RUTGERS UNIVERSITY,
HILL CENTER, ROOM 114
SUNDAY, MONDAY AND TUESDAY,
DECEMBER 16-18, 2007
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)