Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session V22: Biological Computation |
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Sponsoring Units: DBP Chair: Peter Jung, Ohio University Room: LACC 409B |
Thursday, March 24, 2005 11:15AM - 11:27AM |
V22.00001: Computation through the development of synchrony in neural models Jan Engelbrecht, John Hopfield We investigate integrate-and-fire models with an emphases on temporal order. Our goal is to demonstrate that simple models can perform non- trivial computations based on the development of synchrony. While the computational strategies are general, we realize our model in a sensory processing context, particularly olfaction, where we consider recognizing an odor in the presence of a background, using multiple sniffs. This introduces a time-dependent aspect in the stimuli where the advantages of temporal coding may become more apparent. Our synchrony-based computational strategy emphasizes the role of adaptation and also employs the general principle: ``What moves together is an object.'' [Preview Abstract] |
Thursday, March 24, 2005 11:27AM - 11:39AM |
V22.00002: Foamlike disorder in the developing Drosophila embryo Richard Zallen, Jennifer A. Zallen Convergent extension is the cell-rearrangement process by which a developing embryo elongates to establish the body axis. In Drosophila (fruitfly), this occurs within a one-cell-thick epithelial layer. Confocal microscopy was used to image the two-dimensional cell pattern at various stages in the process [1]. Increasing foamlike disorder was observed and analyzed via p(n), the frequency of occurrence of n-sided cells [2], and related statistical measures such as the Shannon entropy. During convergent extension in Drosophila, the peak at p(6) drops from 0.65 to 0.38 and the second moment of p(n) triples to 1.1. An initial degree of hexatic interface-orientation order disappears during the process. [1] J.A. Zallen and E. Wieschaus, Dev. Cell 6, 343 (2004); [2] J.A. Zallen and R. Zallen, J. Phys.: Condensed Matter 16, S5073 (2004). [Preview Abstract] |
Thursday, March 24, 2005 11:39AM - 11:51AM |
V22.00003: How a frog's neuronal wetware learns what is where in the dark J. Leo van Hemmen The clawed frog \emph{Xenopus}, an inhabitant of South-African ponds, locates prey by detecting water waves generated by insects floundering on the water surface. It does so during night by means of 180 lateral-line organs located on its skin, which allow the frog not only to localize prey but also to determine its character. We have shown [1] how it performs both through waveform reconstruction. A key question is now how it gets the appropriate neuronal wetware. In so doing, catching time differences arising from the input on its skin is important. Spike-timing-dependent synaptic plasticity (STDP) [2], which has been experimentally demonstrated, seems to be the natural tool. The development of the frog's synaptic software appears to be ``supervised'' by the visual system during daytime. Here we show how supervised STDP allows a frog to learn what is where in the dark. In addition, the learning procedure is derived from a minimization principle and can be generalized to perform similar tasks elsewhere. Refs: [1] J.-M.P. Franosch, M.C. Sobotka, A. Elepfandt, and J.L. van Hemmen, Phys. Rev. Lett. 91 (2003) 158101; [2] W. Gerstner, R. Kempter, J.L. van Hemmen, and H. Wagner, Nature 383 (1996) 76. [Preview Abstract] |
Thursday, March 24, 2005 11:51AM - 12:03PM |
V22.00004: Modeling spatiotemporal patterns of neocortical activity in epileptic seizures Daisuke Takeshita, Frank Moss, Sonya Bahar Epileptic seizures are characterized by excess and synchronized neural activity. To investigate how seizures initiate and terminate, we develop a model of a neocortical network based on a model suggested by Wilson [1]. We simulate the effect of the potassium channel blocker 4-aminopyridine, which is often used in experiments to induce epileptic seizures, by decreasing the conductance of the potassium channels in a small fraction of neurons in our model. We show that the firing frequency of a single neuron is increased by decreasing the conductance in some cases. By coupling one normal neuron to another neuron which has decreased potassium conductance, changes in behavior such as an increase in firing rate, switching from spiking to bursting, and synchronized activity are observed depending on the coupling strength between the neurons. We will also discuss the effect of decreased conductance on the spread of activity through the network, and on the initiation and termination of seizure-like events. [1] Wilson HR, J. theor. Biol. (1999) 200, 375-388 [Preview Abstract] |
Thursday, March 24, 2005 12:03PM - 12:15PM |
V22.00005: Noise-enhanced periodicity in hair cells and primary afferent neurons Alexander Neiman, Michael Rowe We study oscillatory responses of a primary auditory unit composed from a hair cell and a primary afferent neuron to a broad-band mechanical noisy stimuli using a biophysical model. The model contains two compartments: the hair cell possessing electrical resonance properties and an excitable Hodgkin-Huxley type afferent neuron, coupled with the hair cell through an excitatory synapse. The model predicts the existence of an optimal noise level that maximizes the quality factor of a resonance peak in the power spectrum of the afferent neuron, demonstrating thus a maximal coherence of oscillations (coherence resonance). It also predicts a shift of the peak frequency towards lower frequencies with the increase of noise level. Our experimental results on turtle saccular units support model predictions, demonstrating both the frequency shift and the coherence resonance. [Preview Abstract] |
Thursday, March 24, 2005 12:15PM - 12:27PM |
V22.00006: Axon chemotaxis: Nature's most sensitive gradient detector? Jeffrey Urbach, Will Rosoff, Ryan McAllister, Geoff Goodhill Axonal chemotaxis plays an important role in wiring up the developing and regenerating nervous system, but little is known about the mechanisms by which axons responsd to molecular gradients. We have developed a new assay that allows measurement of the long-term response of axons to gradients of controllable shape in a three-dimensional gel. We show that axons are among the most sensitive chemical gradient detecting devices yet discovered, capable of responding to concentration differences that average less than one molecule across the growth cone, the sensing structure at the tip of the developing axon (Rosoff et al, Nat. Neurosci., 7:678- 682, 2004). We also present a theoretical model of axonal response to gradients in the presence of stochastic receptor binding that quantitatively matches the experimental data. [Preview Abstract] |
Thursday, March 24, 2005 12:27PM - 12:39PM |
V22.00007: Collective Behavior of Amoebae in Thin Films Albert Bae, Bradley Webster, Danica Wyatt, Loling Song, David Reynolds, Eberhard Bodenschatz, Carl Franck We have discovered new aspects of social behavior in Dictyostelium discoideum by culturing high density colonies in liquid media depleted of nutrients in confined geometries by using three different preparations: I. thin (15-40um thick) and II. ultrathin ($<$3um) films of liquid media with a mineral oil overlayer, and III. microfluidic chambers fabricated in PDMS ($\sim $7um tall). We find greatly reduced, if not eliminated, cell on cell layering in the microfluidic system when compared to the wetting layer preparations. The ultrathin films reveal robust behavior of cells despite flattening that increased their areas by over an order of magnitude. We also observed that the earliest synchronized response of cells following the onset of starvation, a precursor to aggregation, was hastened by reducing the thickness of the aqueous culture layer. We were surprised to find that the threshold concentration for aggregation was raised by thin film confinement when compared to bulk behavior. Finally, both the ultra thin and microfluidic preparations reveal, with new clarity, vortex states of aggregation. [Preview Abstract] |
Thursday, March 24, 2005 12:39PM - 12:51PM |
V22.00008: Circadian rhythms and fractal fluctuations in forearm motion Kun Hu, Plamen Ch Ivanov, Zhi Chen, H. Eugene Stanley, Michael F. Hilton, Steven A. Shea Recent studies have shown that the circadian pacemaker --- an internal body clock located in the brain which is normally synchronized with the sleep/wake behavioral cycles --- influences key physiologic functions such as the body temperature, hormone secretion and heart rate. Surprisingly, no previous studies have investigated whether the circadian pacemaker impacts human motor activity --- a fundamental physiologic function. We investigate high-frequency actigraph recordings of forearm motion from a group of young and healthy subjects during a forced desynchrony protocol which allows to decouple the sleep/wake cycles from the endogenous circadian cycle while controlling scheduled behaviors. We investigate both static properties (mean value, standard deviation), dynamical characteristics (long-range correlations), and nonlinear features (magnitude and Fourier-phase correlations) in the fluctuations of forearm acceleration across different circadian phases. We demonstrate that while the static properties exhibit significant circadian rhythms with a broad peak in the afternoon, the dynamical and nonlinear characteristics remain invariant with circadian phase. This finding suggests an intrinsic multi-scale dynamic regulation of forearm motion the mechanism of which is not influenced by the circadian pacemaker, thus suggesting that increased cardiac risk in the early morning hours is not related to circadian-mediated influences on motor activity. [Preview Abstract] |
Thursday, March 24, 2005 12:51PM - 1:03PM |
V22.00009: Entropic Analysis of Electromyography Time Series Miron Kaufman, Ulrich Zurcher, Paul Sung We are in the process of assessing the effectiveness of fractal and entropic measures for the diagnostic of low back pain from surface electromyography (EMG) time series. Surface electromyography (EMG) is used to assess patients with low back pain. In a typical EMG measurement, the voltage is measured every millisecond. We observed back muscle fatiguing during one minute, which results in a time series with 60,000 entries. We characterize the complexity of time series by computing the Shannon entropy time dependence$.$ The analysis of the time series from different relevant muscles from healthy and low back pain (LBP) individuals provides evidence that the level of variability of back muscle activities is much larger for healthy individuals than for individuals with LBP. In general the time dependence of the entropy shows a crossover from a diffusive regime to a regime characterized by long time correlations (self organization) at about 0.01s. [Preview Abstract] |
Thursday, March 24, 2005 1:03PM - 1:15PM |
V22.00010: Probing Vesicle Dynamics in Single Synapses Matthew Shtrahman, Chuck Yeung, Guo-qiang Bi, Xiao-lun Wu The classic mode of communication between neurons occurs via chemical synapses. In this process, vesicles dock at release sites (active zone), and fuse with the cell membrane, emptying neurotransmitter into the synaptic cleft. This process is stochastic, and the fidelity of this synaptic communication depends on the availability of docked vesicles. We use fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP) to study vesicle dynamics inside the synapses of cultured neurons labeled with a fluorescent vesicle marker. These studies show that when the cell is electrically at rest, only a small population of vesicles is mobile, taking seconds to explore the synapse. Applying pharmacological agents causes vesicles to diffuse freely, moving 30 times faster than vesicles in control synapses. These results suggest that vesicles move sluggishly due to binding to structural elements within the synapse. Motivated by these results, a model is constructed consisting of diffusing vesicles that bind reversibly to the cytomatrix. This stick-and-diffuse model agrees with the experimental data, and also predicts the well-known exponential refilling of docked vesicles. [Preview Abstract] |
Thursday, March 24, 2005 1:15PM - 1:27PM |
V22.00011: Astrocytes Potentiate Synaptic Transmission Suhita Nadkarni, Peter Jung A recent experimental study shows that astrocytes, a subtype of glia, are able to influence the spontaneous activity in the brain via calcium dependent glutamate release. We model the coupling mechanism between an astrocyte and a neuron based on experimental data. This coupling is dynamic and bi-directional, such that the modulations in intracellular calcium concentrations in astrocytes affect neuronal excitability and vice versa via a glutamatergic pathway. We demonstrate through simple neural-glial circuits that increases in the intracellular calcium concentration in astrocytes nearby can enhance spontaneous activity in a neuron, a significant mechanism said to be involved in plasticity and learning. The pattern of this marked increase in spontaneous firing rate in our model quantitatively follows that observed in the experiment. Further, depending on the type of synaptic connections diverging from the neuron, it can either inhibit or excite the ensuing dynamics and potentiate synaptic transmission, thus reinstating the integral role played by astrocytes in normal neuronal dynamics. [Preview Abstract] |
Thursday, March 24, 2005 1:27PM - 1:39PM |
V22.00012: {\bf Modelling Shapes of the Mitochondrial Crista Membrane} Jim Nulton, Peter Salamon, Joe Mahaffy, Terry Frey, Arun Kumar, Arlette Baljon Recently, electron tomographs have revealed a novel structure of the inner mitochondrial membrane. They show that the crista membrane contains both tubules and lamellae. The structural organization of mitochondria affects their functionality, for instance it may be important in explaining their role in programmed cell death. A model will be presented to account thermodynamically for the observed uniform radii of the tubules. The model contains two differently shaped lipids, which are allowed to redistribute between the two sides of the membrane. It makes two predictions: (1) there is an osmotic pressure difference of 0.2 atmospheres across the inner membrane as a consequence of the experimentally observed tubular radii of 10 nm; (2) migration of differently shaped lipids causes concentration variations between the two sides of the tubular membrane on the order of 7 percent. [Preview Abstract] |
Thursday, March 24, 2005 1:39PM - 1:51PM |
V22.00013: A non-equilibrium model of capsid assembly Stephen D. Hicks, C.L. Henley In virus capsids, proteins are assembled into a locally regular triangular lattice (quasiequivalence rule), which permits a variety of possible sizes and shapes (regular or irregular) of the capsid: what selects among these? We present an irreversible growth model in which triangular units are added one at a time. After each addition, we relax the intermediate configurations to minimize a discrete elastic Hamiltonian with in-layer stretching and bending terms. The relaxed angles on the growing edge determine the probability of creating coordination-5 defects, the arrangement of which controls the capsid's global shape; its mean size is controlled by a nonzero preferred inter-unit dihedral angle (spontaneous curvature) included in our Hamiltonian. Using this model, we demonstrate large success rates in forming complete capsids with both deterministic and random growth rules, and measure the degree of icosahedral symmetry of the results. We discuss the assembly of retroviruses, exploring scenarios which give rise to the irregular conical shape of the mature HIV-1 capsid and apply several statistical measures of its deviation from a sphere. [Preview Abstract] |
Thursday, March 24, 2005 1:51PM - 2:03PM |
V22.00014: Two-Stage Aggregate Formation via Streams in Myxobacteria Mark Alber, Maria Kiskowski, Yi Jiang In response to adverse conditions, myxobacteria form aggregates which develop into fruiting bodies. We model myxobacteria aggregation with a lattice cell model based entirely on short range (non-chemotactic) cell-cell interactions. Local rules result in a two-stage process of aggregation mediated by transient streams. Aggregates resemble those observed in experiment and are stable against even very large perturbations. Noise in individual cell behavior increases the effects of streams and result in larger, more stable aggregates. {\it Phys. Rev. Lett. 93: 068301 (2004).} [Preview Abstract] |
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