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102nd SMC Program
Invited speaker talks and abstracts
102nd SMC short talk schedule
SMC 102 presentation of talks

Speakers and titles for 102nd Statistical Mechanics Conference

Larry Abbott
Title: Controlling Chaotic Activity in Neural Networks
Abstract: Large, strongly coupled neural networks tend to produce chaotic spontaneous activity. This might appear to make them unsuitable for generating reliable sensory responses or repeatable motor patterns. However, this is not the case. Inputs can induce a phase transition, leading to responses uncontaminated by chaotic "noise". Likewise, appropriately trained feedback units can control the chaos, resulting in a wide variety of repeatable output patterns.

Uri Alon
Title: On the Evolution of Modularity

David Bensimon
Title: Single cell physiology

Bill Bialek
Title: How much can we calculate?: Predicting the structure of genetic networks from an optimization principle

David Botstein
Title: A few examples of quantitative issues in biology

G. Bhanot
Title: Scales of selection events-local or genome wide?
Coauthors: Gabriela Alexe, Anupama Reddy, Michael Seiler, Todd Michael, Lee Cronk, Boris Shraiman, Richard Neher, Lane McIntosh, Ajish George, Ravi Sachidanandam, Arnold J Levine, Gyan Bhanot * Joint first authors
Abstract: Cases of hypercholesterolemia are often associated with fat- and cholesterol-rich diets; in spite of this, the Maasai people of East Africa live on a diet consisting mainly of milk, meat and blood and yet, largely avoid hypercholesterolemia and arteriosclerosis, do not suffer from gallstones, have low blood pressures and low rates of cardiac incidents. In the 1970s, radioactively labeled diet studies identified a negative feedback mechanism in the Maasai which maintained cholesterol homeostasis by co-regulating endogenous cholesterol synthesis and dietary cholesterol absorption. These studies suggested, but did not prove, a genetic origin for this phenomenon. The Maasai were also found to have high serum levels of IgA as compared to Caucasians; selected perhaps on account of the pressure to survive in a highly pathogenic environment. Using a number of association significance tests on the recently released HapMap III data, we identified 5,173 polymorphisms that are significantly associated with the Maasai (MKK) samples in the HapMap III dataset compared to all other samples/populations (p-value 0.95, Wilcoxon p-value10-16). A large numbe of the 5,173 polymorphisms are within or near genes known to be associated with the lipid metabolism pathway. Many are in or close to genes whose dysfunction is known to be associated with arteriosclerosis, coronary artery disease, hypercholesterolemia, hyperlipidemia, hyperlipoprotemia, hypertriglyceridemia, and cardiovascular and metabolic disorders. Many of the other polymorphisms are in regions involving immune system genes. 120 of the 5,173 and 8 of the 697 polymorphisms are located in the human orthologous regions of the "Diet1" locus in mouse strain C57BL/6ByJ (B6By), where polymorphisms are known to induce resistance to diet-induced hypercholesterolemia. Our results strongly suggest that the Maasai have specific genetic alterations compared to other populations in genes involved in metabolic and immune regulation pathways that protect them against hypercholesterolemia and from pathogenic organisms. Such strong selection presumably derives from inbreeding, a relatively small population size, a fat-rich diet, long exposure to a steady but hostile environment, and unusual social customs.

Freeman Dyson
Title: Why Negative Specific Heat is Good for Life

Daniel Fisher
Title: Quantative issues in evolutionary dynamics

Michael Fisher
Title: Biology, Medicine, and Engineering : Roles for Theory ?

Peter Fratzl
Title: Tissue growth and remodelling

Bill Gelbart
Title: What does evolution have to say about our being able to make a virus from scratch?
Abstract: Even though viruses are only arguably alive, they do evolve. And they evolve faster and all-too-often "better" than any living organism (or its immune system). Because they are obligate parasites, depending on their hosts for almost everything, their genomes can be orders of magnitude smaller than those of independent, living, things. Often they involve only a few (i.e., fewer than 10) genes, and consist of just a few components. The first viruses to be reconstituted from purified components were plant viruses consisting of a single RNA molecule and a special number of copies of a single capsid protein that self-organize to form a protective shell for the genome. To date, it has not proved possible to reconstitute an enveloped mammalian virus "from scratch", i.e., to create test-tube conditions for spontaneous self-assembly of the infectious virus from its purified components - RNA genome, virally-encoded capsid protein, lipid bilayer, and virally-encoded membrane proteins. In my talk I describe ongoing efforts to make an enveloped virus without help from its host cell, and discuss what we can learn from our partial successes.

John Hopfield
Title: What is thinking? The dynamics of mental exploration

Mehran Kardar
Title: Thymic Selection of T-Cell Receptors as an Extreme Value Problem
Abstract: T lymphocytes (T cells) orchestrate adaptive immune responses upon activation. T-cell activation requires sufficiently strong binding of T-cell receptors on their surface to short peptides (p) derived from foreign proteins, which are bound to major histocompatibility gene products (displayed on antigen-presenting cells). A diverse and self-tolerant T-cell repertoire is selected in the thymus. We map thymic selection processes to an extreme value problem and provide an analytic expression for the amino acid compositions of selected T-cell receptors (which enable its recognition functions).
A. Kosmrlj, A. K. Chakraborty, M. Kardar, and E. I. Shakhnovich, Phys. Rev. Lett. 103, 068103 (2009). http://link.aps.org/doi/10.1103/PhysRevLett.103.068103

Stefan Klumpp
Title: Transcription of ribosomal RNA - a central task for rapid bacterial growth
Abstract: Synthesis of ribosomes is essential for rapid cell growth and fast growing cells, from bacteria to cancer cells, devote a substantial fraction of their transcriptional activity to making ribosomal RNA (rRNA). Transcription of rRNA is typically characterized by dense traffic of RNA polymerases along the rRNA genes. However, dense traffic is susceptible to traffic jams which may arise inevitably due to stochastic pausing of the polymerases. Theoretical analysis of rRNA synthesis from a "traffic viewpoint" provides a unique perspective towards the physiological constraints and regulatory principles governing ribosome synthesis in bacterial and eukaryotic cells.

Stan Leibler
Title: Selection and survival in microbial populations
Abstract: Synthetic microbial systems present a unique opportunity for a quantitative study of selection in dynamic populations. I will present a short review of some classical arguments in theory of natural selection, in particular of those connected with origins of cooperation. I will show how simple experiments with bacteria could help to make these arguments precise and to "demystify" the whole subject.

This work has been done in collaboration with John Chuang, and Olivier Rivoire.

Raphael Levine
Title: Maximal entropy thermodynamic-like analysis of cell signaling with application to early processes in carcinogenesis
Abstract: Point mutations in the phosphorylation domain of the Bcr-Abl fusion oncogene give rise to drug resistance in chronic myelogenous leukemia (CML) patients. These mutations alter kinase-mediated signaling function and phenotypic outcome. An information theoretic analysis of the correlation of phosphoproteomic profiling and transformation potency of the oncogene in different mutants is presented. The theory seeks to predict the leukemic transformation potency from the observed signaling by constructing a distribution of maximal entropy of site-specific phosphorylation events. The theory is developed with special reference to systems biology where high throughput measurements are typical. We seek sets of phosphorylation events most contributory to predicting the phenotype by determining the constraints on the signaling system. The relevance of a constraint is measured by how much it reduces the value of the entropy from its global maximum, where all events are equally likely. Application to experimental phospho-proteomics data for kinase inhibitor-resistant mutants shows that there is one dominant constraint and that other constraints are not relevant to a similar extent. This single constraint accounts for much of the correlation of phosphorylation events with the oncogenic potency and thereby usefully predicts the trends in the phenotypic output.

Gautam Menon
Title: Stretching Fluctuations and Loop Formation in Short Double-Stranded DNA molecules
Abstract: Many of the physical properties of DNA are well modeled in terms of the mechanics of a homogeneous semi-flexible polymer (the worm-like chain), particularly at scales much larger than the individual base-pair. For very short DNA strands (say 1-20 base pairs), on the other hand, more microscopic atomic-scale descriptions would seem more appropriate. Recent experiments on DNA cyclization and DNA stretching probe a length regime intermediate between these extremes (between 35-90 bp's), providing evidence both for an anomalously enhanced tendency for DNA at this scale to form loops as well as for cooperative stretching fluctuations. Neither of these are explained by conventional approaches based on the worm-like chain model. I will describe our approach to this problem, presenting a comparison of predictions from theory with experimental data, suggestions for new methods of looking at the data itself and a physical picture for the experiments.



Konstantin Mischaikow
Title: A Database Schema for Multiparameter Dynamical Systems

Remi Monasson
Title: Learning in the temporal domain with an integrate-and-fire neuron
Abstract: Twenty years ago E. Gardner showed how statistical mechanics concepts and tools could be used to understand the classification of neural patterns according to their average activity. But what happens if the classification depends on the precise timing of the spikes, and not only the firing rate? I will report some recent results with R. Rubin and H. Sompolinsky on this issue.

Alexander Morozov
Title: Statistical Mechanics of Chromatin Structure
Abstract: Genomic DNA is packaged into chromatin in eukaryotic cells. The fundamental building block of chromatin is the nucleosome, a 147 bp DNA segment wrapped around the surface of a histone octamer. Nucleosomes function to compact DNA and to regulate access to it both by physical occlusion and by providing the substrate for numerous covalent epigenetic tags. We study sequence specificity of intrinsic histone-DNA interactions by using maps of nucleosomes assembled in vitro on genomic DNA. We infer free energies of nucleosome formation with a biophysical model that rigorously takes steric exclusion between neighboring nucleosome particles into account.
Surprisingly, most nucleosomes do not appear to be positioned by periodic dinucleotide distributions or by exclusion of longer sequence motifs such as A-tracts - rather, their locations are simply controlled by the A/T and G/C content of the underlying DNA sequence. A similar sequence signature is observed in nucleosome-free control experiments, likely because intrinsic nucleosome sequence preferences are correlated with those revealed by sonication and micrococcal nuclease digestion assays.

Hong Qian
Title: Nonequilibrium Phase Transition in a Biochemical System: Emerging landscape, time scales, and a possible basis for epigenetic-inheritance
Abstract: We consider a small driven biochemical network, the phosphorylation-dephosphorylation cycle (or GTPase) with a positive feedback. We investigate its bistability, with fluctuations, in terms of a nonequilibrium phase transition based on ideas from large-deviation theory. We show that the nonequilibrium phase transition has many of the characteristics of classic equilibrium phase transition: Maxwell construction, discontinuous first-derivative of the "free energy function", Lee-Yang's zero for the generating function, and a tricritical point that matches the cusp in nonlinear bifurcation theory. As for the biochemical system, we establish mathematically an emergent "landscape" for the system. The landscape suggests three different time scales in the dynamics: (i) molecular signaling, (ii) biochemical network dynamics, and (iii) cellular evolution. For finite mesoscopic systems such as a cell, motions associated with (i) and (iii) are stochastic while that with (ii) is deterministic. We suggest that the mesoscopic signature of the nonequilibrium phase transition is the biochemical basis of epi-genetic inheritance.

• Qian, H. and Reluga, T.C. (2005) Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switch. Phys. Rev. Lett. 94, 028101.

• Ge, H. and Qian, H. (2009) Thermodynamic limit of a nonequilibrium steady-state: Maxwell-type construction for a bistable biochemical system. Phys. Rev. Lett. to appear.

• Ge, H. and Qian, H. (2009) Nonequilibrium phase transition in a mesoscoipic biochemical system: From stochastic to nonlinear dynamics and beyond. Preprint arXiv:0905.3789

Michael Schick
Title: "Rafts" as mixtures of lipids and cholesterol; are we still at sea?"

Boris Shklovskii
Title: Self-assembly of viruses

Boris Shraiman
Title: Evolution, Sex and Statistical Mechanics

Eric Siggia
Title: Geometry and Genetics

Eduardo Sontag, Rutgers University
Title: Interconnections in biochemical networks: signaling, impedance, and insulators
Abstract: When analyzing or designing systems made up of interconnected components, it is desirable to be able to predict global behaviors through a bottom-up analysis, based on the knowledge of the behaviors of the individual components together with the interconnection structure. One potential difficulty in such a modular approach is the existence of "retroactivity" effects, which imply that the behaviors of components may change upon interconnection. Indeed, this is a well-appreciated fact in electrical, mechanical, and other engineering fields, and is the reason that "operational amplifiers" are routinely introduced into circuits in order to enforce "unidirectional signal propagation" through insulation from impedance effects. We will discuss how this phenomenon appears in biomolecular systems, analyze their effects on steady state as well as dynamic behavior, and suggest a design of "biological OpAmps" based on enzymatic futile cycles that may play a role in synthetic as well as natural biological systems.

Harry Swinney
Title: Lethal protein produced in response to competition between bacterial colonies
Abstract: We have conducted experiments on neighboring colonies of /P. dendritiformis /bacteria grown on an agar gel [1]. The colonies mutually inhibit growth through secretions that become lethal if the level exceeds a well-defined threshold. Analysis of the secretions reveals the presence of subtilisin (a protease) and a 12 kDalton protein, which we have named Slf (sibling lethal factor). Subtilisin promotes the growth of the colonies, while Slf is lethal. Slf is found to be encoded by a gene belonging to a large family of bacterial genes of previously unknown function. The experimental results are used to develop a model (six coupled PDEs), which predicts that once subtilisin exceeds a threshold, as occurs at the interface between competing colonies, then Slf is secreted into the medium and rapidly kills cells. Laboratory tests yield results in accord with the predictions of the model. The existence in many bacteria of genes encoding homologs of the gene that encodes Slf suggests that the mechanism we observe for self-regulation of colony growth may well occur in other bacteria.
[1] A Be'er, G Ariel, O Kalisman, Y Helman, A Sirota-Mad, HP Zhang, EL Florin, SM Payne, E Ben-Jacob, and HL Swinney, submitted.

Chao Tang
Title: Linking network function and topology

Yuhai Tu
Title: The dissipative nature of adaptation and its thermodynamic cost
Abstract: In this talk, we will first show the dissipative (nonequilibrium) nature of adaptation kinetics in simple biological signaling networks. Next, we will determine the thermodynamic cost for accurate adaptation in E. coli chemotaxis by using a detailed model for its adaptation process. The computed energy requirement reveals the possible chemical energy source that drives adaptation in E. coli chemotaxis. Our analysis uncovers an interesting connection between adaptation and ultrasensitivity, two seemingly opposite but equally desirable functions of biological signaling systems. Finally, we will discuss characteristic signatures of these dissipative systems which may be used to detect the underlying nonequilibrium effects experimentally.

Eric Vanden Eijnden
Title: Navigating through the maze of rare events
Abstract: Rare events such as conformation change of macromolecules, chemical reactions in solution, nucleation events during phase transitions etc. pose challenges both for computations and modeling. At the simplest level, these events can be characterized as the hopping over a free energy barrier associated with the motion of the system along some reaction coordinate. Indeed this is the viewpoint underlying classical tools such as transition state theory or Kramers reaction rate theory, and it has been successful to explain rare events in a wide variety of context. However this picture presupposes that we know or can guess beforehand what the reaction coordinate of the event is. In many systems of interest -- protein folding, enzyme kinetics, protein-protein interactions, etc. -- making such educated guesses is hard if not impossible. The question then arises whether we can develop a more general framework to describe rare events, elucidate their pathway and mechanism, and give a precise meaning to a concept such as the reaction coordinate. In this talk I will discuss an attempt at such a framework and indicate how it can be used e.g. in the context of molecular dynamics simulations to develop efficient algorithms to accelerate the calculations.

Massimo Vergassola
Title: Bacterial chemotaxis as a game against nature
Abstract: Bacteria respond to chemical cues by performing a biased random walk that enables them to migrate towards attractants and away from repellents. Bias is achieved by regulating the duration of the bacterial runs as a function of the history of chemoattractant detections experienced by the bacterium. This time-signal is processed using a time convolution function that can be assayed measuring the response of the bacterium to short pulses of chemoattractant. The convolution constitutes an elementary form of memory, which is encoded at the molecular level by the processes of (de-)methylation and (de-)phosphorilation of the underlying biochemical network. While the latter is being characterized in increasing detail, the evolutionary and functional reasons shaping the chemotactic response remain largely unknown. We shall show that the response observed experimentally emerges from evolution in hostile natural environments as the game-theoretical MaxiMin strategy. In other words, the observed chemotactic behavior is the response that ensures individual bacteria to uptake the largest minimum amount of chemoattractant in any profile thereof.

Geoffrey West
Title: Damage and Repair; Sleep, Aging and Nucleotide Substitution Rates
Abstract: Damage and repair are ubiquitous across all of biology. The network systems that sustain life are typically dissipative, leading to "wear and tear" at all scales. Metabolism fuels repair to combat entropy production, yet is itself dissipative and a major source of damage. These ideas will be discussed in the context of three examples: sleep, aging and nucleotide substitution rates. What sets the scale of our sleep time, our lifespan and our rate of evolution?

Lai-Sang Young, Courant Institute
Spike-time reliability of neural oscillator networks
Abstract: I will discuss the reliability of large networks of coupled oscillators in response to fluctuating inputs. In this talk, intrinsically active neurons are idealized as phase oscillators, and the networks are assumed to be layered, a "layer" being a group of neurons having similar characteristics and driven by the same source. Reliability is the opposite of trial-to-trial variability; a system is reliable if a signal elicits identical responses upon repeated presentations. The effects of network structure, cell heterogeneity and noise on reliability will be discussed. This is joint work with Kevin Lin and Eric Shea-Brown.

Schedule of Short talks

Session A

A1: Y-J. Chen, Cornell University
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.

1. A. Magni, G. Durin, J. P. Sethna and S. Zapperi, "Visualization of avalanches in magnetic thin films: temporal processing", J. Stat. Mech. (2009) P01020
2. Ryan Gutenkunst. "Sloppiness, Modeling, and Evolution in Biochemical Networks." PhD thesis, Cornell University, 2007.
3. "Bayesian Ensemble Approach to Error Estimation of Interatomic Potentials", Søren L. Frederiksen, Karsten W. Jacobsen, Kevin S. Brown, and James P. Sethna, Phys. Rev. Letters 93, 165501 (2004).

A2: R. Fisch, Princeton University
Title: New Results for the 3D random field XY model
Abstract: For three-dimensional O(n) spin models with n > 1 in the presence of a random field with an isotropic probability distribution, Aizenman and Wehr consider a box of size L3 inside a much larger system. They show that if one averages over the random fields outside the box, the magnetization inside the box will average to zero. What this means is that the surface energy of the box need not become negligible in the limit L -> infinity, contrary to the simple Imry-Ma argument. Therefore, and despite what is stated by Aizenman and Wehr, this means that ferromagnetism can occur. New Monte Carlo results using n=2 spins strongly indicate that a ferromagnetic phase exists for moderately strong random field distributions. However, due to the absence of Kramers degeneracy, there is no critical scaling of the usual sort.

A3: O. Sariyer, Koc University
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.

A4: Y-Y. Anh, Northeastern University
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.

A5: D. Adams, University of Michigan
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.

A6: A. Baule, Rockefeller University
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.

A7: V. Tkachenko, Ben-Gurion University of the Negev, Israel
Title: An inverse problem for 1d ordinary differential operator of order 4
Abstract

A8: A. Toom, UFPE, Brazil
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.

A9: B. Vollmayr-Lee, Bucknell University
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.

A10: Y. Zhang, Fundan University/University of Maryland
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.

1. 1. M. J. I. Muller, S. Klumpp and R. Lipowsky, PNAS, 105, 4609 (2008).
   2. Y. Zhang, Phys. Rev. E. 79, 061918 (2009).

A11: M. Palassini, University of Barcelona
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.

A12: D. Rabson, University of South Florida
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!

1. 1. 1. D.C. Lovelady, T.C. Richmond, A.N. Maggi, C.-M. Lo, D.A. Rabson, Phys. Rev. E 76, 041908 (2007).
      2. D.C. Lovelady, J. Friedman, S. Patel, D.A. Rabson, C.-M. Lo, Biosensors and Bioelectronics 24, 2250 (2009).

A13: T. Reichenbach, Rockefeller University
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.

A14: I. Nemenman, Emory University
Title: Simplicity of Completion Time Distributions of Kinetic Proofreading-Like Biochemical Process
Coauthors: Golan Bel and Brian Munsky, LANL
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.

A15: E.-M. Schoetz, Princeton University
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.

A16: R. Weinkamer, Max Planck Institute of Colloids and Interfaces, Department of Biomaterials
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.

A17: S. Maslov, Brookhaven National Laboratory
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:

1. 1. 1. E van Nimwegen, "Scaling laws in the functional content of genomes", Trends Genet 19:479-84 2003.
      2. S Maslov, S Krishna, T Y Pang, K Sneppen, "Toolbox model of evolution of prokaryotic metabolic networks and their regulation", PNAS 106, 9743-9748 2009.

A18: S. Redner, Boston University
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.

A19: S. Harvey, Georgia Institute of Technology
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 ?S 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.

A20: F. Family, Emory University
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.

Session B

B1: S. Ji, Rutgers University
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

B2: A. Davidson, Rutgers University
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.

B3: J. Bechhoefer, Simon Fraser University
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.

B4: D. David-rus, Ecole Normale Superiere, Paris
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.

B5: M. Barbosa, Cornell University
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.

B6: B. Daniels, Cornell University
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

B7: B. Fernandez, CNRS & NYU
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.

B8: U. Harbola, University of California, San Diego
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.

B9: J. Xing,Virginia Tech.
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.

B10: J. Menche, Max Planck Institute
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.

B11: M. Transtrum, Cornell University
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.

B12: S. Papanikolaou, Cornell Univesity
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.

B13: S. Mishra, Syracuse University
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.

B14: B. Miller, Texas Christian University
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.

B15: R. Bundschuh, Ohio State University
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.

B16: K. Korolev, Harvard University
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.

B17: R. Vandiver, Bryn Mawr College
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.

B18: R. Zia, Virginia Tech
Title: Convection Cells driven by Spontaneous Symmetry Breaking
Coauthors: M.F.J. Pleimling and B. Schmittmann
Abstract: TBA

Session C

C1: C. Henley, Cornell University
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.

C2: J. England, Lewis-Sigler Institute, Princeton University
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."

C3: D. Sisan, NIST
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.

C4: B. Machta, Cornell University
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?

C5: D. Blair, University of Massachusetts, Amherst
Title: Diameter of Random Clusters
Coauthors: Don Blair*, Jon Machta
Abstract: We report on recent measurements of a newly-defined quantity for Potts models: their diameter -- the maximum over all pairs of connected vertices of the minimum path length between those vertices -- in numerical simulations that employ the Swendsen-Wang algorithm to explore the q-state Potts models at criticality in two, three, and four dimensions.

C6: S. Norrelykke, Princeton University
Title: Foraging strategies for starving and feeding Amoeba
Coauthors: Edward C. Cox
Abstract: Do individual cells have a search strategy when their target is outside their range of detection? Does this strategy change when a high density of targets is encountered? To answer these questions, we observed single, well-isolated cells of the social amoeba Dictyostelium as they forage for bacteria on a flat surface. Time-lapse movies of this predator-prey system were recorded and analyzed. By varying the concentration of the food source over several orders of magnitude the dynamics of the amoebae as they responded to their environment could be studied.

C7: R. Movassagh, MIT
Title: Qudit chains and their ground states
Coauthors: Eddie Farhi, Jeffrey Goldstone, Daniel Nagaj, Tobias Osborne, Peter Shor
Abstract: We investigate chains of 'd' dimensional quantum spins (qudits) on a line with generic nearest neighbor interactions without translational invariance. We find the conditions under which these systems are not frustrated, i.e. when the ground states are also the common ground states of all the local terms in the Hamiltonians. The states of a quantum spin chain are naturally represented in the Matrix Product States (MPS) framework. Using imaginary time evolution in the MPS ansatz, we numerically investigate the range of parameters in which we expect the ground states to be highly entangled and find them hard to approximate using our MPS method.

C8: S. J. Rahi, MIT
Title: Scattering theory approach to electrodynamic casimir forces
Abstract: We have recently developed a method for calculating the Casimir force to arbitrary accuracy, for any number of objects, arbitrary shapes, susceptibility functions, and separations. The technique is applicable to objects immersed in media other than vacuum, nonzero temperatures, and spatial arrangements in which one object is enclosed in another. Our method combines each object's classical electromagnetic scattering amplitude with universal translation matrices, which convert between the bases used to calculate scattering for each object, but are otherwise independent of the details of the individual objects.

C9: M. Halter, NIST
Title: Modeling Growth Rates and Division Times of Cells in Culture
Coauthors: John T Elliott; Joseph B Hubbard; Alessandro Tona; Anne L Plant
Abstract: Actively growing and dividing cells in culture exhibit distributions of cell volumes that appear to be stationary, as they are highly reproducible over many population doublings, and are rapidly recovered after perturbation. A possible mechanism by which such variations can arise has been examined by modeling variations in measured cell volumes. A stochastic model will be presented that is based on two physical parameters, rate of cell growth, r, and time for cell division, t. This model describes the observed non-Gaussian, log-normal-like distribution of cell volumes that characterizes an asynchronous population.

C10: C. Franck, Cornell University
Title: Exploration of Transitions to Multicellular Life in Amoeba Colonies
Abstract: The social amoebae system Dictyostelium discoideum has long been a target of inquiry for its dramatic response to starvation: the aggregation on substrates of tens of thousands of hitherto uncorrelated cells in order to form a genomic lifeboat. We have been particularly interested in the limit of low density where intercell communication would be challenging and one would expect continuum models to fail. Besides varying density of cells, we perturbed this transition to collective life in another essential manner by physically altering its chemical signaling channel through variation of channel thickness from on the order of 1000 microns to less than 1 micron. We succeeded in explaining some key observations with a simplified dynamical theory coupled with an analytical solution to the relevant chemical transport problem. Our results force a reexamination of how this model developmental transition is understood to come about in standard protocols. Switching to another problem in the same living system: we reveal key fluctuation effects in cell proliferation for the unstarved state in shaken bulk suspensions. This is a followup to our earlier work (Phys. Rev. E v. 77, 041905 (2008)) which explored a slow-to-fast population growth transition with increasing density which we interpreted as a collective effect. In contrast to the first problem, we believe that here intercell signaling is conducted by means of short range, possibly mechanical events, rather than through the long range exchange of molecules. These projects, collaborations with Xiao-Qiao S. Zhou, Amrish Deshmukh, Elijah Bogart, Sharon Lau, Kayvon Daie, Albert Bae, Bradley Webster, Ryan Monaghan, Wui Ip, Nathan Franck, and Thanhbinh Thi Le are detailed in papers found at http://people.ccmr.cornell.edu/~kip/.

PRESENTATIONS OF TALKS GIVEN AT THE 102nd STATISTICAL MECHANICS CONFERENCE

Larry Abbott
Controlling chaotic activity in neural networks

David Bensimon
Single cell physiology

William Bialek
How much can we calculate?: Predicting the structure of genetic networks from an optimization principle

Mehran Kardar
Thymic selection of t-cell receptors as an extreme value problem

Raphael Levine
Maximal entropy thermodynamic-like-analysis of cell signaling with application to early processes in carinogenesis

Hong Qian
Nonequilibrium phase transition in a biochemical system: emerging landscape, time scales, and a possible basis for epigenetic-inheritance

Michael Schick
"Rafts" mixtures of lipids and cholesterol: Are we still at sea?

Boris Shklovskii
Self-assembly of viruses

Chao Tang
Linking network function and topology

Eric Vanden-Eijnden
Navigating through the maze of rare events