Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Session Q39: Information Processing in Biological Systems |
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Sponsoring Units: GSNP DBP Chair: Madan Rao, Raman Research Institute Room: A124/127 |
Wednesday, March 23, 2011 11:15AM - 11:51AM |
Q39.00001: TBD Invited Speaker: This abstract not available. [Preview Abstract] |
Wednesday, March 23, 2011 11:51AM - 12:03PM |
Q39.00002: Adaptive processing of natural signals in the fly peripheral visual system Liming Zhou, Rob de Ruyter van Steveninck For modest light intensity variations, fly photoreceptors and their postsynaptic targets, the Large Monopolar Cells (LMCs) behave approximately linearly. In this linear and stationary regime, signal transmission is described by a combination of impulse response and noise autocorrelation function. But natural visual signals often show fast and large intensity variations, and cells adapt to cope with such strong variations. As a result, responses to small contrast perturbations are still linear, but the system is no longer stationary. We study signal transfer under these conditions by measuring responses to small pseudorandom contrast perturbations that ride on large cyclically repeated intensity fluctuations. Those measurements allow us to describe signal transmission by matrices representing nonstationary analogs of the impulse response and the noise autocorrelation function. This description makes it possible to quantify information transmission as the system is continuously adapting to large intensity fluctuations, and to study trade off in adaptation and reliable information transmission in a natural context. [Preview Abstract] |
Wednesday, March 23, 2011 12:03PM - 12:15PM |
Q39.00003: Optogenetic dissection of neural circuit underlying locomotory decision-making in Caenorhabditis Elegans Askin Kocabas, Zengcai Guo, Sharad Ramanathan Despite the knowledge of the physical connectivity of the entire nervous system of C.elegans, we know little about how neuronal dynamics results in decision-making. Detailed understanding of functional and dynamic relations of the neural circuitry requires spatiotemporal control of the neuronal activity. Recent discoveries of light gated ion channels have allowed temporal optical control of neural activity. However, excitation of a specific neuron from among many expressing the channel has been a challenge. By combining optogenetic tools, micro mirror array technology and fast real time image processing, we have developed a technique to activate specific single or multiple neurons in an intact crawling animal while tracking its behavior. Using this setup we traced the neural pathway controlling the gradual turning of the animal during the locomotion. We found that the activity of a specific neuronal circuit that receives inputs from sensory neurons is coordinated with head movement. This coordination allows the animal to turn left or right based on the variation of sensory stimulus during head movement. By directly modulating the activity of the neural circuit, we can force the animal to turn in a specific direction independent of sensory stimuli. [Preview Abstract] |
Wednesday, March 23, 2011 12:15PM - 12:27PM |
Q39.00004: Physical limits to concentration sensing in biochemical signaling Nicholas Licata, Sima Setayeshgar In many biological systems, signals are carried by changes in the concentration of diffusable molecules which are transduced by receptors. It has been demonstrated experimentally that many signaling systems, from regulation of gene expression during development to bacterial chemotaxis, operate with remarkable sensitivity as indicated by a reliable response to small fractional changes in concentration. This sensitivity has contributions from an irreducible noise arising from the inherent random nature of the diffusing input signal, as well as from the chemical measurement process. By explicitly evaluating these theoretically derived contributions for the experimentally well- characterized bacterial chemotaxis network and motor response, we show that they are comparable to within factors of order unity, consistent with the observation that the measurement error approaches the physical lower limit set by diffusion. We extend our analysis to a class of ligand-gated ion channels, demonstrating the generality of this result where accuracy is especially important for the signaling system. [Preview Abstract] |
Wednesday, March 23, 2011 12:27PM - 12:39PM |
Q39.00005: Spatial phase patterns in locally coupled Kuramoto oscillators with repulsive interactions Zahera Jabeen, Michael Giver, Dapeng Bi, Bulbul Chakraborty Recent experiments in microfluidic arrays of interacting Belousov-Zhabotinsky droplets, which belong to the class of active emulsions, show a rich variety of spatial patterns [J. Phys. Chem. Lett. 1, 1241-1246 (2010)]. The predominant coupling between these droplets is inhibitory. Motivated by this experimental system, we study repulsively coupled Kuramoto oscillators with nearest neighbor interactions on a triangular lattice in two dimensions. We show that the geometry of the lattice constrains the phase difference between two neighboring oscillators to $2\pi/3$. We report the existence of domains with either clockwise or anticlockwise helicity, leading to defects in the lattice. We study the time dependence of these domains and show that at large coupling strengths the domains freeze due to frequency synchronization. A variant of this model, in which amplitude variations are introduced by an additional Ising-like coupling between the oscillators, explores the strong coupling limit phenomenon in the experimental system. We discuss these results in the context of the experiments. [Preview Abstract] |
Wednesday, March 23, 2011 12:39PM - 12:51PM |
Q39.00006: Monte-Carlo Study of Axonal Transport in a Neuron Uttam Shrestha, Clare Yu, Zhiyuan Jia, Robert Erickson, Steven Gross A living cell has an infrastructure much like that of a city. A key component is the transportation system that consists of roads (filaments) and molecular motors (proteins) that haul cargo along these roads. We will present a Monte Carlo simulation of intracellular transport inside an axon in which motor proteins carry cargos along microtubules and are able to switch from one microtubule to another. The breakdown of intracellular transport in neurons has been associated with neurodegenerative diseases such as Alzheimer's, Lou Gehig's disease (ALS), and Huntingdon's disease. [Preview Abstract] |
Wednesday, March 23, 2011 12:51PM - 1:03PM |
Q39.00007: Phase and frequency entrainment in locally coupled phase oscillators with repulsive interactions Michael Giver, Zahera Jabeen, Bulbul Chakraborty Recent experiments in one and two-dimensional microfluidic arrays of droplets containing Belousov - Zhabotinsky reactants show a rich variety of spatial patterns [J. Phys. Chem. Lett. 1, 1241-1246 (2010)]. These experiments provide the first steps towards creating easily reproducible model active emulsion systems. Motivated by this experimental system, we study repulsively coupled Kuramoto oscillators with nearest neighbor interactions on a linear chain as well as a ring in one dimension. We show using linear stability analysis as well as numerical study, that the stable phase patterns depend on the geometry of the lattice and that a transition to the ordered state does not exist in the thermodynamic limit. We will also present results comparing our Kuramoto model with finite element simulations of the Brusselator model in geometries similar to those of the experiment. [Preview Abstract] |
Wednesday, March 23, 2011 1:03PM - 1:15PM |
Q39.00008: Simulation studies of creeping flexible nematogens: flocking and rectifying barriers Adam Nicholas, Robin Selinger Recent simulation studies of active nematics have focused on rigid rods or swimming bacteria undergoing collisions via simple rules. Here we present a more physically detailed model of self-propelled creeping flexible nematogens. Each segmented ``worm'' is represented as nine interaction sites connected by springs. The springs' equilibrium length is modulated, causing each worm to elongate and contract periodically. Each worm alternately grips the substrate at its leading or trailing end, producing creeping locomotion. Inter-worm interactions are described via the Weeks-Chandler-Anderson potential between nearby interaction sites. Random forces and damping are also added. For worms that reverse crawling direction at random intervals, we observe a homogeneous nematic phase, and study its behavior in the presence of a rectifying barrier. For worms that move only in a single direction, we observe flocking behavior characterized by evolving stripes of densely crowded particles interspersed with low-density regions. We compare these results with relevant experiments and related theory/simulation approaches. [Preview Abstract] |
Wednesday, March 23, 2011 1:15PM - 1:27PM |
Q39.00009: ABSTRACT WITHDRAWN |
Wednesday, March 23, 2011 1:27PM - 1:39PM |
Q39.00010: Glass-like dynamics in collective cell migration Thomas Angelini, David Weitz The collective movement of tissue cells is essential to fundamental biological processes in both health and disease, and occurs throughout embryonic development, during wound healing, and in cancerous tumor invasion. Most knowledge of cell migration, however, comes from single cell studies. Single cells migrate by executing cyclic processes of extension, adhesion, and retraction, during which the cell body fluctuates dramatically and the cell changes direction erratically. These sub-cellular motions must be coupled between neighbors in confluent layers, yet the influence of this coupling on collective migration is not known. In this talk we present a study of motion in confluent epithelial cell sheets. We measure collective migration and sub-cellular motions, covering a broad range of length-scales, time-scales, and cell densities. We find that that collective cell migration exhibits many behaviors characteristic of classical supercooled particulate fluids, including growing dynamic heterogeneities in the migration velocity field, non-Arrhenius relaxation behavior, and peaks in the density of states analogous to the Boson peak. These results provide a suggestive analogy between collective cell motion and the dynamics of supercooled fluids approaching a glass transition. [Preview Abstract] |
Wednesday, March 23, 2011 1:39PM - 1:51PM |
Q39.00011: Active Chemical Thermodynamics promoted by activity of cortical actin Bhaswati Bhattacharya, Abhishek Chaudhuri, Kripa Gowrishankar, Madan Rao The spatial distribution and dynamics of formation and breakup of the nanoclusters of cell surface proteins is controlled by the active remodeling dynamics of the underlying cortical actin. To explain these observations, we have proposed a novel mechanism of nanoclustering, involving the transient binding to and advection along constitutively occuring ``asters'' of cortical actin. We study the consequences of such active actin-based clustering, in the context of chemical reactions involving conformational changes of cell surface proteins. We find that the active remodeling of cortical actin, can give rise to a dramatic increase in efficiency and extent of conformational spread, even at low levels of expression at the cell surface. We define a activity temperature ($\tau_a$) arising due to actin activities which can be used to describe chemical thermodynamics of the system. We plot TTT (time-temparature-transformation) curves and compute the Arrhenius factors which depend on $\tau_a$. With this, the active asters can be treated as enzymes whose enzymatic reaction rate can be related to the activity. [Preview Abstract] |
Wednesday, March 23, 2011 1:51PM - 2:03PM |
Q39.00012: Brown movement in complex asymmetric periodic potential under the influence of colored noise Mikhail Sviridov, Sergey Guz The idea of the molecular motor in an asymmetric periodic potential is a well-known problem. The motion of a Brownian particle is often studied when the system is subjected to the action of white noise. In practical situations noise is colored (``red'') random process. The red noise is the Ornstein-Uhlenbeck process. In this work we consider noise when the spectral density of the external noise is equal to zero on the zeroth frequency. In our previous works such a noise is been called as ``green'' noise. For the analytical study of green noise action, we use an approach based on a Krylov-Bogoliubov averaging method which is modified to study the action of noise with arbitrary intensity. A certain effective potential can be built which determines the basic features of the system dynamics. Further, we compare two numerical cases. The first one is the time-derivative of the Ornstain-Uhlenbeck process (green noise). The complex potentials when the system does not work as a molecular motor in the case of red noise, i.e. the average motion of the particle does not exhibit a drift in a given direction. If green noise operates on the same system, it turn out the effective molecular motor. We demonstrate this fact by a histograms for realizations of these processes. [Preview Abstract] |
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