner, Dominic; Song, Boya; Dunkel, Jörn | In this talk we introduce a topological distance between materials that needs only the coordinates of the centroid of each discrete object, and is based on the local graph structure around each centroid. | Session 29: Mechanics of cells and tissues across scales |
| 481 | Tissue-Tissue Interactions at Boundaries of Colliding Monolayers | Heinrich, Matthew; Cohen, Daniel; Kosmrlj, Andrej; Strain, Jake | Classic ‘wound healing’ studies in epithelial monolayers use a wound or barrier removal to induce and study collective migration, focusing on the migration rather than the ultimate collision and tissue healing. | Session 29: Mechanics of cells and tissues across scales |
| 482 | Patterning Potential of Cell-cell signalling Molecules in Flowing Tissue | BAJPAI, SUPRIYA; Inamdar, Mandar; Prabhakar, Ranganathan; Chelakkot, Raghunath | We present a model which accounts for contact signalling between adjacent cells and between non-adjacent neighbours through long protrusions that occur along the direction of cell polarization. | Session 29: Mechanics of cells and tissues across scales |
| 483 | Formation and Properties of Self-Assembled Nanoparticle-Supported Lipid Bilayer Probed Through Molecular Dynamics Simulations | Jing, Haoyuan; Wang, Yanbin; Desai, Parth; Ramamurthi, Kumaran; Das, Siddhartha | We reveal that the equilibrated self-assembled NPSLBL system demonstrates a larger number of lipid molecules occupying the outer leaflet as compared to the inner leaflet. | Session 30: Membranes and Channels |
| 484 | Leveraging the physics of a barbecue lighter to genetically transform living organisms | Byagathvalli, Gaurav; Sinha, Soham; Zhang, Yan; Styczynski, Mark; Standeven, Janet; Bhamla, Saad | In this talk, we will discuss both the physics of a lighter, as well as the synthetic biology protocol we have developed for electroporation using this frugal device. | Session 30: Membranes and Channels |
| 485 | Listening to lipid membranes | Lee, Kisung; Chommanov, Gurban; Granick, Steve | Listening to lipid membranes | Session 30: Membranes and Channels |
| 486 | Comparing microrheological methods for measuring lipid membrane viscosity | Jahl, Philip; Parthasarathy, Raghuveer | To resolve this discrepancy, we applied both methods simultaneously to the same lipid vesicles, featuring both phase separated domains and bound elliptical beads. | Session 30: Membranes and Channels |
| 487 | Regulated ensembles and lipid membranes | Girard, Martin; Bereau, Tristan | Their composition is highly complex, involving hundreds of different lipid types and the regulation mechanism is still the subject of intense research. | Session 30: Membranes and Channels |
| 488 | Stable fabrication of a various-sized nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules | Yanagi, Itaru; Akahori, Rena; Takeda, Kenichi | In this study, we found that nanopore fabrication by dielectric breakdown of a SiN membrane under high-pH conditions (pH ≥ 11.3) could overcome these two problems and enabled the formation of a single large nanopore up to 40 nm in diameter within one minute. | Session 30: Membranes and Channels |
| 489 | Monte Carlo simulation of pH activated conformational changes of coarse-grained sodium-proton antiporters | Asadi, Mojgan; Warshel, Arieh | In this study, we map the energy landscape between two pH levels for two different conformations of the wild antiporter and a mutated variant using MD with coarse-graining. | Session 30: Membranes and Channels |
| 490 | Multichannel Flow Cell for a Nanopore Array Sensor | Nguyen Pham, Hai Huy; Yanagi, Itaru; Takeda, Kenichi | In this study, the mechanism of those issues is investigated. | Session 30: Membranes and Channels |
| 491 | Interaction of Graphene Oxide with Model Bio-membrane: Insights into the Structure of the Membrane | MANDAL, PRIYA; Ghosh, Sajal Kumar | In present work, the x-ray reflectivity (XRR) and grazing incidence small-angle x-ray scattering (GISAXS) techniques have been used to extract the structural details of the GO-membrane complex. | Session 30: Membranes and Channels |
| 492 | Detection of streptavidin-labeled DNA using solid-state nanopores for target sequence detection | Akahori, Rena; Yanagi, Itaru; Takeda, Kenichi | In this study, the possibility of streptavidin (SA) as a labelled molecule was investigated. | Session 30: Membranes and Channels |
| 493 | Moving while you’re stuck; a mechanical model of binding facilitated transport in biological systems | Koo, Kanghyeon; Lalitha Sridhar, Shankar; Clark, Noel; Vernerey, Franck; Hough, Loren | Here we describe a mechanical model to probe how binding and thermal motion can enable transport. | Session 30: Membranes and Channels |
| 494 | Towards high-sensitivity phase cancellation microscopy | Lyzwa, Dominika; Singh, Vijay; Yaqoob, Zahid; So, Peter | Here, we present a high phase sensitivity, phase cancellation interferometry system. | Session 30: Membranes and Channels |
| 495 | Predicting optimal parameters for ion transport through nanopores and biological channels | Gibby, William; Barabash, Miraslau; Luchinsky, Dmitry; McClintock, Peter | We have derived a statistical and linear response theory that calculates the occupancy and conductivity of nanopores for given parameters including: pore geometry and charge; type of competing ionic species; and bulk concentration [2]. | Session 30: Membranes and Channels |
| 496 | Temperature-dependent Motility in H. pylori | Antani, Jyot; Lele, Pushkar | We will present a quantitative model that accounts for the anisotropic random walk to predict the temperature dependence of the bacterial diffusion. | Session 31: Microbiological Physics |
| 497 | Developing Methods for Two-Way Communication to Explore the Dynamic Sense of Touch in Bacteria | Xu, Zhou; Niu, Wuqi; Rivera, Sylvia; Siegrist, Sloan; Tuominen, Mark; Santore, Maria | In this work, we study the bacterial sense of touch to establish the new research area of sensory-based bacterial communication. | Session 31: Microbiological Physics |
| 498 | Comparative study of bacterial growth on different surfaces and the effect of weak magnetic field on the growth rates | Masood, Samina | We investigate the growth of bacteria on different sufaces. | Session 31: Microbiological Physics |
| 499 | Rigid Body Dynamics of Motile Bacteria Near Surfaces | Shindell, Orrin; Holt, Keaton; Hoang, Quan; Hoang, Nam Dung; Healy, Frank; Nguyen, Hoa | We present results from our analysis for experiments with both wild-type and smooth-swimming E. coli strains. | Session 31: Microbiological Physics |
| 500 | Fast Modulation of Phenotypic Diversity in Bacterial Chemotaxis | Kamino, Keita; Keegstra, Johannes; Long, Junjiajia; Emonet, Thierry; Shimizu, Thomas | In the E.coli chemotaxis pathway, we find that the diversity of a key sensory parameter, the response sensitivity, is modulated depending on the presence or absence of ambient chemoattractant molecules. | Session 31: Microbiological Physics |
| 501 | Flow-induced symmetry breaking in growing bacterial biofilms | Pearce, Philip; Song, Boya; Skinner, Dominic; Mok, Rachel; Hartmann, Raimo; Singh, Praveen; Jeckel, Hannah; Oishi, Jeffrey; Drescher, Knut; Dunkel, Jörn | 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 31: Microbiological Physics |
| 502 | Resource allocation model for bacterial shape control under growth perturbations | Serbanescu, Diana; Ojkic, Nikola; Banerjee, Shiladitya | Here we propose a coarse-grained theory for how bacteria allocate their molecular resources to regulate their cell shapes and growth rates in varying nutrient environments and antibiotic induced perturbations. | Session 31: Microbiological Physics |
| 503 | Multi-scale dynamical description Gram-negative bacterial responses to antibiotics towards drug resistance | Manrique, Pedro; Ganguly, Kumkum; Gnanakaran, S | Here we propose a dynamical model that integrates these scales in the context of bacterial survival and efficacy of drugs. | Session 31: Microbiological Physics |
| 504 | A Facile Accelerated Specific Therapeutic (FAST) Platform that Reverses Carbapenem Resistance in Multi-Drug Resistant E. coli | Aunins, Thomas; Erickson, Keesha; Chatterjee, Anushree | Here, we show that the Facile Accelerated Specific Therapeutic (FAST) platform can use transcriptomic data for the rapid (<1 week) design, synthesis, and testing of antisense inhibitors that are able to re-sensitize a strain of MDR E. coli to carbapenem treatment. | Session 31: Microbiological Physics |
| 505 | A Comparative Analysis of Various Cas Proteins in CRISPRi Gene Circuits | Kreindler, Lior; Lambert, Guillaume | A Comparative Analysis of Various Cas Proteins in CRISPRi Gene Circuits | Session 31: Microbiological Physics |
| 506 | Tuning programmable CRISPR-based toggle switches with buffer sites in Escherichia coli | Xu, Yasu; Lambert, Guillaume | Later, adding a second plasmid that shares the same target as the TS and competes with TS for dCas pool, we can tune the efficiency of each NOT gate via manipulating the number of buffers, and thus the performance of TS. | Session 31: Microbiological Physics |
| 507 | Development of non-linear gradient microfluidic devices | Amarie, Dragos; Harden, Ileene; Diaz, Arturo; Waters, Elijah; Stupack, Dwayne | In this work we present microfluidic devices that generates non-linear chemical gradients. | Session 31: Microbiological Physics |
| 508 | Acoustic Micromotors for Cellular Manipulation | McNeill, Jeffrey; Maaddi, Austin; Das, Sambeeta | Here, we demonstrate the use of acoustically powered micromotors steered by an applied magnetic field for mammalian cell rotation and manipulation. | Session 31: Microbiological Physics |
| 509 | The biophysics of cellular counting — uncovering how viral copy number drives cell-fate decision | Coleman, Seth; Yao, Tianyou; Nguyen, Thu Vu Phuc; Igoshin, Oleg; Golding, Ido | We find that the expression of essential genes in the decision network exhibits power-law scaling with MOI. | Session 31: Microbiological Physics |
| 510 | The role of physical forces in cortical morphogenesis | Holland, Maria | We now consider the more complex, fully three-dimensional pattern of cortical thickness in the brain, and investigate the role of physical forces in its evolution, consistency, and variability. | Session 32: Morphogenesis |
| 511 | New directions for the animal shape analysis | Alba, Vasyl; Carthew, Jamie; Mani, Madhav; CARTHEW, RICHARD | We used a new precise tool to address a question of quantitative description of the morphological traits in biological systems. | Session 32: Morphogenesis |
| 512 | Surface Stresses Drive Morphological Changes in Three-Dimensional Microtissues | Mailand, Erik; Li, Bin; Eyckmans, Jeroen; Bouklas, Nikolaos; Sakar, Mahmut Selman | We developed a high-throughput biomimetic platform for the study of morphogenesis in multilayered 3D microtissues. | Session 32: Morphogenesis |
| 513 | Mechanoregulation of Valvular Morphogenesis | Butcher, Jonathan | Recent studies from our group and others have highlighted that the local mechanical environment within the fetal heart are essential mediators of proper, and when perturbed defective, valvular growth and maturation. | Session 32: Morphogenesis |
| 514 | Organ Size Coordination by Chemical Signaling | Damavandi, Ojan; Lubensky, David | Inspired by this example, we model noisy growth of bilaterally symmetric organs and investigate different mechanisms of organ size coordination using a single coordination signal secreted by the organs. | Session 32: Morphogenesis |
| 515 | Generating Cell Fate Patterns via Mechanical Stress in Stem Cell Colonies | Nunley, Hayden; Xue, Xufeng; Fu, Jianping; Lubensky, David | We propose a mechanical model for neural induction in which cell fate determines active contractility and in which mechanical stress biases cell fate. | Session 32: Morphogenesis |
| 516 | How can proteins take derivatives? | Wigbers, Manon; Tan, Tzer Han; Brauns, Fridtjof; Hermann, Tobias; Fakhri, Nikta; Frey, Erwin | To analyze how the interplay of diffusion and protein interactions on a nanometer scale influence the protein patterns on the cellular scale, the framework of reaction-diffusion models has proven useful. | Session 32: Morphogenesis |
| 517 | Hierarchical “buckling without bending” and brain shape | Schwarz, Jennifer; Gandikota, Mahesh Chandrasekhar; Engstrom, Tyler; Zhang, Teng | This model is now generalized beyond the onset of shape change to predict shape development at later stages. | Session 32: Morphogenesis |
| 518 | Mechanomorphogenesis of bacterial biofilms | Yan, Jing | Here, using Vibrio cholerae as our model system, we combine mechanical measurements, theory and simulation, quantitative image analyses, surface energy characterizations, and mutagenesis to show that mechanical instabilities, including wrinkling and delamination, underlie the morphogenesis program of growing biofilms. | Session 32: Morphogenesis |
| 519 | Quantifying mechanochemical coupling in the actomyosin cortex during early development in vivo | Tekant, Melis; Bacanu, Alexandru; Jung, Yoon; Dunkel, Jorn; Fakhri, Nikta | We generate various Rho-GTP dynamic patterns and map the resulting stress patterns via tracking endogenous tracer particles embedded in the cell cortex. | Session 32: Morphogenesis |
| 520 | The role of environment, material, and function in the morphological diversity of termite mounds | Fagundes, Tadeu; Ordonez, Juan; Yaghoobian, Neda | To explain this diversity, the present work introduces a computational model that couples the mound’s environment, material, and thermal function to its shape. | Session 32: Morphogenesis |
| 521 | Investigation into the dynamics of lipid membrane remodeling | Sharma, Abhimanyu; Nguyen, Henry; Talledge, Nathaniel; McCullough, John; Moss III, Frank; Iwasa, Janet; Vershinin, Michael; Sundquist, Wesley; Frost, Adam | We have used an in vitro GUV system, and investigated the details of membrane reshaping under local mechanical load and in several ESCRT protein backgrounds. | Session 33: Morphogenesis, Tissues, and Cancer |
| 522 | Investigating cell shape changes during organogenesis using a 3D vertex model | Sanematsu, Paula; Erdemci-Tandogan, Gonca; Merkel, Matthias; Amack, Jeffrey; Manning, M. Lisa | Since the KV is inherently 3D, and that 2D and 3D drag forces can be very different, we extend that work by studying drag forces on the KV in a 3D model. | Session 33: Morphogenesis, Tissues, and Cancer |
| 523 | Patterning-Mechanics Feedback Mechanism to Understand Axis Extension during Morphogenesis | Anbari, Samira; Buceta Fernandez, Javier | Here we propose a mechanism of tissue elongation that couples the mechanical properties of cells with the concept of positional information to modulate the former in a location-dependent manner. | Session 33: Morphogenesis, Tissues, and Cancer |
| 524 | Morphogenesis and fractal dimension of bacterial pellicles | Qin, Boyang; Wingreen, Ned; Bassler, Bonnie; Stone, Howard | Here, using a home-made adaptive stereoscope instrument and fluorescent microscopy, we identify a series of mechanical and architectural transitions in Vibrio cholerae pellicles at a liquid-oil interface. | Session 33: Morphogenesis, Tissues, and Cancer |
| 525 | Learning about human development from clinical IVF data | Leahy, Brian; Yang, Helen; Jang, Won-dong; Ben-Yosef, Dalit; Manoharan, Vinothan; Needleman, Daniel | Here, we examine tens of thousands of videos of human embryos recorded during routine clinical IVF procedures. | Session 33: Morphogenesis, Tissues, and Cancer |
| 526 | Emergence of helical growth and morphogenesis in fungal cells from cell wall dynamics | Lalitha Sridhar, Shankar; Lostec, Guillaume; Ortega, Joseph; Vernerey, Franck | In this talk, we will present a novel approach based in statistical mechanics to model the organization and dynamics of microfibrils and tethers in the cell wall of to help explain this phenomenon . | Session 33: Morphogenesis, Tissues, and Cancer |
| 527 | Understanding cell contact constriction in epithelial morphogenesis through data driven reverse-time inference | Lenner, Nicolas; Kong, Deqing; Eule, Stephan; Großhans, Jörg; Wolf, Fred | We here show how our mathematically novel approach of reverse time ensemble inference allows to infer the process of junction shrinkage in reverse time, starting from the endpoint of the dynamic, i.e. the 4-vertex. | Session 33: Morphogenesis, Tissues, and Cancer |
| 528 | Experiments and modeling of “irreversible” brain torsion in early chick embryos | Chen, Zi; Zhang, Hao; Wan, Guangchao; Zeng, Wei; Grover, Hannah; Huang, Shicheng | A computational model is employed to help interpret the findings, in particular the path-dependent, "irreversible" shape evolution. | Session 33: Morphogenesis, Tissues, and Cancer |
| 529 | Dynamics of a single cell fate decision | Freedman, Simon; Johnson, Kristin; LaBonne, Carole; Mani, Madhav | To elucidate these dynamics, we performed bulk RNA sequencing at multiple time points during a single cell fate decision in which pluripotent Xenopus laevis (African frog) cells differentiate to one of two fates: neural progenitor and epidermis. | Session 33: Morphogenesis, Tissues, and Cancer |
| 530 | Binary establishment and maintenance of discrete cell fates in development | Zhao, Jiaxi; Bothma, Jacques; Norstad, Matthew; 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 33: Morphogenesis, Tissues, and Cancer |
| 531 | A variational principle for power dissipation in low frequency conduction in biological tissues. | Solis, Francisco; Jadhao, Vikram | Models for propagation of these signals usually consider tissues as purely conductive materials. | Session 33: Morphogenesis, Tissues, and Cancer |
| 532 | A biophysical model uncovers the size distribution of migrating cell clusters across cancer types | Bocci, Federico; Jolly, Mohit Kumar; Onuchic, Jose | We present a biophysical model that couples intra-tumoral heterogeneity enabled by the epithelial-mesenchymal transition (EMT) with cell migration to explain the modes of individual and collective cancer cell migration. | Session 33: Morphogenesis, Tissues, and Cancer |
| 533 | 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 33: Morphogenesis, Tissues, and Cancer |
| 534 | Computationally tractable mechanistic model of inhomogeneous — anisotropic drug diffusion and tumor ablation | 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 33: Morphogenesis, Tissues, and Cancer |
| 535 | A possible role for epigenetic feedback regulation in the dynamics of the epithelial–mesenchymal transition (EMT) | Jia, Wen; Deshmukh, Abhijeet; Mani, Sendurai; Jolly, Mohit Kumar; Levine, Herbert | Here, we analyzed the effects of epigenetic feedback on EMT through integrating this feedback on various aspects of the miR-200/ZEB loop – a core circuit regulating EMT. | Session 33: Morphogenesis, Tissues, and Cancer |
| 536 | Development and Application of Three-Dimensional Multi-Resolution Imaging | Yang, Haw | In this presentation, we explain how a multi-resolution approach helps to elucidate dynamics in complex systems. | Session 34: Multimodal Optical Trapping/Microscopy/Spectroscopy of Living Matter |
| 537 | Avalanching Upconverting Nanoparticles for Super Resolution Imaging | Xu, Emma; Lee, Changhwan; Yao, Kaiyuan; Cohen, Bruce; Chan, Emory; Suh, Yung Doug; Schuck, P. James | Here, we introduce avalanching upconverting nanoparticles (AUCNPs), NaYF4 nanocrystals doped with Thulium ions. | Session 34: Multimodal Optical Trapping/Microscopy/Spectroscopy of Living Matter |
| 538 | Mechanical unzipping of DNA molecules in parallel using nanophotonic tweezers | Ye, Fan; Inman, James; Wang, Michelle | Here, we present an nSWAT that achieves manipulation forces large enough to mechanically unzip an array of DNA molecules at room temperature. | Session 34: Multimodal Optical Trapping/Microscopy/Spectroscopy of Living Matter |
| 539 | A Simple Approach to Optical Trapping Analysis | Hasbun, Javier; Howard, James; Patterson-Goss, Zachary; Tripathy, Suvranta | We have developed a simplified model of an optically trapped micron-sized particle using a modified version of a numerical approach [2]. | Session 34: Multimodal Optical Trapping/Microscopy/Spectroscopy of Living Matter |
| 540 | Bacterial proteomes are predictable from cellular Raman spectra | Kamei, Ken-ichiro; Kobayashi-Kirschvink, Koseki; Nakaoka, Hidenori; Wakamoto, Yuichi | Using quantitative proteome data of E. coli cultured under various conditions (Schmidt et al., Nature Biotechnology, 2016), we show that proteomes can be linked to and reconstructed from cellular Raman spectra. | Session 34: Multimodal Optical Trapping/Microscopy/Spectroscopy of Living Matter |
| 541 | 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 2-photon microscope to measure realtime gene activity in early fly embryos. | Session 34: Multimodal Optical Trapping/Microscopy/Spectroscopy of Living Matter |
| 542 | The Origin of Enhanced Enzyme Motility Probed with Optical Tweezers | Huang, Tian; Park, Jin Tae; Pak, Hyuk Kyu; Granick, Steve | In this talk, we will discuss our effort to measure these forces by using optical tweezers. | Session 34: Multimodal Optical Trapping/Microscopy/Spectroscopy of Living Matter |
| 543 | Multimodal microscopy through optimal integration of wide-field and focused-beam laser illumination | Lee, Sang-Hyuk | In this talk, I will describe the design of the instrument and its application to the multimodal imaging and spectroscopy of biological systems. | Session 34: Multimodal Optical Trapping/Microscopy/Spectroscopy of Living Matter |
| 544 | Near-field optical interferometer for refractive index sensing | Ghaffari, Abbas; Do, Kevin; Riehn, Robert | Here we introduce a near-field optical interferometer that detects the presence of nanoparticles and proteins by measuring the deflection of a light, and not transmission as commonly performed. | Session 34: Multimodal Optical Trapping/Microscopy/Spectroscopy of Living Matter |
| 545 | 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 might be a useful general metric to describe fluctuations in nonequilibrium steady states. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 546 | Critical Dynamics of Anisotropic Antiferromagnets in an External Field | Tauber, Uwe; Nandi, Riya | We numerically investigate the non-equilibrium critical dynamics in three-dimensionalanisotropic antiferromagnetsin the presence of an external magnetic field. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 547 | Current fluctuations in presence of time-periodic metabolic conditions | Forastiere, Danilo; Falasco, Gianmaria; Esposito, Massimiliano | We show that there exist different regimes, depending on the kinetic rates, in which positive and negative amplitude resonant effects take place, and we provide interpretations for the role that these nonequilibrium effects can play in the metabolic network. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 548 | Large scale kinetic modeling of metabolic networks | CHEN, Yong-Cong; Zhu, Xiaomei; Ao, Ping; Xu, Minjuan | Large scale kinetic modeling of metabolic networks | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 549 | Temperature interfaces in the Katz-Lebowitz-Spohn driven lattice gas | Mukhamadiarov, Ruslan; ., Priyanka; Tauber, Uwe | We explore the intriguing spatial patterns that emerge in a two-temperature Katz-Lebowitz-Spohn (KLS) model in two dimensions, a driven lattice gas with attractive nearest-neighbor interactions and periodic boundary conditions.The domain is split into two regions with hopping rates governed by different temperatures T > Tc and Tc, respectively, where Tc indicates the critical temperature for phase ordering. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 550 | Anomalous heating in a colloidal system: Observation of the inverse Mpemba effect | Kumar, Avinash; Bechhoefer, John | We present the first experimental observation of anomalous heating in colloidal systems, a phenomenon known as the inverse Mpemba effect. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 551 | Decomposition of anomalous diffusion in generalized Lévy walks into its constitutive effects | Adlakha, Vidushi; Meyer, Philipp; Aghion, Erez; Kantz, Holger; Bassler, Kevin | We show that the anomalous diffusive behavior found in these systems can be decomposed into three fundamental constitutive causes. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 552 | A coupled two-species model for the pair contact process with diffusion | Deng, Shengfeng; Tauber, Uwe | We introduce a coarse-grained two-species representation for the PCPD in which single particles B and particle pairs A are coupled according to the processes 2 B→ A, A→ A+ B, A→0, A→2 B, with each type of particles diffusing independently. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 553 | Anomalous Diffusion with an Absorbing Wall | Warhover, Alex; Vojta, Thomas | We employ large scale Monte Carlo simulations to investigate these models in the presence of an absorbing wall. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 554 | Diffusion in dynamic crowded spaces | Yllanes, David; Bendekgey, Harry; Huber, Greg; Yan, Le | Here we propose an extension of commonly used "Swiss-cheese" models to include moving obstacles and study it with numerical simulations in one, two and three dimensions. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 555 | Trajectories and transport characteristics of a Brownian particle in a 1D potential subject to bias. | Jiron, Trey; Schiffbauer, Jarrod | We investigate one-dimensional driven, diffusive motion of a single Brownian particle moving through a periodic lattice potential and subject to a constant, uniform bias using a Langevin equation of motion. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 556 | Fluctuation theorem for geometric pumping processes | Hayakawa, Hisao | We derive an extended fluctuation theorem for an open quantum system coupled with two reservoirs under one-cycle modulation. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 557 | Stochastic Line Integrals as Metrics of Irreversibility and Heat Transfer | Teitsworth, Stephen; Neu, John | In this talk, we provide a framework for understanding general properties of stochastic line integrals and clarify their implementation for experiments and simulations as well as their utility as metrics for quantifying non-equilibrium behavior. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 558 | Minimal Model for Intermittent Dynamics and "Turbulence" in Many-Body Systems | Gogia, Guram; Yu, Wentao; Burton, Justin | Inspired by our previous experimental findings [1], here we present computational results for a particle-based system that exhibits intermittent switching between two distinct phases. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 559 | Stochastic transitions between phase-locked steady states in RF-irradiated graphene Josephson junctions | Larson, Trevyn; Zhao, Lingfei; Arnault, Ethan; Wei, Ming-Tso; Seredinski, Andrew; Li, Hengming; Watanabe, Kenji; Taniguchi, Takashi; Amet, Francois; Finkelstein, Gleb | We investigate the Shapiro steps in a graphene-based Josephson junction with large gap MoRe leads. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 560 | Understanding Stochastic Dynamics in Classical and Quantum Metastable Condensed Matter Systems | Spagnolo, Bernardo | We obtain: (i) exact analytical results of the residence time in the presence of Lévy flights in unstable potential profile, and noise enhanced stability phenomenon is observed in the system investigated and in JJs. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 561 | Anomalous Phase Dynamics of Driven Graphene Josephson Junctions | Kalantre, Sandesh; Yu, Fan; Wei, Ming-Tso; Watanabe, Kenji; Taniguchi, Takashi; Hernandez-Rivera, MIguel; Amet, Francois; Williams, James | In this work, we report on DC and AC Josephson effect of high-mobility, hexagonal boron nitride encapsulated graphene Josephson junctions. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 562 | A theoretical model for ionic transport in a viscosity gradient | Stein, Derek; Wiener, Benjamin | We present an explanation based on the Maxwell-Stefan (MS) theory of diffusion. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 563 | Pulling cargo increases the precision of molecular motor progress | Brown, Aidan; Sivak, David | We find that the widely used "constant-force" approximation for the effect of cargo on motor dynamics leads to a much larger variance of motor step number compared to explicitly modeling diffusive cargo, suggesting the constant-force approximation may be misapplied in some cases. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 564 | Spectral method for estimating entropy production rates in spatially extended systems | Seara, Daniel; Machta, Benjamin; Murrell, Michael | We present a generic method for estimating entropy production rates from stochastic time series data for both random variables and fields while providing insight into the dissipative processes underlying their dynamics. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 565 | Learning the Non-Equilibrium Dynamics of Brownian Movies | Gnesotto, Federico; Gradziuk, Grzegorz; Ronceray, Pierre; Broedersz, Chase | In this talk, we present a new approach that does not rely on the tracking of probes in the system. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 566 | Spectral decomposition of irreversibility reveals structure of nonequilibrium activity in biological systems | Bacanu, Alexandru; Pelletier, James; Jung, Yoon; Horowitz, Jordan; Fakhri, Nikta | Using normal mode decomposition of filament shape fluctuations, we infer the structure of the actomyosin-driven mechanical fluctuations. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 567 | Noisy driven oscillators: Adaptive drives break the fluctuation-dissipation theorem | Sheth, Janaki; Levine, Alex; Bozovic, Dolores | We explore the fluctuations and response functions of intrinsically noisy limit-cycle oscillators starting with models of stereocilium dynamics in the inner ear. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 568 | A generalized theory of interactions for complex multiscale stochastic systems with thermodynamic irreversibility | Núñez-Corrales, Santiago; Jakobsson, Eric | We present ongoing work towards a novel mathematical physics development that aims to capture statistical mechanical properties of complex multiscale stochastic systems driven by irreversible thermodynamics, a generalized theory of interactions (GToI) with a purely relational view in which interactions are fundamental entities, while objects and laws are derived. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 569 | Non-equilibrium response of a strongly coupled rotary motor | Lathouwers, Emma; Lucero, Joseph; Sivak, David | Using a simple model of FoF1-ATP synthase (the primary motor for ATP synthesis), we investigate the interplay between non-equilibrium driving forces, natural equilibrium fluctuations, and interactions between the strongly coupled subsystems of this ingenious rotary machine. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 570 | Stochastic Dynamics and Selection in the One Dimensional Stabilized Kuramoto-Sivashinsky Equation | Saxena, Saloni; Kosterlitz, John | We study coarsening dynamics in the stabilized Kuramoto-Sivashinsky (SKS) equation in one dimension, with and without noise. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 571 | Maxwell’s demons with finite size and response time | Rupprecht, Nathaniel; Vural, Dervis | Here, we focus on its rate of operation. | Session 35: Noise-Driven Dynamics in Far-From-Equilibrium Systems |
| 572 | Mechanics and Elasticity of dynamic cellular monolayers – How Volvox embryos turn inside-out | Hoehn, Stephanie; Haas, Pierre; Goldstein, Raymond | Mechanics and Elasticity of dynamic cellular monolayers – How Volvox embryos turn inside-out | Session 36: Non-Linear Deformations in Biology |
| 573 | A bilayer model of the non-linear elastodynamics of Hydra mouth opening | Goel, Tapan; Tran, Cassidy; Adams, Ellen; Diamond, Patrick; Collins, Eva-Maria | We compare the kinematics generated by radially travelling contraction pulses with that for simultaneous contractions at all radii. | Session 36: Non-Linear Deformations in Biology |
| 574 | Investigation of Rice Root Tip Circumnutation Functions in Heterogeneous Environments | McCaskey, Erin; Taylor, Isaiah; Lehner, Kevin; Benfey, Philip; Goldman, Daniel | In this work we used a clear gel-based media to create a growth environment of two gel layers with varying stiffness, which can model soil horizons with varying compaction. | Session 36: Non-Linear Deformations in Biology |
| 575 | Mechanics of behavior: Comprehensive search behavior encoded in cytoskeletal dynamics of single cell Lacrymaria olor | Flaum, Eliott; Krishnamurthy, Deepak; Coyle, Scott; Prakash, Manu | Our work combines theoretical active filament models with experimental data to unravel how active mechanics leads to emergent behavior in single cells. | Session 36: Non-Linear Deformations in Biology |
| 576 | Functional consequences of microscopic skin features on snake locomotion | Rieser, Jennifer; Li, Tai-De; 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 36: Non-Linear Deformations in Biology |
| 577 | Bioelectrical signaling via domain wall migration | McNamara, Harold; Salegame, Rajath; Al Tanoury, Ziad; Xu, Haitan; Begum, Shahinoor; Ortiz, Gloria; Pourquie, Olivier; Cohen, Adam | Here we show theoretically and experimentally that homogeneous or nearly homogeneous tissues can undergo spontaneous spatial symmetry breaking into domains with different resting potentials, separated by stable bioelectrical domain walls. | Session 36: Non-Linear Deformations in Biology |
| 578 | Modeling the Mechanosensitivity of Crawling Cells | Molina, John; Yamamoto, Ryoichi | In this work, we study the ability of cells to probe and dynamically adapt to the mechanical properties of their surroundings, i.e., their mechanosensitivity. | Session 36: Non-Linear Deformations in Biology |
| 579 | Geometry, Elasticity, Growth: The Connection Between Cowrie Growth Dynamics and Shell Form | Levy, Michael; DeWeese, Michael | We propose a new model illustrating how the physics of bending and wrinkling sheets could underlie the geometry of Cowrie Seashells, offering both qualitative and quantitative insights. | Session 36: Non-Linear Deformations in Biology |
| 580 | Theoretical tool bridging cell polarities with development of robust morphologies | Nissen, Silas Boye; Rønhild, Steven; Trusina, Ala; Sneppen, Kim | Inspired by the progressive role of apical-basal and planar cell polarity in development, we propose that stability, complexity, and diversity are emergent properties in populations of proliferating polarized cells. | Session 36: Non-Linear Deformations in Biology |
| 581 | Spatiotemporal dynamics in synthetic microbial consortia | Bennett, Matthew | In this talk I will discuss how spatiotemporal coordination of gene expression can be achieved even when the spatial extent of the consortium is much greater than the diffusion distance of the signaling molecules. | Session 37: Physics in Synthetic Biology |
| 582 | Synthetic genetic circuits using plant protoplasts | Kiwimagi, Katherine; Antunes, Mauricio; Xu, Wenlong; Kassaw, Tessema; Zalewski, Christopher; Medford, June; Prasad, Ashok | With the help of a mathematical model coupled with stochastic simulations, we were successful in explaining and normalizing the batch effects to make quantitative comparisons between different inducible repressors, and approximately predict quantitative properties of synthetic circuits in stably transformed plants. | Session 37: Physics in Synthetic Biology |
| 583 | Construction and Characterization of a Tunable Plasmid Copy Number System | Rouches, Miles; Lambert, Guillaume | Through randomized mutagenesis of the promoters controlling these RNAs, we have created a library of over 1000 plasmids with copy numbers spanning a range greater than 2 orders of magnitude, allowing plasmid copy number to be used as a tunable parameter in several systems. | Session 37: Physics in Synthetic Biology |
| 584 | Engineering Transcriptional Interference for Genetic Logic Gates | O’Connor, Nolan; Escalas Bordoy, Antoni; Chatterjee, Anushree | Here, we show that rationally controlling RNAP traffic on DNA through TI can lead to diverse gene expression profiles and facilitate the construction of TI-based logic gates. | Session 37: Physics in Synthetic Biology |
| 585 | Multicellular Drug Resistance from Synthetic Mitosis Control in Budding Yeast | Romanyshyn, Oleksandra; Balazsi, Gabor | By deleting the AMN1 (antagonist of mitotic exit network) gene from multicellular S. cerevisiae, we obtained a drug-sensitive unicellular yeast strain. | Session 37: Physics in Synthetic Biology |
| 586 | FAST, Smart Therapeutics | Chatterjee, Anushree | In this talk, I will describe multi-pronged systems, synthetic biology, and nano-biotechnology based approaches being devised in our lab to rationally engineer therapeutics that can overcome antimicrobial resistance. | Session 37: Physics in Synthetic Biology |
| 587 | The effect of time-dependent drive and delayed feedback loop in two-dimensional gene regulatory network | KAITY, BIVASH; SARKAR, RATAN; Mitra, Mithun; Chakrabarti, Buddhapriya | In the present work, we propose a theoretical model based on a two-gene regulatory motif to investigate the role of time delay in the regulation of gene expression level. | Session 37: Physics in Synthetic Biology |
| 588 | Synthetic gene circuits enable quantitative comparison of proteosynthesis rates in mammalian cells | Wan, Yiming; Cohen, Joseph; Smashnov, Alex; Balazsi, Gabor | Here, we establish a synthetic biological framework to enable such comparisons. | Session 37: Physics in Synthetic Biology |
| 589 | Synthetic Gene Circuits Reveal how KRAS(G12V) Affects Cell Proliferation & Migration Patterns | Guinn, Tyler; Coraci, Damiano; Ledalla, Karthik; Balazsi, Gabor | Here we present results from perturbing the levels of proto-oncogene KRAS(G12V). | Session 37: Physics in Synthetic Biology |
| 590 | Improved CRISPRi gene circuit function via 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 37: Physics in Synthetic Biology |
| 591 | Uncovering thermodynamic determinants of CRISPR-Cas gene circuit design. | Lambert, Guillaume; Specht, David; Xu, Yasu | To better evaluate the impact of mismatches on DNA target recognition and binding, we develop a massively parallel CRISPR interference assay to measure the binding energy between tens of thousands of CRISPR RNA and target DNA sequences. | Session 37: Physics in Synthetic Biology |
| 592 | Strategies transcription factors use to gain access to nucleosomal DNA | Poirier, Michael | I will discuss proposed strategies for how transcription factors bind to their sites within compact chromatin, and the differences between activating and pioneering transcription factors. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 593 | Theory and modeling of active nucleosome repositioning | Jiang, Zhongling; Zhang, Bin | For remodeling enzymes, we use a perturbation theory to show that the effect of these enzymes can be well approximated by effective equilibrium models with rescaled temperatures and interactions. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 594 | 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 38: Physics of Genome Organization: From DNA to Chromatin: |
| 595 | Knot dynamics of a DNA strand pushed inside a nanochannel | Rothörl, Jan; Virnau, Peter; Bhattacharya, Aniket | We investigate knot formation for a model DNA polymer pushed inside a square nanochannel whose width is much shorter compared to the contour length of the chain using Brownian dynamics simulation. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 596 | Error-speed correlations in biopolymer synthesis | Pigolotti, Simone; Chiuchiu, Davide; Tu, Yuhai | We study fluctuations of error and speed in biopolymer synthesis and show that they are in general correlated. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 597 | 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 38: Physics of Genome Organization: From DNA to Chromatin: |
| 598 | A Mechanochemical Model of Transcriptional Bursting | Klindziuk, Alena; Meadowcroft, Billie; Kolomeisky, Anatoly | Stimulated by these observations, we developed a stochastic mechano-chemical model of supercoiling-induced transcriptional bursting. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 599 | Field theoretic methods applied to epigenetic models | Sood, Amogh; Zhang, Bin | We introduced a (0+1)-dimensional kinetic model, wherein modified nucleosomes recruit enzymes that similarly modify neighbouring nucleosomes, to investigate the stability and heritability of the states. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 600 | Pulling a DNA through a Double-Nanopore system: A Brownian Dynamics Study | Smucz, Peter; Seth, Swarnadeep; Bhattacharya, Aniket | We study translocation of a model DNA polymer captured in a double nanopore (DNP) system using Brownian dynamics (BD). | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 601 | Loop extrusion in chromatin: A question of time! | Maji, Ajoy; Padinhateeri, Ranjith; Mitra, Mithun | We propose a simple physical answer to this puzzle and show how a naive obstacle view of nucleosomes can be misleading. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 602 | 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 38: Physics of Genome Organization: From DNA to Chromatin: |
| 603 | Extracting the degree of order in the bacterial chromosome using statistical physics | Messelink, Joris; Janssen, Jacqueline; van Teeseling, Muriel; Thanbichler, Martin; Broedersz, Chase | To investigate this, we develop a maximum entropy approach to extract the three-dimensional structure of the bacterial chromosome from such data. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 604 | Direct Quantification of Gene Regulation by Transcription-Factor Binding at an Endogenous Gene Locus | Wang, Jingyao; Dong, Yijing; Bao, Huihan; Yao, Xintao; Sokac, Anna; Golding, Ido; Xu, Heng | Using stochastic theoretical analysis, we show that TF binding follows nonequilibrium multi-state kinetics, breaking the law of mass action. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 605 | On the Border of Order: Chromosomal Organization in Space and Time | Zhang, Yaojun; Khanna, Nimish; Lucas, Joseph; Murre, Cornelis; Dudko, Olga | We address these questions in the context of adaptive immunity – the system that enables the individual to respond to a great variety of pathogens through a diverse repertoire of antibodies. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 606 | A “Tug-of-War” in a three dimensional Double-Nanopore system | Seth, Swarnadeep; Bhattacharya, Aniket | We simulate a model system in three dimensions and use Brownian dynamics to reveal the details of the single file translocation. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 607 | Studies of nucleosome-decorated DNA structures and deformations using a new analytical model | Sabok-Sayr, Seyed Ahmad; Olson, Wilma | We introduce a new analytical treatment of nucleosome-decorated DNA which is made up of three essential parts: nucleosomal DNA; protein-free stretches of DNA; and the intervening connectors. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 608 | Long-lived memory and dynamics of liquefied chromatin | Banigan, Edward; Belaghzal, Houda; Borrman, Tyler; Dekker, Job; Mirny, Leonid | In a heteropolymer simulation model, we find that strong interactions between inactive chromatin segments can lead to slow melting of inactive compartments, as in experiments. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 609 | The Dynamic Archaeal Chromatin “Slinky” | Bowerman, Samuel | Here, we utilize molecular dynamics simulations, cryoEM, and analytical ultracentrifugation to study the inherent dynamics of these putative chromatin slinkies. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 610 | 5-methyl-cytosine binding proteins loop DNA under nanoconfinement | Liu, Ming; Williams, David; Wang, Hong; Riehn, Robert | By using atomic force microscopy (AFM), we determined that the likely mechanism for compaction by MeCP2 is the formation of bridges between distant DNA stretches and the formation of loops. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 611 | Nuclear chromatin patterns: modeling dynamics of intra-chromatin interactions and its impact on structure organization | Laghmach, Rabia; Di Pierro, Michele; Potoyan, Davit | Here, we introduce a mesoscale liquid model of nucleus (MELON) that incorporates dynamic of interactions between A-B-C chromatin compartments of the nucleus, as well as the affinity between constitutive heterochromatin and Lamina at the nuclear envelope and nucleus deformation. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 612 | Long-distance group dynamics of RNA polymerases via DNA supercoiling | Kim, Sangjin | Here, we provide in vitro and in vivo evidence for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances (>2 kb) through transcription-induced DNA supercoiling. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 613 | Interplay of chromatin self-adhesion and lengthwise compaction on interchromosomal organization | Brahmachari, Sumitabha; Contessoto, Vinicius; Di Pierro, Michele; Onuchic, Jose | We use a coarse-grained polymer model for chromosomes where centromeres and telomeres are treated as polymer blocks featuring respective self-adhesion, and simulate multiple chromosomes in a confined volume. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 614 | A minimal model for correlated chromatin dynamics | Liu, Kuang; Patteson, Alison; Banigan, Edward; Schwarz, Jennifer | Therefore, we construct a minimal polymeric model to study the spatiotemporal properties of chromatin by simulating a Rouse chain with excluded volume interactions confined within a rigid, spherical shell that represents the lamina. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 615 | Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity | Le, Tung; Gao, Xiang; Park, Seong ha; Lee, Jaeyoon; Inman, James; Lee, Joyce; Killian, Jessica; Badman, Ryan; Berger, James; Wang, Michelle | By making direct torque measurements, we demonstrated that a single chromatin fiber (as would be located ahead of a replisome) is torsionally soft, while a braided chromatin fiber (as would be located behind the replisome) is relatively stiff. | Session 38: Physics of Genome Organization: From DNA to Chromatin: |
| 616 | A statistical-mechanics approach to microbiome data analysis | Marsland, Robert; Mehta, Pankaj | In this talk, I will draw on conceptual tools from statistical physics, which were designed to answer precisely these sorts of questions. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 617 | Quantifying multi-species bacterial interactions in larval zebrafish | Sundarraman, Deepika; Hay, Edouard; Martins, Dylan; Shields, Drew; Pettinari, Noah; Guillemin, Karen; Parthasarathy, Raghuveer | To address this, we consider commensal intestinal microbes in larval zebrafish, initially raised germ-free to allow introduction of controlled combinations of bacterial species. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 618 | Species covariance in C. elegans microbiome demonstrates existence of bacteria-bacteria and host-bacteria interactions | Martini, K. Michael; Taylor, Megan; Nemenman, Ilya; Vega, Nicole | Here we analyze a simplified community of bacteria in the gut of Caenorhabditis elegans, a roundworm. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 619 | Evidence for a multi-level trophic organization of the human gut microbiome | Wang, Tong; Goyal, Akshit; Dubinkina, Veronika; Maslov, Sergei | Here, using a simplified model, we provide quantitative support for a multi-level trophic organization of the human gut microbiome, where microbes consume and secrete metabolites in multiple iterative steps. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 620 | Regime shifts in a phage-bacterial ecosystem and strategies for its control | Maslov, Sergei; Sneppen, Kim | We propose and study a successful control strategy via short population pulses aimed at inducing the desired regime shifts. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 621 | Biophysical consequences of sublethal antibiotics on gut bacterial persistence and transmission | Schlomann, Brandon; Wiles, Travis; Wall, Elena; Guillemin, Karen; Parthasarathy, Raghuveer | A biophysical model, reminiscent of models of polymer growth and gelation, describes microbial dynamics and makes testable predictions of aggregation properties. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 622 | Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations | Hallinen, Kelsey; Karslake, Jason; Wood, Kevin | In this work, we show the dynamics of E. faecalis communities exposed to antibiotics can be surprisingly rich, as increasing population size or delaying drug exposure can promote population collapse. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 623 | Predicting microbial community metabolic function from genomic structure | Gowda, Karna; Ping, Derek; Troyer, Laura; Mani, Madhav; Kuehn, Seppe | We approach this prediction problem using denitrification as a model metabolic process. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 624 | Cross-feeding is not necessarily evolutionarily stable | Liu, Bo; Li, Zhiyuan; Wingreen, Ned | To address this question, we constructed a minimum metabolic model of cross-feeding, with trade-offs in enzyme allocation and reversible energy-producing reactions. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 625 | Percolation transition of pusher-type microswimmers | Schwarzendahl, Fabian Jan; Mazza, Marco | In this talk I will present the presence of a continuum percolation transition in model suspensions of pusher-type microswimmers. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 626 | Biphasic Chemotaxis of E. coli to the Microbiota Metabolite Indole | Yang, Jingyun; Chawla, Ravi; Rhee, Kathy; Gupta, Rachit; Manson, Michael; Jayaraman, Arul; Lele, Pushkar | I will discuss analytical models to explain these and other physiological responses to indole. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 627 | Dynamic motility selection drives population segregation in a bacterial swarm | Wu, Yilin; Zuo, Wenlong | Ecological models usually take growth rate fitness as the essential driver of population dynamics. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 628 | Continuum modeling of bacterial biofilm development | Fei, Chenyi; Alert, Ricard; Qin, Boyang; Bridges, Andrew; Bassler, Bonnie; Wingreen, Ned | To understand the role of mechanics in shaping the biofilm, we develop a multiphase continuum model of biofilm development. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 629 | E. coli Bacteria near "Black Hole" | Phan, Trung; Morris, Ryan; Black, Matthew; Lin, Ke-Chih; Bos, Julia; Austin, Robert | 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 39: Physics of Microbiomes and Bacterial Communities |
| 630 | Microbial communities governed by interplay of bacterial interaction and biofilm mechanics | Steinbach, Gabi; Siulung, Michael; Crisan, Cristian; Hammer, Brian; Yunker, Peter | Here, we show that mechanics and social interactions can be strongly interrelated and their combination can crucially impact biofilm formation and dynamics. | Session 39: Physics of Microbiomes and Bacterial Communities |
| 631 | Unifying criticality and the neutral theory of neural avalanches | Matin, Sakib; Tenzin, Thomas; Klein, W. | We study a model of the brain for which the dynamics are governed by neutral theory and find that the scale-free behavior is controlled by the proximity to a critical point. | Session 40: Physics of Neural Systems |
| 632 | Spontaneous spatial symmetry breaking in excitatory neuronal networks and its effects in sparsely connected networks. | Bibireata, Mihai; Slepukhin, Valentin; Levine, Alex | We explore the dynamics of the preBötzinger complex, the mammalian central pattern generator with N ∼ 10 3 neurons, which produces a collective metronomic signal that times the inspiration. | Session 40: Physics of Neural Systems |
| 633 | A model for oscillatory gating of information flow between neural circuits as a function of local recurrence | Khona, Mikail; fiete, Ila | We present a mechanistic neural model of communication, regulated by oscillations. | Session 40: Physics of Neural Systems |
| 634 | Quasicriticality or Criticality in the brain? | Fosque, Leandro; Beggs, John; Ortiz, Gerardo; Williams-Garcia, Rashid | Quasicriticality or Criticality in the brain? | Session 40: Physics of Neural Systems |
| 635 | Compression as a path to simpler models of collective neural activity | Ramirez, Luisa; Bialek, William | But making models that capture the behavior of these real neural networks easily leads to a combinatorial explosion of complexity and we need explicit strategies for simplification. | Session 40: Physics of Neural Systems |
| 636 | Effects of local excitations on large-scale brain network dynamics: Insights from coupled Wilson-Cowan oscillators under perturbative stimulation | Papadopoulos, Evangelia; Lynn, Christopher; Battaglia, Demian; Bassett, Danielle | By employing computational modeling, we examine how the impacts of excitations depend on the location of the perturbation, and, crucially, on the baseline state of the system. | Session 40: Physics of Neural Systems |
| 637 | Robust simplicity in the multimodal sensory control of insect flight. | Sponberg, Simon; Sharma, Varun | Using an agile hawk moth, Manduca sexta, tracking a robotic flower during foraging behavior we have shown that the underlying frequency response is linear, time invariant on the scale of 10’s of seconds, and relies on the linear superposition of vision and touch (via the moth’s long proboscis). | Session 40: Physics of Neural Systems |
| 638 | Scalable maximally informative dimensions analysis of deep neural networks | Kim, Jimmy; Schwab, David | Here, we present a method based on variational lower bounds of mutual information that allows for the efficient extraction of large number of informative dimensions. | Session 40: Physics of Neural Systems |
| 639 | Inferring structure-function relationships in neural networks from geometric features of their error landscapes | Fitzgerald, James; Biswas, Tirthabir | Here we introduce a geometric framework for calculating and analyzing connectivity constraints in nonlinear recurrent neural networks of rectified linear units. | Session 40: Physics of Neural Systems |
| 640 | An olfactory pattern generator for functional neural circuit analysis in Drosophila larva | Si, Guangwei; Baron, Jacob; Feng, Yu; Samuel, Aravinthan | Here, we present a stimuli method that project activity pattern directly onto the olfactory receptor neurons. | Session 40: Physics of Neural Systems |
| 641 | Sequential and efficient neural-population coding of complex task information | Koay, Sue Ann; Thiberge, Stephan; Brody, Carlos; Tank, David | We found that the neural encoding implied that correlated task variables were represented by uncorrelated modes in an information-coding subspace, which can in theory enable optimal decoding directions to be insensitive to neural noise levels. | Session 40: Physics of Neural Systems |
| 642 | Heterogeneity of timescales in random networks with bistable units | Istrate, Nicolae; Stern, Merav; Mazzucato, Luca | We provide a biophysical interpretation for the bistable units in our rate network in terms of Hebbian assemblies. | Session 40: Physics of Neural Systems |
| 643 | Recurrent Neural Networks Learn Simple Computations on Complex Time Series through Examples | Kim, Jason; Lu, Zhixin; Bassett, Danielle | Here, we explain how a neural network further learns the underlying computations performed on the observed outputs. | Session 40: Physics of Neural Systems |
| 644 | 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 | Here we report measurements of trophallaxis and face-to-face event durations of honeybees show that its distribution is heavy-tailed as in human face-to-face interactions. | Session 40: Physics of Neural Systems |
| 645 | Social inhibition maintains adaptivity and consensus of honey bees foraging in dynamic environments | Bidari, Subekshya; Kilpatrick, Zachary; Peleg, Orit | We address this problem in the context of honey bee colonies whose inhibitory social interactions promote adaptivity and consensus needed for effective foraging. | Session 40: Physics of Neural Systems |
| 646 | Is the endoplasmic reticulum an obstacle to intracellular diffusion? | Huber, Greg | We analyze diffusion on a surface with locally helicoidal topological dislocations, and use the results to argue that the Terasaki ramps facilitate an efficient transport of water-soluble molecules both within the lumen of the endoplasmic reticulum, and in the adjacent cytoplasmic space. | Session 41: Physics of Organelles |
| 647 | Dynamics of and on the endoplasmic reticulum | Weiss, Matthias; Speckner, Konstantin; Stadler, Lorenz | Using time-resolved imaging, we have analyzed the dynamics of ER junctions and of ERES domains as well as the self-organization of ERES on the ER network. | Session 41: Physics of Organelles |
| 648 | Fundamental limits to organelle biogenesis control in Saccharomyces cerevisiae | Panjtan Amiri, Kiandokht; Kalish, Asa; Mukherji, Shankar | In particular, our framework suggests that organelle size increases in random bursts from a limited pool of building blocks, which in turn imposes an asymmetry in optimal organelle number and size control. | Session 41: Physics of Organelles |
| 649 | Decoding the variance in intracellular organization of the undifferentiated hiPS cell | Viana, Matheus; Rafelski, Susanne | We are now applying these analyses to develop biophysical models of nuclear shape. | Session 41: Physics of Organelles |
| 650 | Modelling membrane-bound cellular organelles with non-equilibrium dynamics | Sens, Pierre; Vrel, Jean-Patrick; Vagne, Quentin | In this talk, I will discuss a conceptual model of organelle biogenesis and maintenance that include vesicular exchange (budding, transport, and fusion) and biochemical maturation, i.e. the change of identity of an organelle over time (early to late endosomes, cis to trans Golgi cisternae…). | Session 41: Physics of Organelles |
| 651 | The key differences in protein x-ray crystal and solution NMR structures | Treado, John; Mei, Zhe; Grigas, Alex; Levine, Zachary; Regan, Lynne; O’Hern, Corey | To address this important question, we compiled a dataset of paired high-resolution x-ray crystal structures and high-quality NMR structures to determine whether there are any systematic differences between the structures solved using the two experimental techniques. | Session 42: Physics of Protein Structure, Folding and Design |
| 652 | Decoy Detection of Computational Protein Designs | Grigas, Alex; Mei, Zhe; Treado, John; Levine, Zachary; Regan, Lynne; O’Hern, Corey | In this work, we apply this framework to the decoy detection problem and find that state-of-the-art protein predictions in the CASP11, 12 and 13 competitions often have core regions that are overpacked, due to overlapping residues. | Session 42: Physics of Protein Structure, Folding and Design |
| 653 | Low-Force Elasticity Reveals Complex Structure of an Intrinsically Disordered Protein | Truong, Hoang; Morgan, Ian; Saleh, Omar | Here, using a high-resolution single-molecule magnetic tweezer, we stretch a polypeptide construct derived from the neurofilament tail domains and study its conformations. | Session 42: Physics of Protein Structure, Folding and Design |
| 654 | ProSPr: Protein Structure Prediction via Interatomic Distances | Billings, Wendy; Hedelius, Bryce; Millecam, Todd; Wingate, David; Della Corte, Dennis | Here we present ProSPr, a network representing the first part of the AlphaFold pipeline for predicting interatomic distances, and demonstrate its abilities in the contact prediction task relative to other state-of-the-art methods. | Session 42: Physics of Protein Structure, Folding and Design |
| 655 | Landscapes, Nonlinearity, and Biomolecular Energy Redistribution | Elenewski, Justin; Velizhanin, Kirill; Zwolak, Michael | In this talk, I will discuss how topological features, nonlinearities, and energy landscape architecture can collude to define biomolecular heat propagation [1]. | Session 42: Physics of Protein Structure, Folding and Design |
| 656 | Understanding the native fluctuations of protein cores | Mei, Zhe; Treado, John; Levine, Zachary; Regan, Lynne; O’Hern, Corey | In this work, we carry out all-atom molecular dynamics simulations to study the fluctuating conformational dynamics of wildtype globular proteins, as well as mutants, in aqueous solvent at room temperature. | Session 42: Physics of Protein Structure, Folding and Design |
| 657 | Steric Equation of State for Monoclonal Antibodies from Low to High Concentrations | Shahfar, Hassan; Roberts, Christopher | Steric Equation of State for Monoclonal Antibodies from Low to High Concentrations | Session 42: Physics of Protein Structure, Folding and Design |
| 658 | Origins of Critical Phenomena in the Folding Phase Diagram of Proteins | Gasic, Andrei; Cheung, Margaret | Based on our theory, we show that the separation of T between the folding and collapse transition temperatures ( TF and T Θ, respectively) lead to a critical transition. | Session 42: Physics of Protein Structure, Folding and Design |
| 659 | Dissimilar ligands bind in a similar fashion: guiding the ligand binding mode prediction | Xu, Xianjin; Zou, Xiaoqin | In this study, a strategy was introduced for comparing the binding modes of ligands with different molecular structures for the first time. | Session 42: Physics of Protein Structure, Folding and Design |
| 660 | An escape rate analysis for pulling experiments based on energy landscapes in two reaction coordinates | Adhikari, Sudeep; Beach, Kevin | We present an analytical framework for the well escape rate in the context of an effective 2D landscape. | Session 42: Physics of Protein Structure, Folding and Design |
| 661 | Principles governing catalytic activity of self-assembled short peptides | Dong, Hao | In this work, the atomic structure of the aggregates was determined by using molecular modelling and further validated by solid-state NMR experiments, where the fibril with high activity adopts twisted parallel configuration within each layer, and the one with low activity is in flat antiparallel configuration [1]. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 662 | Representation of the Conformational Ensemble of Peptides in Coarse Grained Simulations | Sayar, Mehmet | We demonstrate here, that the structure/physics based approach used in the original parameterization of our CG model, strongly depends on the reference system chosen and excluded volume interactions. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 663 | Polarization of Intrinsically Disordered Proteins in the Presence of Charged Biopolymers: the Case of Tau Protein | Ruffin, Isabel; Aponte-Rivera, Christian; Rubinstein, Michael | We study tau protein conformations and polarization using molecular dynamics simulations. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 664 | Strategic incorporation of fluorinated prolines can lead to faster folding and stable proteins | Muralidharan, Ajay; Schmidt, JR; Yethiraj, Arun | In this work we use quantum chemistry and QM/MM methods coupled with accelerated sampling to study the static and dynamic properties of proline containing peptides in water, with a focus on the effect of fluorination on the free energy surface and conformational properties. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 665 | Low Temperature Protein Refolding Suggested by Molecular Simulation | Kozuch, Daniel; Stillinger, Frank; Debenedetti, Pablo | To investigate this question, we use molecular simulation to explore the behavior of a model protein, Trp-cage, as low as 70 K below the freezing point of the solvent. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 666 | van der Waals Forces in Biomolecular Systems: from Solvation to Long-range Interaction Mechanisms | Stoehr, Martin; Gori, Matteo; Kurian, Philip; Tkatchenko, Alexandre | Here, we employ the Many-Body Dispersion framework to investigate the vdW interaction in biomolecular systems and its spatial and spectral aspects. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 667 | The Assessment of MD Force Fields with Respect to Alanine Conformations in Aqueous Solutions | Zhang, Shuting; Schweitzer-Stenner, Reinhard; Urbanc, Brigita | The Assessment of MD Force Fields with Respect to Alanine Conformations in Aqueous Solutions | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 668 | Developing an explicit solvent model for protein aggregation | Luettmer-Strathmann, Jutta | In this work, we start from an off-lattice, mesoscale protein model with implicit solvent to develop an explicit solvent model that reproduces the equilibrium conformational and aggregation properties of the original model. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 669 | A kinetic analysis of local fluctuations in ubiquitin by combining the LE4PD normal modes and Markov state modeling | Beyerle, Eric; Guenza, Marina | Here, we model the fluctuation dynamics and kinetics of the protein ubiquitin using a coarse-grained description of the protein’s dynamics, the Langevin Equation for Protein Dynamics (LE4PD), which decomposes the dynamics of a protein into dynamical pathways that explore mode-dependent free-energy surfaces. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 670 | Non-additive effects of denaturing and protective cosolvents on protein stability | Ganguly, Pritam; Shea, Joan-Emma | We find that the pure and the mixed solutions of urea and GdmCl denature Trpcage as a whole, but remarkably, the helical segment 1NLYIQWL 7 of Trpcage is stabilized in mixed GdmCl-urea solutions. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 671 | Short peptides assemble to produce enzyme-like catalysts. | Korendovych, Ivan | We will present applications of a minimalistic approach to design of artificial enzymes. | Session 43: Physics of Proteins: Peptides and Small Proteins |
| 672 | Lessons from Designing Optogenetic Tools | Woolley, Andrew | I will describe how following up on some odd behaviour observed while trying to engineer photoactive yellow protein as a light-controlled switch, led to interesting, perhaps, general new insights into the behavior of these remarkable moelcules | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 673 | Engineering and application of a biosensor with focused ligand specificity | Della Corte, Dennis | We here solved the structure of the transcriptional regulator LysG of Corynebacterium glutamicum detecting all three basic amino acids. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 674 | Spontaneous Rupture and Entanglement of Human Neuronal Tau Protein Induced by Piconewton Compressive Force | Roy Chowdhury, Susovan; Lu, H Peter | We have observed abrupt and spontaneous tau protein ruptures under a compressive force ranging from ∼5 to ∼125 pN, at a biologically available force amplitude range in living cells, using a home-modified atomic force microscopy single-molecule manipulation. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 675 | Allosteric communications via substrate and linker between domains modulate protein function | SARKAR, SUSANTA | Here we show that inter-domain dynamics of matrix metalloprotease-1 (MMP1) on collagen fibrils are correlated with activity. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 676 | Disordered Protein Folding and Solubility as a Determinant of Human Disease | Levine, Zachary | In this talk, I will summarize our efforts to leverage molecular models of IDPs that populate vast free energy landscapes, reconciling how disordered and often soluble protein intermediates contribute to human disease. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 677 | Is the Protein Dynamical Transition Useful? | Sharma, Akansha; George, Deepu; Markelz, Andrea | Typically the THz measurements are performed using solutions, however there is some question as to whether the freezing of the solution effects protein structure or dynamics. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 678 | Anti-cancer drug containing apolipoprotein B refolding through first-order-like phase transition process | Cheng, Chia Hsin; Chang, Wei-Ping; Lin, Po Yen; Liang, Yu Chuan; Chen, Caleb G.; Chang, Chia-Ching | In this study, we refolded apoB with anti-cancer drug from denatured state to functional state follow a first-order-like state transition model. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 679 | Integrative structural biology: insights from photoactive yellow protein | Wu, Yichao; Kumauchi, Masato; Li, Wenfei; Xie, Aihua; Hoff, Wouter | We report such an integrative structural biology approach using a bacterial photoreceptor (photoactive yellow protein) as an accessible model system. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 680 | Decoupling between translation al and rotation al motions of water in the proximity of a protein molecule | Tan, Pan; Hong, Liang | By performing neutron scattering on a perdeuterated protein at various hydration levels, we characterized the dynamics of water in each molecular layer surrounding the biomolecule . | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 681 | Probing Temperature-Dependent Dynamics of Hemoglobin and Water Molecules in the Hydration Shells Using High Sensitivity Dielectric Spectroscopy | Doan, Luan; Singh, Abhishek; Wen, Chengyuan; Cheng, Shengfeng; Nguyen, Vinh | Employing high-sensitivity dielectric megahertz-to-terahertz frequency-domain spectroscopy, we have systematically examined the dynamics of hemoglobin and the water molecules in their hydration shells as a function of temperature at the molecular level. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 682 | Single Molecule Studies of DNA-Histone Interactions | Gaire, Santosh | Here we present preliminary data characterizing the mechanical properties of DNA molecules bound to native and post-translationally modified histones. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 683 | The Incredible Secret Electronic Life of Proteins | Lindsay, Stuart | 2 We find that nS conductances over distances of many nm are common. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 684 | Time-resolved Infrared Structural Biology of Proteins: Bringing New Light to Protein Structural Dynamics and Function | Xie, Aihua | In my talk, I will discuss important challenges we are facing in protein structural biology, and how to overcome some of these challenges using time-resolved infrared structural biology of proteins. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 685 | Domain Swapping in Crystallin Proteins Can Drive Early Stages of Cataract Formation | Patluri, Govardhan | Using molecular dynamics simulations and coarse-grained protein model of human γC and γD Crys, we identified the aggregation prone misfolded states present in the unfolding pathways of these proteins. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 686 | Evaluating molecular simulations of protein dynamics using novel experimental data | McGough, Lauren; Kim, Justin; Klyshko, Eugene; Ranganathan, Rama; Rauscher, Sarah | We present a comparative analysis between MD and experiment using data from X-ray diffraction studies reporting electric field-stimulated excited state motions. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 687 | Effects of artificial mutations on topological features of proteins | Negami, Haru | In this research we investigated the topological features of artificial proteins and showed the topological traits of mutants which have a drug resisitant to antibiotics. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 688 | Using Molecular Dynamics to Improve Molecular Docking | Morris, Connor; Della Corte, Dennis | We have been developing an improved method of protein-ligand docking. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 689 | Marburg VP24 Protein K-loop Cysteine Interactions with the Human Keap1 Protein | Bhattarai, Nisha; Gerstman, Bernard; Chapagain, Prem | In this work, we investigate the molecular level details of the interactions between Marburg and Ebola VP24 proteins and Keap1 using molecular dynamics simulation. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 690 | Anomalous kinetics on low-fouling surfaces | Krapf, Diego; Hedayati, Mohammadhasan; Kipper, Matt | This work reveals a mechanistic origin for anomalous adsorption/desorption kinetics that can be employed to define design principles for non-fouling surfaces and to predict their performance. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 691 | Single polypeptide antibody functionalized electrochemical probe development for enterovirus detection | Lu, Yi-Xiang; Chang, Chia-Yu; Fan, Wen-Bin; Yang, Jyh-Yuan; Chang, Chia-Ching | We have developed a single polypeptide antibody for enterovirus 71 detection. | Session 44: Physics of Proteins: Progress on Structure-Function Relationships |
| 692 | Collective Behavior in Growth-Driven Systems | Meroz, Yasmine | Here we set the stage for the study of emergent growth-driven structures by developing a model for interacting growth-driven organs. | Session 45: Physics of Social Interactions |
| 693 | Collective Aggregation via Directed Pheromone Signaling in Honeybee Swarms | Nguyen, Dieu My; Iuzzolino, Michael; Mankel, Aaron; Peleg, Orit | Using honeybees as a model organism, we study the communication network of honeybee swarms that locate their queen by tracking her pheromones. | Session 45: Physics of Social Interactions |
| 694 | Social context alters behavioral interactions in bumblebees | McKenzie-Smith, Grace; Wang, Yan; Cho, Jean; Pereira, Talmo; Kocher, Sarah; Shaevitz, Joshua | In this study, we investigate how social context alters behavioral interactions among bumblebee ( Bombus impatiens) workers by probing the behavior of differently aged bees either alone or paired with another bee. | Session 45: Physics of Social Interactions |
| 695 | Brownian motion of fire ants hinders raft formation | Ko, Hungtang; Hu, David | In this study, we observe individual fire ants perform random walk on the water surface. | Session 45: Physics of Social Interactions |
| 696 | Behavioral plasticity in jackdaw flocks | Ouellette, Nicholas; Ling, Hangjian; McIvor, Guillam; Westley, Joseph; Van der Vaart, Kasper; Vaughan, Richard; Thornton, Alex | I will present evidence from field studies of jackdaws, a highly social corvid species, that indeed flocks of this single species display different interaction rules in different ecological contexts. | Session 45: Physics of Social Interactions |
| 697 | Shared behavioral mechanisms underlie C. elegans aggregation and swarming | Ding, Serena; Schumacher, Linus; Javer, Avelino; Endres, Robert; Brown, Andre | Here, we investigate collective feeding in the roundworm C. elegans at this intermediate scale, using quantitative phenotyping and agent-based modeling to identify behavioral rules underlying both aggregation and swarming—a dynamic phenotype only observed at longer timescales. | Session 45: Physics of Social Interactions |
| 698 | Predicting residential segregation using statistical physics approaches | Chen, Yuchao; Kinkhabwala, Yunus; Gaspard, Mallory; Hall, Matthew; Arias, Tomas; Cohen, Itai | We introduce a statistical physics based method to predict racial residential segregation in human populations. | Session 45: Physics of Social Interactions |
| 699 | Leader cells in collective chemotaxis: optimality and trade-offs | Hopkins, Austin; Camley, Brian | We use a simple mathematical model to find when specialization would be advantageous. | Session 45: Physics of Social Interactions |
| 700 | One fish, two fish, win fish, lose fish: Imaging and analyzing the fighting behavior of zebrafish in 3D | O’Shaughnessy, Liam; Izawa, Tatsuo; Masai, Ichiro; Shaevitz, Joshua; Stephens, Greg | We describe a custom tracking apparatus consisting of multiple fast cameras, a large imaging volume, and a transparent interior cage to avoid reflection artifacts. | Session 45: Physics of Social Interactions |
| 701 | A Foraging Approach to Analyzing Infant and Caregiver Vocal Behavior | Vallomparambath PanikkasserySu, Ritwika; M. Pretzer, Gina; Mendoza, Sara; Shedd, Christopher; T. Kello, Christopher; Gopinathan, Ajay; S. Warlaumont, Anne | Previous research on infant vocal development suggests that human infants and adult caregivers search for sounds that have social value. | Session 45: Physics of Social Interactions |
| 702 | The Superorganism’s Circulatory System: Collective control of development through a socially exchanged fluid | LeBoeuf, Adria | In carpenter ants, we’ve shown that components of trophallactic fluid can influence larval development, regulating the number of new adults produced. | Session 45: Physics of Social Interactions |
| 703 | A structured representation of odors in the fly mushroom body | Yang, Jie-Yoon; Hong, Elizabeth | We present a method using genetically enabled, in vivo two-photon functional imaging to measure near complete population representations of odors in KCs. | Session 46: Physics of the Brain: Structure and Dynamics |
| 704 | Inferring causality in highly-synchronized dynamics | Calderon, Josuan; Berman, Gordon | Causality methods provide a powerful tool for the characterization of these functional circuits by identifying directed functional interactions from time-series data. | Session 46: Physics of the Brain: Structure and Dynamics |
| 705 | Modularity allows classification of human brain networks during music and speech perception | Bonomo, Melia; Karmonik, Christof; Brandt, Anthony; Frazier, J | Here, we investigated a means to quantify individual differences in functional brain activity while subjects listened to a variety of auditory pieces. | Session 46: Physics of the Brain: Structure and Dynamics |
| 706 | Synchronization, waves and stochasticity in spatially structured neuronal networks | Ranft, Jonas; Kulkarni, Anirudh; Hakim, Vincent | In order to shed light on these data, we have revisited the synchronization properties of distinct oscillating local Excitatory-Inhibitory (E-I) modules induced by distance-dependent long-range excitation. | Session 46: Physics of the Brain: Structure and Dynamics |
| 707 | Searching for emergent long time scales without fine tuning | Chen, Xiaowen; Bialek, William | We will give a progress report on the more realistic, and challenging, case of asymmetric interactions. | Session 46: Physics of the Brain: Structure and Dynamics |
| 708 | Margin learning in spiking neural networks | Gütig, Robert | Recently, we have introduced the spike-threshold-surface to define a continuous distance between the responses of spiking neurons. | Session 46: Physics of the Brain: Structure and Dynamics |
| 709 | Randomly connected networks generate emergent selectivity and predict decoding properties of large populations of neurons | Sederberg, Audrey; Nemenman, Ilya | Modern recording methods enable sampling of thousands of neurons during the performance of behavioral tasks, raising the question of how recorded activity relates to theoretical models. | Session 46: Physics of the Brain: Structure and Dynamics |
| 710 | Impact of correlated connections in large recurrent networks with mesoscopic structure | Kuczala, Alexander; Sharpee, Tatyana | We address this deficiency by investigating the impact of correlations between forward and reverse connections, which may depend on the neuronal type. | Session 46: Physics of the Brain: Structure and Dynamics |
| 711 | Relationships Between Lognormal Distributions of Neural Properties and Connectivities | Robinson, Peter; gao, xiao; Han, Yinuo | Relationships Between Lognormal Distributions of Neural Properties and Connectivities | Session 46: Physics of the Brain: Structure and Dynamics |
| 712 | Directed effective connectivity of in vitro neuronal networks revealed from electrophysiological recordings | Sun, Chumin; Lin, K.C.; Huang, Yu-Ting,; Ching, Emily S.C.; Lai, Pik-Yin; Chan, C.K. | We present a method that makes explicit use of a theoretical result that effective connectivity is contained in the relation between time-lagged cross-covariance and equal-time cross-covariance. | Session 46: Physics of the Brain: Structure and Dynamics |
| 713 | A Quantitative Kinematic Movement Biomarker Characterizing Neurodevelopmental Disorders | Jose, Jorge | In this lecture I will describe the nature of experiments we carry out, the importance of fully filtering out the external electronic noise from neuronal noise. | Session 46: Physics of the Brain: Structure and Dynamics |
| 714 | Latent fields lead to emergence of scaling in simulated neurons | Morrell, Mia; Sederberg, Audrey; Nemenman, Ilya | We conducted simulations of conditionally independent binary neurons coupled to a small number of long-timescale stochastic fields with and without periodic spatial stimuli (depicting neural place cells) and replicated the coarse-graining shown in [1]. | Session 46: Physics of the Brain: Structure and Dynamics |
| 715 | Architectural Principles and Predictive Modeling of the Mammalian Connectome | Toroczkai, Zoltan; Molnar, Ferenc; Ribeiro Gomes, Ana-Rita; Ercsey-Ravasz, Maria; Knoblauch, Kenneth; Kennedy, Henry | We hypothesize the existence of network architectural organizational principles in the mammalian brain, critical for efficient and hierarchically modular information processing. | Session 46: Physics of the Brain: Structure and Dynamics |
| 716 | A 2D Stochastic Lattice Model Describing the Self-Assembly of Synaptic Membrane Protein Domains | Law, Everest | Inspired by the interactions between glycine receptors and gephyrin scaffolds, we present a stochastic lattice reaction-diffusion model explaining receptor domain formation. | Session 46: Physics of the Brain: Structure and Dynamics |
| 717 | Dynamics of the intrinsically disordered proteins and neurodegeneration | Cieplak, Marek | We demonstrate this picture explicitly by studying networks defined on the discretized plane: conformational end-to-end distances vs. radii of gyration. | Session 46: Physics of the Brain: Structure and Dynamics |
| 718 | Alpha rhythm shapes the correlation landscape of avalanche dynamics across resting wakefulness | Lombardi, Fabrizio; De Arcangelis, Lucilla; Herrmann, Hans; Shriki, Oren | In this talk I will show that, while the scale-free properties are universal and preserved across sleep and wake, avalanche dynamics is intimately connected to the dominant brain rhythm characterizing each of those physiologic states, and shows unique features in the resting awake state. | Session 46: Physics of the Brain: Structure and Dynamics |
| 719 | Non-perturbative renormalization group analysis of strongly-coupled spiking networks | Brinkman, Braden | Given a model of neural dynamics and their synaptic connections, we would in principle achieve this goal by calculating the statistical and response functions of the network—a notoriously intractable task for all but the simplest models. | Session 46: Physics of the Brain: Structure and Dynamics |
| 720 | Representation of nearby and infinitely far reference frames in the brain | Dhingra, Shonali; Shahi, Mina; Mehta, Mayank | Our work shows that hippocampal cells recognize space as a vector! | Session 46: Physics of the Brain: Structure and Dynamics |
| 721 | How behavioral and evolutionary constraints sculpt early visual processing | Palmer, Stephanie | We use techniques from statistical physics and information processing to assess how efficient, predictive vision emerges from these imperfect component parts. | Session 46: Physics of the Brain: Structure and Dynamics |
| 722 | Tubulin shape controls the kinetics and mechanism of microtubule depolymerization | Bollinger, Jonathan; Imam, Zachary; Stevens, Mark; Bachand, George | Both methods reveal exponential decay in the kinetics of depolymerization corresponding to the relative number of uncompressed dimers. | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 723 | Stutter: a Transient Microtubule Dynamic Instability Phase that is Strongly Associated with Catastrophe | Mahserejian, Shant; Scripture, Jared; Mauro, Ava; Lawrence, Elizabeth; Zanic, Marija; Alber, Mark; Goodson, Holly | To address these problems, we developed STADIA (Statistical Tool for Automated Dynamic Instability Analysis). | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 724 | Molecular dynamics study of Katanin oligomeres: A MT-severing enzyme | Damre, Mangesh; Varikoti, Rohith Anand; Dima, Ruxandra | We will describe our all-atom molecular dynamics simulations performed on the apo, the ATP bound, and minimal substrate-bound states of katanin. | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 725 | Role of substrate cooperativity and motor concentration in microtubule severing | Varikoti, Rohith Anand; Ross, Jennifer; Dima, Ruxandra | Due to the large size of the system, we employed coarse grained molecular simulations of different MT lattices and at varying concentration of severing enzymes. | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 726 | Dynamic stability of actin cytoskeletal networks with mixed geometries | Tabatabai, Pasha; Lanier, Laura; Murrell, Michael | With this system, we investigate the effect of coexistence of networks with different geometries and growth rates on steady-state structure. | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 727 | Actin crosslinking controls mobility, microtubule crosslinkers control co-localization in a composite cytoskeletal network | Farhadi, Leila; Rust, Michael; Das, Moumita; Robertson-Anderson, Rae; Ross, Jennifer | We use biotin-NeutrAvidin crosslinkers to irreversibly crosslink actin and MAP65, an antiparallel microtubule crosslinker to bundle microtubules. | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 728 | Avalanches in simulations of branched actomyosin networks with the Arp2/3 complex | Liman, James; Bueno, Carlos; Eliaz, Yossi; Schafer, Nicholas; Waxham, Neal; Wolynes, Peter; Levine, Herbert; Cheung, Margaret | In this work, we simulate the spatiotemporal configurations of actomyosin networks with and without the Arp2/3 complex. | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 729 | A dynamic contractile F-actin network reconstituted in Xenopus egg extract | Zhao, Jianguo; Schmidt, Christoph | We observed steady state directed flows and non-equilibrium phase separation. | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 730 | Controlling ‘cell’ size and shape to elucidate the mechanics of microtubule aster positioning | Gatlin, Jay; Sulerud, Taylor; Sami, Abdullah; Geisterfer, Zach; Oakey, John | To address this gap in our collective understanding, we have combined photo-labile hydrogels with cell-free extracts in a new experimental platform that affords exquisite control of “cell” shape and volume. | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 731 | Active Composites of Actin and Kinesin-driven Microtubules | Berezney, John; Fraden, Seth; Dogic, Zvonimir | To demonstrate some of the mechanics governing the active reorganization of these materials, we have built a polymer blend of kinesin-driven microtubule networks which reorganize a passive entangled actin network. | Session 47: Physics of the Cytoskeleton Across Scales: Enzymes to Networks |
| 732 | Harmonic oscillation frequencies of cellular contractility support a wave shape model | Werner, Michael; Ray, Dylan; Breen, Coleman; Sattler, Adam; Jug, Florian; Shaub Madox, Amy | We propose that the latter reflects the Rho pacemaker driving contractility, and that the harmonic is emergent due to non-linearities in the system. | Session 48: Physics of the Cytoskeleton Across Scales: In vivo |
| 733 | Actomyosin-driven mechanics of starfish oocytes | Foster, Peter; Fakhri, Nikta | Here, we address this issue using oocytes from the starfish Patiria miniate. | Session 48: Physics of the Cytoskeleton Across Scales: In vivo |
| 734 | Spatiotemporal dynamics of the neuronal cytoskeleton across scales during development | O’Neill, Kate; Robinson, Emily; Losert, Wolfgang | Using live confocal imaging, we study how the dynamics of actin change as cultures of in vitro primary rat cortical neurons develop. | Session 48: Physics of the Cytoskeleton Across Scales: In vivo |
| 735 | Computational model of mitotic spindle positioning in polarized cells | Moore, Jeffrey; Lamson, Adam; Glaser, Matthew; Betterton, Meredith | We present results from simulations of a minimal spindle positioning model in a polarized cell driven by interactions between astral filaments, motorized tethers, and cortical binding domains. | Session 48: Physics of the Cytoskeleton Across Scales: In vivo |
| 736 | Flagellar length control in biflagellate eukaryotes : Cooperative phenomena of generating and regenerating the flagellum | Patra, Swayamshree; Julicher, Frank; Chowdhury, Debashish | Combining the dynamics of trafficking intraflagellar transport trains, the pool and the kinetics of flagellar assembly and disassembly, we have developed a stochastic model for understanding the collective phenomena of flagellar length control. | Session 48: Physics of the Cytoskeleton Across Scales: In vivo |
| 737 | Bridging microtubules promote centering of kinetochores by length-dependent pulling forces | Bosilj, Agneza; Tolić, Iva; Pavin, Nenad | We predict that stable antiparallel overlaps exert length-dependent forces on kinetochores to navigate their positioning in the center of the metaphase plate. | Session 48: Physics of the Cytoskeleton Across Scales: In vivo |
| 738 | Effects of rapid impact loading on neural progenitor cells | Rodriguez, Delany; Patterson, Luke; Walker, Jennifer; Rodriguez-Mesa, Evelyn; Shields, Kevin; Foster, John; Doyle, Adele; Foster, Kimberly; Valentine, Megan | We recently developed a high throughput microfluidic MEMS device, the μHammer, to subject individual cells to rapid impact loading, at strains of up to 40% over typical impact durations of ~10 μs. | Session 48: Physics of the Cytoskeleton Across Scales: In vivo |
| 739 | Assemblies of Calcium/Calmodulin Dependent Kinase II with Actin and Their Dynamic Regulation by Calmodulin in Dendritic Spines | Wang, Qian; Chen, Mingchen; Schafer, Nicholas; Bueno, Carlos; Song, Sarah; Hudmon, Andy; Wolynes, Peter; Waxham, Neal; Cheung, Margaret | Assemblies of Calcium/Calmodulin Dependent Kinase II with Actin and Their Dynamic Regulation by Calmodulin in Dendritic Spines | Session 48: Physics of the Cytoskeleton Across Scales: In vivo |
| 740 | A generalized clutch model to explain cell adhesion mechanics | Venturini, Chiara; Saez, Pablo | In summary, we proposed a model that unifies our current understanding of cell adhesion architecture and turnover while replicating previous experimental results. | Session 48: Physics of the Cytoskeleton Across Scales: In vivo |
| 741 | A mechanistic view of collective filament motion in active nematic networks | Striebel, Moritz; Graf, Isabella; Frey, Erwin | To address this question we study a minimal but generic model for a nematic network where filament sliding is driven by the action of motor proteins. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 742 | Time varying mechanical response of cytoskeletal networks | Das, Moumita | This talk will discuss an integrated approach consisting of theory and experiments, that seeks to address these questions. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 743 | Microrheology of active actin-microtubule networks | Lee, Gloria; Ricketts, Shea; Rust, Michael; Das, Moumita; Ross, Jennifer | Here, we create active actin-microtubule networks by adding the motor protein myosin. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 744 | Probing length scale-dependent viscoelasticity from bending fluctuations of filaments | Nishi, Kengo; Raja, Sufi; MacKintosh, Fred; Schmidt, Christoph | Here, we introduce the use of semi-flexible filaments/tubes to probe scale-dependent dynamics. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 745 | Triggering salt-induced contraction of cytoskeletal networks with microfluidics | Ricketts, Shea; Khanal, Pawan; Currie, Christopher; Rust, Michael; Das, Moumita; Ross, Jennifer; Robertson-Anderson, Rae | Here, we use microfluidics and confocal fluorescence microscopy to show that increasing salt concentration triggers contraction of cytoskeleton networks in the absence of motor proteins. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 746 | Slow stress relaxation of transient-crosslinked biopolymer networks | Chen, Sihan; Markovich, Tomer; MacKintosh, Frederick | In this talk I will propose a microscopic theory for the rheology of transient networks under prestress. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 747 | Electric Field Guidance of Actin Waves | Yang, Qixin; Hourwitz, Matt; Campanello, Leonard; Sharif, Bedri; Devreotes, Peter; Fourkas, John; Losert, Wolfgang | By quantifying spatial-temporal actin wave patterns, we show that DC EFs can guide actin wave propagation, lead to inhomogeneous activities of actin waves, and alter cell migratory modes. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 748 | Exploring the effects of actin-binding proteins on the percolation of actin networks using a mean field model | Bueno, Carlos; Liman, James; Schafer, Nicholas; Cheung, Margaret; Wolynes, Peter | In this work we model an actin system and its interaction with α-actinin, myosin and Arp2/3 using ordinary differential equations and stochastic mechanochemical simulations. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 749 | Mechanical stability of microtubule lattices under high crowdedness | Szatkowski, Lukasz; Varikoti, Rohith; Dima, Ruxandra | We present a modified indentation protocol to determine the mechanical response of MT lattices under conditions which mimic high confinement. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 750 | Understanding the Topology of Microtubules | Subramanyan, Varsha; Krishnan, Kesav; Kirkpatrick, Kay; Vishveshwara, Saraswathi; Vishveshwara, Smitha | We show the emergence of topological edge modes, and propose the modelling of dynamic instability as a phase transition. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 751 | The role of multivalent actin-binding proteins in remodeling actomyosin networks | Eliaz, Yossi; Cheung, Margaret | We explore the contribution of multivalent actin-binding proteins (ABPs) in remodeling actomyosin networks by using mesoscopic computer simulations. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 752 | Mechanical properties of branched actin networks | Bouzid, Mehdi; Valencia-Gallardo, Cesar; Koehler, Lara; Foffi, Giuseppe; Heuvingh, Julien; Du Roure, Olivia; Lenz, Martin | Through experiments, simulations and theory, we show that their elasticity crucially involves reversible entanglements between their filaments. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 753 | Hydrodynamic effects on the motility of crawling eukaryotic cells | Mai, Melissa; Camley, Brian | We study the relationship between hydrodynamics and adhesion that describe whether a cell is swimming, crawling, or combining these motions. | Session 49: Physics of the Cytoskeleton Across Scales: Mechanics and Rheology |
| 754 | Microtubules Regulate Localization and Availability of Insulin Granules in Pancreatic Beta Cells | Holmes, William | We demonstrate that microtubule (MT) motor transport dynamics have a critical role in regulating both factors. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 755 | Anomalous transport across scales in crosslinked actin-microtubule composites | Anderson, Sylas; Garamella, Jonathan; McGorty, Ryan; Robertson-Anderson, Rae | Specifically, we investigate the impact of permanently crosslinking actin to actin, microtubules to microtubules, and actin to microtubules. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 756 | Spreading through the cell via non-canonical modes of transport | Koslover, Elena | This talk will focus on two examples of multi-modal transport: combining motor-driven motion, diffusion, and fluid flow for efficient dispersion of particles within the cell. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 757 | MEMBRANE CHOLESTEROL IS A NOVEL CONTROL FOR KINESIN-BASED TRANSPORT | Li, Qiaochu; Wilson, John; Tseng, Kuo-fu; Qiu, Weihong; Vershinin, Michael; King, Stephen; Xu, Jing | We found that coupling motors via a biomimetic membrane significantly enhanced the transport of cargos along tau-decorated microtubules. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 758 | Effect of membrane fluidity on the multi-motor transport of intracellular cargoes | Sarpangala, Niranjan; Gopinathan, Ajay | We developed a stochastic dynamical simulation of kinesin-based cargo transport along microtubules that explicitly considers the Langevin dynamics of motors on the cargo surface to answer these questions. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 759 | The Dynein Catch Bond: Implications for cooperative transport | Mitra, Mithun; Puri, Palka; Chaudhuri, Abhishek; Muhuri, Sudipto | Motivated by these experiments, we propose a phenomenological model for catch bonding in dynein. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 760 | Tracking Down the Fast and Superprocessive KIF1A with Gold Scattering Microscopy | Gicking, Allison; Zaniewski, Taylor; Hancock, William | Single molecule studies observe KIF1A velocities > 1 mm/s and average run lengths > 5 mm, making KIF1A one of the fastest and most processive members of the kinesin superfamily; however, the mechanistic basis of these high speeds and long run lengths is unknown. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 761 | Investigating the Effect of Cargo-Motor Linkage Stiffness on Cellular Functions of Myosin VI | Shrivastava, Rachit; Rai, Ashim; Salapaka, Murti; Sivaramakrishnan, Sivaraj | We examine the effect of cargo-motor linkage stiffness on the mechanobiological properties of the molecular motor Myosin VI. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 762 | Deviations from Arrhenius behavior of Kinesin-1 at low temperatures | Doval, Florence; Ori-McKenney, Kassandra; McKenney, Richard; Vershinin, Michael | We investigated the enzymatic activity of KIF5A at even lower temperatures and have observed a break in the Arrhenius trend, corresponding to higher activation energy at lower temperature. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 763 | Cargo diffusion shortens single-kinesin runs at low viscous drag | Wilson, John; Xu, Jing; Quint, David; Gopinathan, Ajay | We found that cargo diffusion significantly shortens single-kinesin runs. | Session 50: Physics of the Cytoskeleton Across Scales: Transport |
| 764 | Immune repertoire dynamics out of steady state | Gaimann, Mario; Desponds, Jonathan; Mayer, Andreas | Here, we show how such long tails can emerge out of steady state from a simple neutral model for immune repertoire formation. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 765 | The role of drug kinetics on the evolution of resistance. | Nande, Anjalika; Nowak, Martin; Hill, Alison | We find that there exists an initial time-frame after treatment initiation that has the most influence on the establishment probability of the drug resistant strain. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 766 | The Dynamics of Human Society Evolution: An Energetics Approach | Poudel, Ram; McGowan, Jon | In this paper, we will demonstrate that Lotka-Volterra type equations can be derived from the Hamiltonian equation in the social field. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 767 | Understanding the Dynamics of Antibiotic Resistance in Microbial Communities using Tensor Methods | De Jong, Max; Wood, Kevin | We develop several methods to deconstruct this tensor into quantities that allow us to gain insight into the evolutionary dynamics of the system as it reaches fixation. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 768 | Evolving generalists in optimal cycling environments | Wang, Shenshen | Using a generative approach, we find that switching between environments neither too similar nor too different can efficiently evolve fit generalists, via dynamically enlarging their attractor basins in sequence space. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 769 | Search strategies that find generalists in time varying environments | Kutasov, Jonathan; Husain, Kabir; Wang, Shenshen; Murugan, Arvind | We find that a class of biased random walks that we call `directed’ are naturally driven towards generalists by time varying environments at intermediate timescales; this class includes classic E. coli chemotaxis with run times modulated by food availability and constant tumble times. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 770 | Time-Dependent Effective Sampling Bias in Populations with Broad Offspring Numbers | Okada, Takashi; Hallatschek, Oskar | Here, we establish a number of new scaling relations about the fixation probability, the extinction time and the site frequency spectrum that arise when offspring numbers are distributed according to a power law with divergent variance. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 771 | Using environmental noise to hedge one’s evolutionary bets | Xue, BingKan; Sartori, Pablo; Leibler, Stanislas | We show that, even when the signal is extremely noisy and uninformative of the true environment, the organism can still benefit from the signal by using it as a source of randomness for bet-hedging. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 772 | Clocks, Anticipation, and Growth in Bacteria | Monti, Michele; Ten Wolde, Pieter; Lubensky, David | Here, we use mathematical modeling to address this question for nitrogen-fixing cyanobacteria.1 By extending recent work on growth laws in E. coli,2 we show that it is difficult to change the composition of the proteome when the growth rate is small, and thus that the average growth rate can be increased by using a clock to anticipate the onset of darkness by switching to a dark-adapted proteome late in the day, when growth rates are still large.1 M. Monti, D.K. Lubensky, and P.R. ten Wolde, arXiv:1805.04538. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 773 | Minimal model reveals key features of vaccination protocols that optimally elicit broadly neutralizing antibodies | Ganti, Raman; Kardar, Mehran; Chakraborty, Arup | Minimal model reveals key features of vaccination protocols that optimally elicit broadly neutralizing antibodies | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 774 | Predicting antibiotic resistance evolution | Pinheiro, Fernanda; Warsi, Omar; Andersson, Dan; Lässig, Michael | Here we develop a fitness model that predicts dosage-dependent growth rates of common resistance mutations. | Session 51: Population Dynamics in Antibiotics and Time-Varying Environments |
| 775 | Silk-inspiration: hierarchy, assembly, and mechanics in polyurea-polypeptide hybrids | Korley, LaShanda; Jang, Daseul | Inspired by spider silk, we have designed a series of polymer-peptide polyurethane/ureas to explore the hierarchical arrangement critical to energy absorption and mechanical enhancement. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 776 | Osmotic Swelling Behavior of Ionic Cylindrical Microgels | Alziyadi, Mohammed; Denton, Alan | Within a cell model, we derive an exact statistical mechanical theorem for the electrostatic osmotic pressure of a cylindrical microgel to study the dependence of microion distribution and osmotic pressure on equilibrium size. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 777 | Swelling-induced Morphological Deformation and Constitutive Relation of Soft Materials in Micro-patterned Hydrogel | Bae, Jung Gun; Lee, Won Bo | In this presentation, we propose modified nonlinear stress-strain relationship of our synthesized gels in scope of both continuum and molecular scales and compare it with our experimental results. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 778 | Dynamics of 3D polymer gel with reversible linkers | Biswas, Santidan; Yashin, Victor; Balazs, Anna | We utilize the gel lattice-spring approach to develop the 3D computational model of polymer gels containing the temporary crosslinks. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 779 | Phototunable Viscoelasticity in Hydrogels Through Thioester Exchange | Carberry, Benjamin; Rao, Varsha; Anseth, Kristi | We present a cell culture substrate based on thioester exchange chemistry where viscoelasticity of the biophysical environment can be modulated in situ with light and the photoinitiated thiol-ene ‘click’ reaction. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 780 | Toughening mechanism of tough and self-healing physical hydrogels | CUI, KUNPENG; Gong, Jian Ping | In this work, we used real time small-angle X-ray scattering (SAXS) to study the toughening mechanism of PA hydrogels. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 781 | Anisotropic Hollow Microgels That Can Adapt Their Size, Shape, and Softness | Nickel, Anne; Scotti, Andrea; Houston, Judith; Crassous, Jerome; Pedersen, Jan Skov; Richtering, Walter | With such models, we demonstrated the existence of the cavity and simultaneously the anisotropic character of the microgels. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 782 | Osmotic Pressure of Permeable Ionic Microgels | Denton, Alan; Alziyadi, Mohammed | Within the cell model, we derive the electrostatic contribution within Poisson-Boltzmann (PB) theory, by minimizing a free energy functional with respect to electrostatic potential, and extract the gel pressure from the pressure tensor. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 783 | Tuning Diblock Copolymer Morphologies by Stimuli-Responsive Supramolecular Interactions | Zhang, Xiangyu; Zong, Jing; Meng, Dong | To offer microscopic insights into this process, here we present a simulation study of diblock copolymers blended with homopolymers that are associative to one of the blocks through supramolecular forces. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 784 | On the solvation of elastin-like polypeptides in aqueous mixtures | Zhao, Yani; Singh, Manjesh; Kremer, Kurt; Cortes Huerto, Robinson; Mukherji, Debashish | In this work, we compare conformational behavior of ELPs in aqueous-ethanol and -urea mixtures using explicit solvent generic simulations. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 785 | Chemomechanical origin of directed gel locomotions driven by intenal chemical pulses | Gao, Qingyu; Ren, Lin; Epstein, Irving | Our previous work reported the directed locomotion of self-oscillating polymer gels in asymmetric environments, such as retrograde and direct wave locomotion, reciprocal migration, photophobic and phototropic movement. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 786 | Competition between Hydrophobic and Electrostatic Interactions determine pH-responsive Supramolecular Self-assembly | Chakraborty, Saikat; Berac, Christian; Besenius, Pol; Speck, Thomas | We present results from a molecular dynamics simulations study, inspired by experiments on pH-regulated self-assembly into filaments. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 787 | Detection of Polypeptide Conformational Transitions in Solution via Sound Velocity and Optical Rotation | Blake, Alyssa; Parkinson, Graham; Russo, Paul | Detection of Polypeptide Conformational Transitions in Solution via Sound Velocity and Optical Rotation | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 788 | Giant hyaluronan polymer brushes display polyelectrolyte brush polymer physics behavior | Faubel, Jessica; Patel, Rhiddi; Curtis, Jennifer; Brettmann, Blair | In this study, we explored the stimulus response of the brush to ionic strength and solvent changes. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 789 | Detecting Bacteria with Plasmonic Microcapsules | Dreyfus, Remi; Burel, Céline; Murray, Christopher; Donnio, Bertrand | Here, we show how to combine optically active plasmonic gold nanoparticles and pH-responsive thin shells into “plasmocapsules”. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 790 | Enzyme-Responsive Materials for Regenerative Medicine | Heilshorn, Sarah | Enzyme-Responsive Materials for Regenerative Medicine | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 791 | Shape Control of Charge-patterned Nanocontainers | Brunk, Nicholas; Jadhao, Vikram | Shape Control of Charge-patterned Nanocontainers | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 792 | A simple mechanical model for synthetic catch bonds | Dansuk, Kerim; Keten, Sinan | Here, we have demonstrated that a simple mechanical design based on a tweezer-like mechanism can exhibit catch bond characteristics under thermal excitations. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 793 | Towards Tumor pH Detection Using Plain Radiography: An Injectable pH-Responsive Polyacrylic Acid Based Hydrogel Biosensor | Kiridena, Sachindra; Wijayaratna, Uthpala; Arifuzzaman, Md.; Anker, Jeffrey | Towards Tumor pH Detection Using Plain Radiography: An Injectable pH-Responsive Polyacrylic Acid Based Hydrogel Biosensor | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 794 | Modulation of hydrogel biophysical properties using photoadaptable chemistry improves formation of intestinal organoids | Yavitt, Max; Brown, Tobin; Hushka, Ella; Dempsey, Peter; Anseth, Kristi | We use the adaptable allyl sulfide (AS) photochemistry to tune hydrogel biophysical properties through on demand network reorganization. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 795 | Biosensor physics: DNA folding in a crowded environment | Taylor, Mark; Paul, Wolfgang | We develop a coarse-grained model for ssDNA (based on a flexible hard-sphere chain with square-well patch interactions that accounts for both H-bonding and base-pair stacking) and use it to examine the entropic effects associated with surface crowding. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 796 | Effect of Nanoparticle Surface Functionality on Magnetic and Interfacial Properties of Iron Oxide–Poly(ethylene oxide) Nanocomposites | Weiblen, Donovan; Gionta, Grace; Rende, Deniz; Akcora, Pinar; Ozisik, Rahmi | In the current work, the impact of surface coating of iron oxide (Fe 3O 4) NPs on interfacial heat transfer, bulk magnetization properties, and structure of poly(ethylene oxide), PEO, nanocomposites was explored. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 797 | Ordering hard-sphere particle suspensions by medium crystallization: Effect of size and interaction strength | Gimenez-Pinto, Vianney | Here, I numerically investigate the effect of particle-size and solvent-size in the process of solidification templating by implementing a simple coarse-grain model for the kinetics of hard-sphere particles at the melt/crystal interface. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 798 | Exploring Solution Behavior of Fully Rigid “Block Copolymers” with Sphere-Rod Molecular Architecture | LUO, JIANCHENG; Liu, Tong; Cheng, Stephen; Liu, Tianbo | Here, we explore solution behavior of fully rigid“block copolymers”hybrid macromolecules based on spherical polyoxometalates and rod-like oligofluorenes. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 799 | Stimuli-responsive phase behavior of block copolymers in ionic liquids | Seitzinger, Claire; Hall, Cecilia; Lodge, Timothy | We explore the light-mediated phase behavior of a diblock copolymer, poly(methyl methacrylate)- b-poly(benzyl methacrylate- s-4-phenylazophenyl methacrylate), in a selective ionic liquid solvent, 1-alkyl-3-methyl imidazolium bis(trifluoromethylsulfonyl)imide. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 800 | Exploring the Limits of Actuation Force Output of Stretch-based Deformation of Liquid Crystalline Elastomers | MCCRACKEN, JOSELLE; Lynch, Kelsey; White, Timothy | We describe several facile approaches for accessing thick LCE actuators (>30x a standard film), including the preparation of devices with interlaid compliant electrodes that allow rapid electrothermal deformation in the multi-laminate LCEs. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 801 | Electro-responsive Ionic Liquid Crystal Elastomers | Feng, Chenrun; Rajapaksha, Chathuranga Prageeth; Kaphle, Vikash; Lussem, Bjorn; Kyu, Thein; Jakli, Antal | We will describe the preparation, physical properties and electric bending actuation of a new class of active materials – ionic liquid crystal elastomers (iLCEs). | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 802 | Voltage-induced deformation in soft dielectric elastomers | Ghosh, Abhishek; Basu, Sumit | We have modelled the behaviour of a soft deformable dielectric body under the combined effect of mechanical loading and electric field through non-linear finite element analysis.These materials are capable of large voltage-induced deformation, but achieving it in practice poses serious challenge due to electromechanical instability and electric breakdown. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 803 | Tough, Responsive and Soft Biomaterials for Tissue Repair and Regeneration | Li, Jianyu | This talk will highlight how to leverage a variety of physical, chemical and mechanical cues to finely tune the interactions between tissues and biomaterials to promote tissue repair and regeneration. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 804 | Flexoionic effect of Ionic Liquid Crystal Elastomers | Rajapaksha, Chathuranga Prageeth; Feng, Chenrun; Piedrahita, Camilo; Albehaijan, Hamad; Kaphle, Vikash; Paudel, Pushpa; Lussem, Bjorn; Kyu, Thein; Jakli, Antal | Here we report the flexoionic effect of iLCEs. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 805 | Statistical field theory model for Liquid Crystal Elastomers | Khandagale, Pratik; Dayal, Kaushik; Majidi, Carmel | We develop a statistical mechanics-based field theoretic model for LCE response to enable us to probe these questions. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 806 | Branching out and back: Reconfigurable nematic drops driven by molecular heterogeneity | Wei, Wei-Shao; Xia, Yu; Ettinger, Sophie; Wang, Yuchen; Yang, Shu; Yodh, Arjun | Here we report reconfigurable nematic liquid crystal oligomer drops, which reveal, surprisingly, that molecular heterogeneity facilitates equilibrium transitions among dramatically different morphological structures, via spatial segregation. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 807 | Imaging crack propagation in tough model gels by ultrasound elastography | Le Blay, Heiva; Deffieux, Thomas; Tanter, Mickael; Marcellan, Alba | This approach offers new insights into soft matter fracture. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 808 | Photoisomerization in a Glassy Matrix: Predicting a Broad Distribution of Dynamics with Machine Learning | Salerno, Kenneth; Sirk, Timothy; De Pablo, Juan | We apply methods from structural analysis of an ideal disordered solid [1] to an all-atom molecular system for the first time, predicting a propensity to isomerize as an analog to “softness.” | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 809 | Response of Polymer Conformations to Crowded Environments | VanDonselaar, Kurt; Kurtti, Matthew; Denton, Alan | To efficiently study conformations of crowded polymers in good solvents, we adopt a coarse-grained model of a polymer as a penetrable ellipsoid whose size and shape fluctuate according to the statistics of a self-avoiding walk [1]. | Session 52: Responsive Polymers, Soft Materials, and Hybrids |
| 810 | Molecular Simulations of Poly[n]catenane Dynamics and Rheology | Rauscher, Phillip; Schweizer, Kenneth; Rowan, Stuart; De Pablo, Juan | We observe unusual monomer diffusion and present a Rouse-like model that can qualitatively explain the results. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 811 | Graft Polymers and Entanglements: From Linear Chains to Filaments | Dobrynin, Andrey; Liang, Heyi; Grest, Gary | Graft Polymers and Entanglements: From Linear Chains to Filaments | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 812 | Effect of Head-to-Head Association/Dissociation on Relaxation of Entangled Chains | Watanabe, Hiroshi; Matsumiya, Yumi; Kwon, Youngdon | Effect of Head-to-Head Association/Dissociation on Relaxation of Entangled Chains | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 813 | Unified analytic expressions for the entanglement length, tube diameter, and plateau modulus in polymer melts | Hoy, Robert; Kröger, Martin | By postulating that the contributions to the dimensionless plateau modulus from flexible-, semiflexible-, and stiff-chain entanglement mechanisms combine additively (in parallel), and testing this postulate with molecular dynamics simulations and topological analyses of Kremer-Grest bead-spring polymer melts, we obtain analytic expressions that quantitatively predict the plateau modulus G, the entanglement length N e, and the tube diameter a in melts that span three orders of magnitude in l K /p, where l K and p are respectively the Kuhn and packing lengths. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 814 | The Source of Strain Hardening in Glassy Polymers Investigated by Molecular Dynamics and Brownian Dynamics Simulations | Larson, Ronald; Hoy, Robert; Moghadam, Soroush; Zou, Weizhong | Using both fine-grained Molecular Dynamics (MD) simulations and coarse-grained simulations we show how strain hardening in polymeric glasses under uniaxial extension arises from highly stretched strands that form as the polymer chains deform subaffinely on increasing length scales as strain increases. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 815 | Predicting time-temperature-superposition breakdown near the glass transition with the Heterogeneous Rouse Model | Simmons, David | Here, we report on predictions of TTS breakdown by the Heterogeneous Rouse Model, which generalizes the Rouse model to incorporate dynamic heterogeneity – the emergence of a distribution of segmental relaxation times at low temperature. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 816 | Relationship Between Large Amplitude Oscillatory Strain (LAOS) Experiments and Commercial Pressure Sensitive Adhesives Applications Testing | Nakatani, Alan; Zhang, Sipei; Ozair, Sehban; Peera, Asghar; Young, Owen; Manning, Kylie; Pearson, Cachae; Ray, Himal | Historically, analytical test methods on pressure sensitive adhesives (PSA’s) have shown poor correlation to applications test results. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 817 | Polymer rheology predictions from first-principles using the slip-link model | Becerra, Diego; Cordoba, Andres; Katzarova, Maria; Andreev, Marat; Venerus, David; Schieber, Jay | Nonetheless, the work demonstrates that theory predictions without adjustable parameters should be possible. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 818 | A priori Determination of the Extensional Viscosity of Polydisperse Linear Polymer Melts | Dorgan, John; Szfranski, John | The algorithm captures molecular details of extensional flow in three dimensions for entangled polymer melts of arbitrary molecular weight distribution across multiple flow regimes from the correct low deformation limit, through the strain-hardening regime, to the high deformation rate strain softening region. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 819 | Thinning and break up of freestanding polymer solutions | Vermant, Jan; Chatzigiannakis, Emmanouil | We have studied the thinning dynamics of concentrated polymer-solutions liquid films experimentally using a modified thin film balance technique. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 820 | Uniaxial Extensional Rheology of Associating Polymers: from Processing to Performance | Hinton, Zachary; Alvarez, Nicolas | In this work, we use filament stretching uniaxial extension to probe the processing window of strongly associating polymers. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 821 | Liquid to soft solid transition in block polymers via low strength magnetic fields | Suresh, Karthika; Calabrese, Michelle | Here, we identify substantial field-induced rheological and structural changes in several coil-coil BCP variants using magneto-rheology and small-angle neutron scattering (SANS). | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 822 | Multiscale simulation of a well-entangled polymer melt flow in between two coaxial cylinders under non-isothermal condition | Hamada, Yuji; Sato, Takeshi; Taniguchi, Takashi | It is also found that the temperature-dependent reptation-time-based Weissenberg number is a suitable measure to understand how extent polymer chains are deformed in a range of the shear rate used in this study. | Session 53: Rheology and Dynamics of Polymer Liquids and Glasses |
| 823 | 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 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 824 | Measuring packing length in simulations for different polymer architectures | Bobbili, Sai Vineeth; Milner, Scott | In this work, we measure the packing length, as the typical distance of closest approach of two polymer strands in a simulated bead-spring melt. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 825 | Influence of Sodium Salts on the Swelling and Rheology of Hydrophobically Crosslinked Hydrogels Determined by QCM-D | Vogt, Bryan; Zhang, Mengxue; Douglas, Jack | Here, we investigate model hydrogels with three different sodium salts with anions chosen from the classic Hofmeister series to determine how these counterions influence the swelling and mechanical properties of neutral hydrogels. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 826 | Effects of humidity on the rheology of supramolecular organogels | Vlassopoulos, Dimitris; Vereroudakis, Emmanouil | Specifically, we investigate the properties of biphenyl tricarboxamides (BPTA) in dodecane which exhibit structural transitions with varying temperature. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 827 | Rheology of Jammed Silicone Microgels | Duraivel, Senthilkumar; Angelini, Thomas | In this presentation, we will describe our investigations of polydimethylsiloxane (PDMS) microgels. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 828 | Predicting the plateau modulus from molecular parameters of conjugated polymers | Fenton, Abigail; Colby, Ralph; Gomez, Enrique | Using small angle neutron scattering (SANS), static light scattering (SLS), and oscillatory shear rheology along with the freely rotating chain model we have shown that nine non-crystalline conjugated polymers and three aromatic polymers not only populate a large part of this gap, but that they follow the proposed relationship between b, p, and GN° as well. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 829 | Accessing Viscoelasticity of PDMS at MHz Frequencies: Physically Intuitive Continuum Mechanics Model for QCM Able to Treat Film Resonance Region | Gagnon, Yannic; Burton, Justin; Roth, Connie | We present a physically intuitive continuum mechanics model with no small frequency-shift approximations that can numerically treat film resonance, accessing a wider range of film thicknesses. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 830 | Viscoelastic properties of tightly entangled polymeric systems | Inoue, Tadashi | In this talk, by combining simultenous mesurement of strain-induced birefringence, the mode separation of orientation, bending, and tension is carried out on on the linear viscoelasticity of the model materials, and the contribution of each mode is quantitatively discussed. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 831 | Microphase Separation in Entangled Polymeric Solutions in Extensional Flows | Nafar Sefiddashti, Mohammad Hadi; Edwards, Brian; Khomami, Bamin | To address these questions, we performed a series of NEMD simulations for entangled C 1000H 2002 polyethylene solutions in oligomeric C 16H 32 and benzene solvents. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 832 | Predicting the Microstructure of Bottlebrush Copolymers | Tabedzki, Christian; Riggleman, Robert | In this talk, we present a field-theoretic model for the structure of bottlebrush copolymers. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 833 | Interactions between two knots in a stretched DNA molecule | Klotz, Alexander; Soh, Beatrice; Doyle, Patrick | We use microfluidic devices to stretch viral genomic DNA molecules in an elongational electric field, and observe the molecules using fluorescence microscopy. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 834 | Diffusion of knots in DNA molecules confined in nanochannels | Ma, Zixue; Dorfman, Kevin | We present experimental data on the diffusion of knots in single DNA molecules via a combination of a nanofluidic "knot factory" device and fluorescence microscopy. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 835 | Dynamics of DNA-bridged particle dumbbells in well-entangled, shear-banding polymer solutions under large amplitude oscillatory shear (LAOS) | Shin, Seunghwan; Dorfman, Kevin; Cheng, Xiang | To elucidate the microscopic dynamics of entangled chains in shear-banding flows, we study the dynamics of DNA-bridged particle dumbbells in the shear-banding flow of well-entangled double-stranded DNA (dsDNA) solutions under LAOS using a rheo-confocal shear cell. | Session 54: Rheology and Dynamics of Polymers and Polyelectrolytes |
| 836 | Adaptive robot morphology and behavioral control policy through responsive composite materials | Kramer-Bottiglio, Rebecca | In this talk, I will introduce several soft robot platforms that can adapt both their shape and behavior to accommodate different tasks or environments. | Session 55: Robophysics |
| 837 | Robots and animals transition from less to more favorable modes to traverse obstacles | Othayoth Mullankandy, Ratan Sadanand; Thoms, George; Li, Chen | To understand what governs the direction of locomotor transitions between modes, we developed and studied a robophysical model traversing beams of variable stiffness. | Session 55: Robophysics |
| 838 | Active adjustments help cockroaches traverse obstacles by lowering potential energy barrier | Wang, Yaqing; Othayoth Mullankandy, Ratan Sadanand; Li, Chen | We are developing a robotic physical model instrumented with force sensors to test this hypothesis. | Session 55: Robophysics |
| 839 | A template model reveals self-righting mechanism of a winged robot | Xuan, Qihan; Li, Chen | We used the model to calculate the potential energy barrier the body must overcome, mechanical energy input by the wings and leg, and energy dissipation due to collision and friction. | Session 55: Robophysics |
| 840 | Testing the effect of scaling on microrobot locomotion performance | Jayaram, Kaushik; Wood, Robert | Here, we present the newly designed HAMR-Jr, a 22.5mm, 320mg quadrupedal microrobot. | Session 55: Robophysics |
| 841 | Tail control decreases jamming of a mechanics-dominated legged robot on rough terrain | Soto, Daniel; Goldman, Daniel | To develop robot locomotion principles which leverage mechanics to simplify control, we study a minimally aware quadrupedal RHex-type robot (~3kg, 20 cm long) walking on a rough terrain composed of blocks with Gaussian height distribution with mean and variance approximately leg length and one-quarter leg length respectively. | Session 55: Robophysics |
| 842 | Modulation of robot orientation by exploiting leg-obstacle collisions through successive choices of gait | Qian, Feifei; Guo, Yongxin; Kathail, Anmol; Koditschek, Daniel | In this study, we show that the basins around these fixed-point headings depend sensitively on the locomotor gaits. | Session 55: Robophysics |
| 843 | A systematic approach to creating terrain-capable hybrid soft/hard myriapod robots | Ozkan-Aydin, Yasemin; Aydin, Enes; Chong, Baxi; Goldman, Daniel | To examine how the variation in body/limb forms of legged animals affects the mechanics of terrestrial locomotion, we built a multi-legged hybrid (soft/rigid) robot that has 8 segments (9 cm/segment), each with two out of phase legs. | Session 55: Robophysics |
| 844 | Basilisk Lizard Bipedal Locomotion on Sand, Mud, and Water: An Insight to Future Morphing Amphibious Robots | Bagheri, Hosain; Gambatese, Marcus; Lentink, David; Marvi, Hamidreza | Basilisk Lizard Bipedal Locomotion on Sand, Mud, and Water: An Insight to Future Morphing Amphibious Robots | Session 55: Robophysics |
| 845 | 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 |
| 846 | Hopping with Elastic Restitution Is More Difficult Than It Seems | McLaughlin, Taylor; Anderson, Marion; Revzen, Shai | We present five generations of three-legged hoppers: four have actuators in series with springs. | Session 55: Robophysics |
| 847 | Recovery of Behaviors of Robots without Dynamics | Council, George; Revzen, Shai | We instead suggest a method that leverages data from examples of successful motion to produce "behavior specifications" as constraints on outputs and states. | Session 55: Robophysics |
| 848 | Modeling of the Primary Animal Gaits by Coupled Identical Raleigh-Van der Pol Oscillators | Asadi-zeydabadi, Masoud; Saffari-Parizi, Mozhdeh; Tagg, Randall | Modeling of the Primary Animal Gaits by Coupled Identical Raleigh-Van der Pol Oscillators | Session 55: Robophysics |
| 849 | Centipede locomotion in varying terrains | Carruthers Ferrero, Alexandra; Diaz, Kelimar; Ozkan-Aydin, Yasemin; Mendelson, Joseph; Goldman, Daniel | We hypothesize that the centipedes will modulate the use of their limbs in order to overcome heterogeneities. | Session 55: Robophysics |
| 850 | Modeling Locomotion in a Segmented Soft Robot using Planar Discrete Elastic Rods | Goldberg, Nathaniel; Huang, Xiaonan; Majidi, Carmel; Novelia, Alyssa; O’Reilly, Oliver; Paley, Derek; Scott, William | In this talk, we describe a simplified planar version of Bergou et al.’s theory and show how it can be used to model soft robots that are composed of segments of soft material folded and bonded together. | Session 55: Robophysics |
| 851 | Geometric mechanics reveals optimal coordination of limb and body waves during centipede locomotion | Chong, Baxi; Schiebel, Perrin; Ozkan-Aydin, Yasemin; Brown, Malcolm; Carruthers, Alexandra; Rieser, Jennifer; Sponberg, Simon; Goldman, Daniel | We decomposed the centipede locomotion into body undulation and leg stepping waves, and used the mathematical framework of geometric mechanics to study body-leg coordination. | Session 55: Robophysics |
| 852 | Geometric Gait Optimization with a five-link wheeled snake | Bittner, Brian; Revzen, Shai | Here, we present a case study on a physical five-link wheeled snake robot. | Session 55: Robophysics |
| 853 | Directional Compliance in Snake Robot Obstacle-Aided Locomotion | Wang, Tianyu; Whitman, Julian; Travers, Matthew; Choset, Howie | To address this problem, we introduce a biologically inspired strategy called directional compliance, which selectively allows some portions of the robot to comply to the environment, while others remain stiff to push off for forward progression. | Session 55: Robophysics |
| 854 | Body compliance helps oscillating snake robots reduce roll instability to traverse large steps | Fu, Qiyuan; Li, Chen | Here, to understand stability principles, we developed a snake robot as a physical model and tested two hypotheses: (1) roll stability diminishes as step becomes higher; and (2) body compliance helps maintain contact and reduce roll instability. | Session 55: Robophysics |
| 855 | Exploring the role of passive mechanics in limbless locomotors via a novel robophysical snake. | Maisonneuve, Marine; Schiebel, Perrin; Goldman, Daniel | To explore the implications of this scheme we developed a robophysical model with passive mechanical flexibility. | Session 55: Robophysics |
| 856 | Amplitude modulation enhances obstacle negotiation for sidewinders | Kaba, Abdul; Rieser, Jennifer; Paez, Veronica; Astley, Henry; Mendelson, Joseph; Goldman, Daniel | To test this, we created a sidewinding robot from a chain of 14 servo motors with alternating direction of actuation. | Session 55: Robophysics |
| 857 | Springs and Wings: Elastic Energy Exchange in Insect Flight | Gau, Jeffrey; Lynch, James; Gravish, Nick; Sponberg, Simon | 2) Does a simple damped elastic model describe bulk mechanical behavior? | Session 55: Robophysics |
| 858 | Springs and Wings: Robophysical investigation of unsteady flapping wing dynamics | Lynch, James; Gau, Jeffrey; Sponberg, Simon; Gravish, Nick | In this talk, we describe experiments to study the control implications of operating spring-wing transmissions on and off resonance. | Session 55: Robophysics |
| 859 | Springs and wings: robophysical and biological investigations inform the design, energetics, and control space for effective flapping wing flight | Lynch, James; Gau, Jeffrey; Sponberg, Simon; Gravish, Nick | Here we present an overview of how elastic structures in flapping wing flight can improve flight energetics while at the same time altering control capabilities. | Session 55: Robophysics |
| 860 | Biologically inspired vision based aerial robot perching | Zhang, Haijie; Zhao, Jianguo | In this research, we propose an optimized two-stage time-to-contact based guidance law. | Session 55: Robophysics |
| 861 | 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 55: Robophysics |
| 862 | Collective Robot Sex on Dynamic Resource Landscapes | Wang, Gao; Phan, Trung; Austin, Robert; Qu, Junle; Liu, Liyu | We present a community of robots (“Jeeps”), which move over a resourc landscape consisting of a large light-emitting diode (LED) light board whose local RGB intensity represents fitness, the local intensity can change due to robot local presence, making the landscape dynamic. | Session 55: Robophysics |
| 863 | Delay Induced Swarm Pattern Bifurcations in Mixed Reality Experiments | Edwards, Victoria; Schwartz, Ira; Szwaykowska, Klementyna; Hindes, Jason; Hsieh, M.; Triandaf, Ioana | We show that multiple rotation patterns persist in the presence of collision-avoidance and uncertainties in the real robot dynamics. | Session 55: Robophysics |
| 864 | Robotic control of live jellyfish swimming to enhance propulsion | Xu, Nicole; Dabiri, John | We demonstrate that by integrating onboard microelectronics into live jellyfish, we can enhance propulsion up to threefold, using only 10 mW of external power input to the microelectronics and at only a twofold increase in cost of transport to the animal. | Session 55: Robophysics |
| 865 | Neuromuscular actuation of biohybrid motile bots | Gazzola, Mattia; Adyin, Onur; Zhang, Xiaotian; Saif, Taher | As a step toward this goal, we computationally designed, optimized, and implemented light-sensitive flagellar swimmers driven by on-board neuromuscular units. | Session 55: Robophysics |
| 866 | Gait coordination and hydrodynamic performance of a quadriflagellate robophysical model | Robinson, Tommie; Diaz, Kelimar; Ozkan-Aydin, Yasemin; Wan, Kirsty; Goldman, Daniel | To study quadriflagellate gait coordination, we developed a robophysical model which replicates quadriflagellate swimming at low-Reynolds number. | Session 55: Robophysics |
| 867 | Locomotion of Soft Robots with Flexible Uni-flagellum in low Reynolds Number Fluid | Du, Yayun | Locomotion of Soft Robots with Flexible Uni-flagellum in low Reynolds Number Fluid | Session 55: Robophysics |
| 868 | Simply controlled 1DOF adaptive soft robotic fish with multiple swimming behaviors | Liu, Bangyuan; Goldman, Daniel; Hammond III, Frank | Research in robotic grasping and soft machines has demonstrated that the use of “smart” mechanical structures in robotic systems can enable complex behaviors in dynamically changing, uncertain environments without the need for complicated, low-level control strategies. | Session 55: Robophysics |
| 869 | Magnetic Actuation and Biological Sensing for Soft Micro Bio Robots | Hunter, Elizabeth; Steager, Edward; Kumar, Vijay | In this talk, we will discuss our distinct approach to actuation and sensing through the design and fabrication of soft micro bio robots composed of an organic hydrogel embedded with iron oxide nanoparticles. | Session 55: Robophysics |
| 870 | Surface electrochemical actuators for micron-scale fluid pumping and autonomous swimming | Reynolds, Michael; Cortese, Alejandro; Liu, Qingkun; Wang, Wei; Cao, Michael; Muller, David; Miskin, Marc; Cohen, Itai; McEuen, Paul | Our ultimate goal is to create fully autonomous swimming microrobots with onboard electronics that can sense and respond to their environment in complex ways, yet are too small to be resolved by the naked eye. | Session 55: Robophysics |
| 871 | Material remodeling on granular terrain yields robustness benefits for a robophysical rover | Shrivastava, Siddharth; Karsai, Andras; Ozkan-Aydin, Yasemin; Pettinger, Ross; Bluethmann, William; Ambrose, Robert; Goldman, Daniel | We created a miniature rover (2.1 kg) as a robophysical model of RP-15 and conducted systematic and automated experiments in a tilting bed containing a model granular medium (poppy seeds) to discover gaits which allow progress in various conditions. | Session 55: Robophysics |
| 872 | Investigating Growth and Granular Fluidization in a Minimally Invasive Burrowing Robot | Naclerio, Nicholas; Murray-Cooper, Mason; Karsai, Andras; Ozkan-Aydin, Yasemin; Goldman, Daniel; Hawkes, Elliot | Here we present a paradigm for minimally invasive robotic burrowing that results in movement an order of magnitude faster and deeper than previous low-impact approaches. | Session 55: Robophysics |
| 873 | Force response of running up a sand dune | Chang, Brian; Greenwood, Alexander; Nowayti, Waleed; Hsieh, Tonia | In this study, we experimentally examined the impact force normal to a flat plate against a bed of poppy seeds, to determine how intrusion kinematics affect force generation. | Session 55: Robophysics |
| 874 | Generation GrowBots: learning from plants how to design self-morphing, growing robots | Mazzolai, Barbara; Del Dottore, Emanuela; Margheri, Laura; Mondini, Alessio; Tramacere, Francesca | For the first time, we have proposed a growing robot inspired by the movements and the behaviors of plant roots, able to create its own structure exploiting a 3D printer-like system integrated into its tip and depositing a thermoplastic material. | Session 55: Robophysics |
| 875 | Controlling robot dynamics via environmental deformations | Gynai, Hussain; Li, Shengkai; Ozkan-Aydin, Yasemin; Dominguez, Camila; 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 robot driving on a deformable spandex membrane (d=2.4m) with a static central depression (Li et al., 2019). | Session 56: Robophysics IV and Animal Behavior |
| 876 | Modeling and simulation of complex dynamic musculoskeletal architectures | Zhang, Xiaotian; Chan, Fan Kiat; Parthasarathy, Tejaswin; Gazzola, Mattia | In order to facilitate the understanding of the biophysical mechanisms at play and to streamline their potential use in engineering applications, we present here a versatile and robust numerical approach to the simulation of musculoskeletal architectures. | Session 56: Robophysics IV and Animal Behavior |
| 877 | Chrono: A multi-physics engine for simulation of robophysical systems | Rakhsha, Milad; Serban, Radu; Negrut, Dan | We present the latest capabilities of a multi-physics platform, called Chrono, that allows for computer modeling and simulation of such systems. | Session 56: Robophysics IV and Animal Behavior |
| 878 | Synchrono: A simulation framework for machine learning in multi-robot applications. | Elmquist, Asher; Serban, Radu; Negrut, Dan | We present here a simulation infrastructure designed to allow for safe, low-cost, and rapid development, testing, and evaluation of robot control strategies particularly in scenarios that are difficult or impossible to test in reality. | Session 56: Robophysics IV and Animal Behavior |
| 879 | Learning to locomote in the presence of symmetry | Kelly, Scott | This talk will discuss the use of symmetry to improve the economy with which a physical robot can learn to locomotive efficiently. | Session 56: Robophysics IV and Animal Behavior |
| 880 | Nonlinear distance and velocity estimation from optic flow | van Breugel, Floris | We propose that this approach to integrating multiple sensory modalities during dynamic motion, which we refer to as idiokinemetry, is likely a general feature of how animals perceive the world, and may inspire the development of smaller and more robust robotic systems. | Session 56: Robophysics IV and Animal Behavior |
| 881 | Raising head facilitates antenna cleaning in a honey bee | Zhang, Wei; Wu, Jianing; Wu, Zhigang | By high-speed imaging, we find that the honey bee raises its head while grooming antennae by forelegs. | Session 56: Robophysics IV and Animal Behavior |
| 882 | Large scale quantitative phenotyping of aversive behaviour and habituation in C. elegans | Feriani, Luigi; Barlow, Ida; McDermott-Rouse, Adam; Brown, Andre | We have combined robotic liquid handling, multi-camera imaging systems, and tracking software in a high-throughput pipeline that can record from about 500 samples simultaneously. | Session 56: Robophysics IV and Animal Behavior |
| 883 | Using robotics and physics to understand the evolution of novel functional morphologies | Flammang, Brooke; Gamel, Kaelyn; Garner, Austin | Herein, we translated fundamental biological principles into engineering design rules and show that a passive model system can autonomously achieve adhesive forces measured in live remoras in any environment. | Session 56: Robophysics IV and Animal Behavior |
| 884 | Electrically Programmable Micro-Scale Shape Memory Devices | Liu, Qingkun; Wang, Wei; Reynolds, Michael; Miskin, Marc; Cao, Michael; Muller, David; McEuen, Paul; Cohen, Itai | We demonstrate microscale shape memory devices capable of achieving micrometer bending radius with a holding time of several tens of hours. | Session 56: Robophysics IV and Animal Behavior |
| 885 | The radical pair mechanism can provide a sensitive and robust magnetic compass for birds. | Strausser, Shawn; Ritz, Thorsten | The radical pair mechanism can provide a sensitive and robust magnetic compass for birds. | Session 56: Robophysics IV and Animal Behavior |
| 886 | Breathing from Underground: Diurnal Variability in the Ventilation Mechanism of Termite Mounds | Saxena, Saurabh; Yaghoobian, Neda | This study investigates the underlying physics of the ventilation mechanisms in termite mounds. | Session 56: Robophysics IV and Animal Behavior |
| 887 | Specialisation and plasticity in a primitive social insect | Patalano, Solenn; Alsina, Adolfo; Reik, Wolf; Rulands, Steffen | We show that stability of the nest relies on epigenetic DNA modifications that suppress transcriptional noise. | Session 56: Robophysics IV and Animal Behavior |
| 888 | Hydrodynamics of sheep herds | Sarfati, Raphael; de Marcken, Marine; Peleg, Orit | By employing optical flow methods to measure the velocity field of dense sheep herds, we construct a hydrodynamics framework to study the collective motion of living systems flowing like liquids. | Session 56: Robophysics IV and Animal Behavior |
| 889 | The decision-making and mechanics of honey bee swarm formation | Nave, Gary; Peleg, Orit | In this work, we present both experimental results and computational modeling on the process of swarm formation to address questions of decision-making as bees join the swarm and the mechanical properties of bees within the swarm. | Session 56: Robophysics IV and Animal Behavior |
| 890 | Using Information Geometry to find simple models of complex processes | Transtrum, Mark | Often, these models are related through a hierarchy of simplifying approximations that formally justify their respective domains of validity. | Session 57: Searching for Simplicity: Information Geometry and Model Reduction |
| 891 | Finding and explaining structural hierarchies in models of complex systems | Quinn, Katherine | By unifying information geometric interpretations of sloppiness with Chebyshev approximation theory, I will derive a formal and systematic explanation of why sloppiness occurs. | Session 57: Searching for Simplicity: Information Geometry and Model Reduction |
| 892 | Identifiability, uncertainty, and parameter reduction in mathematical biology | Eisenberg, Marisa | In this talk, I will discuss some of the ideas and methods from identifiability, how they link to ideas of model reduction and model selection, and present public health applications to recent epidemics of polio and cholera. | Session 57: Searching for Simplicity: Information Geometry and Model Reduction |
| 893 | Manifold Learning for Parameter Reduction | Kevrekidis, Yannis | Here, we explore systematic, data-driven parameter reduction by means of effective parameter identification, starting from current nonlinear manifold-learning techniques enabling state space reduction. | Session 57: Searching for Simplicity: Information Geometry and Model Reduction |
| 894 | How do cells control the length of their flagella? | Kar, Prathitha; Fai, Thomas; Mohapatra, Lishibanya; Kondev, Jane; Amir, Ariel | Here, we show that within a wide class of models, length-control of multiple flagella can only occur if the disassembly (depolymerization) of the flagella is length-dependent. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 895 | Size regulation of multiple intracellular structures self-assembled from a shared resource pool | Banerjee, Deb; Banerjee, Shiladitya | Here we present a physical theory for non-equilibrium self-assembly and size regulation of sub-cellular structures, based on negative feedback between structure size and growth rate. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 896 | Energy cost of protein gradient formation in cells | Datta, Arnab | In this talk I examine different mechanisms of gradient formation in cells and estimate the energy costs associated with them. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 897 | First passage times in multi-protein self-assembly | MISHRA, BHAVYA; Johnson, Margaret | We formulate the self-assembly of protein binding pairs as first-passage problems and calculate the mean time to approach the thermodynamic equilibrium. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 898 | Quantifying kinetics of multi-protein self-assembly, remodeling, and disassembly | FU, YIBEN; Johnson, Margaret | We show here using reaction-diffusion simulations how the kinetics of these assembly and disassembly processes can be sensitively tuned by the binding kinetics and cooperative interactions of the coat components and the molecules linking them to the membrane. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 899 | Theoretical principles of viral shell assembly and self-organization | Zandi, Roya | We find that the ground states consist of positive disclination defects and that the ground states with icosahedral subgroup symmetries in caps arise across a range of curvatures, even far from the closure point of complete shells. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 900 | Computational modeling to explain Hepatitis-B Virus capsid assembly, dimorphism, and disruption by antiviral drugs | Mohajerani, Farzaneh; Tyukodi, Botond; Schlicksup, Christopher; Hadden, Jodi; Zlotnick, Adam; Hagan, Michael | In this talk we will describe dynamical computer simulations of HBV assembly, using a model which is minimal and highly computationally tractable, but has parameters learned from atomistic simulation data of whole HBV capsids. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 901 | Thermodynamic and kinetic aspects of polymorphism in core controlled assembly of virus-like particles | Ramezani, Alireza; Karachalios, Orfeas Agis; Van der Schoot, Paul; Zandi, Roya | Our goal is to understand how protein concentration, stoichiometry and preferred curvature of capsids influence the prevalence of one shell size over another one. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 902 | RNA-mediated capsid nucleation of bacteriophage MS2 coat proteins confers RNA packaging selectivity | Chiang, Timothy; Garmann, Rees; Goldfain, Aaron; Williams, LaNell; Manoharan, Vinothan | Using interferometric scattering microscopy and quantitative gel electrophoresis, we show that the RNA-mediated nucleation-and-growth assembly pathway of MS2 coat proteins can drive preferential encapsidation of cognate RNA, and hence selective packaging. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 903 | Role of C-Terminal "Arms" in the Assembly and Stability of SV40 Polymorphs | Waltmann, Curt; Olvera De La Cruz, Monica; Asor, Roi; Raviv, Uri | We study SV40 polymorphs by simulating the templated assembly process of VP1 pentamers. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 904 | Linking Capsomere Elasticity with Virus Capsid Size and Patterning | Nilsson, Lauren; Kadupitiya, JCS; Jadhao, Vikram | We introduce SOUFFLE, a molecular dynamics simulation method with elastic capsomeres, to investigate capsid assembly. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 905 | Bulk light-scattering measurements of viral capsid self-assembly around RNA. | Williams, LaNell; Chiang, Timothy; Garmann, Rees; Manoharan, Vinothan | To better understand this process, we modify the interactions between coat proteins and between the coat proteins and RNA of MS2 bacteriophage in vitro by varying the ionic strength and pH, and we study the assembly using dynamic and static light scattering. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 906 | Membrane tubulation induced by chiral crescent-shaped proteins | Noguchi, Hiroshi | We studied the protein assembly and membrane remodeling using coarse-grained meshless membrane simulations. | Session 58: Self-Limiting Assemblies: Functional Structures in Biology |
| 907 | Finite-Size Colloidal Constructs Designed through Self-Assembly of Defective Colloidal Molecules | Parvez, Nishan; Zanjani, Mehdi | In this study, we use computational techniques to identify, investigate, and exploit self-assembly paradigms that are made possible through the use of defective colloidal molecules. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 908 | Self-assembly of protein-made structures | Curatolo, Agnese; Goodrich, Carl; Kimchi, Ofer; Brenner, Michael; Hsia, Yang; Chen, Zibo; Boyken, Scott; Baker, David | Here I will present different approaches that one can take to predict the yield of protein-made structures and address the difficulties of relating statistical mechanics models and real world experiments. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 909 | Programmable self-assembly of DNA origami capsids based on the principles of virus structure. | Fraden, Seth | We provide a general and modular solution for building synthetic icosahedral shells on the scale of 100 nm, motivated by the 1962 Caspar and Klug theory of virus structure. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 910 | Functionalized DNA origami shells for cargo encapsulation | Aghvami, S.Ali; SIgl, Chris; Willner, Elena; Dietz, Hendrik; Fraden, Seth | We demonstrate a robust method for self-assembly of virus like DNA origami capsids of various sizes by designing specific capsomers with programmable shape complementary lock and key interactions. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 911 | Structural and mechanical properties of nucleic acid nanotubes: A combined all-atom and coarse-grained molecular dynamics study | Naskar, Supriyo; Joshi, Himanshu; Gosika, Mounika; Chakraborty, Banani; Seeman, Nadrian; Maiti, Prabal | In this work, we introduce a computational framework to model nucleic acid nanotubes and estimate their mechanical properties using various levels of theory. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 912 | Self-assembly of DNA origami particles into self-limited surfaces | Hayakawa, Daichi; Hall, Douglas; SIgl, Chris; Grason, Gregory; Rogers, William | In this talk, I will present experimental results showing that we can mimic these features using DNA origami. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 913 | Frustration in the absence of Gaussian Curvature: what we learned from colloidal crystallization on a cylinder | Tanjeem, Nabila; Wilkin, William; Rycroft, Christopher; Manoharan, Vinothan | We demonstrate the effects of a closure constraint on a crystal in the absence of Gaussian curvature. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 914 | Self-Assembly of Triply-Periodic Minimal Surfaces, An “Inverted” Caspar-Klug Approach | Duque, Carlos; Hall, Douglas; Tyukodi, Botond; Hagan, Michael; Grason, Gregory; Santangelo, Christian | In this work, we are interested in studying an “inverted” Caspar-Klug problem, focussed primarily on structures with negative Gaussian curvature. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 915 | Colloidal crystallization on a cone | Sun, Jessica; Tanjeem, Nabila; Manoharan, Vinothan | We study the self-assembly of colloidal spheres on the surface of a cone, which has zero Gaussian curvature but varying mean curvature. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 916 | Programming extrinsic geometry to control membrane self-assembly | Hall, Douglas; Stevens, Mark; Grason, Gregory | In this talk, we show how an additional molecular shape parameter separately controls the extrinsic geometry (i.e. the directionality of curvature axis relative to inter-block packing directions), modulates the intrinsic frustration energetics and influences the size scale over which frustration stress accumulate in the assembly. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 917 | Dynamical and equilibrium calculations of self-limited assembly through geometric frustration | Tyukodi, Botond; Mohajerani, Farzaneh; Grason, Gregory; Hagan, Michael | In this talk, we use a recently developed dynamical MC algorithm and free energy calculations to study the assembly of subunits that undergo frustrated assembly. | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 918 | Emergence of fiber in frustrated self assembly | Le Roy, Hugo; Lenz, Martin; Terzi, Mert | In this work, we use statistical physics tools to investigate the thermodynamic stability of such fibers in more realistic conditions | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 919 | Role of Geometrical Frustration in Self-limiting Enantioselective Synthesis of Chiroptical Helices | kumar, prashant; Yan, Jiao; Simon, Alexander; Katz, Daniel; Hall, Douglas; Grason, Gregory; Kotov, Nicholas | Herein, we present a colloidal synthesis route for enantiopure bow-ties by guiding the electrostatic and coordination interactions between cadmium ions and chiral amino acid cysteine (Cys). | Session 59: Self-Limiting Assemblies: Programmable Assemblies |
| 920 | Pitch-balanced helical motifs in tightly packed lamellar structures | Efrati, Efi | In this talk, I will show that the lamellar structures that house photosynthesis in some plants, the thylakoid, also display right and left-handed motifs. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 921 | Colloidal membrane thickness sets critical surface area for vesicle formation | Robaszewski, Joanna; Jia, Leroy; Powers, Thomas; Pelcovits, Robert; Dogic, Zvonimir | We use colloidal membranes as experimental models to study the forces governing vesicle formation. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 922 | How Curvature and Tension Direct Morphology and Interactions of Solid Membrane Domains in Fluid Vesicles | Santore, Maria; Xin, Weiyue; Wan, Hao | The curvature imposed we show that at sufficiently high tensions, the curvature imposed by global vesicle shape influences the growth of solid domains, producing deviations from hexagon domain shape to include edge instabilities that appear as flowers. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 923 | Collapse and folding of flexible colloidal polymers | McMullen, Angus; Brujic, Jasna | Unlike periodically repeating structures, here we introduce a new paradigm of self-assembly in which flexible colloidal polymers find a ‘fold’, similar to the way polypeptides fold into proteins. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 924 | Dissolving a DNA liquid through competition | Abraham, Gabrielle; Saleh, Omar | Here, we employ a model DNA liquid system and quantify the dissolution by short nucleic acids. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 925 | Theory and simulation of reaction diffusion models of self-limiting droplet formation | GrandPre, Trevor; Limmer, David | We discuss ways in which macroscopic domains can be avoided by slow coarsening dynamics accompanying gelation or active processes that modulate Ostwald ripening. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 926 | Nonequilibrium Variational Control Forces for Self-Limited Colloidal Assembly | Das, Avishek; Limmer, David | We discuss a variational principle for the optimization of interparticle and nonequilibrium driving forces, which lead to robust assembly of self-limited clusters. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 927 | Kinetic entrapment: a mechanism for periodic one-dimensional growth | Witten, Thomas; Lenz, Martin | Here we propose a common kinetic mechanism in which the next growth site is a generic, deterministic function of the current aggregate configuration. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 928 | Pattern recognition through molecular self-assembly | Evans, Constantine; O’Brien, Jackson; Winfree, Erik; Murugan, Arvind | We test the system with numerous concentration patterns and confirmed nucleation-based pattern recognition through Atomic Force Microscopy (AFM) and fluorescence measurements. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 929 | Strain-Adaptive Self-Assembled Networks of Linear-Bottlebrush-Linear Copolymers | Liang, Heyi; Wang, Zilu; Dobrynin, Andrey | We study the strain-adaptive behavior of the self-assembled networks of linear-bottlebrush-linear ( LBL) triblock copolymers using a combination of analytical calculations and molecular dynamics simulations. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 930 | Self-directed Self-assembly of Block Copolymers | Huang, Hejin; Alexander-Katz, Alfredo | Here, we introduce a novel method, which enables self-directed self-assembly of 3D tailored nanostructures. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 931 | Identification of a Frank–Kasper Z phase from shape amphiphile self-assembly | Cheng, Stephen; Huang, Mingjun; Su, Zebin | Identification of a Frank–Kasper Z phase from shape amphiphile self-assembly | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 932 | Theory of Complex Spherical Packing Phases in Surfactant Systems | Xie, Jiayu; Lai, Chi To; Shi, Anchang | Theoretically, we model the surfactant molecules by short diblock copolymers composed of a hydrophilic head and a hydrophobic tail. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 933 | Predictive Modeling of Dendrimer Directed Nanoparticle Self-Assembly | Vo, Thi; Elbert, Katherine; Krook, Nadia; Zygmunt, William; Park, Jungmi; Yager, Kevin; Composto, Russell; Glotzer, Sharon; Murray, Christopher | Here, we present a combined experimental and theoretical study in which a series of dendrimer ligands are used to direct the assembly of nanoplates into 2D and 3D geometries. | Session 60: Self-Limiting Assemblies: Soft Assemblies and In and Out of Equilibrium |
| 934 | Multi-scanning of single DNA Molecules in a Dual Nanopore Device | Liu, Xu; Zimny, Philip; Zhang, Yuning; Rana, Ankit; Nagel, Roland; Reisner, Walter; Dunbar, Willam | Here we present a single-molecule manipulation and sensing approach based on a dual nanopore device that can linearize DNA and improve read quality by enabling repeated scanning at reduced speeds of the same molecule. | Session 61: Single-Molecule Techniques and Enzymes |
| 935 | Computational design and interpretation of single-RNA translation experiments. | Aguilera, Luis; Raymond, William; Lyon, Kenneth; Morisaki, Tatsuya; Stasevich, Timothy; Munsky, Brian | With this, we present an interpretation for the well-established experimental procedures, including Correlation Spectroscopy, ribosome Run-Off Assays, and FRAP (Aguilera, L., et al., 2019, Plos Comp Biology). | Session 61: Single-Molecule Techniques and Enzymes |
| 936 | Single-Molecule Sensitivity in Mass Spectrometry Using Nanoscale Ion Sources | Drachman, Nicholas; LePoitevin, Mathilde; Wiener, Benjamin; Stein, Derek | We have shown that a nanoscale ion source allows ions to evaporate directly off of the meniscus, bypassing the wasteful droplet evaporation process. | Session 61: Single-Molecule Techniques and Enzymes |
| 937 | Brownian motion alone may not be sufficient to supply ribosomes with tRNA during translation elongation | Maheshwari, Akshay; Gonzalez Gonzalez, Emma del Carmen; Sunol, Alp; Endy, Drew; Zia, Roseanna | To test our hypothesis we introduce translation elongation in E. coli as a model system. | Session 61: Single-Molecule Techniques and Enzymes |
| 938 | Enhanced diffusion and enzyme dissociation at high substrate concentration | Jee, Ah-Young; Chen, Kuo; Tlusty, Tsvi; Zhao, Jiang; Granick, Steve | Here we show that urease and certain other oligomeric enzymes of high catalytic activity above kM dissociate into their smaller subunit fragments that diffuse more rapidly, thus providing a simple physical mechanism of enhanced diffusion in this regime of concentrations. | Session 61: Single-Molecule Techniques and Enzymes |
| 939 | Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells | Chen, Kevin; Zuckerman, Daniel; Nelson, Phil | After introducing the stochastic simulation algorithm, we give two case studies, involving gene expression and error correction, respectively. | Session 61: Single-Molecule Techniques and Enzymes |
| 940 | Single-pair measurements of nonradiative energy transfer efficiency between quantum dots and organic dyes reveals orientational variation | Shatery Nejad, Nooshin; Etson, Candice | We used two methods to construct these assemblies. | Session 61: Single-Molecule Techniques and Enzymes |
| 941 | Bayesian nonparametrics allow for super resolution microscopy without photo-switching | Sgouralis, Ioannis | In the talk, I will walk through recent modeling advances and highlight how Bayesian nonparametrics can be used to achieve super resolved localization of single molecules without photo-switching and so allowing for super resolution microscopy with less specialized fluorophores and significantly shorter experiments. | Session 61: Single-Molecule Techniques and Enzymes |
| 942 | Intensity Distribution of a Dilute Solution of Point Emitters under Gaussian Detection | Strey, Helmut | Here we develop a general framework for calculating the intensity distribution of a dilute solution of Point emitters under Gaussian Detection. | Session 61: Single-Molecule Techniques and Enzymes |
| 943 | Reliable Imaging of Dynamic Structures in Live-Cell Super-Resolution | Andrews, J Owen; Cisse, Ibrahim | In this talk, I will present a metric for assessing image reliability, based on robust estimation of the density of detected molecules. | Session 61: Single-Molecule Techniques and Enzymes |
| 944 | Controlled sliding of DNA knots in solid-state nanopores | Sharma, Rajesh; Agrawal, Ishita; Dai, Liang; Doyle, Patrick; Garaj, Slaven | Recently, we showed nanopores that probe the equilibrium structures of DNA knots in solutions. | Session 61: Single-Molecule Techniques and Enzymes |
| 945 | Optimal Control and Reinforcement Learning of Regulation and Enzyme Activities | Britton, Samuel; Alber, Mark; Hurley, Jennifer; Jankowski, Meaghan; Zucker, Jeremy; Baker, Scott; Kelliher, Tina; Dunlap, Jay; Cannon, William | In this study, we use statistical thermodynamics and metabolic control theory as a theoretical framework to calculate enzyme regulation policies for controlling metabolite concentrations to be consistent with experimental values. | Session 61: Single-Molecule Techniques and Enzymes |
| 946 | Binding Energies of Fn Cas12a | Rigas, Pete | Thermodynamically, we can model determinants of binding energies for different sites of the genome with a partition function that reflects energetic costs associated with base pair mismatches. | Session 61: Single-Molecule Techniques and Enzymes |
| 947 | Statistical Physics of Noninteracting Bacterial Populations | Jafarpour, Farshid | In this talk, I will take these phenomenological models as the microscopic dynamics of individual cells to quantitatively predict the macroscopic properties of populations both in batch and chemostat settings. | Session 62: Statistical Physics of Large Populations of Cells: from Microbes to Tissues |
| 948 | Optimal segregation of key proteins in microbes | Min, Jiseon; Amir, Ariel | We study the population growth in the presence of asymmetric segregation and find, generically, a phase transition occurring between a regime where asymmetry is beneficial to one where it is detrimental. | Session 62: Statistical Physics of Large Populations of Cells: from Microbes to Tissues |
| 949 | Understanding Cell Size Homeostasis and Phenotypic Switching Dynamics during Bacterial Filamentation | Chen, Yanyan; Buceta Fernandez, Javier | To answer these questions, we have modeled the bacterial growth and division processes during filamentation and performed analyses of experimental phenotypic lineage trees. | Session 62: Statistical Physics of Large Populations of Cells: from Microbes to Tissues |
| 950 | Effect of non-genetic inheritance dynamics on the variation in cellular traits | Vashistha, Harsh; Kohram, Maryam; Salman, Hanna | In this talk, we will introduce a new experimental technique based on trapping sister bacterial cells in microfluidic channels immediately after they separate from a single mother. | Session 62: Statistical Physics of Large Populations of Cells: from Microbes to Tissues |
| 951 | A large deviation principle linking lineage statistics to fitness | Levien, Ethan; GrandPre, Trevor; Kondev, Jane; Amir, Ariel | Using a large deviation approach, we present a procedure for inferring a population’s fitness from lineage statistics that is independent of the model specifics. | Session 62: Statistical Physics of Large Populations of Cells: from Microbes to Tissues |
| 952 | A Sensitivity Analysis of Growth Rate to Perturbations in Essential Gene Expression | Bardetti, Paola; Rojas, Enrique | To elucidate the genetic basis for cell growth, we performed an essential genome-wide stability analysis of single-cell growth rate upon CRISPRi-mediated perturbation in gene expression. | Session 62: Statistical Physics of Large Populations of Cells: from Microbes to Tissues |
| 953 | Modeling and Optimizing Treatments of Bacterial Infections by Phage and Phage-Antibiotic Combinations | Leung, Chung Yin; Rodriguez-Gonzalez, Rogelio; Li, Guanlin; Wardi, Yorai; Weitz, Joshua | In such cases, we consider two strategies proposed to enhance the robustness of phage therapy: combining phage with antibiotics and combining different strains of phage (phage cocktail). | Session 62: Statistical Physics of Large Populations of Cells: from Microbes to Tissues |
| 954 | New homeostatic principles in biology – how cells go back to their normal size without feedback | Jun, Suckjoon | In this talk, I will focus on cell-size control and homeostasis, a fundmental problem that has been rapidly transforming just in the past few years. | Session 62: Statistical Physics of Large Populations of Cells: from Microbes to Tissues |
| 955 | Scattering of a fast-swimming bacterium off of a surface | Petroff, Alexander; Mcdonough, Schuyler; Roque, Benjamin | Here we present the first experimental observations of the scattering of a fast-swimming bacterium off of a flat surface. | Session 63: Swimming, Motility, & Locomotion |
| 956 | Optically-Powered Microscopic Bubble Rockets | Norris, Samantha; Reynolds, Michael; Cortese, Alejandro; McEuen, Paul | In this talk, we demonstrate a new optically-powered approach to catalyst-free bubble self-propulsion that works in a broad range of fluids, including deionized water. | Session 63: Swimming, Motility, & Locomotion |
| 957 | Antagonism in multiple-cue chemotaxis in breast cancer cells | Saha, Soutick; Moon, Hye-ran; Han, Bumsoo; Mugler, Andrew | We used triple-negative breast cancer cells to study chemotaxis towards cues formed by multiple growth factors and found, surprisingly, that the bias in the movement was less pronounced when we combine two attractant gradients compared to when we have individual gradients. | Session 63: Swimming, Motility, & Locomotion |
| 958 | A universal mechanism for chiral swimming at low Reynolds number | Cortese, Dario; Wan, Kirsty | We combine theory and experiment to reveal how Chlamydomonas actively modulates asymmetries in flagellar beating to produce axial rotation and steering. | Session 63: Swimming, Motility, & Locomotion |
| 959 | Bacterial swarming: Motion under extreme forces? | Gudavadze, Irakli; Korf, Janelle; Florin, Ernst-Ludwig | Here we present a novel method for measuring film thickness with tens of nanometer precision. | Session 63: Swimming, Motility, & Locomotion |
| 960 | Analysis of run-reverse-reorient motility of Helicobacter pylori and its ΔChePep mutant1 | Liao, Wentian; Constantino, Maira; Amieva, Manuel; Bansil, Rama | We analyze translational and cell body rotational motility data obtained by phase contrast microscopy to compare the speed and turn angle distribution of the wild type (WT) with the ΔChePep mutant and compare with run-reversal-reorient model and Resistive Force Theory calculations of torque. | Session 63: Swimming, Motility, & Locomotion |
| 961 | Force and torque on a rotating helical flagellum near a boundary | Rodenborn, Bruce; Romero, Cesar; Lee, Jin; Nguyen, Hoa; Shindell, Orrin | We show that all of the data can be collapsed onto a single curve by non-dimensionalizing the force, torque and boundary distance appropriately. | Session 63: Swimming, Motility, & Locomotion |
| 962 | A minimal neural reaction-diffusion model which generates C. elegans undulation | Hastings, Harold; Magnes, Jenny; Susman, Kathleen; Congo, Cheris; Hulsey-Vincent, Miranda; Singhvi, Anshul; Tasnim, Rifah; Negassa, Naol | We describe a minimal reaction-diffusion model for the C. elegans central pattern generator (CPG) (c.f. Xu et al. 2018, Wen et al. 2012). | Session 63: Swimming, Motility, & Locomotion |
| 963 | Swimmers at low Reynolds number driven by Quincke rotation | Han, Endao; Zhu, Lailai; Shaevitz, Joshua; Stone, Howard | Here we present an artificial swimmer at low Reynolds number driven by an elasto-electro-hydrodynamic instability [1] based on Quincke rotation: a sphere in oil rotates in the presence of a high DC electric field. | Session 63: Swimming, Motility, & Locomotion |
| 964 | Aerotaxis in Sinorhizobium meliloti, a soil bacterium | Bouvard, Julien; Moisy, Frederic; Auradou, Harold | To study and compare this not yet referenced aerotaxis to the already found chemotaxis, we made a few experimental set-ups. | Session 63: Swimming, Motility, & Locomotion |
| 965 | Pairwise and Collective Interactions of a Model Swimmer at Intermediate Reynolds Numbers | Dombrowski, Thomas; Bhalla, Amneet Pal Singh; Griffith, Boyce; Klotsa, Daphne | In this presentation, we investigate pairwise interactions between reciprocal, asymmetric dumb-bell swimmers at intermediate Reynolds numbers (Re). | Session 63: Swimming, Motility, & Locomotion |
| 966 | Hydrodynamics of biomimetic propulsion using externally and internally actuated fins | Demirer, Ersan; Alexeev, Alexander | We combine experiments and computer simulations to examine the hydrodynamics of two different actuation types that can be used to actuate an elastic plate to serve as a biomimetic propulsor in robotic fish. | Session 63: Swimming, Motility, & Locomotion |
| 967 | The ecology and evolution of collective behavior | 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 64: The Many Dimensions of Evolution |
| 968 | 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 64: The Many Dimensions of Evolution |
| 969 | 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 64: The Many Dimensions of Evolution |
| 970 | 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 64: The Many Dimensions of Evolution |
| 971 | Phenotypic heterogeneity between genetically identical cells permits growth with lethal levels of formaldehyde stress | Lee, Jessica; Riazi, Siavash; Nemati, Shahla; Bazurto, Jannell; Vasdekis, Andreas; Ridenhour, Benjamin; Remien, Christopher; Marx, Christopher | Here, we report the discovery of a novel example of microbial phenotypic heterogeneity in which cells are distributed along a gradient of phenotypes, ranging from low to high tolerance of a toxic chemical. | Session 64: The Many Dimensions of Evolution |
| 972 | Self-driven phase transitions in living matter | Shaevitz, Joshua | I will present an overview of how these cells move and how they regulate that motion to produce different phases of collective behavior. | Session 65: Theory Meets High-Precision Biology: Emergent Simplicity in Stochastic Organismal Dynamics |
| 973 | Stochastic intergenerational cell size homeostasis: Precision measurements, exact kinematics and emergent simplicities | Iyer-Biswas, Srividya | In this talk I will first establish that intergenerational bacterial cell size homeostasis is maintained under appropriate growth conditions, using our high-precision data on growth and division of individual C. Crescentus cells. | Session 65: Theory Meets High-Precision Biology: Emergent Simplicity in Stochastic Organismal Dynamics |
| 974 | Jamming and dynamic arrest in sheltered microbial communities | Hallatschek, Oskar | By monitoring and modeling microbial populations under controlled microfluidic confinement, we find a rich spectrum of dynamical patterns that are controlled by the competition between density-dependent outflow and population growth. | Session 65: Theory Meets High-Precision Biology: Emergent Simplicity in Stochastic Organismal Dynamics |
| 975 | How cell growth triggers cell division | Skotheim, Jan; Zatulovskiy, Evgeny; Xie, Shicong; Zhang, Shuyuan; Koivomagi, Mardo; Topacio, Benjamin; Berenson, Daniel | Rather, we found that cell growth acts in the opposite manner. | Session 65: Theory Meets High-Precision Biology: Emergent Simplicity in Stochastic Organismal Dynamics |
| 976 | Stress and velocity fluctuations in photoelastic granular avalanches | Vriend, Nathalie; Thomas, Amalia; Daniels, Karen | In this study, we analyze the correlation between velocity fluctuations and stress fluctuations in both the quasi-steady layer (close to the rough base) and the flowing layer (near the free surface). | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 977 | Photoelastic Analysis of Cohesive Granular Aggregates | Patterson, Carter; Kollmer, Jonathan; Brzinski, Theodore | We present photoelasticimetric force measurements of systems of particles which exhibit attractive interparticle forces, and contrast the structure of force networks in these systems with the networks in purely repulsive aggregates. | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 978 | Optical characterization of underwater contact mechanics | Sun, Mengyue; Kaur, Sukhmanjot | Here, we present a simple, FTIR-based imaging technique to spatially resolve and quantify thickness of nanoscopic puddles formed between two solids in contact under water. | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 979 | Worms in Jell-O: Using photoelastic stress analysis to measure burrowing forces | Dorgan, Kelly | Worms in Jell-O: Using photoelastic stress analysis to measure burrowing forces | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 980 | Exploiting photoelasticity to characterize dynamics of polymer networks | Szczepanski, Caroline; Leslie, Kelsey-Ann; Doane-Solomon, Robert; Arora, Srishti; Driscoll, Michelle | In this work, we exploit the photoelastic behavior of polymer networks to characterize internal stresses that develop during swelling and subsequent rupture of hydrogels. | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 981 | The local mechanics of macroscopic heterogeneous photoelastic polymer networks | Boots, Johannes N.M.; Schaap, Jorik; Dijksman, Joshua; Van der Gucht, Jasper; Kodger, Thomas | We will present the comparisons between simulations/experiments and explore the underlying mechanics of a polymer network in both the linear and non-linear regime just before network failure. | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 982 | Direct force measurement of microscopic droplets pulled along soft surfaces | Khattak, Hamza; Dalnoki-Veress, Kari | We explore droplet dynamics on soft materials using a micropipette-based technique to simultaneously image, and measure the forces on, a microscopic droplet dragged along a soft interface. | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 983 | Experimental Studies on Slow Impacts and Interaction with Regolith Covered Surfaces in Low Gravity | Kollmer, Jonathan | This talk I will give an overview of some recent experiments that explore ejecta generation and material redistribution from slow impacts into a granular bed under realistic space condtions. | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 984 | Optical spatio-temporal control of active matter systems in 2-D. | Senbil, Nesrin; Lemma, Linnea; Dogic, Zvonimir; Fraden, Seth | Our goal is to control the defect velocity and their direction to guide them towards a certain destination. | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 985 | Dynamical Inference of Forces Using Three-dimensional Tomographic Imaging of Dusty Plasmas | Yu, Wentao; Gogia, Guga; Mendez, Joshua; Wu, Brady; Burton, Justin | The method is robust to noise in the data, and can be applied to other many-body systems with complex interactions. | Session 66: Visualizing Forces in Soft Materials via Photoelastic and Other Optical Techniques |
| 986 | Three-dimensional imaging of force-generating molecular networks inside of cells using cryo-electron tomography | Swulius, Matthew | Three-dimensional imaging of force-generating molecular networks inside of cells using cryo-electron tomography | Session 67: Visualizing the Physics Behind Cell Biology Through Cryo-Electron Tomography |
| 987 | Opening a new window into the cell with super-resolution imaging and in situ cryo-electron tomography | Carter, Stephen; Hampton, Cheri; Langlois, Robert; Melero, Roberto; Farino, Zachary; Calderon, Michael; Li, Wen; Wallace, Callen; Grassucci, Robert; Rice, William; Aridor, Meir; Fish, Kenneth; Fass, Deborah; Wolf, Sharon; Watkins, Simon; Carazo, Jose Maria; Jensen, Grant; Frank, Joachim; 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 67: Visualizing the Physics Behind Cell Biology Through Cryo-Electron Tomography |
| 988 | Automatic analysis of cryo-electron tomography using computer vision and machine learning | Zeng, Xiangrui; Min, Xu | We developed and adapted a suite of computer vision and machine learning methods for such analysis. | Session 67: Visualizing the Physics Behind Cell Biology Through Cryo-Electron Tomography |
| 989 | Visualizing mitochondrial division machinery in situ | Grotjahn, Danielle | 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 67: Visualizing the Physics Behind Cell Biology Through Cryo-Electron Tomography |
| 990 | Electric Fields, Reorientation, and Water at the Air-water Interface of Iron and other Salt Solutions | Allen, Heather | We report evidence of interfacial iron (III) speciation and other ions and their interfacial hydration effects. | Session 68: Water Dynamics in Different Environments: Experiment and Theory I. Interfacial Water |
| 991 | The structure and polarization of the water-graphene interface from molecular dynamics simulations and X-ray reflectivity experiments | Jimenez-Angeles, Felipe; Harmon, Katherine; Nguyen, Trung; Fenter, Paul; Olvera De La Cruz, Monica | Here we study the water structure and polarization next to uncharged graphene surfaces by means of molecular dynamics simulations and X-ray reflectivity experiments. | Session 68: Water Dynamics in Different Environments: Experiment and Theory I. Interfacial Water |
| 992 | Polarizable Potentials For Metals: The Density Readjusting Embedded Atom Method (DR-EAM) | Bhattarai, Hemanta; Gezelter, J.; Newman, Kathie | We present a modification of the embedded atom method (EAM) which allows for electronic polarization of the metal by treating the valence density around each atom as a fluctuating dynamical quantity. | Session 68: Water Dynamics in Different Environments: Experiment and Theory I. Interfacial Water |
| 993 | Orientational Dynamics of the Hydrogen-bonded OH of Interfacial Water | McGuire, John; Figge, Florian | We report on the orientational dynamics of the bonded OH (bOH) of interfacial water, i.e., the OH groups in which the H atom participates in a hydrogen bond (HB). | Session 68: Water Dynamics in Different Environments: Experiment and Theory I. Interfacial Water |
| 994 | Why are Water-Hydrophobe Interfaces Electrically Charged? | Nauruzbayeva, Jamilya; Sun, Zhonghao; Gallo Junior, Adair; Ibrahim, Mahmoud; Santamarina, J. Carlos; Mishra, Himanshu | Why are Water-Hydrophobe Interfaces Electrically Charged? | Session 68: Water Dynamics in Different Environments: Experiment and Theory I. Interfacial Water |
| 995 | Free Energy of Water Dissociation at the Water – TiO2 Interface from Ab Initio Deep Potential Molecular Dynamics | Selloni, Annabella | Free Energy of Water Dissociation at the Water – TiO2 Interface from Ab Initio Deep Potential Molecular Dynamics | Session 68: Water Dynamics in Different Environments: Experiment and Theory I. Interfacial Water |
| 996 | Laser-Assisted Dissolution of Geological Samples Submerged in Water: Evidence of Hydrothermal Processing | Durrant, Chad; Mariella, Raymond; Combitsis, Jordan; Weisz, David | We propose a mechanism, a hydrothermal surface interaction, by which this laser-assisted dissolution process occurs. | Session 68: Water Dynamics in Different Environments: Experiment and Theory I. Interfacial Water |
| 997 | Intrinsic pH of water/vapor interface revealed by ion-induced water alignment | Chiang, Kuo-Yang; Dalstein, Laetitia; Wen, Yu-Chieh | Here we utilize phase-sensitive sum-frequency vibrational spectroscopy to quantify the surface density of protons (or their hydronium form) at the intrinsic water/vapor interface, through inspecting the surface-field-induced alignment of water molecules in the electrical double layer of ions. | Session 68: Water Dynamics in Different Environments: Experiment and Theory I. Interfacial Water |
| 998 | The behavior of water confined between two hydrophobic surfaces with grafted polymeric segments studied using molecular simulations | Mehrani, Ramin; Sharma, Sumit | We have performed Indirect Umbrella Sampling (INDUS) molecular simulations to calculate the free energy barrier of evaporation of water confined between two hydrophobic surfaces grafted with polymeric segments. | Session 68: Water Dynamics in Different Environments: Experiment and Theory I. Interfacial Water |
| 999 | Interfacial water: from atmospheric ice nucleation to nano-confinement | Michaelides, Angelos | Recent work from our research group in which we are trying to understand the intimate molecular level details of water freezing will be discussed. | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1000 | Atomic imaging of edge structure and growth of a two-dimensional hexagonal ice | Ma, Runze; Cao, Duanyun; Zhu, Chongqin; Tian, Ye; Peng, Jinbo; Guo, Jing; Chen, Ji; Li, Xin-Zheng; Francisco, Joseph; Zeng, Xiao; Xu, Limei; Wang, Enge; Jiang, Ying | Here we show that noncontact atomic force microscopy with a CO-terminated tip allows real-space imaging of the edge structures of a 2D bilayer of hexagonal ice grown on an Au(111) surface. | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1001 | Simulating Energy Relaxation in Pump–Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids | Dettori, Riccardo; Ceriotti, Michele; Hunger, Johannes; Colombo, Luciano; Donadio, Davide | We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1002 | Complete Lattice Vibration Dispersion Curves (36 Branches) for the Frozen (T=0K) Bernal-Fowler Hexagonal Close Packed Crystalline Ice with Four Water Molecules in One Primitive Unit Cell Containing 8 Protons and 4 Oxygen Nuclei | Jie, Bin; Jie, Cindy Tianhui; Sah, Chih-Tang | This talk gives the computed 36 branches of dispersion curves of Ice Ih at 0K, using six prime force constants, four values of which from isolated water molecule, further proving the connection of water’s crystalline solid phase and single molecule gas phase, by our 2013 melted-ice lattice model for the liquid phase of water. | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1003 | Probing interfacial water by H-sensitive and non-invasive scanning probe microscopy | Jiang, Ying | In order to overcome these two grand challenges, we have developed a new-generation SPM based on a qPlus sensor, which is sensitive to H and non-invasive to water structure [1]. | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1004 | Computed Lattice Vibration Frequency Spectra Explain the Abnormally High Electrical Mobilities of Positive and Negative Ions in Pure Liquid Water Using the Vibrational Force Constants of Oxygen and Hydrogen (Proton) Nuclei in its Solid and Gas Phases. | Sah, Chih-Tang; Jie, Cindy Tianhui; Jie, Bin | Our 2013 melted ice model extends the 1933 Bernal-Fowler Hexagonal Close Packed Ice crystal model to pure liquid water (0-100C). | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1005 | Nanoindentation of Ice Ih – Atomistic simulations | Santos-Flórez, Pedro; Ruestes, Carlos; De Koning, Maurice | Using molecular dynamics simulations we study the mechanical response of ice Ih through nanoindentation tests perpendicular to the basal plane. | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1006 | Sum Frequency Generation Spectroscopy of Ice/Air and Water/Air Interfaces from Ab Initio Deep Potential Molecular Dynamics | Andrade, Marcos; Zhang, Linfeng; Selloni, Annabella; Car, Roberto | We here overcome this difficulty using Deep Neural Networks (DNN) to represent the ab initio potential energy surface. | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1007 | How crystals form: a theory of nucleation pathways. | Lutsko, James | Classical Density Functional theory is combined with fluctuating hydrodynamics to describe nucleation in general and crystallization in particular. | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1008 | Surface and bulk contributions to sum-frequency vibrational spectroscopy of single crystalline ice | Xiaofan, Xu; Shen, Yuen-Ron; Tian, Chuanshan | We study the bulk and surface contributions to the sum-frequency vibrational spectroscopy (SFVS) of ice I h(0001) interfaces in the bonded OH stretching band at 223K. | Session 69: Water Dynamics in Different Environments: Experiment and Theory II. Ice |
| 1009 | Investigating graphene oxide-aqueous interfaces | Kumar, Revati; David, Rolf; Subasinghege Don, Visal | Our efforts are focused on gaining molecular level insight into the interfacial ordering using molecular simulations. | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1010 | Viscoelasticity and dynamics of nanoconfined water by atomic force microscopy | Hoffmann, Peter; Kramkowski, Edward; Khan, Shah | Here we will present an overview of our findings, including the observation of dynamic solidification, the effect of ions on ordering and dynamics, and the recent observation of the compression rate dependence of the effective viscosity. | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1011 | Hydrogen bonding structure of confined water templated by a metal-organic framework with open metal sites | Hunter, Kelly; Rieth, Adam; Dinca, Mircea; Paesani, Francesco | Here, we investigate structural and dynamical properties of water adsorbed in Co 2Cl 2BTDD as a function of relative humidity using many-body molecular dynamics simulations with the MB-pol model. | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1012 | Vibrational dynamics and quantum tunneling of water molecules in bassanite | Kolesnikov, Alexander; Anovitz, Lawrence {Larry}; Irle, Stephan | Using inelastic neutron scattering (INS) we studied dynamics of bassanite (CaSO 4*0.5H 2O), a structure of which has channels formed by CaO 8 and CaO 9 polyhedra with water molecules residing in the channels and occupying two different positions. | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1013 | Structure and Dynamics of Aqueous Solutions in Carbon Nanotubes: Insights from First-Principles Simulations | Aydin, Fikret; Zhan, Cheng; Schwegler, Eric; Pham, Tuan Anh | We find that polarizable ions exhibit a stronger adsorption at the interfaces and these effects are found to be significantly enhanced under confinement. | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1014 | One atom thick angstrom-scale capillaries: Water flow | Boya, Radha | We have developed a method for fabrication of narrow and smooth angstrom (Å) scale capillaries through van der Waals assembly of 2D-materials, with atomically flat sheets at the top and bottom separated by spacers made of 2D-crystals with a precisely controlled number of layers. | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1015 | Nano-confined water and ions in cement pores | Goyal, Abhay; Palaia, Ivan; Ioannidou, Katerina; Trizac, Emmanuel; Pellenq, Roland; Del Gado, Emanuela | We use numerical simulations to study the behavior of water confined by planar surfaces in the presence of divalent ions. | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1016 | Microscopic study of proton kinetic energy anomaly for confined water | Moid, Mohammad; Finkelstein, Yacov; Moreh, Raymond; Maiti, Prabal | We used classical MD method to deduce Ke(H) by calculating the proton vibrational density of states, H-VDOS, for the case of water inside single wall carbon nanotubes (SWCNT) of varying diameters. | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1017 | Water dynamics in Evaporating Nanodroplets | Ruiz Pestana, Luis; Head-Gordon, Teresa | At the nanoscale, however, where large surface to volume ratios govern the behavior, and fluctuations play a major role, it remains unclear whether the continuum theories can be applied to predict the the response. | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1018 | A molecular view of glycerol-water hydrogen bonding patterns | Mackie, Cameron; Xu, Bo; Kostko, Oleg; chari, nikhil; zhang, emily; Head-Gordon, Martin; Ahmed, Musahid | A molecular view of glycerol-water hydrogen bonding patterns | Session 70: Water Dynamics in Different Environments: Experiment and Theory III. Nanoconfined Water |
| 1019 | Systematic optimization of atomistic water models for molecular simulation using liquid/vapor surface tension data | Wang, Lee-Ping; Qiu, Yudong; Head-Gordon, Teresa; Nerenberg, Paul | To test this hypothesis we implemented new functionality into the automated ForceBalance optimization procedure for using surface tension data, and parameterized revised three-point and four-point rigid, fixed charge water models named TIP3P-ST and TIP4P-ST. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1020 | Kosmotrope and Chaotrope Salts Influence on Water Structural Relaxation and hydrogen Bond Dynamics Investigated by Coherent Quasielastic Neutron Scattering | Faraone, Antonio; Senses, Erkan; Mamontov, Eugene | Using coherent quasielastic neutron scattering, we have investigated the dynamics of NaCl/D O and KCl/D O, NaCl being a kosmotrope and KCl being a chaotrope, respectively. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1021 | The SCAN330 dataset of first-principles molecular dynamics simulations of water | LaCount, Michael; Gygi, Francois | We present the SCAN330 dataset of first-principles molecular dynamics simulations of liquid water [1] obtained using the Qbox code [2] and the SCAN meta-GGA density functional [3] at a temperature of 330 K. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1022 | Sensitizing Hydration Shells of Ions by Analyzing Water Dynamics Using High Sensitive Dielectric Spectroscopy | Lou, Djamila; DOAN, LUAn; Kesting, Henry; Nguyen, Vinh | In response, we have employed a highly sensitive, high-resolution, frequency domain, MHz to THz dielectric spectrometer that is sensitive to int ermolecular dynamics. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1023 | Spatio-temporal analysis of water molecules around DNA employing extended MHz-THz spectroscopy and MD simulations | Singh, Abhishek K; DOAN, LUAn; Nguyen, Vinh | Here we present a temperature-dependent study for dynamics of water molecules around salmon testes DNA, employing extended megahertz-terahertz dielectric spectroscopic technique and Fourier transform infrared spectroscopy supported by MD simulations. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1024 | Transient Anisotropy of Liquid Water | Novelli, Fabio; Ruiz Pestana, Luis; Bennett, Kochise; Dessmann, Nils; Sebastiani, Federico; Adams, Ellen; Saeedi Ilkhchy, Kamyar; Stavrias, Nikolas; Eless, Viktoria; Ockelmann, Thorsten; Colchero, Alejandro; Hoberg, Claudius; Schwaab, Gerhard; Head-Gordon, Teresa; Havenith, Martina | Here we report unprecedented non-linear THz experiments on water molecules in the liquid phase. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1025 | Strong orbital interactions of the Zundel cation H5O2+ with hydration shell water | Ekimova, Maria; Kleine, Carlo; Ludwig, Jan; Ochmann, Miguel; Gustafsson, Thomas A.; Kozari, Eve; PINES, EHUD; Huse, Nils; Wernet, Philippe; Odelius, Michael; Nibbering, Erik T. J. | With our flatjet system for x-ray absorption spectroscopy in transmission, now succesfully operating for the polar acetonitrile solvent, and in combination with previously obtained laboratory infrared spectroscopic data, we can establish a systematic structural approach to hydrated proton structures in solution. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1026 | Molten hydrate clathrates as a new class of macromolecular fluids. | Lopez-Bueno, Carlos; Herreros-Lucas, Carlos; Bittermann, Marius; Amigo, Alfredo; Woutersen, Sander; Giménez-López, Maria del Carmen; Rivadulla, Francisco | Here we demonstrate the formation of a supramolecular liquid in ≈1.4-2.2m aqueous solutions of tetrabutyl ammonium bromide. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1027 | A New Model for the Structure and Dynamics of the Hydrated Proton in Liquid Acetonitrile and Water | Kozari, Eve; Sigalov, Mark; Pines, Dina; Fingerhut, Benjamin; PINES, EHUD | A new proton-solvation and -transport model in aqueous solutions is proposed based on our combined NMR and IR experiments and theoretical quantum–classical-molecular-dynamics findings. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1028 | Determination of Ion–Water Correlated Motions in Aqueous Salt Solutions | Shinohara, Yuya; Matsumoto, Ray; Thompson, Matthew; Dmowski, Wojciech; Ryu, Chae Woo; Iwashita, Takuya; Ishikawa, Daisuke; Baron, Alfred; Cummings, Peter; Egami, Takeshi | We report on the real-space correlated motion of water molecules and ions in an aqueous salt solution. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |
| 1029 | Lysozyme Solution-State Tertiary Structure Measured in Protic and Aprotic Ionic Liquid Aqueous Mixtures | Reyes, Ian; Banuelos, Jose | Aqueous protic ionic liquid (PIL) mixtures are interesting solvent media for the stabilization of proteins over wide temperature ranges, which may help develop long term protein storage methods or high temperature catalysis applications. | Session 71: Water Dynamics in Different Environments: Experiment and Theory IV. Bulk Water and Solute Hydration |