Bulletin of the American Physical Society
APS March Meeting 2018
Volume 63, Number 1
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session V53: Nonequilibrium Statistical Mechanics and Hydrodynamics of Active Matter IV |
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Sponsoring Units: GSOFT GSNP DFD Chair: Katherine Klymko, Univ of California - Berkeley Room: LACC 513 |
Thursday, March 8, 2018 2:30PM - 2:42PM |
V53.00001: Can one hear the hydrodynamics of an active liquid ? Delphine Geyer, Denis Bartolo From water to vine to bourbon and vodka, most of the fluids we are familiar with are characterized by two material constants: their density and their shear viscosity. In stark constrast, all hydrodynamic theories of active liquids involve a host of hydrodynamic coefficients that have been out of reach of conventional rheological characterization. |
Thursday, March 8, 2018 2:42PM - 2:54PM |
V53.00002: Thermodynamically Consistent Coarse Graining of Biocatalysts beyond Michaelis--Menten Massimiliano Esposito Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Moreover, we identify the conditions under which a relation between fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux--force relation. |
Thursday, March 8, 2018 2:54PM - 3:06PM |
V53.00003: Reynolds vs. Peclet - Finite acceleration in the Stokes regime from slowly relaxing gradients Joseph Albert, Vincent Crespi Several models of diffusiophoretic particles exhibit spontaneous symmetry breaking - directed motion occurs even if the particle itself is isotropic. We present one such model, formulated as a system of delay differential equations. Analysis shows a critical Péclet number beyond which the stationary solution is unstable and sustained motion is possible. Beyond this critical value, simulations reveal an intermediate-Péclet regime exhibiting 'inertial' behavior - despite existing at zero Reynolds number by construction, particles do not immediately reach a steady state in response to external forces, permitting, for example, circular orbits in a central potential. In the limit of infinite Péclet number, we find that trajectories become approximately self-avoiding. |
Thursday, March 8, 2018 3:06PM - 3:18PM |
V53.00004: Enhanced Diffusion of Molecular Catalase Mengqi Xu, Jennifer Ross Active matter, which focuses on ensembles of self-propelled elements, has shown unique emergent activities making them excellent candidates for novel materials of the future. One of these emergent activities is how active materials couple together to harvest energy to perform work from athermal noise. Biological systems do this routinely to perform work used in cell division and cell motility. Enzymes are non-equilibrium proteins that use substrates and release products asymmetrically. Recent work has shown that enzymes, such as catalase, urase, and adolase, can causes enhanced diffusion in bulk depending on the substrate concentration. We are using catalase, an common asymmetric enzyme, and its substrate, hydrogen peroxide, as the basic model system, to demonstrate the work-harvesting from noisy on molecular-scale. Using TIRF microscopy, we can measure the diffusion of individual catalase molecules to test for enhanced diffusion as a function of substrate concentration to check if diffusion of individual molecules is enhanced, or if the phenomena is purely an ensemble activity. This work will pave the way to determining the mechanism for the enhanced diffusion and ultimately enable a system that can harness the non-equilibrium noise of enzymes into mechanical work. |
Thursday, March 8, 2018 3:18PM - 3:30PM |
V53.00005: Passive colloids in an active fluid: fluctuation induced interaction, self-propulsion, and pressure Amit Singh, Jacques Prost, Madan Rao We describe the hydrodynamics of passive colloids in a viscous fluid with active stress fluctuations by coupled Langevin equations with multiplicative noise. These active fluctuations give rise to effective interactions which can either be long-range (between colloid-wall), or short-range (between two colloids). We show that the steady state distribution in position of the colloid is not Boltzmann, from which implications follow. First, the noised induced mechanical pressure on the wall depends on the particle-wall interaction potential, hence it is not a state variable. Second, a dimer of two spheres of different sizes, interacting harmonically, acts like a self propelled particle, with a mobility that increases with the strength of the noise. Our results highlight the interplay between hydrodynamic interactions and active noise, with direct relevance to the dynamics of rigid and soft ``inclusions'' in cells and tissues. |
Thursday, March 8, 2018 3:30PM - 3:42PM |
V53.00006: Ballistic flight of enzymes away from reactants Jee Ah-Young, Sandipan Dutta, Tsvi Tlusty, Steve Granick Too much remains speculative about how the internal dynamics of enzymes relates to catalytic function, owing to lack of appropriate methods to detect millisecond time scales over sufficiently small observation windows. Here, we used super-resolution microscopy (stimulated emission-depletion fluorescence correlation spectroscopy, STED-FCS) to observe an active enzyme spontaneously migrate toward the direction of lower reactant (substrate) concentration using the run-and-tumble method, which is a strategy similar to that of swimming microorganisms. This we modeled theoretically to explain why it leads to anti-chemotaxis. Experimentally, we showed that enhanced enzyme mobility is generated by super-diffusive kicks at the substrate turnover frequency. The results help us understand activities of enzymes, and furthermore to design and use a synthetic self-propelled swimmer relevant to “active matter.” |
Thursday, March 8, 2018 3:42PM - 3:54PM |
V53.00007: Universal Dynamic Self-assembly: From Colloids to Microorganisms to Sub-10 nm Particles Serim Ilday, Evren Engin, Ghaith Makey, Ozgun Yavuz, Denizhan Kesim, Onur Tokel, Oguz Gulseren, Fatih Ilday Arguably, the ultimate goal for self-assembly research is to develop a methodology that can be applied to almost any material, where the dynamics are largely independent of the initial conditions of the system, applicable at the smallest scale as well as the largest. Here, we show a universal dynamic/dissipative self-assembly methodology in a highly nonlinear and highly stochastic system operating far from equilibrium where we demonstrate exotic patterns and behaviour emerging from (i) simple polystyrene colloids with diameters ranging from 250 nm to 1 µm, (ii) three different microorganisms namely, immotile S. cerevisiae that are elliptical in shape, ~7 µm in diameter, immotile M. luteus that are spherical in shape, ~500 nm in diameter and motile E. coli that are rod-like with dimensions of ~1 µm x 2 µm, (iii) gold nanoparticles with 5 nm in diameter. Furthermore, all these different materials can be spatially arranged in a fashion to do specific movements such as rotary motion. |
Thursday, March 8, 2018 3:54PM - 4:06PM |
V53.00008: Measuring fluctuations and dissipation in an ATP-chemostated system Alexandru Bacanu, James Pelletier, Junang Li, Todd Gingrich, Jordan Horowitz, Nikta Fakhri Many biological systems act as ATP chemostats, regulating metabolism to maintain the ATP/ADP ratio at constant levels, driving nonequilibrium activities. In chemostats with multiple dissipative processes, it remains unclear how a specific process contributes to the global dissipation of the system. Using actin-intact cytoplasmic extract from Xenopus laevis frog eggs as a model system, we measure how a specific dissipative process - local actomyosin fluctuations – relates to the global dissipation. To estimate local dissipation, we image conformational fluctuations of single-walled carbon nanotubes (SWNTs) embedded in the actomyosin network, and we analyze breaking of detailed balance in the space of normal modes. To estimate global dissipation and the chemical potential gradient, we quantify the global ATP turnover, as well as ATP and ADP concentrations, using fluorimetric assays. To vary the chemical potential, we introduce apyrase, which provides an additional exogenous dissipative pathway by catalyzing the hydrolysis of ATP. We thus reveal how a specific, local dissipative process is a function of the global dissipation of the system. |
Thursday, March 8, 2018 4:06PM - 4:18PM |
V53.00009: Active droplets as model of bacterial colonies Hui-Shun Kuan, Frank Julicher, Vasily Zaburdaev Examples of active systems appear in various biological settings, such as flocks of birds, cell cytoskeleton and bacterial colonies. These out-of-equilibrium systems constantly transduce and dissipate energy and may exhibit phase separation, which in active matter can differ fundamentally from passive phase separation governed by free energy minimization. In this talk, we focus on phase separation occurring in bacterial colonies due to intracellular force generation. We use a continuum approach, representing bacterial colonies as active materials, which exhibit different surface profiles and position-dependent motility gradients. Moreover, the coalescence of two such droplets exhibits two time scales which cannot be solely understood by surface tension and viscosity. Our theoretical framework of active droplets provides a means of describing bacterial colony formation and can be extended to other cellular aggregates. |
Thursday, March 8, 2018 4:18PM - 4:30PM |
V53.00010: Dynamical self-consistent mean-field theory for interacting self-propelled rods Drake Lee, Robert Wickham We derive a dynamical self-consistent field theory (dSCFT) for interacting, self-propelled rods by applying an extremal principle to the collective variables in an exact Martin-Siggia-Rose functional integral arising from the microscopic equations for the many-body Brownian dynamics of self-propelled rods. In dSCFT, the problem reduces to that of the motion of one self-propelled rod under the influence of dynamical forces and torques from other rods computed within a self-consistent mean-field approximation. A key quantity in the theory is the time-dependent rod position-orientation distribution function, that satisfies a Smoluchowski equation. Our derivation provides a clean, systematic, and direct route from the microscopic equations of rod motion to this continuum dynamical theory. This connection will enable us to efficiently and quantitatively simulate dSCFTs for biological systems of increasing complexity and realism. We present simulations that aim to understand the fascinating large-scale collective structures and group dynamics seen in studies of the surface motility of Pseudomonas aeruginosa bacteria colonies. |
Thursday, March 8, 2018 4:30PM - 4:42PM |
V53.00011: Instabilities, rheology and spontaneous flows in magnetotactic bacterial suspensions. Roberto Alonso, David Saintillan Magnetotactic bacteria are motile prokaryotes, mostly present in marine habitats, that synthesize intracellular magnetic membrane-bounded crystals known as magnetosomes. They behave as self-propelled permanent magnetic dipoles that orient and migrate along the geomagnetic field lines of the Earth. In this work, we analyze the macroscopic transport properties of suspensions of such bacteria in microfluidic devices. When placed in an external magnetic field, these microorganisms feel a net magnetic torque which is transmitted to the surrounding fluid, and can give rise to a net unidirectional fluid flow in a planar channel, with a flow rate and direction that can be controlled by adjusting both the magnitude and orientation of the external field. Using a continuum kinetic model, we provide a physical explanation for the onset of these spontaneous flows. We also study the rheological properties and stability of these suspensions in both an applied shear flow and in pressure-driven flow. |
Thursday, March 8, 2018 4:42PM - 4:54PM |
V53.00012: Light-Switchable Collective Behavior in Photoactive Microalgae Alexandros Fragkopoulos, Christine Linne, Johannes Frey, Oliver Baeumchen In their natural habitats, many biological microorganisms are exposed to variable light conditions throughout the day. For light-sensitive microbes, these can be of paramount importance since their biological functions change with the illumination conditions. Here we present that Chlamydomonas, a unicellular soil-dwelling microalgae, form regions of high and low cell density in the absence of light, while in a uniform illumination the active suspension becomes homogeneous. We find that the emerging pattern follows the shape of the compartment that encloses the motile cells by staying a typical distance away from the compartment wall. As result, we find that for circular confinement, the pattern transitions from a disk to a ring morphology depending on the compartment size and cell density. The effect is completely reversible and we explore the spatial characteristics of the patterns as well as the time scales associated to the emergence of this collective behaviour. Our results suggest that the mechanism of this light-switchable collective behaviour is unrelated to phototaxis but rather linked to cells' metabolic and/or chemotactic activity in certain light conditions. |
Thursday, March 8, 2018 4:54PM - 5:06PM |
V53.00013: Geometry and mechanics of micro-domains in growing bacterial colonies Luca Giomi, Zhihong You, Daniel Pearce, Anupam Sengupta Bacterial colonies are abundant on living and non-living surfaces and are known to mediate a broad range of processes in ecology, medicine and industry. Although extensively researched, from single cells to demographic scales, a comprehensive biomechanical picture, highlighting the cell-to-colony dynamics, is still lacking. Here, using experiments, molecular dynamics simulations and continuous modelling, we investigate the geometrical and mechanical properties of a bacterial colony growing on a substrate with free boundary, and demonstrate that such an expanding colony self-organizes into a "mosaic" of micro-domains consisting of highly aligned cells. The emergence of micro-domains is mediated by two competing forces: the steric forces between neighboring cells which favour cell alignment, and the extensile stresses due to cell growth that tend to reduce the local orientational order, and thereby distort the system. This interplay results into an exponential distribution of the domain areas, and sets a characteristic length scale proportional to the square root of the ratio between the system orientational stiffness and the magnitude of the extensile active stress. |
Thursday, March 8, 2018 5:06PM - 5:18PM |
V53.00014: Non-Gaussian properties of transport in active systems Eli Barkai, Stanislav Burov Appearance of non-Gaussian features for transport in systems with active elements becomes less an exception but rather a rule. Examples include transport mediated by molecular motors and diffusion in a bacteria suspension. Experimentally obtained single particle trajectories reveal presence of prolonged jumps, an effect that is frequently attributed to active processes, e.g. adherence of a bead to a moving bacteria. Number of such "active" events fluctuates from one trajectory to another. We present a simple model of a random walk with random number of jumps. Analytically obtained results show that non-Gaussian features, like exponential decay of the displacement probability density function, naturally appear in the model. Moreover the model predicts that close to exponential behavior of the tails of the displacement distribution is an attractor for a wide class of systems. |
Thursday, March 8, 2018 5:18PM - 5:30PM |
V53.00015: Rényi Entropy of the Totally Asymmetric Exclusion Process Anthony Wood, Richard Blythe, Martin Evans I will present our analytic work on the totally asymmetric exclusion process (TASEP), where we have calculated a measure known as the Rényi entropy. This is a generalisation of the more common Shannon entropy, that has a neat interpretation for equilibrium systems. Away from equilibrium (the case for any real system e.g. biological processes), a physical interpretation remains elusive. However, we suspect the nonanalyticities of a given system’s Rényi entropy may serve as an indicator as to whether a system is in or out of equilibrium. |
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