Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session V29: Nonlinear Phenomena & Pattern Formation in Biology |
Hide Abstracts |
Sponsoring Units: DBP DCMP Chair: Igor Aronson, Argonne National Laboratory Room: Baltimore Convention Center 326 |
Thursday, March 16, 2006 11:15AM - 11:27AM |
V29.00001: Thermally activated escape rate for a Brownian particle in a double-well potential for all values of the dissipation William Coffey, Yuri Kalmykov, Sergey Titov The translational Brownian motion in a (2-4) double-well potential is considered. The escape rate, the position correlation function and correlation time, and the generalized susceptibility are evaluated from the solution of the underlying Langevin equation by using the matrix continued fraction method. The escape rate and the correlation time are compared with the Kramers theory of the escape rate of a Brownian particle from a potential well as extended by Mel'nikov and Meshkov [J. Chem. Phys. \textbf{85}, 1018 (1986)]. It is shown that in the low temperature limit, the universal Mel'nikov and Meshkov expression for the escape rate provides a good estimate of both escape rate and inverse position correlation time for all values of the dissipation including the very low damping (VLD), very high damping (VHD), and turnover regimes. Moreover, for low barriers, where the Mel'nikov and Meshkov method is not applicable, analytic equations for the correlation time in the VLD and VHD limits are derived. [Preview Abstract] |
Thursday, March 16, 2006 11:27AM - 11:39AM |
V29.00002: The spectra of spiral wave breakup Dwight Barkley, Paul Wheeler It has been known for many years that spiral waves in excitable reaction-diffusion systems can break up into a state of spatio-temporal chaos. The breakup may occur near the spiral tip (core breakup) or far from the tip (far-field breakup). Past analyses of these phenomena have been almost exclusively based on the study of 1D wave trains. This talk focuses on the computation of linear stability spectra and nonlinear simulations of spiral waves on large 2D disks. Through such computations we determine point eigenvalues associated with both types of breakup and show that these are near to, but not in, the absolute spectra. Hence spiral breakup occurs before the crossing of the absolute spectrum, contrary to prediction. Both types of breakup appear to be simply due to subcritical Hopf bifurcations. [Preview Abstract] |
Thursday, March 16, 2006 11:39AM - 11:51AM |
V29.00003: Pattern Formation without Patterning Proteins in Cyanobacteria Jun Allard, Andrew Rutenberg Filaments of cyanobacteria respond to nitrogen starvation by differentiating one cell in ten into a heterocyst, which is devoted to fixing atmospheric nitrogen. This is an example of self-organized pattern formation. We present a dynamical model explaining the initial selection of heterocysts in mutated cyanobacteria that are effectively without normal patterning proteins. Our simulations of this model produce distributions of heterocyst spacings that are consistent with experimental data, and lead to new qualitative predictions on the mechanisms of pattern formation in filamentous cyanobacteria. We discuss possible experimental tests of our results. [Preview Abstract] |
Thursday, March 16, 2006 11:51AM - 12:03PM |
V29.00004: Experimental studies of large-scale collective swimming in dense suspensions of bacteria Andrey Sokolov, Igor Aranson, Raymond Goldstein, John Kessler We conducted experimental investigation of large-scale collective swimming in dense suspensions of \textit{Bacillus subtilis}. This microorganism is flagellated, rod-shaped objects, 5-10 microns long and capable of swimming up to 20 microns/second. The hydrodynamic and chemical interactions between individual cells results in remarkably rich collective behavior; self-concentration due to gradients of dissolved oxygen or pH level; phase transitions and self-organization in confined geometries. The self-organization often takes the form of coherent structures with typical sizes that are many times larger than those of the individual bacteria. The studies were performed in thin liquid film with controlled thickness. We explored experimentally the dependence of the scales of large-scale flow structures on the concentration of cells. The experimental results are compared with the predictions of continuum mathematical model of this phenomenon. [Preview Abstract] |
Thursday, March 16, 2006 12:03PM - 12:15PM |
V29.00005: Fiber optical measurements of electrical activity in canine ventricular preparations Amgad Squires, Gisa E. Luther, Michael Enyeart, Robert F. Gilmour, Eberhard Bodenschatz, Stefan Luther Ventricular fibrillation (VF) is a cardiac arrhythmia that kills over 300,000 people every year in the US alone, yet efforts at finding a cure have been stymied by our incomplete information about patterns of electrical activity in the whole heart. As an excitable medium, the heart is a pattern forming system; but only a very limited subset of patterns is compatible with life. In particular, spiral waves have been associated with both tachycardia and VF, but their origin and spatial and temporal dynamics is not fully understood. We propose a novel measurement technique that combines optical mapping of the epicardial surface with data from intramural fiber optical probe arrays. The data obtained from the fiber optical probes is sparse in space but dense in time. The data processing is based on sequential data assimilation using an ensemble Kalman filter. The ensemble Kalman filter provides a numerically efficient (sub-) optimum state space estimate based on the available spatial and temporal observations. The feasibility of the method is demonstrated with numerical data and arterially perfused canine heart preparations. [Preview Abstract] |
Thursday, March 16, 2006 12:15PM - 12:27PM |
V29.00006: Motion artifact removal in the optical mapping of cardiac tissue Gisa E. Luther, Amgad Squires, Michael W. Enyeart, Robert F. Gilmour, Eberhard Bodenschatz, Stefan Luther Optical mapping provides measurements of the transmembrane potential in cardiac tissue with high spatial and temporal resolution using voltage senitive dye. However, the contractile motion of cardiac tissue causes substantial artifacts in optical recordings. On the other hand, mechanical or pharmacological inhibition of motion is known to promote ischemia or alter the electrophysiological properties of the tissue and therefore limits the application of the optical mapping technique. Motion artifacts arise due to two dominant mechanisms: (a) Relative motion of the tissue with respect to the optical imaging system or the fiber optical probe. (b) Change of the optical properties of the tissue and of the dye associated with the variation of the tissue’s mean density. We present a novel model based algorithm, which accounts for both mechanisms. It combines a Lukas-Kanade feature tracking with two-wavelength ratiometric imaging. The robustness and accuracy of this approach is validated using numerical and experimental data. Our approach allows to rephrase the contamination of the signal with motion artifacts as a nonlinear mixing process. De-mixing the signal opens the perspective of retrieving information on both the transmembrane potential and contractile force. [Preview Abstract] |
Thursday, March 16, 2006 12:27PM - 12:39PM |
V29.00007: Compact Dynamical Equations for Brain Activity Jong Won Kim, Peter A. Robinson A continuum model of brain dynamics has recently been developed to reproduce and unify many features of electroencephalographic (EEG) signals. We further investigate the model and propose a new, more compact, model based on a single delay differential equation which captures the essential features, such as rapid corticocortical feedbacks and delayed feedbacks from extra cortical pathways. Experimentally observed frequency spectra of EEGs, including resonances, are reproduced in relevant regions of parameter space. In the nonlinear regime, onsets of seizures, which often show limit cycles, are explained by the instabilities of resonances at the boundary of a stability zone in the parameter space. This compact model also shows several other points of agreement with previous models and experiments, and thus provides a theoretical basis for analyzing complex brain activities, especially when they exhibit low-dimensional dynamics. [Preview Abstract] |
Thursday, March 16, 2006 12:39PM - 12:51PM |
V29.00008: Pattern recognition through collective behaviour in neural networks Jan R. Engelbrecht We investigate how collective order in networks of integrate-and-fire neurons can lead to computation. Specifically we show that patterns in static and dynamic sensory stimuli can be recognized through the development of synchrony in a simple neural network with a hierarchy of layers. The recognition events ultimately trigger activity in `grandmother' neurons in the last layer. [Preview Abstract] |
Thursday, March 16, 2006 12:51PM - 1:03PM |
V29.00009: Modeling of Protein Subcellular Localization in Bacteria Xiaohua Xu, Rahul Kulkarni Specific subcellular localization of proteins is a vital component of important bacterial processes: e.g. the Min proteins which regulate cell division in {\it E. coli} and Spo0J-Soj system which is critical for sporulation in {\it B. subtilis}. We examine how the processes of diffusion and membrane attachment contribute to protein subcellular localization for the above systems. We use previous experimental results to suggest minimal models for these processes. For the minimal models, we derive analytic expressions which provide insight into the processes that determine protein subcellular localization. Finally, we present the results of numerical simulations for the systems studied and make connections to the observed experiemental phenomenology. [Preview Abstract] |
Thursday, March 16, 2006 1:03PM - 1:15PM |
V29.00010: Quantitative measures for mitotic spindle pattern formation structures Stuart Schaffner, Jorge Jose Recently introduced biophysical models successfully reproduce the basic spindle patterns found in \textit{in-vitro} meiotic experiments. Numerical simulations of the model show the detailed behavior of microtubules and positive and negative walking molecular motors as they interact to form spindle patterns. Previous results were mostly qualitative in nature, but we are now developing quantitative measures to characterize the formation of spindle structures. In particular, minus-directed crosslinking motors bind microtubules together in pairs. This pairwise binding can be represented by a graph where the vertices are microtubules and the edges are crosslinking motors. Highly interconnected components of this graph correspond to bundles of motion-correlated microtubules. Numerical simulations show that these bundles are a prominent feature of spindle pole assembly. Using general ideas of random graph theory, we can measure deviations from random connectivity. We also calculate an approximation of the strain energy induced by contact forces between the microtubules and make estimates that could be tested experimentally. [Preview Abstract] |
Thursday, March 16, 2006 1:15PM - 1:27PM |
V29.00011: Stability and Perturbation Analysis on a Model of Cell Chemotaxis Colin McCann, Ron Skupsky, Wolfgang Losert, Ralph Nossal Many eukaryotic cells respond with directional movement to spatial and/or temporal gradients of small molecules that bind to cell surface receptors. The computational model of a chemotaxing cell developed in [1], which models cells such as neutrophils or Dictyostelium discoideum, is investigated with regard to stability and response to perturbations. A formal stability analysis finds that, when placed in an initial linear gradient, the model is most sensitive to perturbations at a 60-90 degree offset from the direction of the initial gradient. The model also responds most quickly and strongly to external point sources placed in that direction. These responses hold for all four of the model variants developed in [1]. This suggests that the observed `zigzag' behavior of real cell movement in a gradient may be influenced by the nature of the biochemical reactions that control a cell's chemotactic response. This research was funded in by the National Institutes of Health (NIH) and the National Institute of Standards and Technology (NIST). [1] Skupsky, R., W. Losert, and R.J. Nossal. 2005. ``Distinguishing modes of eukaryotic gradient sensing''. Biophys. J. 89:2806--2823 [Preview Abstract] |
Thursday, March 16, 2006 1:27PM - 1:39PM |
V29.00012: Raman Correlation Spectroscopy Edward Van Keuren, Maki Nishida We have developed a simple method for measurement of diffusion coefficients of specific components in complex mixtures of suspended particles in a liquid. The method, a variation of photon correlation spectroscopy (PCS), uses temporal fluctuations of Raman scattered light to characterize the particle Brownian motion. This is possible due to the key fact that Raman scattering is a coherent process, which is necessary for meaningful photon autocorrelation functions to be obtained. The time autocorrelation functions of Raman emission lines will yield information similar to that obtained by PCS. However, since the scattering at a particular wavelength is usually specific to only one type of molecule, only the diffusion coefficient of the particles containing that chemical species will be measured. We demonstrate this method with several multicomponent nanoparticle dispersions. [Preview Abstract] |
Thursday, March 16, 2006 1:39PM - 1:51PM |
V29.00013: A New Paradigm for Nanoparticle Biosensing: Magnetically Driven Critical Phase Slipping Brandon H McNaughton, Raoul Kopelman Could a single opto-magnetic micro or nanoparticle be used as a noninvasive nanobiosensor? In this work, we imitated micro-organism or bacteria sensing by binding a micron sized sphere to a larger rotating magnetic particle. The magnetic particle exhibits a nonlinear rotational behavior that marks a crossover from phase-locking to phase slipping with a remote rotating magnetic field. This critical transition is very sensitive to volume and shape changes, allowing for the detection of an attaching particle or biomolecule. Further miniaturization, combined with the remote sensing ability of this probe, could allow for measurements of viruses or biomolecules like DNA or proteins in a variety of environments, including closed biological systems. [Preview Abstract] |
Thursday, March 16, 2006 1:51PM - 2:03PM |
V29.00014: Sum frequency generation microscopy for imaging chirality Na Ji, Kai Zhang, Haw Yang, Yuen-Ron Shen Optically active sum frequency generation microscopy was demonstrated for the first time. Using films of solution of chiral 1,1'-bi-naphthol molecules with microstructures, we showed that sum frequency generation microscopy can image molecular chirality with three-dimensional sectioning capability and sub-micron spatial resolution. Because the image contrast originates from the intrinsic chirality of the system, no staining is required. Our microscopy scheme also allows the simultaneous detection of two-photon fluorescence. As a result, optically active sum frequency generation microscopy can be potentially very useful for live cell imaging. Preliminary results of applying this technique to DNA conformation study will also be described. [Preview Abstract] |
Thursday, March 16, 2006 2:03PM - 2:15PM |
V29.00015: Upconversion-Detected Ultrafast Two-Dimensional Infrared Spectroscopy Kevin Kubarych, Manuel Joffre Two-dimensional infrared (2DIR) spectroscopy provides direct access to ultrafast molecular dynamics by measuring time- and structure-dependent couplings between vibrational transitions. Biological molecules, such as proteins, have rich vibrational spectra that relate to key structural elements including secondary structure ($\alpha $-helix, $\beta $-sheet), hydrogen bonding and protonation state. The ability to reliably measure 2DIR spectra in biological molecules represents a major step towards an atomic-level picture of biochemical dynamics. A key limitation of ultrafast IR spectroscopy has been the measurement of the spectrum in a grating-based spectrometer due to HgCdTe detectors limited to linear arrays of 128 or fewer pixels. We have circumvented this problem by converting the coherently generated four-wave mixing 2DIR signal into the visible spectrum, and recording it using a 1340x100 pixel silicon CCD camera. The IR signal is mixed in a MgO:LiNbO$_{3}$ crystal with a chirped, $<$10 $\mu $J, 0.5 ns, 800 nm pulse. Signal detection is sufficient to measure single-shot dispersed vibrational echo spectra, as well as heterodyne detected 2DIR in Mn$_{2}$(CO)$_{10}$. The IR emission temporally overlaps only a narrow frequency range of the chirped near-IR pulse resulting in negligible spectral broadening. [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