Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session Y06: Disordered, Glassy, and Jammed Behavior in Biological MatterFocus
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Sponsoring Units: DBIO Chair: Andrei Gasic, Rice University Room: Room 129 |
Friday, March 10, 2023 8:00AM - 8:36AM Author not Attending |
Y06.00001: Nontrivial effects of activity on the glassy dynamics of active self-propelled particles Invited Speaker: Saroj K Nandi Effects of activity on the glassy dynamics are crucial for several critical biological processes, such as wound healing, cancer progressions, embryogenesis, Etc. It also extends the scope and extent of the as-yet mysterious physics of glass transition. Theories of equilibrium glassy dynamics have been extended for the active glasses where the constituent particles have a self-propulsion force, f0, and a persistence time, τp, of their motion. While f0 always drives the system away from the glassy regime, the effects of τp are more complex and depend on the activity details. The relaxation dynamics of active glassy systems seem qualitatively similar to that in an equilibrium system at an effective temperature. However, activity has nontrivial complex effects on the dynamical heterogeneity. In this talk, I will discuss some of these effects and show that mode-coupling theory, extended for active systems, can surprisingly capture both these aspects of activity. |
Friday, March 10, 2023 8:36AM - 8:48AM |
Y06.00002: Criticality of isotropic stress percolation during glass to fluid transition in active cell layers Siavash Monfared, Guruswami Ravichandran, Jose E Andrade, Amin Doostmohammadi The transition between solid-like to fluid-like states in cellular systems is of relevance to a range of biological processes, including cancer metastasis, wound healing and tissue morphogenesis. However, our fundamental understanding of how cells collectively switch between these two states remains limited. Using a three-dimensional phase-field based representation of confluent cell layers, we map the amorphous solid to fluid phase transition in active cell layers onto the two-dimensional (2D) site percolation universality class. To achieve this, we use two distinct and independent paths to model this transition based on increasing (1) cell-cell adhesion and (2) active traction forces. Our findings provide a new perspective on the fundamental mechanical mechanisms associated with the solid-like to fluid-like transition in active cell layers. |
Friday, March 10, 2023 8:48AM - 9:00AM |
Y06.00003: From cells to tissue: decoupling cell-adhesion and contractile forces in a model epithelial tissue framework Anshuman Pasupalak Epithelial cells in monolayers undergo rearrangements, also known as T1 transitions that facilitate their motility during various developmental processes. Such rearrangements are a result of many cellular properties as well as their interactions. It is difficult to isolate the effects of such properties in Vertex/Voronoi-based models of epithelial tissues, as a cell cannot be defined in isolation and there is a lack of control over the various dynamics of individual cells and their interactions. |
Friday, March 10, 2023 9:00AM - 9:12AM |
Y06.00004: Glass-like dynamics in plant cells Maziyar Jalaal, Nico Schramma, Cintia Perugachi Israels Photosynthesis is essential for all life on earth. Plants have evolved multiple mechanisms to adapt their photosynthetic performance to ever-changing light conditions: from the active motion of their leaves during the day to directed growth towards light. However, such adaptation could also occur on a cellular scale, via the motion of chlorophyll-containing organelles - chloroplasts. A plant-specific light-controlled actin-binding mechanism enables chloroplasts to individually move towards or away from light, depending on the light intensity. This mechanism enables chloroplasts to collectively self-organize into different light-adapted configurations. |
Friday, March 10, 2023 9:12AM - 9:24AM |
Y06.00005: Distinguishing jammed monomer and polymer packings in three dimensions Jack Logan, Alex T Grigas, Mark D Shattuck, Corey S O'Hern Proteins are geometrically and physically complex structures made from combinations of amino acids. When a protein folds, stereochemical, steric, and other atomic interactions determine the possible conformations. A polymer chain of spherical monomers is an overly simplified approximation of a protein, but even at this coarse-grained level, the differences in the structural and mechanical properties of packings made from folding a polymer of spherical monomers and packings made from individual spherical monomers are not fully understood. In this work, we seek to discern the fundamental differences between packings of spherical monomers and packings of polymers with short-range attractive interactions. We start by modeling the polymer as a freely jointed chain of spherical monomers, and then consider freely rotating chains of spherical monomers with fixed bend angles. In future studies, we will consider non-spherical monomers that can mimic the backbone and side chains of individual amino acids. While still a coarse-grained approximation of a true protein core, the inclusion of bend angles and non-spherical monomers provides an in-depth investigation into the core packings of collapsed polymers that can begin to elucidate how the presence of a backbone can change the packing landscape in proteins. |
Friday, March 10, 2023 9:24AM - 9:36AM |
Y06.00006: Emergence of bacterial glass: two-step glass transition in 2D bacterial suspension Kazumasa A Takeuchi, Hisay Lama, Masahiro J Yamamoto, Yujiro Furuta, Takuro Shimaya An interesting question in active matter physics is what states of matter may arise in active matter and how different they are from thermal systems. Bacterial populations are particularly interesting in this context, as they are known to show a plethora of collective phases, yet it remains challenging to characterize dense states of bacteria, partly because it is experimentally difficult to realize a uniform growth condition for dense populations. |
Friday, March 10, 2023 9:36AM - 9:48AM |
Y06.00007: Polymer collapse and jamming: The role of the backbone connectivity and adhesive interactions in determining the properties of the cores of collapsed polymers and folded proteins Alex T Grigas, Mark D Shattuck, Corey S O'Hern Proteins are important biopolymers that not only reliably fold to stable conformations, but also possess collective dynamics and response that are essential for performing biological functions. Previous work has shown that the interiors of proteins are densely packed, i.e. similar to jammed packings of purely repulsive amino acid-shaped particles. Therefore, soft matter approaches are uniquely positioned to model the structural and mechanical properties of protein cores. While much work over the past two decades has explored the properties of jammed packings of disconnected repulsive particles, complexities emerge when applying these approaches to collapsed biopolymers due to open boundary conditions, polymer backbone connectivity, and attractions between monomers. Here, we generate jammed packings of repulsive monomers and of a repulsive polymer chain and thermally collapsed systems of sticky monomers and a sticky polymer chain. Two main questions arise: 1. How similar is the thermal collapse of sticky particles to jamming of repulsive particles under isotropic compression? and 2. How do connectivity and adhesive interactions impact the structural and mechanical properties? To this end, we analyze the interior packing fraction, number of contacts above isostaticity, and the emergence of excess low-frequency modes in the vibrational density of states. |
Friday, March 10, 2023 9:48AM - 10:00AM |
Y06.00008: How do changes in the spatial and temporal correlations arising from activity affect the glass transition? Francesco Arceri, Corey S O'Hern, Mark D Shattuck Assemblies of active colloidal particles serve as model systems for the heterogeneous, collective dynamics of self-propelled, living materials, such as flocking in bacterial films and correlated cell motion during wound healing and embryogenesis. Despite recent advances, the effects of activity on the glassy dynamics of dense active matter are still largely debated. Using numerical simulations of active brownian particles, we study how activity affects the dynamical slow-down near the glass transition as a function of the temperature of the thermal bath, particle packing fraction, and Peclet number. We focus on measurements of the spatial and temporal Fourier transforms of the kinetic K(q,omega) and potential U(q,omega) energies of the system. We take a stepwise approach, first measuring K(q,omega) and U(q,omega) in systems at constant energy, then in the presence of a Langevin thermostat near the glass transition, and finally with active forces with a given strength and persistence time. We find that the active forces can either enhance or disrupt the two step-relaxation of glass-forming liquids, and connect this behavior to changes in the spatial and temporal correlations of the system. This work offers fundamental insights into the differences between the glassy dynamics that occurs in thermal energy-driven versus activity-driven systems, an important step forward in modeling active motion in living and non-living materials. |
Friday, March 10, 2023 10:00AM - 10:12AM |
Y06.00009: Branching fractional Brownian motion as a model of serotonergic neurons Reece D Beattie-Hauser, Gaurav R Khairnar, Jonathan House, Skirmantas Janusonis, Ralf Metzler, Thomas Vojta Fractional Brownian Motion (FBM) is a stochastic process with long-time correlations which has been used to model anomalous diffusion in numerous biological systems. Recently, it has been used to study the distribution of serotonergic fibers in the brain [1,2]. To better represent the biological process we are trying to simulate, we introduce the concept of branching FBM (bFBM). In this stochastic process, individual particles perform FBM but may randomly split into two. Here, we study bFBM in one space dimension in the subdiffusive and superdiffusive regimes, both in free space and on finite intervals with reflecting boundaries. We examine three possible types of behavior of the correlations (memory) at a branching event: both particles keep the memory of the previous steps, only one particle keeps the memory, and no particles keep the memory. We calculate the mean-square particle displacement, the corresponding probability distribution, and displacement correlation function. We find that the qualitative features of the bFBM process strongly depend on the type of branching event. We also discuss implications of our results for the distribution of serotonergic fibers, and we discuss possible future refinements of the model, including interactions between different fibers. |
Friday, March 10, 2023 10:12AM - 10:24AM |
Y06.00010: Topological packing statistics distinguish living and non-living matter Dominic J Skinner, Hannah Jeckel, Adam C Martin, Knut Drescher, Jorn Dunkel How much structural information is needed to distinguish different multicellular materials? Here, we show that the statistical properties of Delaunay tessellations suffice to differentiate prokaryotic and eukaroytic cell packings from a wide variety of inanimate physical structures. By introducing a mathematical framework for measuring topological distances between general 3D point clouds, we construct a universal topological atlas encompassing bacterial biofilms, zebrafish brain matter and embryonic tissues as well as colloidal packings, glassy materials, and stellar configurations. Living systems are found to localize within a bounded island-like region, reflecting that growth memory essentially distinguishes multicellular from physical packings. By detecting subtle topological differences, the underlying metric framework enables a unifying classification of 3D disordered media, from microbial populations, organoids and tissues to amorphous materials and astrophysical systems. |
Friday, March 10, 2023 10:24AM - 10:36AM |
Y06.00011: Rheological aging of viscoelastic glasses Andrei G Gasic, Peter G Wolynes Glassy materials age; i.e., their rheology and dynamical properties depend on the time spent waiting before a measurement is taken. Furthermore, aging occurs through two relaxation processes: i.) primary, which involves activated events involving compact regions, and ii.) secondary, which is a faster relaxation governed by string-like clusters. There is a fundamental interest in understanding how both primary and secondary relaxations affect aging of glassy materials, which also applies to biological matter such as biocondensates and jammed actin networks. In this talk, we present a theory of aging for viscoelastic glasses that incorporates both relaxation processes. Using random first-order transition theory, we consider the local fluctuations in the driving force to account for the glassy material's heterogeneity and non-exponential relaxation rates. We also examine the nonequilibrium, protocol-dependent properties of the system. Our model demonstrates how the stress response and other mechanical properties vary with age. We also discuss general insights into the physics of aging motivated by biological materials. |
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