Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session M13: Physics of Biological Active Matter III: Liquids and Model SystemsFocus Session Live
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Sponsoring Units: DBIO DPOLY DSOFT Chair: Ricard Alert, Princeton University |
Wednesday, March 17, 2021 11:30AM - 12:06PM Live |
M13.00001: From topological defects to fruiting bodies in bacterial colonies Invited Speaker: Ricard Alert The soil bacterium Myxococcus xanthus lives in colonies of millions of cells that migrate on surfaces. When nutrients are scarce, M. xanthus colonies develop droplet-like multicellular aggregates called fruiting bodies. To develop these three-dimensional aggregates, the colony sequentially forms new cell layers on top of an original cell monolayer. However, how new cell layers form is poorly understood. In this talk, I will show that, in each layer, the rod-shaped M. xanthus cells are densely packed, aligned with neighboring cells, and motile. Thus, the colony forms an active nematic liquid crystal. New cell layers preferentially form at topological defects, i.e. points at which the nematic alignment is locally lost. Defects with topological charge +1/2 and -1/2 lead to the formation of new layers and new holes, respectively. We explain these findings by modeling the bacterial colony as an extensile active nematic fluid with anisotropic friction. In agreement with our experimental measurements, the model predicts an influx of cells toward +1/2 defects and an outflux of cells from −1/2 defects. Our results suggest that cell motility and mechanical cell-cell interactions are sufficient to promote the formation of cell layers at topological defects, thereby seeding fruiting bodies in the bacterial colony. |
Wednesday, March 17, 2021 12:06PM - 12:18PM Live |
M13.00002: Dynamic coacervation of a DNA Liquid Gabrielle Abraham, Aria Chaderjian, Dan T Nguyen, Omar A. Saleh Dynamic condensation is one of many ways that gene expression is regulated. In this, RNA and proteins, the very products of gene expression, drive the phase separation of genes of different expression levels. However, a gene’s expression level and its state can change, causing the other, intertwined property to change as well. We aim to mimic this dynamic, self-regulating system using a model DNA liquid system that is transformed by RNA produced from in vitro transcription. This liquid is composed of DNA nanostars, four-armed star shaped structures created by the hybridization of four strands. Each arm ends in a palindromic, single-stranded sequence that allows nanostars to interact and condense into droplets which previous work has confirmed to share similar physical properties and spatial control as intracellular droplets (i.e., specific molecules are enriched or depleted in the droplet phase). We use confocal and fluorescence microscopy to track changes in the nanostar liquid system, like droplet size, with the creation of RNA transcripts. |
Wednesday, March 17, 2021 12:18PM - 12:30PM Live |
M13.00003: A theoretical framework for active chiral filaments Aleksandra Plochocka, Sebastian Fuerthauer, Michael Shelley The cell cytoskeleton - the active structure that drives cellular motion - is an active chiral fluid. Chirality refers to the breaking of left-right symmetry and can be observed in in-vitro experiments where the kinesin-14 motor walks helically around microtubules with a right-handedness. Here, we develop a framework for coarse graining chiral filament-filament interactions to obtain an active gel theory for living chiral materials. We identify the conditions under which microscopic chirality can be inherited by macro-scales and determine couplings between chiral, extensional, and compressive degrees of freedom in active gels. Our work enables the quantitative understanding of the molecular basis of chiral phenotypes of cellular structures, such as the spindle, and of chiral motions in vitro. |
Wednesday, March 17, 2021 12:30PM - 12:42PM Live |
M13.00004: Controlling membrane-less organelles via chemical reactions Jan Kirschbaum, David Zwicker Liquid-like droplets, formed by phase separation, play a crucial role in the spatiotemporal organization of membrane-less organelles inside cells. While passive phase separation is well understood, the interaction with the non-equilibrium environment inside biological cells is not. We investigate how fuel-driven chemical reactions influence the properties of those organelles when the droplet material can switch between a phase separating and a soluble form. We model this non-equilibrium system based on the chemical potential as a driving force for both the reaction and diffusion. First, we show how driven chemical reactions can control the total amount of phase separating material. We then, motivated by experiments, introduce heterogeneously distributed enzymes, which lead to spatial varying reaction rates. In this case, the system reaches a non-equilibrium steady state in which the diffusive and reactive fluxes are constant. The balance of these fluxes can lead to a collective state where multiple droplets of the same size coexist. The model also allows us to characterize the energy consumption and entropy production rate to quantify the cost of maintaining a fixed droplet size. |
Wednesday, March 17, 2021 12:42PM - 12:54PM Live |
M13.00005: A data-driven statistical field theory of active matter Ahmad Borzou, J. M. Schwarz One of the major challenges in modeling biological systems is that some of the key players and their interactions are not fully understood. With the advent of high throughput experiments, and in the age of big data, data-driven methods are on the rise. However, although machine-learning approaches have been useful so far, they do not necessarily shed light on the underlying principles of such systems. To begin to illuminate the underlying principles, I will present a data-driven statistical field theory for active matter---a leading candidate for quantifying living systems. The method is first developed analytically. The parameters of the model will be learned from observations of the active matter system of interest. I then validate the approach with several simulations. |
Wednesday, March 17, 2021 12:54PM - 1:06PM Live |
M13.00006: Kinetics of light-switchable surface association of C. reinhardtii populations Rodrigo Catalan, Alexandros Fragkopoulos, Simon Kelterborn, Peter Hegemann, Oliver Baeumchen Bacterial and microalgal colonization on surfaces produce favorable and adverse effects in technological and medical settings. Consequently, the fundamental aspects of biofilm formation on solid substrates are actively studied. While bacteria have been the main focus of research to understand microbial surface colonization, analogous studies using archetypes in microalgae are thus far elusive. It is known that the flagellar adhesion of the microalga C.reinhardtii is switched on in blue light and switched off under red light [Kreis et al., Nature Physics, 2018]. We exploit the ability to switch the adhesiveness of C. reinhardtii to study the kinetics of adsorption and desorption of cell suspensions on glass using bright field microscopy and image analysis. We observe that both processes exhibit a lag response relative to the time at which blue- or red-light conditions are set and we model this feature using time-delayed Langmuir kinetics. We find that adsorption occurs significantly faster than desorption, with the delay to be an order of magnitude larger. Adsorption experiments of phototactically blind C.reinardtii mutants show that phototaxis does not affect the kinetics of either process. Hence, our method can be used as an assay for characterizing surface colonization. |
Wednesday, March 17, 2021 1:06PM - 1:18PM Live |
M13.00007: Comparison of different approaches to single-molecule imaging of enhanced enzyme diffusion Mengqi Xu, W. Benjamin Rogers, Wylie Ahmed, Jennifer L Ross Enzymes have been shown to diffuse faster in the presence of their substrates. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT). In our prior work, we used a polymer-brush coated surface and a large viscous polymer, methylcellulose, to slow diffusion and facilitate tracking. Here, we simplify our system by using supported lipid bilayer (SLB) coated surface, and a small viscous molecule, glycerol. Using this newly-designed lipid-coated/glycerol chamber, we compare two different analysis approaches for SPT: the mean-squared displacement (MSD) analysis and the jump-length analysis. We find that the MSD analysis requires high viscosity and large particles to accurately report the diffusion coefficient, while jump-length analysis depends less on the viscosity or size limitation. Furthermore, lipid-coated/glycerol chambers fail to reproduce enhanced diffusion due to the presence of glycerol inhibiting enzyme activity. To avoid adding glycerol and to constrain the diffusion to two dimensions, we tether enzymes directly to the lipid bilayer. This approach recovers the 3-fold enhancement in diffusion of enzymes with the presence of their substrate as we observed before. |
Wednesday, March 17, 2021 1:18PM - 1:30PM Live |
M13.00008: Layered Liquids: A complex tensor theory of simple smectics Jack Paget, Tyler N Shendruk Liquid crystals are ubiquitous in nature, often appearing in biological and industrial systems. Proper hydrodynamic study and simulation of these materials requires an appropriate order parameter capable of describing their complex internal structures. The strength of the Q-tensor for nematic phases arises from the tensor’s ability to simultaneously describe both the local degree of nematic order and orientation. Smectic phases, however, break both translational and rotational symmetry so require a more composite order parameter. |
Wednesday, March 17, 2021 1:30PM - 1:42PM Live |
M13.00009: Active carpets drive non-equilibrium transport and feature self-cleaning properties Francisca Guzman-Lastra, Hartmut Löwen, Arnold Mathijssen Biological activity is often highly concentrated on surfaces, across the scales from molecular motors and ciliary arrays to sessile and motile organisms. These 'active carpets' locally inject energy into their surrounding fluid. Whereas Fick's laws of diffusion are established near equilibrium, it is unclear how to solve non-equilibrium transport driven by such boundary-actuated fluctuations. Here, we derive the enhanced diffusivity as a function of distance from an active carpet and, following Schnitzer's telegraph model, we cast these results into generalised Fick's laws. Two archetypal problems are solved using these laws: First, considering sedimentation towards an active carpet, we find a self-cleaning effect where surface-driven fluctuations can repel particles. Second, considering diffusion from a source to an active sink, say nutrient capture by suspension feeders, we find a large molecular flux compared to thermal diffusion. Hence, our results could elucidate certain non-equilibrium properties of active coating materials and life at interfaces. |
Wednesday, March 17, 2021 1:42PM - 1:54PM Live |
M13.00010: Role of Active Trafficking Dynamics on the Shape and Morphogenesis of Subcellular Compartments Alex Rautu, Madan Rao We study the role of membrane trafficking on the morphology of subcellular comparments, such as those encountered within the eukaryotic cell. These continuously interchange material amongst themselves via small transport vesicles, along closely regulated trafficking pathways. The processes of fission and fusion are orchestrated by a highly complex biochemical network of proteins. We develop a general theory which allows us to study the dynamical interplay of such active processes of fusion and fission with the membrane morphology as well as the hydrodynamics of the ambient fluid. This is facilitated by an appropriate coarse-graining over the microscopic biochemical reactions, which provides us with the large-scale properties of such active membranes. Here, the activity leads to a dynamical renormalization of the membrane parameters, which in turn drives the membrane to nonequilibrium steady-states with distinct morphologies that have no analogue in equilibrium physics. For instance, even under conditions of spatially isotropic activity, the membrane may spontaneously acquire a drift. We believe that these biophysical processes could play an important role to organelles such as golgi and endosomes. |
Wednesday, March 17, 2021 1:54PM - 2:06PM Live |
M13.00011: Dynamic Mode Structure of Bacterial Turbulence Olivia Martin, Richard Henshaw, Jeffrey S. Guasto Dense suspensions of swimming bacteria exhibit chaotic flow patterns that promote mixing and transport of resources and signaling chemicals within cell colonies. Whilst the importance of this so-called “bacterial turbulence” is widely recognized, the structure of the resulting flow is not well understood. Here, we extend the use of modal decomposition to study the dynamical flow structure of this model active matter system. Particle image velocimetry (PIV) quantifies the two-dimensional velocity field of dense bacterial suspensions of the rod-shaped Bacillus subtilis. The dominant spatial structures of the velocity and vorticity fields are extracted using proper orthogonal decomposition (POD) and ranked in order of energy and enstrophy magnitude, respectively. The time-dependent amplitudes of the spatial structures reveal velocity fluctuation frequencies within the turbulent system. We also examine the spatial mode structure and fluctuation frequency as a function of mean cell swimming speed to characterize changes in the kinetic energy distribution with cell activity. These results contribute to the fundamental understanding of active matter system dynamics and chaotic flow structures responsible for mixing. |
Wednesday, March 17, 2021 2:06PM - 2:18PM Live |
M13.00012: Stochastic Spatial Modeling of Attachment and Detachment Processes in Molecular Motor-Cargo Systems Peter Kramer, Abhishek Choudhary, Yushen Huang Intracellular transport is conducted largely by molecular motor proteins which process along cytoskeletal filaments, from which they can attach or detach. We describe an analytical framework to characterize motor attachment or reattachment times to microtubules in a parallel architecture as a function of the physical and geometric properties of the motor, the cargo to which it is attached, and possibly a second motor attached to the same cargo and a microtubule. The biophysical model is coarse-grained at the level of the macromolecular motors and formulated in terms of stochastic differential equations. Various asymptotic approximations based on ``small target'' first passage time calculations are possible depending on the relationship of the motor-cargo tether length, the distance between microtubules, whether the cargo has a rigid or lipid membrane surface, and the initial configuration of the motor and cargo relative to the parallel microtuble network. The same methodology also allows the computation of the probability distribution for which nearby microtubule a motor will attach next. |
Wednesday, March 17, 2021 2:18PM - 2:30PM Live |
M13.00013: Photoisomerization-induced wrinkling and leakage in azobenzene-based photoswitchable solid lipid bilayer membranes Arash Manafirad, Christopher Paul Oville, Anthony Duprat Dinsmore UVC-induced morphological changes were observed in giant unilamellar vesicles (GUVs) composed of lipid mixtures of dipalmitoyl-phosphocholine (DPPC) and photoswitchable azobenzene-based phospholipid (azo-PC). The morphological changes varied considerably and depended on azo-PC's molar fraction, which undergoes a reversible trans-to-cis isomerization upon ultraviolet irradiation. Notable non-spherical morphologies, including wrinkling, swelling, elongation, and budding, were induced at nominal azo-PC concentrations of 30 mol% and above, with characteristic effects present at each concentration. Bright-field and fluorescence confocal microscopy were used to determine the GUV morphology. Over a broad range of, we found phase separation into solid DPPC domains and azo-PC enriched domains. In GUVs with near 30 mol%, rapid and reversible membrane wrinkling was observed. For above 30 mol%, vesicle swelling was observed with varying degrees. The wrinkling and leakage responses were not observed in mixtures of azo-PC with lipids that form the fluid phase. The solid (gel) DPPC-rich phase's role and the implications for designing stimuli-responsive materials will be discussed. |
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