List of short talk requests

RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY
HILL CENTER, ROOM 114
SUNDAY, MONDAY AND TUESDAY
DECEMBER 13-18, 2008

List of Short talk requests

Below is a list of short talk requests along with titles & abstracts. The short talk schedule will be posted the week of December 7th

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D. Adams, University of Michigan
Talk preference: Session A or B
Title: The barrier method: a new algorithm to measure rare transitions in non-equilibrium systems with applications to a model by Maier and Stein
Coauthors: L. M. Sander and R. M. Ziff
Abstract: In 1993, Maier and Stein introduced a simple non-equilibrium bistable stochastic model to study exit phenomena in the absence of detailed balance. A number of theoretical predictions were made for exit times and exit paths that have been difficult to verify because those predictions are only valid in the low-noise limit, which is not accessible to brute-force simulations. We present a new rare-event algorithm, which we call the barrier method. This algorithm allows us to verify some of the predictions in the low-noise limit by speeding up calculations by several orders of magnitude.

Y-Y. Anh, Session A
Talk preference: Session A
Title: Link communities reveal multi-scale complexity in networks
Coauthors: James P. Bagrow and Sune Lehmann
Abstract: Networks have become a key approach to understanding systems of interacting objects, unifying the study of diverse phenomena including biological organisms and human society. One crucial step when studying the structure and dynamics of networks is to identify communities; groups of related nodes that correspond to functional subunits such as protein complexes or social spheres. Communities in networks often overlap such that nodes simultaneously belong to several groups. Meanwhile, many networks are known to possess multi-scale, hierarchical organisation, where communities are recursively grouped into a hierarchical structure. However, the fact that many real networks have communities with pervasive overlap, where each and every node belongs to more than one group, has the consequence that a global hierarchy of nodes cannot capture the relationships between overlapping groups. Here we reinvent communities as groups of links rather than nodes and show that this unorthodox approach successfully reconciles the antagonistic organising principles of overlapping communities and hierarchy. In contrast to the existing literature, which has entirely focused on grouping nodes, link communities naturally incorporate overlap while revealing hierarchical organisation. We find biologically relevant link communities in protein-protein interaction and metabolic networks and show that a large social network contains hierarchically organised, community structures spanning inner-city to regional scales while maintaining pervasive overlap. Our results imply that link communities are fundamental building blocks that reveal overlap and multi-scale hierarchical organisation in networks to be two aspects of the same phenomenon.

M. Barbosa, Cornell University
Talk preference: Session B or A
Title: A linear relation between solvation free energy and the potential of mean force in a lattice model of fluid
Coauthors: Marco Barbosa* and Benjamin Widom, Cornell University
Abstract: The solvation of an apolar solute in a solvent medium represented by a simple lattice gas is investigated in the Bethe lattice. We follow a previous study on the hydrophobic effect [Widom et al., Phys. Chem. Chem. Phys. (2003)] which found an almost linear relation between the solvation free energy and the potential of mean force at contact. In the mean field limit, the model studied here obeys an exact linear relation for those two quantities.

A. Baule, Rockefeller University
Talk preference: Session A
Title: Path integral approach to random motion with nonlinear friction
Coauthors: E. G. D. Cohen, H. Touchette
Abstract: Using a path integral approach, we derive an analytical solution of a nonlinear and singular Langevin equation, which has been introduced previously by P.-G. de Gennes as a simple phenomenological model for the stick-slip motion of a solid object on a vibrating horizontal surface. We show that the optimal (or most probable) paths of this model can be divided into two classes of paths, which correspond physically to a sliding or slip motion, where the object moves with a non-zero velocity over the underlying surface, and a stick-slip motion, where the object is stuck to the surface for a finite time. These two kinds of basic motions underlie the behavior of many more complicated systems with solid/solid friction and appear naturally in de Gennes' model in the path-integral framework.

J. Bechhoefer, Simon Fraser University
Talk preference: Session B
Title: Defects in DNA Replication: A tale of two regimes?
Abstract: In higher organisms, a vast amount of DNA must be replicated in a short time. The cell thus initiates replication at many distinct "origins" that are dispersed throughout the genome. After initiation, "forks" (domain boundaries) spread out bi-directionally from the origin site until they eventually coalesce with another fork. Unfortunately, defects along the DNA (such as single-strand DNA lesions or double-strand breaks) can temporarily block replication forks. We propose a formalism to model the effects of defects such as fork blocks and find that there are two qualitatively different regimes: a low-defect-density regime, where defects perturb replication locally and a high-defect-density regime, where replication changes qualitatively. Experimental evidence suggests that in normal cells, the defect density is just below the crossover between the two regimes.

R. Bundschuh, Ohio State University
Talk preference: Session A or B(Session C only if its early)
Title: Flexibility of short DNA
Coauthors: Robert Forties, Ralf Bundschuh*, and Michael Poirier Abstract: Protein-bound duplex DNA is often bent or kinked. Yet, quantification of intrinsic DNA bending that might lead to such protein interactions remains enigmatic. DNA cyclization experiments have indicated that DNA may form sharp bends more easily than predicted by the established worm-like chain (WLC) model. One proposed explanation suggests that local melting of a few base pairs introduces flexible hinges. We have expanded this model to incorporate sequence and temperature dependence of the local melting, and tested it for three sequences at temperatures from 23 degrees C to 42 degrees C. We find that small melted bubbles are significantly more flexible than double-stranded DNA and can alter DNA flexibility at physiological temperatures. However, these bubbles are not flexible enough to explain the recently observed very sharp bends in DNA.

J. England, Lewis-Sigler Institute, Princeton University
Talk preference: Session A or B
Title: An Exactly Solvable Model of Structure from Sequence: The Solution to a Gaussian Folding Problem
Abstract: We suggest a Hamiltonian for a harmonically-bonded polymer with heterogeneous solvophobicity along its length exploring different conformations in a collapsed globule state. By computing the partition function in the physically meaningful parameter regime, we show that the structural ensemble of states can be derived from the eigensystem of a one-dimensional Schroedinger equation for a particle in a potential determined by the heteropolymer's "amino acid sequence."

Y-J. Chen, Cornell University
Talk preference: Session A
Title: Merging theory with experiment: improving the accuracy of scaling theories.
Coauthors: Stefanos Papanikolaou, James P. Sethna (Cornell University), Gianfranco Durin (INRIM and ISI foundation, Torino, Italy), Stefano Zapperi(INFM-CNR, Modena and ISI foundation Torino, Italy)
Abstract: Motivated by the experimental problem of analyzing data of crackling noise collected through a limited field of view[1], we have developed a flexible software environment, SloppyScaling, which fits multi-variable scaling functions to both experimental and simulation data. We've used this to test our proposed two-variable scaling functions against simulations on interface depinning models, enabling experiments to make better predictions. Importance sampling algorithms[2] allow us to estimate exponents with honest error bars[3]and improved confidence. Furthermore, we've discovered its utility as a theorist's playground: it allows us to easily identify corrections to scaling, add them to our theory, and explore crossovers away from well-understood scaling behavior.

B. Daniels, Cornell University
Talk preference: Session B or A
Title: Statistical mechanics of the DNA supercoiling transition Coauthors: James P. Sethna
Abstract: When overtwisted, DNA forms the same wound coils that are familiar from phone cords and water hoses. Since DNA lives at the nanometer scale, however, it is subject to significant thermal fluctuations, and the machinery of statistical mechanics becomes necessary to accurately describe its behavior. We are specifically interested in the transition that occurs as turns are added to straight fluctuating DNA, when it suddenly nucleates a coiled structure known as a plectoneme. Single molecule experiments have shown that this nucleation is thermally activated, with hopping near the transition between states with and without a plectoneme. Combining techniques from polymer physics and transition state theory to characterize motion over the free energy barrier at the transition, we aim to explain why the experimentally measured rate of hopping is so slow, happening on the human-sized timescale of about 1 Hz. Positions_Wanted: Seeking a postdoctoral position. I have experience in applying statistical physics ideas to biological problems, including DNA supercoiling and many-parameter complex network models. See http://www.physics.cornell.edu/~bdaniels

D. David-rus, Ecole Normale Superiere, Paris
Talk preference: Session B or A
Title: Understanding regulation of the states of DARPP-32 phosphorylations- a stochastic approach
Abstract: In this work, I study a stochastic process that describes DARPP-32 phosphorylation states. I solve the steady state of the model for a particular choice of states and transition rules that describes DARPP-32 phosphorylation states when the number of phosphorylated states is very large. Regulation of this states provides a mechanism for integrating information arriving at dopaminoceptive neurons, in multiple brain regions, via a variety of neurotransmitters. DARPP-32 has been established as a crucial mediator of the biochemical,electrophysiological, transcriptional, and behavioral effects of dopamine. Understanding the nature of dopaminergic neurotransmission is important for understanding Parkinson disease, Huntington's chorea, and virtually all antischizophrenic drugs that are influenced by dopamine receptors.
I thank you for suggestions in the analytical calculations to Prof. J.L.Lebowitz and Prof. Larry Shepp.

A. Davidson, Rutgers University
Talk preference: Session A or B
Title: Energy-dependent and pathway-specific transitions of RNA levles in budding yeast induced by glucose-galactose shift
Coauthors: Davidson*, A., Chin, P., Patel, D., Shah, R., So, K., and Ji, S.
Abstract: When glucose is replaced with galactose in the growth medium, budding yeast cells exhibit genome-wide changes in the intracellular levels of RNA molecules, which have been measured using DNA microarrays at 0, 5, 120, 360, 450 and 850 minutes after the nutritional shift (Garcia-Martinez et al., Mol. Cell 15, 303-313, 2004). The results can be displayed as a set of over 6000 RNA trajectories, each of which in turn can be represented as a point in a 6-dimensional RNA concentration space (6DRCS). The distance between any pair of the points in 6DRCS is thought to be inversely proportional to the phenotypic similarity between the paired RNA molecules. When all the possible phenotypic distances of a given metabolic pathway are plotted as a frequency vs. phenotypic distance histogram (FvsPDH), a relatively smooth distribution was obtained which was found to fit a Planck radiation law-type equation (see S. Ji and K. So, this Conference). The FvsPDH of the glycolytic pathway can be divided into two FvsPDHs, one belonging to the energy-poor early phase (0 to 120 min) and the other belonging to the energy-rich late phase (360-850 min). The former FvsPDH was found to contain more RNA pairs separated by short phenotypic distances than the latter, indicating that glycolytic pathway is more active in the late phase than in the early phase. Almost exactly opposite changes were found for the oxphos pathway. Thus, the energy- dependent and metabolic pathway-specific RNA level changes in whole cells measured with DNA microarrays can be conveniently analyzed in terms of the changes in the position and the shape of the FvsPDHs which may serve a role in whole-cell metabolism that is analogous to the role of atomic spectra which revolutionized physics in the early decades of the 20th century.

F. Family, Emory University
Talk preference:Session A
Title: A Statistical Physics Look at Macular Degeneration
Coauthors: Fereydoon Family*, Hans Grossniklaus, Miguel Arizmendi, Karina Mazitello, James Glazier
Abstract: Age-related macular degeneration (AMD) is the leading cause of blindness in the adult population. Choroidal neovascularization, which is the abnormal growth of blood vessels in the choroidal region, is the most common cause of AMD. CNV is produced with age by accumulation of residual material in the retinal pigment epithelium cells (RPE). With time, incompletely degraded membrane material build up in the RPE in the form of lipofuscin, cause abnormal growth of blood vessels that break through the Bruch's membrane, and raise the macula and eventually lead to blindness. The fact that a number of far from equilibrium dynamical processes are involved in the formation and growth of AMD makes this a rich field for application of many techniques of statistical mechanics. I will give some examples of the open problems and mention the results of a deposition and aggregation model of lipofuscin formation in the RPE cells, as well as both two and three-dimensional models of the formation of CNV, that we have recently developed.

B. Fernandez, CNRS & NYU
Talk preference: Session A or B
Title: Athermal dynamics of strongly coupled stochastic three-state oscillators
Coauthors: Bastien Fernandez* and Lev Tsimring
Abstract: We study the collective behavior of a globally coupled ensemble of N cyclic stochastic three-state systems with rates of transition from state i-1 to state i proportional to the number of systems already in state i. While the mean field theory predicts only decaying oscillations in this system, direct numerical simulations indicate that the mean field exhibits stochastic oscillations even in the large N limit. The order parameter characterizing the level of synchrony among oscillators, increases monotonously with the coupling strength. We derive the exact solution of the full master equation for the stationary probability distribution and find the analytical expression for the order parameter.

U. Harbola, University of California, San Diego
Talk preference: Session A or B
Title: Fluctuation Theorems and Electron Counting Statistics
Coauthors: Shaul Mukamel, Massimiliano Esposito
Abstract: Fluctuation Theorems (FTs) describe universal properties of non-equilibrium fluctuations. We present a unified approach to the FTs by introducing a two-point measurement process.Application to electron counting statistics are discussed.

S. Harvey, Georgia Institute of Technology
Talk preference: Session A or B
Title: The Entropic Penalty of Confining a Polymer into a Very Small Space
Coauthors: Mark R. Smyda
Abstract: Determination of the entropic penalty of confinement of a chain polymer into a very small space is an important unsolved problem in polymer statistical mechanics. We present a method for calculating ΔS for the confinement of an elastic polymer of persistence length P in the long-chain limit, when volume exclusion effects are ignored. We consider three geometries: (1) parallel planes separated by a distance d; (2) a circular tube of diameter d; and (3) a sphere of diameter d. We provide results over the range of d/P from 0.01 to 100.

C. Henley, Cornell University
Talk preference: Session B or C
Title: Possible mechanisms to determine macroscopic left-right asymmetry in animals and plants
Abstract: How can systematic L/R asymmetry of the body plan be brought up from molecular to macroscopic scales? Basic symmetry principles suggest that the usual ``biological'' mechanisms Diffusion and gene regulation are insufficient to implement the "right-hand rule"; physical mechanisms involving the cytoskeleton seem always to be involved. I will mention two kinds of dynamic arrays of fibers in the cell wall that might be involved, respectively, in the handedness of snails and of growing plants.

S. Ji, Rutgers University
Talk preference: Session A or B
Title: The universal law of thermal transistions applicable to blackbody radiation, single-molecule enzymology and whole-cell metabolism Coauthors: Sungchul Ji* and Kenneth So
Abstract

K. Korolev, Harvard University
Talk preference: Session A or B
Title: Genetic Waves under Strong Noise
Coauthors: Oskar Hallatschek
Abstract: The rate at which a new advantageous mutation takes over the population is an important quantity because it sets the time scale of evolutionary change. In a spatially extended habitat, a beneficial mutation creates a genetic wave expanding from the location where the mutation occurred. The spreading of beneficial mutations or infectious diseases can usually be tackled when randomness is small, but chance often plays a major role in nature. We studied how an advantageous mutation spreads in the limit of strong number fluctuations. Mathematically, this spreading is described by the stochastic Fisher-Kolmogorov-Petrovsky-Piscounov equation, a classical model in nonequilibrium physics, which is also used in chemical kinetics, ecology, and nuclear physics. We developed a powerful technique to analyze systems in which the effects of chance dominate deterministic forces and calculated the expansion velocity in one and two spatial dimensions. We also analyzed the population structure in the hybrid zone, where both the mutants and the wild type are present. Instead of a stationary, smooth transition region predicted by the classical no-noise approximation, we found non-trivial dynamics of a few rugged kinks that diffuse, give birth by division, and annihilate upon encounter.

B. Machta, Cornell University
Talk preference: Session A or C
Title: Criticality in Biological Membranes
Coauthors: Stefanos Papanikolaou, Sarah Veatch, Jim Sethna
Abstract: All cells are surrounded by a lipid bilayer membrane. This two-dimensional liquid is composed of thousands of lipids and proteins and is home to a host of biological functions. Recent work in giant plasma membrane vesicles (GPMVs) isolated from living cells demonstrates that these GPMVs can be tuned with a single parameter (temperature) to liquid-liquid criticality in the 2D Ising universality class, not far from in vivo temperatures [1,2]. Criticality requires the fine-tuning of two parameters suggesting important biological function, and its presence resolves many of the paradoxes associated with putative lipid rafts. Here we look at the significance of this proximity to criticality, both for understanding surprising features in membrane experiments, as well as from a more theoretical perspective. Why would a cell want to have a nearly critical membrane?

S. Maslov, Brookhaven National Laboratory
Talk preference: Session A or B
Title: "Home depot" model of evolution of prokaryotic metabolic networks and their regulation
Coauthors: Sandeep Krishna,Tin-Yau Pang, Kim Sneppen
Abstract: It has been reported [1] that in prokaryotes the number of transcription factors scales approximately quadratically with the total number of genes. As a consequence the fraction of transcriptional regulators among all genes in small bacterial genomes (< 500 genes) is less than 0.5%, while in large genomes (~10,000 genes) it reaches as high as 10%.
We recently proposed [2] a general explanation of this empirical scaling law and illustrated it using a simple model in which metabolic and regulatory networks co-evolve together. In this model prokaryotic organisms acquire new metabolic functions by the virtue of horizontal gene transfer of entire co-regulated metabolic pathways from a shared gene pool (the "universal metabolic network") followed by removal of redundant enzymes. This process can be compared to a homeowner buying a tool set from a hardware store (hence our "Home Depot" metaphor) and later returning duplicate or unnecessary items.
We view the full repertoire of metabolic enzymes (or more generally any non-regulatory proteins) encoded in the genome of an organism as its collection of tools. Adapting to a new environmental condition (e.g. learning to use a new nutrient source) involves acquiring new enzymes as well as reusing some of the enzymes/tools that are already encoded in the genome. As the toolbox of an organism grows larger, it can reuse its existing tools more often, and thus needs to acquire fewer new enzymes to master each new regulated task. From this analogy it follows that, in general, the number of regulators in an organism should scale faster than linearly with its total number of proteins.
Our model faithfully reproduces the empirically observed [1] quadratic scaling between these two numbers. Furthermore, the distribution of lengths of co-regulated pathways in our model approximately agrees with that in real-life metabolic network of E coli. Thus, the toolbox analogy provides a conceptual explanation for the empirically observed broad distribution of regulon sizes. I will describe several possible regulatory architectures ensuring proper coordination of activity of metabolic pathways with each other. It remains to be determined which of them (if any) are realized in real-life prokaryotes.
References:

J. Menche, Max Planck Institute
Talk preference: Session A or B
Title: Activity patterns on scale-free networks
Coauthors: Angelo Valleriani, Reinhard Lipowsky
Abstract: We study the activity patterns of a generic two-state system on scale-free networks. The states of neighboring vertices interact according to a simple majority rule that is equivalent to Glauber dynamics at zero-temperature in Ising spin systems. On uncorrelated networks, this dynamics only exhibits two stable fixed points, where all vertices are in the same state. This situation changes when correlations between the degrees of adjacent vertices are introduced: With increasing correlations a growing number of additional attractors emerges. Most attractors are found in maximally correlated network configurations. We characterize the properties of these attractors in terms of the underlying network structure and give estimates for their total number. In networks with positive correlations the number of attractors grows with network size. This is not the case in networks with negative correlations, where a maximal number of attractors is reached at intermediate network sizes.

B. Miller, Texas Christian University
Talk preference: Session A or B
Title: A Minimal Model for the Study of Polychronous Groups
Coauthors: Bruce N. Miller * and Willard Maier
Abstract: The concept of a polychromous group in a neural network was introduced by Izhikevich as a model to facilitate learning. Here we present a minimal model of polychronous groups. The model is computationally efficient and allows the study of polychronous groups independent of specific neuron models.Computational experiments were performed with the model in one- and two-dimensional neural architectures to determine the dependence of the number of polychronous groups on various connectivity options. The possibility of using polychronous groups as computational elements will also be discussed.

S. Mishra, Syracuse University
Talk preference: Session A or B
Title: Pattern formation and traveling bands in dense layers of self-propelled rods
Coauthors: Aparna Baskaran, M. Cristina Marchetti
Abstract: A collection of interacting self-propelled (SP) hard rods in two dimensions can be used as a minimal model for a variety of active systems, including bacterial suspensions and vibrated granular layers. Hydrodynamics equations for SP rods were derived in A. Baskaran et al.[PRL 101, 268101 (2008)]. In the bulk limit the rods exhibit a mean-field transition from an isotropic to a polarized state at a density \rho_c . Linear stability analysis indicates that the uniform polarized (hence moving) state in unstable above a critical value v_0 ≃ (\rho_0 − \rho_c )^{-1} of the self-propulsion speed, with \rho_0 the mean density of rods. The numerical solution of the full nonlinear equations shows that above a critical value v_c (\rho_0 ), the system phase separates into traveling bands of ordered and disordered bands. The ordered bands are polarized along the direction of motion, transverse to the long direction of the bands. Similar patterns have been obtained from numerical studies of Vicsek-type models and in actin motility assays.

I. Nemenman, Emory University
Talk preference: Session A or B
Title: Simplicity of Completion Time Distributions of Kinetic Proofreading-Like Biochemical Process
Abstract: Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the precise construction of specific macromolecules. Here we show that, for a wide range of parameters, as the system size grows, the completion time for such processes attains a simple, almost universal distribution: it becomes either deterministic or exponentially distributed, with a very narrow transition between the two regimes. These findings suggest not only that one may not be able to understand individual elementary reactions from completion time observations, but also that such understanding may be unnecessary.

M. Palassini, University of Barcelona
Talk preference: Session A
Title: Delay and noise in negative-feedback genetic regulatory loops
Coauthors: Marta Dies
Abstract: Stochastic effects are important in gene regulation due to the small number of molecules involved. Another important, often neglected aspect of regulatory dynamics is the large separation of time scales between slow processes, such as transcription and translation, and fast processes, such as protein degradation. We consider a generic birth-and-death stochastic model of a negative- feedback loop, in which the separation of time scales is incorporated via an explicit delay in one of the loop arms. We show, both from exact simulation of the delayed Master Equation and from a Van Kampen volume expansion, that noise-sustained oscillations occurs quite generally in such a model. We propose that this mechanism might explain the experimentally observed temporal oscillations in the concentration levels of proteins p53 and Mdm2 in cells subjected to DNA damage, as well as similar oscillations observed in other genetic regulatory negative-feedback loops.

S. Papanikolaou, Cornell Univesity
Talk preference: Session A or B
Title: Beyond scaling: The average avalanche shape
Coauthors: Felipe Bohn, Rubem Luis Sommer, Gianfranco Durin, Stefano Zapperi and James P. Sethna
Abstract: Universality, scaling, and the renormalization group claim to predict all be- havior on long length and time scales asymptotically close to critical points. In practice, large simulations and heroic experiments have been needed to un- ambiguously test and measure the critical exponents and scaling functions. We announce here the measurement and prediction of universal corrections to scaling, applied to the temporal average shape of Barkhausen noise avalanches. We bypass the confounding factors of time-retarded interactions (eddy currents) by measuring thin permalloy films, and bypass thresholding effects and amplifier distortions by applying Wiener deconvolution. We show experimental shapes that are approximately symmetric, and measure the leading corrections to scal- ing. We solve a mean-field theory for the magnetization dynamics and calculate the relevant demagnetizing-field correction to scaling, showing qualitative agree- ment with the experiment. In this way, we move toward a quantitative theory useful at smaller time and length scales and farther from the critical point.

D. Sisan, NIST
Talk preference: Session B or A
Title: Event ordering in live cell imaging determined from temporal cross correlation asymmetry
Coauthors: Defne Yarar, Clare M. Waterman, and Jeffrey S. Urbach
Abstract: We use the temporal asymmetry of the cross-correlation function to determine the temporal ordering of spatially localized cellular events in live cell multi-channel fluorescence imaging. Temporal ordering, a term commonly used in cell biology, requires a nonequilibrium biochemical flux, which is quantifiable through the cross-correlation asymmetry. I'll briefly describe how the approach was applied to extract the temporal ordering of three proteins in the endocytic pathway: actin, sorting nexin 9, and clathrin.

V. Tkachenko, Ben-Gurion University of the Negev, Israel
Talk preference: Session A
Title: An inverse problem for 1d ordinary differential operator of order 4
Abstract

D. Rabson, University of South Florida
Talk preference: Session A
Title: Sometimes the Noise is the Signal
Coauthors: Chun-Min Lo, Douglas Lovelady
Abstract: Since 1984, electric cell-substrate impedance sensing (ECIS) has been used to monitor cell behavior in culture and has proven sensitive to morphological changes and cell mobility. Several authors have associated fluctuations in the measured impedance with cellular micromotion; however we are unaware of any previous work applying statistical techniques in order to distinguish two different cell types. We have demonstrated a method for distinguishing cancerous from non-cancerous cultures of human ovarian surface epithelial cells [1]; applying similar ideas, we have also determined the presence and concentration of the toxin cytochalisin B in cultures of 3T3 fibroblasts at levels lower than the detection thresholds of other techniques [2]. Measures of short-time and long-time correlation confirm that the noise from non-cancerous cultures has a higher degree of temporal order, order which we argue, based on a statistical-mechanical model, might arise from greater coordination of motion between healthy cells than between cancerous ones. The moral of the story: apply easy statistics to a field where people haven't previously!

S. Redner, Boston University
Talk preference: Session A
Title: Distribution of Species Body Masses
Coauthors: A. Clauset
Abstract: We present a model for the evolution of body masses of related species, in which mass M evolves by speciation-driven branching, multiplicative diffusion, and an extinction probability that increases weakly with mass, leading to a convection-diffusion equation for ln M. The resulting steady-state behavior agrees well with empirical data on recent terrestrial mammals, and the time-dependent behavior also agrees with data on extinct mammal species between 95-50 Myr ago.

T. Reichenbach, Rockefeller University
Talk preference: Session A or B
Title: A ratchet mechanism for low-frequency hearing in mammals
Coauthors: A. J. Hudspeth
Abstract: The sensitivity and frequency selectivity of hearing result from tuned amplification by an active process in the mechanoreceptive hair cells. The nature of the active process in the mammalian cochlea is intensely debated, for outer hair cells exhibit two forms of mechanical activity, active hair-bundle motility and membrane-based electromotility. Here we show theoretically that active hair-bundle motility and electromotility can together implement an efficient mechanism for amplification that functions like a ratchet: sound-evoked forces acting on the basilar membrane are transmitted to the hair bundles while electromotility decouples the active hair-bundle forces from the basilar membrane. Through a combination of analytical and computational techniques we demonstrate that the ratchet mechanism can naturally account for a variety of unexplained experimental observations from low-frequency hearing.

O. Sariyer, Koc University
Talk preference: Session A
Title: Charge-Ordered Phases of the $d = 3$ Spinless Falicov-Kimball Model: Renormalization-Group Theory
Coauthors: Ozan S. Sariyer*, Michael Hinczewski, and A. Nihat Berker
Abstract: The global phase diagram of the spinless Falicov-Kimball model in $d = 3$ spatial dimensions has been obtained by renormalization-group theory. This global phase diagram exhibits five distinct phases. Four of these phases are charge-ordered (CO) phases, in which the electron hopping strength diverges under repeated renormalizations. In the other ($\delta$) phase, the hopping strength vanishes under repeated renormalizations. The phase boundaries are second-order, except for an intermediate-temperature regime, where a first-order phase boundary between two CO phases occurs. The first-order phase boundary is delimited by bicritical points. The cross-sections of the global phase diagram with respect to the chemical potentials of the localized and mobile electrons, at all representative temperatures and hopping strengths, are calculated and exhibit four distinct topologies.

E.-M. Schoetz, Princeton University
Talk preference: Session A
Title: Dynamics of asexual reproduction in flatworms
Coauthors: Jared Talbot and Joern Dunkel
Abstract: Flatworms can reproduce by transverse fission (i.e. they simply split themselves in two) because they can regenerate the missing body parts. Naively, one would think that this kind of reproduction could be captured by models for cell growth in bacteria or other simple organisms. However, we find that there is much more to the story by monitoring >10 generations of individuals as well as the behavior of worm populations under different environmental conditions, such as temperature, feeding frequency and crowding.

A. Toom, UFPE, Brazil
Talk preference: Session A or B
Title: Non-Ergodicity and Growth Are Compatible for 1-D local Interaction
Coauthors: Alex D. Ramos (UFPE)
Abstract: We present results of Monte Carlo simulation and chaos approximation of a class of Markov processes. Each of their states can be written as a finite or infinite in both direction sequence of pluses and minuses As continuous time goes on,our sequence undergoes the following three types of local transformations: The first one, called flip, changes any minus into plus and any plus into minus with a rate beta. Another, called annihilation, eliminates two neighbor components with a rate alpha whenever they are in different states. The third one, called mitosis, doubles any component with a rate gamma. All of them occur at any place of the sequence independently. Our simulations and approximations suggest that with approprate positive alpha, beta and gamma this process has the following two properties. Growth: In the finite case, as the process goes on, the length of the sequence tends to infinity with a probability, which tends to 1 as the length of the initial sequence tends to infinity. Non-ergodicity: the infinite system is ergodic and the finite system keeps most of the time at two extremes, occasionally swinging from one to the other.

M. Transtrum, Cornell University
Talk preference: Session A or B
Title: Differential Geometric Approach to Fitting Data
Coauthors: Benjamin Machta, James Sethna
Abstract: Fitting nonlinear functions to experimental data can be a very difficult task. Standard algorithms are usually unreliable to automatically find fits, often requiring many adjustments by hand in order to converge. By considering the manifold of model predictions in data space, we find that the ideal path an algorithm should follow is a geodesic. The standard Levenberg-Marquardt algorithm approximately follows a geodesic path, but will often fail to converge because the geodesic intersects the boundaries of the manifold. When this happens, the algorithm "evaporates" parameters, pushing them to unphysical values, without finding a good fit. Typical multi-parameter models have boundaries with a hierarchy of widths, forming a long, narrow hyper-ribbon which is difficult for standard algorithms to navigate. We explain the origin of these boundaries in terms of the analyticity of the fitting function and suggest that they should guide the design of algorithms to improve the fitting process.

R. Vandiver, Bryn Mawr College
Talk preference: Session A or B
Title: On the mechanical stability of growing arteries
Coauthors: Alain Goriely
Abstract: Arteries are modeled, within the framework of nonlinear elasticity, as incompressible two-layer cylindrical structures that are residually stressed through differential growth. These structures are loaded by an axial force, internal pressure and have nonlinear, anisotropic, hyperelastic response to stresses. Parameters for this model are directly related to experimental observations. The mechanical stability of growing arteries and the role of residual stresses is investigated. It is shown that residual stress lowers the critical internal pressure leading to buckling and that a reduction of axial loading may lead to a buckling instability which may eventually lead to arterial tortuosity.

B. Vollmayr-Lee, Bucknell University
Talk preference: None given
Title: Coarsening Dynamics in a Chaotic Flow
Coauthors: *Benjamin Vollmayr-Lee, Bucknell and Daniel Beller, Brandeis
Abstract: We study the phase separation dynamics of a binary fluid system advected by a chaotic flow. The chaotic flow stretches and rips apart domains, and thus competes with the thermodynamic coarsening to yield a nonequilibrium steady state. We calculate local measures such as the finite-time Lyapunov exponent field and the local free energy density to characterize this steady state.

R. Weinkamer, Max Planck Institute of Colloids and Interfaces, Department of Biomaterials
Talk preference: Session A
Title: Control of bone remodeling
Coauthors: M. Rusconi, A. Valleriani, J.W.C. Dunlop, J. Kurths
Abstract: Trabecular bone is the network-like bone built from struts called trabeculae found inside vertebrae and close to joints. This spongy bone is continuously renewed during life by means of resorption and deposition of bone packets from and onto its surface. We developed a stochastic model, allowing us to extract information about the control of this remodeling process based on experimentally measured frequency distributions of the thickness of the trabeculae.

J. Xing,Virginia Tech.
Talk preference: Session A or B
Title: Mapping between stochastic dissipative and Hamiltonian systems
Abstract: Biological systems are away from equilibrium. Here we prove that a system described by stochastic differential equations can be mapped to a Hamiltonian system, at least for the case the stationary distribution exists. We used the result to obtain a generalized fluctuation-dissipation relation, and to derive the Zwanzig-Mori projection formula for general non-Hamiltonian systems.

Y. Zhang, Fundan University/University of Maryland
Talk preference: Session A
Title: A tug of war model for organelle transport can display three stable steady states
Abstract: Motion of organelles and vesicles moved by motor proteins in cells can be modeled by a tug-of-war model developed by M¨¹ller, Klumpp and Lipowsky [1]. By detailed theoretical analysis, we find that this model can, depending on the single-motor parameters and external force, exhibit one, two or three stable steady states [2]. The steady state motion of the cargo is determined by the initial numbers of the motors bound to the track. The three states correspond, respectively, to the cargo moving to the right, to the left or remaining stationary. Thus our study indicates that the possible motions of the cargo are determined by the intrinsic parameters of the tug-of-war model, while the final motion is determined by the initial conditions. Monte Carlo simulations confirm that our results are accurate when there are a large number of motors. When the number of motors is small, the cargo motion may change from one steady state to another. It is planned to study the transition times between the different steady states.

R. Zia, Virginia Tech
Talk preference: Session A or B
Title: Convection Cells driven by Spontaneous Symmetry Breaking
Coauthors: M.F.J. Pleimling and B. Schmittmann
Abstract: TBA ________________________________