Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session U22: Transport and Kinetics in Biological Systems |
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Sponsoring Units: DBP GSNP Chair: Uwe Tauber, Virginia Tech Room: LACC 409B |
Thursday, March 24, 2005 8:00AM - 8:36AM |
U22.00001: Asymmetric exclusion process models for translation and biological transport Invited Speaker: In the totally asymmetric simple exclusion process (TASEP), particles travel unidirectionally along a one-dimensional lattice and interact with each other by hard-core exclusion. Variants of the TASEP have been used to model the movement of molecular motors along biopolymers, including ribosomes on mRNA and various motors on cytoskeletal filaments. Ribosomes synthesize proteins as they traverse an mRNA molecule, so their motion is important in understanding the kinetics of protein production. We model protein synthesis as a TASEP with quenched disorder in the particle hopping rates. The hopping rates are determined by gene sequences and the availability of biomolecules. We use a statistical ensemble method in fitting the model to experimental data. The model is able to explain much of the nonlinear relationship between mRNA and protein levels. [Preview Abstract] |
Thursday, March 24, 2005 8:36AM - 8:48AM |
U22.00002: Diffusion and binding of finite-size particles through tubes Mark Henle, Ajay Gopinathan, Christian Santangelo The classical treatment of the diffusion of particles through their environment ignores all of the interactions between these particles. The diffusion of biological particles, however, often occurs in crowded environments (e.g. the cellular matrix), where steric interactions between particles are important. In this talk, we investigate the effects of steric interactions on diffusion by considering the diffusion of finite-size particles within a tube whose diameter is comparable to the size of the particles. When the particles diffuse freely through the tube, steric interactions have only a trivial effect on their diffusion; however, steric interactions dramatically alter the diffusion when the particles can reversibly bind to the walls of the tube. Using a simple lattice model of this process, we calculate the steady-state current and density of particles in the tube. We also perform simulations of this system, and find excellent agreement with our analytical results. [Preview Abstract] |
Thursday, March 24, 2005 8:48AM - 9:00AM |
U22.00003: Nucleation and Transport in a Low-Dimensional Driven System Ivan Georgiev, Beate Schmittmann, Royce Zia Based on high precision Monte Carlo simulations, we discuss the formation of domains in a quasi one-dimensional model of two species driven in opposite directions. We argue that the presence of a single macroscopic cluster is an intermediate stage of a complex nucleation process. A careful finite size analysis reveals many interesting properties: for small systems the single cluster destabilizes and on large systems we observe the formation of many clusters. We also show results for the dependence of the cluster growth exponent on the stochastic parameters and on different lattice geometries. [Preview Abstract] |
Thursday, March 24, 2005 9:00AM - 9:12AM |
U22.00004: Exact Solution for a class of Mass Transport Models, Condensation Transitions, and the Nature of the Condensate M.R. Evans, S.N. Majumda, R.K.P. Zia We study the phenomenon of real space condensation in the steady state of one dimensional mass transport models. These models, including the Zero-Range Process and the Asymmetric Random Average Process, have been used to describe a variety of physical systems, e.g., bio-molecular motors, vehicular or pedestrian traffic, force propagation through granular media, etc. The dynamics consists of stochastically transferring a portion of the mass, from site to neighboring site, according to some prescribed distribution. For a class of these models, we find an easy test to check if the steady state (full multi-site) distribution is `factorizable,' and if so, a simple method to construct the solution explicitly. Based on this approach, we not only verify the criterion for the existence of a condensation transition (where, a la Bose-Einstein, a finite fraction of the total mass condenses into a single site) but also elucidate the nature of the condensate. Specifically, we find two regimes: one where the mass of the condensate is Gaussian distributed with normal fluctuations, and a second regime with non-Gaussian distributions and anomalously large fluctuations. [Preview Abstract] |
Thursday, March 24, 2005 9:12AM - 9:24AM |
U22.00005: Will jams get worse when slow cars move over? B. Schmittmann, J. Krometis, R.K.P. Zia Motivated by an analogy with traffic, we simulate two species of particles (`vehicles'), moving stochastically in opposite directions on a two-lane road. In this simple modification of the asymmetric exclusion process, each species prefers one lane over the other, controlled by a parameter $0 \leq b \leq 1$ such that $b=0$ corresponds to random lane choice and $b=1$ to perfect `laning'. We find that the system displays one large cluster (`jam') whose size increases with $b$, contrary to intuition. Even more remarkably, the lane `charge' (a measure for the number of particles in their preferred lane) exhibits a region of negative response: even though vehicles experience a stronger preference for the `right' lane, more of them find themselves in the `wrong' one! For $b$ very close to $1$, a sharp transition restores a homogeneous state. Various characteristics of the system are computed analytically, in good agreement with simulation data. [Preview Abstract] |
Thursday, March 24, 2005 9:24AM - 9:36AM |
U22.00006: Subcellular protein localization in {\it E. coli}: diffusion and membrane attachment of MinD molecules Rahul Kulkarni, Kerwyn Huang, Morten Kloster, Ned Wingreen In {\it E. coli}, accurate cell division depends upon the oscillation of Min proteins. We provide a model for polar localization of MinD based only on diffusion, a delay for nucleotide exchange, and different rates of attchment to the bare membrane and occupied membrane. We derive analytically the probability density, and correspondingly the length scale, for MinD attachment zones. Our simple analytical model illustrates the processes giving rise to the observed localization of cellular MinD zones. [Preview Abstract] |
Thursday, March 24, 2005 9:36AM - 9:48AM |
U22.00007: Molecular trafficking in tissue engineered cartilage constructs Enrica De Rosa, Cristina Borselli, Paolo Antonio Netti Tissue processing in vitro requires an effective trafficking of biologically active agents within three-dimensional constructs for induction of appropriate and enhanced cellular growth, biosynthesis and tissue remodeling. Moreover, nutrients and waste products need to move freely through the cellular constructs to minimize the presence of regions with necrotic and/or apoptotic cells. In tissue-engineered cartilage, for example, during the time of culture, cells seeded within the three-dimensional constructs lay-down their own extracellular matrix and this may lead to a heterogeneous distribution of transport properties both in time and space. In this work the diffusion coefficient of BSA and 500kDa dextran has been measured with FRAP thecnique in agarose gel chondrocytes constructs at different position and time during the culture. The diffusion coefficient of both molecular probes within the developing tissue well correlated with the ECM production and assembly. Moreover the comparision between BSA and dextran transport parameters revealed a selective hindrance effect of the neo tissue on high interacting molecules. [Preview Abstract] |
Thursday, March 24, 2005 9:48AM - 10:00AM |
U22.00008: Minimal Model for Noise-Driven Locomotion Madan Rao, Sriram Ramaswamy We consider a pair of dissimilar particles, bound to each other by a non-centrosymmetric pair potential and restricted to move on a line, in the presence of white noise and nonlinear damping. We show analytically and numerically that the absence of an equilibrium fluctuation-dissipation relation, together with the asymmetry of the pair potential, causes the relative coordinate of the pair to drive a systematic mean motion of the centre of mass, without the aid of an external ratchet potential. This remarkably simple model of noise-driven self-propulsion illustrates a principle that should apply to a variety of driven systems, from biology to granular matter. [Preview Abstract] |
Thursday, March 24, 2005 10:00AM - 10:12AM |
U22.00009: Queueing and Cooperativity in Ligand-Receptor Binding Maria D'Orsogna, Tom Chou We compare the kinetics of two types of receptors: receptors that only allow ligands to attach to the binding sites in a specific order, and those that allow binding in any order. For equivalent rate constants and cooperativities, we find that receptors with sequential ligand binding are more likely to have all of its binding sites fully occupied than receptors that bind ligands in any order. The mean occupation of sequentially loaded receptors is also higher. However, starting from a totally empty receptor, we find that the mean first passage time to full occupancy is smaller for low-mean-occupation, random adsorption receptors. Our results are contrasted with Hill-like descriptions of receptor occupancy. Scenarios in which distinction of receptor types may be important are also discussed. [Preview Abstract] |
Thursday, March 24, 2005 10:12AM - 10:24AM |
U22.00010: A model of the kinetic cycle of single cytoplasmic Manoranjan P. Singh, Roop Mallik, Steven P. Gross, Clare Yu We use Monte Carlo simulations to model molecular motor function at the single molecule level. For kinesin, we show that the simulations of the kinetic cycle reproduces accurately the dependence of velocity on ATP concentration and applied load, described by Michaelis-Menten kinetics. More importantly, the Monte Carlo approach allows us to implement nonlinear models of more complicated branching enzymatic pathways, like those found in enzymes such as cytoplasmic dynein. Our dynein simulations reproduce the main features of recent single molecule experiments that found a discrete distribution of dynein step sizes depending on load and ATP concentration. The theory relates dynein's chemical/enzymatic properties to its mechanical force production. It proposes the existence of negative cooperativity of ATP binding at secondary binding sites, which is required to reproduce the experimentally observed step distribution and improves dynein's ATP economy by suppressing small steps under high-ATP/ no-load conditions. [Preview Abstract] |
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U22.00011: Probing convection and diffusion in macromolecular gels Enrica De Rosa, Paolo Antonio Netti Transport of molecules within three-dimensional biological tissue occurs by both diffusion and convection. While diffusion is relatively well studied in the literature, there is a paucity of data on convection parameters, even if is the most effective transport mechanism for large molecules. Pressure-driven flow through complex macromolecular gels can provide different probe velocity depending on the diffusant molecule and matrix interaction and so far no specific measurements have been performed. Furthermore the complexity or heterogeneity of the system may cause differences with the position in the convection properties of the sample. In this study both diffusion coefficient and velocity of several fluorescent probes in macromolecular gels have been measured with a high spatial resolution (100$\mu $m). The macromolecular velocity has been evaluated by adopting the video-FRAP technique, through an algorithm to separate the fluorescence recovery due to the brownian motion and that due to a bulk convection. Combination of the two transport process is very relevant in tissue engineering and drug delivery application. [Preview Abstract] |
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U22.00012: Dynamics of rigid and flexible extended bodies in viscous films and membranes Alex J. Levine, T.B. Liverpool, Fred C. MacKintosh The mobility of inclusions (e.g. proteins or lipid ``rafts'') in membranes is a fundamental physical parameter controlling a number of cellular processes. In this talk, we examine the motion of rod-like inclusions in continuum viscous films and membranes as a representative example of the general problem of determining the mobility of arbitrarily shaped, extended bodies moving in membranes or at liquid/liquid interfaces. We demonstrate an important difference between rod mobilities in films/membranes and in bulk fluids, which is present even when the dissipation is dominated by the fluid stress: For large inclusions we find that rotation and motion perpendicular to the rod axis exhibit purely local drag, in which the drag coefficient is algebraic in the rod dimensions. We also study the dynamics of the undulation modes of a semiflexible filament embedded in the membrane and find two dynamical regimes in the relaxation spectrum. [Preview Abstract] |
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