98th Statistical Mechanics
Conference

## Short Talk Schedule

SESSION A, Monday 8:30-10:30
*For Author Presenting the Talk

• A1- *W. Ellenbroek, Ellak Somfai, Martin van Hecke, Wim van Saarloos
Title: A diverging length scale in the response of granular media near unjamming
Abstract: Granular model systems of smooth soft spheres display a well-defined jamming transition as a function of density. At the transition the spheres form a marginally connected disordered solid. Many properties of this transition are reminiscent of critical phase transitions. We show direct evidence for a length scale governing the elastic behavior of the system on the jammed side of the transition which diverges as the transition is approached.

• A2- *N. Xu, V. Vitelli, M. Wyart, A. J, Liu, S. R. Nagel, University of Chicago and University of Pennsylvania
Title: Energy transport in jammed systems
Abstract: We performed computer simulations to calculate the thermal diffusivity of vibrational modes in jammed sphere packings near the jamming transition (Point J). The diffusivity $d(\omega)$ is low for all modes, including those at low frequency $\omega$, and appears to be finite in the zero frequency limit. In ordinary solids, by contrast, $d(\omega)$ diverges at low frequencies due to long wavelength plane waves. The low-frequency modes near Point J are very different from plane waves: they are quasi-localized with large anharmonic corrections. Thus, these modes, which can be viewed as harmonic precursors to two-level systems, are poor conductors of energy.

• A3 - *T. Haxton, A. J. Liu, University of Pennsylvania
Title: Activated dynamics and effective temperature in a steady state sheared glass Abstract: We conduct nonequilibrium molecular dynamics simulations to measure the shear stress, the average inherent structure energy E_IS, and the effective temperature T_eff of a sheared model glass as a function of bath temperature T and shear strain rate. Above the glass transition temperature T_0, the rheology approaches a Newtonian limit and T_eff approaches T at low strain rate, while for T < T_0, the shear stress approaches a yield stress and T_eff approaches a limiting value near T_0. In the shear-dominated regime at high T, high strain rate or at low T, we find that T_eff and E_IS each collapse onto a single curve as a function of T_eff. This indicates that T_eff is controlling behavior in this regime.

• A4- *L. Daniels, Y. Park, T.C. Lubensky, D.J. Durian, University of Pennsylvania
Title: Bipolar Rods in a Fluidized Bed
Abstract: We study a driven, non-equilibrium quasi-two-dimensional system of bipolar rods in a gas-fluidized bed. By tracking the position and orientation of the particles in time, we are able to measure the dynamics of the particles with the advantage that our temporal resolution allows us to observe ballistic motion at the shortest time scales. We calculate the mean squared displacement in both the lab frame and the particle's body frame in which displacements are measured as either perpendicular or parallel to the rod's long axis. In the body frame, equipartition of energy fails and we do not observe long-time diffusive behavior in the parallel component. To probe the extent to which the observed behavior is otherwise analagous to that of a thermal particle, we apply a Langevin formalism. We observe rotational-translational coupling consistent with expectations for rotational Brownian motion.

• A5- *E. Rericha, A. Pomerance, D. Sisan, R. McAllister, J. Urbach, W. Losert, University of Maryland
Title: Relaxation from micron scale perturbations in actin networks
Abstract: The cytoskeleton of motile cells is dynamic and spatially heterogeneous. Internal stresses and external forces on the cell can generate large deformations and rearrangements of the cytoskeleton, but the underlying mechanics of stress propagation and relaxation in heterogeneous polymer networks is not well understood. Using a laser tweezer integrated into a fast confocal microscope, we have directly visualized the response of in vitro actin networks to stresses imposed by moving microspheres. We find that the force needed to impose a strain increases with strain and strain rate. When the bead is displaced then held fixed, the network stress rapidly dissipates with at least two time scales. The fast time scale we attribute to the reduction in viscous contribution of the actin gel and the slower time scale we associate with network expansion. In a cross linked network the strain relaxation is dependent on strain rate. Cross-linking the network increases the time needed for network expansion and rearrangements. Our results suggest that the strain relaxation of the network is strongly influenced by the topology of the actin network and concentration of cross linkers, allowing the cell to set the relaxation dynamics by associated actin proteins independent of the forcing environment.

• A6- *A. Kabakcioglu, D. Balcan, M. Mungan, A. Erzan
Title: Yeast's Regulatory Network Topology from Regulatory DNA Sequences
Abstract: We present an information theoretic approach to modeling transcriptional regulatory networks, in terms of a sequence-matching rule and the statistics of the occurrence of binding sequences of given specificity in random promoter regions. The crucial biological input is the distribution of the amount of information coded in the DNA segments recognized by regulatory proteins and the length distribution of the promoter regions. We provide an analysis of the transcriptional regulatory network of yeast Saccharomyces cerevisiae, with respect to the degree distribution, clustering coefficient, degree correlations, rich-club coefficient and the k-core structure. We find that all of these topological features are in remarkable agreement with those predicted by our model.

• A7- *S. Mukhopadhyay, Bob Behringer and Tom Witelski
Title: Dynamics of Circular Contact lines
Abstract: Understanding and controlling instabilities in driven fluid flows is an area of active research. We will give a short overview of novel experimental results obtained on fingering instabilities when a perfectly wetting fluid is driven by a combination of centrifugal forces and radial temperature gradients.

• A8- *B. Goncalves, Stefan Boettcher, Emory University
Title: Hierarchical Small World Graphs
Abstract: We introduce a class of recursively defined small world graphs that has proven amenable to different forms of analysis.

• A9- *P. De Gregorio, A. Lawlor, K. A. Dawson, Cornell University
Title: Finite size effects in some bootstrap percolation and kinetically constrained models

Abstract: Highly constrained kinetic-lattice-gas models are among the simplest prototypes of dynamically slowing-down systems. The connection between bootstrap percolation and kinetically constrained models has been recognized since their earliest studies. Several different bootstrap (or kinetic) rules can be defined. Depending on what they are, and on the dimensionality, the critical concentration of a finite-sized system scales (in the examples discussed here) as the inverse of an iterated logarithm of the box size, to some power. The convergence therefore can be so slow that the asymptotic description is, quantitatively, often incomplete. Rigorous mathematical results, and simulation results, have invariably confirmed this problematic feature, already in two dimensions. Despite all that, a different theoretical approach exists, and is here described, that has allowed us to carry out the full (non-asymptotic) calculation, and which exploits numerically an exact recursion formula. The calculation has been carried out in two dimensions for one bootstrap percolation and for one kinetically constrained model. Recent work in probability theory (Gravner and Holroyd) has led to a rigorous result consistent with one of our earlier predictions.

• A10- *T. Brzinski, T.A. Brzinski and D.J. Durian, University of Pennsylvania
Title: Drag Forces in a Gas Fluidized Granular Bed
Abstract: We use a rheometer to measure the torque acting on a rotating bar in a bed of gas-fluidized glass beads. We vary rotation rate from .001-10rps, vary depth from 1-10 cm, and increase the fluidizing gas flow from no flow well into the fluidized regime. We observe that at high rotation rates the drag is roughly proportional to velocity squared. At low rates we can rescale the measured torque by depth, and observe a collapse of the data. These results agree with the predictions of a granular drag force model which has proven effective in predicting granular impact dynamics. The model consists of an inertial drag term, which is depth-independent and scales as velocity squared, and a frictional drag term, which is independent of rate and varies linearly with depth. We find, as expected, that while the frictional term is airflow-dependent the inertial term is uncoupled from the fluidization.

• A11- K. Nordstrom, B. Polak, P. Arratia, A. Alsayed, J. Gollub, and D. Durian, University of Pennsylvania
Title: Microfluidic Jamming
Abstract: Thermoresponsive microgels offer a unique way to study the jamming transition as a function of density. We consider a flowing suspension of these particles in a microfluidic channel.

• A12- *J. Quintana, J. C Armas and L. Gonzalez-Lee, University of Mexico
Title: Chiral Segregation of Two Dimensional Models
Abstract: Two dimensional models with chiral and anisotropic features are studied via Monte Carlo simulations. Evidence of chiral segregation is found for some molecular geometries. This conclusion is not obviously correlated to the degree of chirality of the models. Because of the anisotropy of the models we also found some evidence of liquid crystalline phases.

• A13- Z-F. Huang, Wayne Statae University
Title: Defect dynamics in stripe phases of nonpotential, patterning forming systems
Abstract: We study nonpotential models of pattern formation in nonequilibrium systems to address the motion and decay of grain boundaries separating domains of stripe configurations. One of the models allows for mean flows and can lead to the formation of spiral defect chaos. We identify three different regimes as a function of the distance to the stripe phase threshold and initial wave number. They are associated with several decay modes including long wavelength undulations of the moving boundary, and interestingly, the formation and motion of localized defects (disclinations). The correlation of these findings with domain morphology and evolution in large aspect ratio systems as well as the onset of spiral defect chaos is also discussed.

• A14- *S. Boettcher, E. Marchetti, Emory University
Title: Thermal-to-Percolative Crossover in Dilute Lattice Spin Glasses Abstract: Ground states of bond-dilute lattice spin glasses with more than 108 spins are sampled at pc to obtain the thermal-to-percolative crossover exponent . in dimensions d=2,...,7. We make experimentally testable predictions in d=3 for the shape of the spin-glass phase boundary, Tg.(p-pc)., near pc, and we study the mean-field limit d

• A15- *B. Miller, J-L Rouet and E. Le Guirriec, Texas Christian University
Title: Emergence of Fractal Geometry in a Toy Model of the Expanding Universe
Abstract: Concentrations of matter in the universe, such as galaxies and galactic clusters, originated as very mall density fluctuations in the early universe. The fluctuation spectrum is revealed by studies of the angular correlation of CBM across the sky with WMAP. The existence of galaxy clusters and super-clusters suggests that a natural scale for the matter distribution may not exist. A point of controversy is whether the distribution is fractal and, if so, over what range of scales. The assumed source of fractal behavior is the lack of a length scale in the two body gravitational interaction. However, even with new, larger, sample sizes from recent surveys, it is difficult to extract information concerning fractal properties with confidence. Similarly, simulations with a billion particles only provide a thousand particles per dimension, far too small for accurate conclusions. With one dimensional "toy models" we can overcome these limitations by carrying out simulations with on the order of a quarter of a million particles. Here we present the recent results* of our ongoing investigation of the fractal geometry of one dimensional models of the expanding universe. * PHYSICAL REVIEW E 76, 036705 _2007

• A16- *M. Pleimling, L. Kornyei and F. Igloi, Virginia Tech
Title: Nonequilibrium critical dynamics of the two-dimensional Ising model quenched from a correlated initial state
Abstract: The universality class, even the order of the transition, of the two-dimensional Ising model depends on the range and the symmetry of the interactions (Onsager model, Baxter-Wu model, Turban model, etc.), but the critical temperature is generally the same due to self-duality. Here we consider a sudden change in the form of the interaction and study the nonequilibrium critical dynamical properties of the nearest-neighbor model. The relaxation of the magnetization and the decay of the autocorrelation function are found to display a power law behavior with characteristic exponents that depend on the universality class of the initial state.

• A17- *J. Joo, S. Plimpton and J.-L. Faulon, Sandia National Laboratories
Title: Interplay of noise and time-delayed negative feedback loops in a biochemical signaling network
Abstract: Many processes in biology involve time-delayed negative feedback loops from networks of biochemical reactions. Crucial molecules are present in small numbers, raising questions about noise and stability of time-delayed dynamics on such networks. I will address this problem in the context of NF-kappaB signal transduction network.

• A18- M. Hagan, Brandeis Physics
Title: Dynamic models for templated viral capsid assembly
Abstract: I will present coarse-grained computational and theoretical models that describe the assembly of solubilized subunits around polymers and rigid spheres. These models are motivated by experimental model systems in which viral proteins encapsidate polyelectrolytes and inorganic nanoparticles. Model predictions demonstrate that cooperative interactions between disparate assembling components can overcome some limitations of spontaneous assembly, but the complexity of multicomponent assembly introduces new limitations. These findings have implications for the dynamic encapsidation of the viral genome during viral assembly.

• A19- A. Rutenberg, G. Ryan
Title: Bacteriophage control of bacterial lysis timing
Abstract: Bacteriophage are viruses that infect and kill bacteria. Phage lambda lyses its host bacterium at a precisely scheduled time after infection. Lysis timing is determined by the action of phage holins, small proteins that induce hole formation in the bacterium's inner membrane. We present a two-stage nucleation model of lysis timing, with the nucleation of condensed holin domains on the membrane followed by the nucleation of holes within holin domains. We recover the accurate lysis timing seen experimentally, and show that the timing accuracy is approximately optimal for the phage.

• A20- *P. Viot and A. Burdeau
Title: Gaussian velocity distribution in a vibrated granular bilayer system
Abstract: We show by using a Discrete Element method that, in a bilayer of vibrated granular bidisperse spheres, the horizontal velocity distribution of the top layer particles has a Gaussian shape. These results are in a very good agreement with the observations obtained by Baxter and Olafsen. A microscopic analysis of the trajectories reveals the mechanism of randomization leading to this result. (arXiv:0711.1497)

• A21- *Y. Shokef, Y. Han, A. Alsayed, P. Yunker, T. Lubensky, and A. Yodh
Title: Geometrical Frustration in Buckled Colloidal Monolayers
Abstract: Geometrically frustrated lattices have been investigated mostly in the context of quantum magnetic systems. Recently, single-particle visualization of frozen frustrated states has become viable in various artificially fabricated materials comprised of macroscopic building blocks. We present experiments on a self-organized colloidal system that exhibits geometrical frustration reminiscent of antiferromagnetic Ising spins on a triangular lattice. Our detailed Monte-Carlo simulations exhibit the antiferromagnetic order observed experimentally and capture the formation of stripes that randomly zigzag around the system. Simple free volume arguments explain both the mapping to the Ising model at moderate confinement and the partial removal of frustration at high confinement due to lattice distortions which favor striped configurations. We conclude by analyzing the dynamics of individual 'spin-flips' for particles with different degrees of local frustration.

• A22- *D. Abraham, F. H. L. Essler and A. M. Maciolek, University of Oxford, England
Title: Forces between Colloidal Particles trapped at interfaces

• A23- *G. Hentschel, I. Procaccia, Emory University
Title: Dielectric Relaxation in Glass-Forming Hydrogen-Bonded Liquids Near the Glass Transition
Abstract: We address the relaxation dynamics in hydrogen-bonded super-cooled liquids near (but above) the glass transition, measured via Broad-Band Dielectric Spectroscopy (BDS). We propose a theory based on decomposing the relaxation of the macroscopic dipole moment into contributions from hydrogen bonded clusters of s molecules, with smin < s < smax. We construct the statistical mechanics of the super-cooled liquid to estimate the temperature-dependent density of clusters of size s. With a theoretical estimate of the relaxation time of each cluster we provide predictions for the real and imaginary part of the frequency dependent dielectric response. The predicted spectra and their temperature dependence are in accord with measurements, explaining a host of phenomenological fits like the Vogel-Fulcher fit and the stretched exponential fit. Using glycerol as a particular example we demonstrate quantitative correspondence between theory and experiments. The theory also demonstrates that the . peak and the "excess wing" stem from the same physics in this material. The theory also shows that in other hydrogen-bonded glass formers the "excess wing" can develop into a . peak, depending on the molecular material parameters (predominantly the surface energy of the clusters). Finally we discuss the dc part of the BDS spectrum and argue why it scales with the frequency of the . peak, providing an explanation for the remarkable data collapse observed in experiments.

• A24- *C. Henley, S. Hicks, Cornell University
Title: Virus capsid elasticities: atomistic to coarse-grained I. Triangulated network models
Abstract: Virus capsids are modeled with elastic network models in which a handful of parameters determine transitions in assembly and morphology. We introduce an approach to compute these parameters from the microscopic structure of the proteins involved, starting by defining an initial coarse-graining of each protein as one or a few rigid bodies with very general interactions.

• A25- *S. Hicks, and C. Henley, Cornell University
Title: Virus capsid elasticities: atomistic to coarse-grained: II. Extracting parameters from MD simulations
Abstract: We begin with a coarse-grained network of proteins and parametrize the interactions by fitting simulated equilibrium fluctuations (relative translations and rotations) of a pair of proteins (or fragments) to a 6-dimensional Gaussian. We then compose these generalized springs to determine the continuum elastic parameters. We demonstrate how this approach can be applied to HIV capsid protein.

SESSION B, Tuesday 8:30 - 10:15
* For Author Presenting the Talk

• B1- S. Ji, Rutgers University
Title: A definition of complexity, emergence and information based on the triadic metaphysics of Peirce
Abstract: The terms, complexity, emergence and information, frequently occur together in many contemporary discourses in natural, computing, and social sciences, but the relation among them has not yet been clearly defined, to the best of my knowledge. To rigorously define the relation among these terms, it may be necessary to utilize a table organized according to the triadic metaphysics of Firstness, Secondness, and Thirdness enunciated by the American chemist-logician-philosopher, C. S. Peirce (1839-1914). See web page for rest.

• B2- *C. Haselwandter, M. Kardar, R. da Silveira, and A. Triller, MIT
Title: Reaction-diffusion model for formation of a neuronal synapse
Abstract: Neurotransmitter receptor molecules are crucial for the synaptic conversion of chemical to electric signals. It has long been assumed that receptor molecules are concentrated at synapses due to a stable binding to scaffold molecules. However, recent experiments have demonstrated [A. Triller and D. Choquet, Trends Neurosci. 28, 133 (2005)] that receptor molecules diffuse rapidly into and out of the synapse, whereas synaptic weights can be stable over a lifetime. We describe a simple reaction-diffusion model for the dynamics of receptor-scaffold aggregation in the chemical synapse. The model exhibits a Turing bifurcation which leads to stable patterns in the presence of high diffusion rates, in accord with the experimental findings.

• B3- *C. Chatelain, M. Kardar, Y. Kantor, MIT
Title: Probability distributions for polymer translocation
Abstract: Translocation, the passage of a polymer through a membrane pore, is a sub-diffusive process. We perform Monte Carlo simulations for a self avoiding polymer in two dimensions, and measure probability distributions for two important indicators of translocation: the survival time T, and the coordinate s labeling the surviving monomer. The probability p(T) has an exponential tail, unlike the solution to a sub-diffusive Fokker-Planck equation. The probability p(s,t) is Gaussian at short times with a variance growing as t^(0.8), but saturates to a non-trivial form at large times.

• B4- *Q. Zhang, K.-Y. Chan, University of Hong Kong
Title: Alternating Current Non-Equilibrium Molecular Dynamics Simulations of Yttria-Stabilized Zirconia
Abstract: Yttria-stabilized zirconia (YSZ) is well known as a solid electrolyte material used in solid oxide fuel cells (SOFC) and oxygen sensors for its very high oxygen ions conductivity. YSZ has high oxygen conductivity due to the vacancies of electrons induced by the doped yttrium In this work, an alternate current non-equilibrium molecular dynamics (AC-NEMD) simulation technique is used to study the oxygen anion conduction behavior of 8% mol yttria-stabilized zirconia(YSZ). With ohmic heat generated by the external field, a constant temperature is effectively maintained by both the Anderson and Nose-Hoover thermostats. Both thermostats yield similar results. The simulation results indicate a resistance-capacitance (RC) circuit behavior at low frequency and resistance-inductance (RL) circuit behavior at high frequency. The transition between RC and RL behavior is connected with the time of oxygen ions transport between oxygen vacancies in YSZ.

• B5- *J. Hoffman, R.K.P. Zia, Virginia Tech
Title: First Order Transition in a Quasi-one-dimensional ABC Model
Abstract: We consider the ABC model (Evans, Kafri, Koduvely and Mukamel, PRL+PRE, 1998), a one-dimensional lattice of particle transport which displays an order-disorder transition. In the ordered state, each of the species into macroscopic clusters (jams). We generalize this to a 2-lane system, in which particles exchange freely and symmetrically (i.e., undergo ordinary diffusion) within the second lane. Across the two lanes, particles exchange with probability s without bias. We find that, for parameters when the ABC model is ordered, the 2-lane system displays two phases: For s << 1, the stationary state consists of a distribution of small clusters. For larger s, aligned macroscopic jams fill both lanes. The transition appears to be first order, in that hystersis is observed. The wider context of study is: How do systems in equilibrium and non-equilibrium steady states behave when they are coupled together?

• B6- *A. Angel, R. K. P. Zia, Virginia Tech
Title: Power Spectra of the Occupation of a Segment of a Totally Asymmetric Zero-Range Process on a Ring
Abstract: The zero-range process (ZRP) is a paradigmatic model in the study of nonequilibrium condensation transitions. We study the dynamics of a totally asymmetric ZRP on a ring lattice by measuring the power spectra of the time series of the occupation of a segment of the lattice. Interesting structure is observed in the form of two distinct decaying-oscillation components. A simple theoretical treatment appears to capture the qualitative aspects of this behavior.

• B7- A. Toom, A. V. Rocha and A. Dias-Ramos, UFPE, Brazil
Title: Approximation of measures by words
Abstract: A is a finite set called alphabet. Its elements are called letters. Z is the set of integer numbers. A to the power of Z is the set S of bi-infinite sequences of letters. A measure on S (on the sigma-algebra generated by cylinder sets) is called uniform if it is translation invariant. All finite sequences of letters are called words. A uniform measure is determined by its values on words. A sequence of words may approximate a uniform measure (like a sequence of growing tables of random numbers). We provide a definition and some properties of this approximation.

• B8- *O. Sariyer, A. Nihat Berker and M. Hinczewski, Istanbul Technical University
Title: Spin-Wave Stiffnesses, Excitation Spectrum Gap and Algebraic Crossovers, and Finite-Temperature Quantum Effects in the XXZ Heisenberg Chain
Abstract: The spin-1/2 XXZ Heisenberg chain, for both the ferromagnetic and antiferromagnetic systems, is studied for all anisotropies using global renormalization-group theory.[1] We obtain, for all anisotropies, the antiferromagnetic spin-liquid spin-wave stiffness and the Isinglike ferromagnetic excitation spectrum gap, exhibiting the spin-wave to spinon crossover. We find that the latter crossover is tracked by a crossover in the leading algebraic behavior of the specific heat. A number of finite-temperature quantum effects are found: When all interactions are ferromagnetic, the spin component with the weakest coupling in fact has antiferromagnetic correlations. Other cross-component correlations, counter to classical intuition, occur at finite temperatures. Again contrary to classical intuition, the specific heat peak and position values are oppositely affected, in the ferromagnetic and antiferromagnetic systems, by spin anisotropy.
1.O.S. Sariyer, A.N. Berker, and M. Hinczewski, arXiv:0704.1064v1 [cond-mat.stat-mech] (2007).

• B9- *A. Malakis, A.N. Berker, N.G. Fytas, I.A. Hadjiagapiou and S.S. Martinos, University of Athens
Title: Wang-Landau Studies of Pure and Quenched Random Systems
Abstract: Random walk processes in energy space, such as the Wang-Landau and Lee-processes, are implemented in their final "entropic stage" for the accumulation of histogram data and the estimation of thermal and magnetic properties for pure and quenched random Ising models. Using these implementations, numerical results have been obtained and finite-size analysis of thermal and magnetic anomalies have been recently carried out for several classical models of statistical mechanics. Some examples are: (I) The behavior of the square and triangular Ising models with next-nearest-neighbor interactions in the superantiferromagnetic regime. (II) The behavior of the pure 2D and 3D Blume-Capel models in their first-order regime. (III) The effects of quenched bond randomness on the first-order transitions of the 2D Blume-Capel and the triangular n and S. Ugur, Technische Universitaet Muenchen

• B10- *C.N. Kaplan, A. Nihat Berker, Koccedil University, Istanbul
rtyTitle: Quantum Induced Asymmetric Phase Diagrams of Spin-Glass Systems
Abstract: The spin-1/2 quantum Heisenberg spin-glass system is studied in all spatial dimensions d by renormalization-group theory.[1] Strongly asymmetric phase diagrams in temperature and antiferromagnetic bond probability p are obtained in dimensions d>=3. The asymmetry at high temperatures approaching the pure ferromagnetic and antiferromagnetic systems disappears as d is increased. However, the asymmetry at low but finite temperatures remains in all dimensions, with a reentrant antiferromagnetic phase receding from the ferromagnetic phase. Accordingly, in the p=1/2 system, with an equal number of randomly distributed ferromagnetic and antiferromagnetic bonds, as temperature is lowered, a finite-temperature phase transition occurs to the FERROMAGNETIC phase.
1. C.N. Kaplan and A.N. Berker, arXiv:0709.3589v1 [cond-mat.dis-nn] (2007).

• B11- *A. Erbas, A. N. Berker, H. Aktug, A. Dörtyön and S. Ugur, Technische Universitaet Muenchen
Title: Two-Level Simulated Annealing Solution of Delivery System in Metropolitan Istanbul
Abstract: A two-level simulated annealing is developed for the home delivery system of Migros supermarkets in metropolitan Istanbul. The outer level is the distribution of adresses between trucks and the inner level is the adress sequencing for each truck. Each level has its own simulated annealing temperature, with the inner level temperature going to its full cycle to zero for each outer level temperature step. Typically a 20% improvement is obtained over the greedy algorithms. With the inclusion of locally varying traffic factors, the random-bond traveling salesman problem is studied. Our results are now being installed for commercial implementation.

• B12- *C. Guven, (KoU), A. Nihat Berker (KoU), M. Hinczewski and H. Nishimori (Tokyo Inst. Tech.)
Title: Reentrant and Forward Phase Diagrams of the Anisotropic Three-Dimensional Ising Spin Glass
Abstract: The uniaxially anisotropic d = 3 Ising spin glass is solved on a hierarchical lattice. In the global phase diagram, 5 different ordered phases, namely ferromagnetic, columnar, layered, antiferromagnetic, and spin-glass phases, are found. The boundary between the ferromagnetic and spinglass phases can be either reentrant or forward, that is either receding from or penetrating into the spin-glass phase as temperature is lowered, depending on whether the multicitical point is or is not on the Nishimori symmetry line. A distinctive phase diagram, with a new multicritical point between the ferromagnetic, layered, and paramagnetic phases, is found in the Nishimori symmetry surface in the global phase diagram.

• B13- W. Guo, B. Nienhuis,W. Guo*, H. W. J. Bloete, Beijing Normal University
Title: Tricritical O(n) Models in Two Dimensions
Abstract: We show that the exactly solved low-temperature branch of the two-dimensional O($n$) model is equivalent with an O($n$) model with vacancies and a different value of $n$. We present analytic results for several universal parameters of the latter model, which is identified as a tricritical point. These results apply to the range $n \leq 3/2$, and include the exact tricritical point, the conformal anomaly and three scaling dimensions, associated with temperature, magnetic field and the introduction of an interface. These results are verified by means of numerical transfer-matrix calculations. We formulate the mapping of the low-temperature branch of the O($n$) model on the dilute O($n$) model also for the case of the honeycomb O($n$) lattice.

• B14- R. Fisch, Princeton University
Title: Structure Factor of the 3D Random Field XY Model
Abstract: We have performed Monte Carlo studies of the 3D random field $XY$ model on $L \times L \times L$ simple cubic lattices, with random field strengths of $h_r$ = 1 and 2. We present results for the angle-averaged magnetic structure factor, $S ( k )$ at $L = 64$. Our results appear to indicate a phase transition into a ferromagnetic state. This is made possible by the existence of a Griffiths singularity. It appears that at the phase transition $M2$ jumps to zero discontinuously, with a latent heat which is probably subextensive. See arXiv:0709.4658

• B15- *S. Durukanoglu, O.S. Trushin, and T.S. Rahman, MIT and Istanbul Tech University
Title: Molecular Static Calculations of Activation Energy Barriers on Cu(111)
Abstract: We study the activation energy barriers for a single atom diffusing around step edges on the (111) low Miller-index surface of Cu, with a particular interest in determining the possible single atom diffusion mechanisms leading to an explanation for the observed rapid decay of double-layer islands on Cu(111). The minimum energy paths for the diffusion processes are determined by using the nudged elastic band method with the interaction potentials based on the embedded atom method. Our calculations reveal that the Erhlich-Schwoebel (ES) barrier for an adatom to diffuse between two neighboring step edges, either by jump or exchange mechanism, is independent of the separation between the steps unless they are at two-atom width apart, in which case the barrier is significantly larger than that for an isolated step. Since the molecular static calculations yield a hindering role for the ES barrier in mass transport phenomenon, temperature-dependent calculations on double-layer island decay are needed to further digest the observed fast-decay double-layer islands. Calculations along this line are on the way.

• B16- M. Hinczewski, A. N. Berker, F. Gursey Research Center
Title: High-Precision Thermodynamic and Critical Properties from Tensor Renormalization-Group Flows
Abstract: The recently developed tensor renormalization-group (TRG) method provides a highly precise technique for deriving thermodynamic and critical properties of lattice Hamiltonians. The TRG is a local coarse-graining transformation, with the elements of the tensor at each lattice site playing the part of the interactions that undergo the renormalization-group flows. These tensor flows are directly related to the phase diagram structure of the infinite system, with each phase flowing to a distinct surface of fixed points. Fixed-point analysis and summation along the flows give the critical exponents, as well as thermodynamic functions along the entire temperature range.[1] Thus, for the ferromagnetic triangular lattice Ising model, the free energy is calculated to better than 10(.5) along the entire temperature range. Unlike previous position-space renormalization-group methods, the truncation (of the tensor index range D) in this general method converges under straightforward and systematic improvements. Currently, our best results are easily obtained with D = 24, corresponding to 4624-dimensional renormalization-group flows.
1. M. Hinczewski and A.N. Berker, arXiv:0709.2803v1 [cond-mat.stat-mech] (2007).

• B17- *A.N. Berker, and M. Hinczewski, Koc University
Title: d=3 tJ Model Global Phase Diagram with Quenched Random Impurities: Renormalization-Group Calculation
Abstract: The phase diagram of the d=3 tJ model with frozen impurities is obtained from the global renormalization-group flows of the quenched probability distribution of the interactions. We find several features with close experimental parallels: (1) Away from half-filling we see the rapid destruction of a spin-singlet liquid phase (analogous to the superconducting phase in cuprates) which is eliminated for impurity concentration p = 0.05. (2) In the same region for these dilute impurity concentrations we observe an enhancement of antiferromagnetism. (3) The antiferromagnetic phase near half-filling is robust against impurity addition, and disappears only for p = 0.40.
1. M. Hinczewski and A.N. Berker, arXiv:cond-mat/0607171v1 [cond-mat.str-el] (2006).

• B18- *C. Franck, W. Ip, A. Bae, N. Franck, E. Bogart, and T. Lee., Cornell University
Title: When Cells Collide: Evidence for Cell-Assisted Cell Growth Based on Direct Contacts
Abstract: Although intercellular communication is frequently viewed as involving the transport of small signal molecules through an intracellular fluid medium, biologists have proposed signaling with specificity due to chemical recognition through direct cell-to-cell contacts. Considering the collective computation behind the decision of a cell to divide when it senses the presence of a sufficient number of like neighbors, we offer data and a model along these lines for the transition from slow to exponential growth in shaken suspension cell culture of the model eukaryote, Dictyostelium discoideum. Besides exploring an elegantly simple example of multicellular life, this discussion might well prove useful in considering the limits of cell culture on the small spatial scales required for contemporary massively parallel biotechnology. This work is available as an online preprint at people.ccmr.cornell.edu/~kip/ .

• B19- *L. Guzman, and M. Santillan, Instituto Politecnico Nacional, Mexico
Title: Comparative study of two transcriptional regulatoy networks: E. coli and S. cerevisiae
Abstract: We compare the statistical properties of two transcriptional regulatory networks: one for the bacterium Escherichia coli, and one for the budding yeast Saccharomyces cerevisiae. We measure several network properties for the original bipartite networks and for the networks projected to the transcription factors and to the regulated genes. In particular, we calculate the clustering coefficient, the degree distribution, the efficiency and cost. We also construct random networks with the same degree distributions and compare with the original networks. Finally, we tested network robustness to random failures and attacks.

• B20- Z. Konkoli, Chalmers, Gothenurg, Sweden
Title: Diffusion controlled reactions in small and structured spaces as a tool for describing living cell biochemistry
Abstract: Chemical reaction kinetics in vivo differs significantly from the one in pipette and care has to be taken when devising computational frameworks or experimental setup to deal with such environment. For example, geometry can be quite complicated and there is an experimental evidence that cell is structured in many ways, already starting that the cytoplasm level. Cytoplasm is not smooth and homogeneous; for a single cell total amount of protein content can be as high as 17-30% by weight which results in extremely structured and crowded space. In addition, cell interior (roughly 10 in diameter) is further partitioned in smaller spaces such as organelles (e.g. mitochondria with 50 nm in diameter), and roughly 50% of cell volume is filled by organelles. Also, for typical physiological concentrations of individual proteins of 1nM one gets Nprot. 1nM(10mmmmm)3. 1000 copies of individual protein. This can result in large spatial fluctuations of protein number across the cell interior and delivery of proteins can become an issue.
1. Konkoli, Z., Interplay between chemical reactions and transport in structured spaces. Physical Review E, 2005. 72(1): p. 011917.
2. Konkoli, Z., Diffusion-controlled reactions in small and structured spaces as a tool for describing living cell biochemistry. Journal of Physics-Condensed Matter, 2007. 19(6): p. 065149.

• B21- *R. Zia, J.J. Dong, and B. Schmittmann, Virginia Tech
Title: Applying TASEP to Modify Production Rates of Real Proteins
Abstract: The totally asymmetric simple exclusion process was generalized in two non-trivial ways so as to model protein synthesis more realistically. One is particles of length greater than unity, to model ribosomes covering 10-12 codons. The other is inhomogeneous hopping rates, associated with the concentrations of aa-tRNA's in the cell. Since the correspondence between codons and amino-acids are n-1 (n up to 6), any specific protein can be synthesized by a huge variety of codes. As a result, the particle current (i.e., protein production rate) is far from unique. We study 10 genes of E. coli by simulations and found that wild type-[i.e., naturally occurring-codes are generally closer to being "optimal" (highest current) than "abysmal" (lowest current). A few strategically chosen replacement-codons can enhance or suppress the current significantly. Obvious implications for biotechnology will be noted.

SESSION C, 3:40 - 4:35
*For Author Presenting the Talk
• C1- *M. Lavrentovich, R. K. P. Zia, Kenyon College
Title: Exact energy flux through the steady state of a non-equilibrium 1-D Ising chain
Abstract: A one-dimensional Ising model is constructed as a non-equilibrium system by coupling the spins in the two halves of the chain to two thermal baths at different temperatures. The spins interact with the baths via Glauber spin-flip dynamics and with their nearest neighbors via ferromagnetic interactions. We analyze the steady state solution to the energy fluxes between the spins and thermal baths. An exact expression for the fluxes is derived for a special case of the bath temperatures. We find a transition between fast and slow energy flux decays as the temperature difference between the baths approaches a maximum. Finally, the analytical expressions are compared to results from a Monte Carlo simulation of the chain.

• C2- J. Park, and A.-L. Barabasi, Northeastern University
Title: Distribution of Node Characteristics on Complex Networks
Abstract: Our enhanced ability to map the structure of various complex networks is accompanied by the capability to independently identify the functional characteristics of each node, leading to the observation that nodes with similar characteristics show tendencies to link to each other. Examples can be easily found in biological, technological, and social networks. Here we propose a tool to quantify the interplay between node properties and the structure of the underlying network. We show that when nodes in a network belong to two distinct classes, two independent parameters are needed. We find that the network structure limits the values of these parameters, requiring a phase diagram to uniquely characterize the configurations available to the system. The phase diagram shows independence from the network size, a finding that allows us to estimate its shape for large networks from their samples. We study biological and socioeconomic systems, finding that the proposed parameters have a strong discriminating power.

• C3- *J. Basner, and C. Jarzynski, University of Maryland
Title: Unbiased Estimation of the Potential of Mean Force
Abstract: An identity is derived that expresses the equilibrium probability distribution of a reaction coordinate as an ensemble average of an observable quantity. This leads to a "binless" method for estimating the potential of mean force, eliminating the need to construct histograms. The potential of mean force is expressed as an arbitrary reference, or guess, potential plus a correction term. Rapid convergence of the unbiased estimator is demonstrated for three simulation conditions. An extension that augments sampling efficiency is also presented.

• C4- *A. Taloni, M. Kardar and M. Andersen Lomholt
Title: Langevin Formulation for Single File Diffusion
Abstract: The single file model describes a system of N identical unit-mass Brownian particles moving on a ring. A hard core interaction ensures that the particles retain their ordering throughout the motion. It's well-known that the mean square displacement of a tagged particle grows sub-diffusively, asymptotically as the square root of time. We propose a stochastic (Langevin) equation equation for the motion of the tagged particle that quantitatively captures the three regimes of ballistic, diffusive and subdiffusive motion, and the corresponding crossover times. We numerically verify several properties such as linear response, the fluctuation-dissipation connections, and a generalized Einstein relation for this process.

• C5- *B. Vollmayr-Lee, S. Yasuda and A. Rutenberg, Bucknell University
Title: Phase Ordering Dynamics: the Influence of Asymmetric Mobility
Abstract: Phase ordering dynamics with a locally conserved order parameter is believed to yield asymptotically a universal domain structure. We argue on theoretical grounds that an asymmetric mobility is one of the few relevant parameters affecting the domain structre. To test this, we simulated an asymmetric Cahn-Hilliard equation and found no measurable influence of the mobility asymmetry on the structure factor, and yet a strikingly large influence on the domain size distribution.

• C6- *R. Akiyama, N. Fujino, K. Kaneda and M. Kinoshita, Kyushu University
Title: Attractive Force between Like-Charged Colloidal Particles Arising Solely from Solvent Granularity
Abstract: Effective interaction between like-charged colloidal particles in aqueous electrolyte solution is studied using the HNC-OZ theory. Although the van der Waals attraction between colloidal particles is omitted in the present model, attractive regions appear in the interaction. In particular, the interaction at small separations is significantly attractive and the contact of colloidal particles is stabilized, when the electrolyte concentration is sufficiently high. This interesting behavior arises from the translational motion of solvent molecules. (R. Akiyama, N. Fujino, K. Kaneda, M. Kinoshita, Condensed Matter Physics, accepted)

• C7- *J-C. Domenge, C. Lhuillier, L. Messio, L. Pierre and P. Viot, Rutgers University
Title: Chirality and Z2 vortices in a Heisenberg spin system on the kagomé lattice
Abstract: We investigated the phase diagram of the classical J1-J2 Heisenberg model on the kagomé lattice using extensive Monte Carlo simulations. This O(3)-invariant model has a low-temperature chiral-ordered phase in a wide range of ferromagnetic J1 and antiferromagnetic J2. Contrary to simple expectations, the phase transition is not Ising-like. It is shown that Z2 vortices are at the origin of a weak first-order phase transition. The gap to the vortex excitations decreases when approaching the Quantum Critical Point (QCP) where it presumably goes to zero. In the neighborhood of the QCP the system is a fully disordered Spin Liquid. This situation could be typical of a large class of frustrated magnets.

• C8- *T. Burkhardt, G. Györgyi, N.R. Moloney, and Z. Rácz
Title: Extreme Value Statistics in Correlated Systems
Abstract: We consider the process dnx/dtn = (t), where (t) is Gaussian white noise and n is an arbitrary. For paths x(t) with periodicity T, we study the distribution of the quantity m = maxt[x(t)x(0)], i.e., of the maximum displacement relative to the initial value. For n = 0, 1, 2, and , exact analytical expressions for the distribution are obtained, and for other n it is determined numerically. The distribution is not the same as the distribution of the maximum value of x(t) relative to its average value in the interval 0 < t < T, recently calculated for n = 1 by Majumdar and Comtet. For a detailed account of our results see PRE 76, 041119 (2007).

• C9- G. Tellez,
Title: Charge inversion of a guest charge in a +2:-1 electrolyte
Abstract: We study the screening of a "guest" charge immersed in an electrolyte composed of two species of ions with valencies +2 and -1. This statistical mechanic system is equivalent to the complex Bullough-Dodd quantum field theory. In the two-dimensional version of the problem, the corresponding quantum field theory is integrable. This allows us to obtain explicit analytic expressions for the density profiles of ions and the electrostatic potential at large distances from the guest particle.

• C10- *S. Lehmann, M. Schwartz and L. K. Hansen, Northeastern University
Title: Bi-clique communities
Abstract: A novel method for detecting communities in bipartite networks is presented. Based on a generalization of the k-clique community detection algorithm suggested by Palla et al., we demonstrate how modular structure in bipartite networks presents itself as overlapping bicliques. The biclique community detection method has the advantages of the k-clique method, but augments it with respect to one critical aspect; the algorithm presented here utilizes bipartite network information in order to investigate aspects of community structure in sparse network regions, where the k-clique algorithm is unable to detect communities.

• C11 - A. Ayyer, Rutgers University
Title: Exact Solution for a TASEP with Three Kinds of Particles
Abstract: We use the matrix method of Derrida, Evans, Hakim and Pasquier to find an exact solution for a three species open system consisting of first and second class particles and holes. The dynamics are those of the totally asymmetric exclusion process (TASEP) but with the second class particles confined to the system. Their density is fixed at some value n. The phase diagram is similar to that found by Derrida et al, to which it reduces when n=0. (joint work with Joel Lebowitz and E.R. Speer)