Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session V40: Mechanics of Biomolecular Systems II |
Hide Abstracts |
Sponsoring Units: DBP Chair: Andrew Rutenberg, Dalhousie University Room: 412 |
Thursday, March 19, 2009 8:00AM - 8:12AM |
V40.00001: Non-monotonic wave dispersion in one-dimensional spiral track of cardiac cells Tae Yun Kim, Okyu Kwon, Kyoung J. Lee Alternans, periodic cardiac beat-to-beat alternation, is an important precursor to cardiac fibrillation. The underlying mechanism for this phenomenon has been discussed mostly based on the electro-chemical kinetics of constituent cells (myocytes) that comprise the heart system. An important unexplored aspect of this phenomenon is the role of wave dispersion that reflects the cell-to-cell coupling as well as the local kinetic properties. A recent modeling study in fact suggests that a non-monotonic wave dispersion can be a source for alternans. We have designed and built very long ($\sim $ 15 cm) in vitro quasi-one dimensional tracks of rat ventricular cells for elucidating the instability responsible for the transition to alternans. One dimensional tracks are favorable, since it excludes the effect of local wave curvature. Systematic investigations based on S1-S2 stimulation protocols are carried out and here we present some preliminary evidence of non-monotonicity in cardiac wave dispersion. [Preview Abstract] |
Thursday, March 19, 2009 8:12AM - 8:24AM |
V40.00002: Periodic reversals allow bacteria to swarm Yilin Wu, Dale Kaiser, Yi Jiang, Mark Alber Many bacteria can rapidly traverse surfaces from which they are extracting nutrient for growth. They generate flat, spreading colonies, called swarms because they resemble swarms of insects. We seek to understand how members of any dense swarm track their neighbors while interfering minimally with the motion of others'. We choose myxobacteria as our model system. Individual myxobacteria cells regularly reverse their gliding directions. With a cell- and behavior-based computational model, we show that reversals of gliding direction are essential for swarming and that reversals increase the outflow of cells across the edge of the swarm. We also find that the reversal period predicted to maximize the outflow of cells is the same (within the errors of measurement) as the period observed in experiments with normal myxobacteria cells. This coincidence suggests that the circuit regulating reversals evolved to its current sensitivity under selection for growth achieved by swarming. Our work suggests a crucial componentin the general behavioral algorithm governing bacterial swarming. [Preview Abstract] |
Thursday, March 19, 2009 8:24AM - 8:36AM |
V40.00003: Do Recurved Sensory Organs in Drosophila Form Through a Turing-Type Bifurcation? Huifeng Zhu We study the recurved bristles on {\it Drosophila} wing margin of wild-type and mutant.The expression levels of the {\it achaete-scute} complex protein determine the epidermal or neural fate of a pro-neural cell. In wide-type flies, the development ends in a state where a recurved bristle grows out nearly every fifth cell. Recent experiments have shown that the frequency of recurved bristles can be changed by adjusting the mean concentrations of the zinc-finger transcription factor {\it Senseless} and the micro\_RNA miR-9a. With reduced levels of miR-9a, mutant flies grow regular organization of recurved bristles, but with a lower periodicity. We argue that the characteristics of bristle organization are signatures of a Turing-type bifurcation which emerges from a uniform background in reaction-diffusion process, in continua. In contract, fly wing margin consists of a discrete array of cells with possible cross-species interactions. Further, proteins do not diffuse between cells. We argue that the intracellular actions can play the role of diffusion in a discrete cell array. However, the analogs of diffusion coefficients can be positive or negative. Intracellular actions should give a conserved cell number periodicity. We introduce a simple model to study pattern formation in such cellular arrays based on intracellular actions. Also, we observe that periodicity both in length and cell numbers from different group of flies. [Preview Abstract] |
Thursday, March 19, 2009 8:36AM - 8:48AM |
V40.00004: Sisyphus at the Nanoscale: Bacterial Topotaxis in a Microfabricated Environment Guillaume Lambert, Peter Galajda, David Liao, Robert H. Austin The ballistic-like motion of self-propelled particles at low-Reynolds number can be exploited to influence their direction of motion. In particular, it has been demonstrated that by using the right topology (in this case a micro-fabricated array of funnel-like asymmetrical barriers), {\it E.coli} bacteria can be ``pumped'' between two adjacent regions (Galajda 2007, Wan 2008). We built upon this idea and developed a micro-habitat array in which chemotaxis and topotaxis --nutrient- and topology-driven motion, respectively-- are in opposition, leading to an inherently unstable environment in which a bacterium is constantly pushed away from the fitness landscape's summit in a Sisyphean fashion. Surprisingly, we find that the bacterial population as a whole is able to overcome the rectifying array. An in-depth microscopic analysis of the swimmer's motion is used to quantify the strategies adopted by the bacteria. [Preview Abstract] |
Thursday, March 19, 2009 8:48AM - 9:00AM |
V40.00005: Microrheology of swimming bacteria suspension. Andrey Sokolov, Igor Aronson We study rheology of suspension of swimming bacteria Bacillus Subtilis at high concentrations. Experiments were performed in a free standing fluid film contained in a transparent chamber with adjustable Oxygen/Nitrogen ratio. The swimming velocity of bacteria is controlled by the concentration of dissolved Oxygen: it reduces to zero when Oxygen is completely replaced by Nitrogen. Macroscopic flow in a film is produced by oscillations and rotations of magnetic particles by rotating external magnetic field. To extract the effective viscosity, we measured macroscopic velocity field generated by the particles using PIV of fluorescent markers seeded to the film. We discovered that viscosity of bacterial suspension is increasing with decreasing swimming speed of bacteria due lack of Oxygen. [Preview Abstract] |
Thursday, March 19, 2009 9:00AM - 9:12AM |
V40.00006: Microrheology of Actin Network Depends on Probe Size, Surface Chemistry and Depletion Effect Jun He, Jay Tang Microrheological properties of F-actin were measured by video particle tracking using beads with different size and surface chemistry. We found that the mean square displacements of probe particles scale with bead diameter with an exponent of about -0.45 instead of -1. This scaling behavior results in the measured shear moduli of F-actin network varying with the probe size. The main features of our data can be accounted for by the probe surface stickiness and the opposing depletion effect, both of which are confirmed by confocal imaging of beads in the actin network. [Preview Abstract] |
Thursday, March 19, 2009 9:12AM - 9:24AM |
V40.00007: Mechanics of biomimetic systems propelled by actin comet tails Hyeran Kang, Dhananjay Tambe, Vivek Shenoy, Jay Tang The motility of intracellular bacterial pathogens such as \textit{Listeria monocytogenes} is driven by filamentous actin comet tails in a variety of trajectories. Here, we present the \textit{in vitro} study on the actin-based movements using spherical beads of different sizes coated with VCA protein, a partial domain of N-Wasp, in platelet extracts. Long term two-dimensional trajectories of the spherical beads motility show characteristic difference than those observed for bacteria, which have both elongated shape and asymmetric expression of the polymerization inducing enzyme. The trajectories also vary sensitively with the bead size and shape. These results provide a useful test to our new analytical model including the rotation of the bead relative to the tail. [Preview Abstract] |
Thursday, March 19, 2009 9:24AM - 9:36AM |
V40.00008: Generalized rules for the optimization of elastic network models Timothy Lezon, Eran Eyal, Ivet Bahar Elastic network models (ENMs) are widely employed for approximating the coarse-grained equilibrium dynamics of proteins using only a few parameters. An area of current focus is improving the predictive accuracy of ENMs by fine-tuning their force constants to fit specific systems. Here we introduce a set of general rules for assigning ENM force constants to residue pairs. Using a novel method, we construct ENMs that optimally reproduce experimental residue covariances from NMR models of 68 proteins. We analyze the optimal interactions in terms of amino acid types, pair distances and local protein structures to identify key factors in determining the effective spring constants. When applied to several unrelated globular proteins, our method shows an improved correlation with experiment over a standard ENM. We discuss the physical interpretation of our findings as well as its implications in the fields of protein folding and dynamics. [Preview Abstract] |
Thursday, March 19, 2009 9:36AM - 9:48AM |
V40.00009: Pulling helices inside bacteria: imperfect helices and rings Andrew Rutenberg, Jun Allard We study steady-state configurations of intrinsically-straight elastic filaments constrained within rod-shaped bacteria that have applied forces distributed along their length. Perfect steady-state helices result from axial or azimuthal forces applied at filament ends, however azimuthal forces are required for the small pitches observed for MreB filaments within bacteria. Helix-like configurations can result from distributed forces, including co-existence between rings and imperfect helices. Levels of expression and/or bundling of the polymeric protein could mediate this co-existence. [Preview Abstract] |
Thursday, March 19, 2009 9:48AM - 10:00AM |
V40.00010: Bending rigidity of type I collagen homotrimer fibrils Sejin Han, Sergey Leikin, Wolfgang Losert Normal type I collagen is an $\alpha $1(I)$_{2}\alpha $2(I) heterotrimeric triple helix, but $\alpha $1(I)$_{3}$ homotrimers are also found in fetal tissues and various pathological conditions, e.g., causing bone fragility and reducing tendon tensile strength. It remains unclear whether homotrimers alter mechanical properties of individual fibrils or affect tissues by altering their organization at a higher level. To address this question, we investigated how homotrimers affect fibril bending rigidity. Homotrimer fibrils have been shown to be more loosely packed so that we expected them to be more susceptible to bending. However, homotrimer fibrils were more rigid despite being thinner and more hydrated. To quantify fibril rigidity, we analyzed their shape by Fourier decomposition, determined the correlation function for the direction along each fibril, and calculated the distribution of local fibril curvature. The estimated persistence length of homotrimer fibrils was 3 $\sim $ 10 times longer than for heterotrimer fibrils, indicating much higher bending rigidity of homotrimer fibrils. [Preview Abstract] |
Thursday, March 19, 2009 10:00AM - 10:12AM |
V40.00011: Surface manipulation of protein filaments Laurent Kreplak, Douglas Staple, Marko Loparic, Hans-Juergen Kreuzer Within mammalian tissues, cells move by actively remodeling a dense network of collagen fibrils. In order to study this situation, we analyze the force response of two types of filamentous protein structures, desmin intermediate filaments 12 nm in diameter and collagen fibrils 80 nm in diameter. Both types of filaments were adsorbed at a solid-liquid interface and locally moved with an AFM tip at constant velocity against surface friction in the interfacial plane. In the case of collagen fibrils, that have an extensibility below 30{\%} extension, we observed that microns long fibrils could be moved by the tip and deformed into shapes that could not be explain by the linear elastic theory for a stiff rod. In the case of desmin filaments that can be stretched up to 3.5 times there length, we observed local stretching of the filaments and discreet steps in the torsional force measured with the cantilever. In order to describe both types of filaments' behaviors, we described the protein filaments as a chain of beads of mass $m$ linked together by a mass-less polymer linker. By solving the Newtonian equations of motions for the coupled beads in the presence of a point load and a viscous drag due to the surface-filament interactions we were able to reproduced our experimental data and extract information on friction. [Preview Abstract] |
Thursday, March 19, 2009 10:12AM - 10:24AM |
V40.00012: Multiscale Mechanics of Fibrin Polymer Andre Brown, Rustem Litvinov, Dennis Discher, Prashant Purohit, John Weisel Blood clots and thrombi consist primarily of fibrin, a branched, open mesh of polymeric fibers made of protein monomers, with a remarkable and unexplained extensibility and elasticity. Understanding the origin of fibrin mechanics may ultimately be significant for modulating thrombosis and bleeding. We propose that the unique mechanical properties of fibrin are based on its ability to undergo concerted structural rearrangements at the network, fiber, and molecular levels. Stretching of a whole fibrin clot is followed by clot shrinkage, fiber alignment and bundling, and extension of the constituent fibrin molecules. We develop constitutive models that integrate these quantitative observations and suggest that fibrin extensibility and elasticity are largely manifestations of protein unfolding. [Preview Abstract] |
Thursday, March 19, 2009 10:24AM - 10:36AM |
V40.00013: Cardiomyocytes beat best on a matrix with heart-like elasticity -- Molecular mechanics of the changes Christine Carag, Adam Engler, Dennis Discher Cardiomyocytes derived from embryos beat spontaneously in culture, but it is shown here with a series of flexible substrates that matrices which mimic the elasticity of the developing heart are optimal for 1-Hz beating, for transmitting contractile work to the matrix, and for promoting actomyosin striation. On hard matrices that mechanically mimic a post-infarct fibrotic scar, cells overstrain themselves, lack striated myofibrils and stop beating; on very soft matrices, cells preserve contractile beating for days in culture but do very little work. Optimal matrix leads to a strain match between cell and matrix, and suggests dynamic differences in intracellular protein structures. A novel `cysteine shotgun' method of labeling the in situ proteome reveals differences in assembly or conformation of several abundant cytoskeletal proteins, including vimentin, filamin and myosin. [Preview Abstract] |
Thursday, March 19, 2009 10:36AM - 10:48AM |
V40.00014: Dynamic Viscoelasticity of Individual Bacterial Cells Virginia Vadillo-Rodriguez, John Dutcher We have used an AFM-based approach to probe the mechanical properties of single bacterial cells (gram-negative \textit{Escherichia coli }K12) by applying a constant compressive force to the cell under fluid conditions while measuring the time-dependent displacement (creep) of a colloidal AFM tip due to the viscoelastic properties of the cell. We observed that the cells exhibited a viscoelastic solid-like behavior with retarded elasticity, i.e. both an instantaneous and a delayed elastic deformation, which is well described by a three-parameter mechanical model. Using the best fit parameter values, we have calculated the dynamic viscoelastic behavior of the cells over a wide range of frequencies based on a numerical time-frequency transform technique and we have compared the calculated behavior with that measured experimentally. Comparison of the results obtained for \textit{E. coli }with previously reported data on the mechanical properties of others gram-negative cells and their isolated surface layers suggests that the elastic component of the cell viscoelastic response is dominated by the properties of the peptidoglycan layer, whereas the viscous component likely arises from the liquid-like character of the cell membranes. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700