Three-state active lattice gas: A discrete Vicsek-like model with excluded volume.

We study a discrete-space model of active matter with excluded volume. Particles are restricted to the sites of a triangular lattice and can assume one of three orientations. Varying the density and noise intensity, Monte Carlo simulations reveal a variety of spatial patterns.

Steady-state thermodynamics: Description equivalence and violation of reservoir independence.

For stochastic lattice models in spatially uniform nonequilibrium steady states, an effective thermodynamic temperature T and chemical potential μ can be defined via coexistence with heat and particle reservoirs. We verify that the probability distribution P_{N} for the number of particles in the driven lattice gas with nearest-neighbor exclusion in contact with a particle reservoir with dimensionless chemical potential µ^{*} possesses a large-deviation form in the thermodynamic limit. This implies that the thermodynamic properties determined in isolation (fixed particle number representation) and in contact with a particle reservoir (fixed dimensionless chemical potential representation) are equal.

Percolation in two-species antagonistic random sequential adsorption in two dimensions.

We consider two-species random sequential adsorption (RSA) in which species A and B adsorb randomly on a lattice with the restriction that opposite species cannot occupy nearest-neighbor sites. When the probability x_{A} of choosing an A particle for an adsorption trial reaches a critical value 0.626441(1), the A species percolates and/or the blocked sites X (those with at least one A and one B nearest neighbor) percolate.

Data-Driven Models of Efficient Chromatic Coding in the Outer Retina.

Recent experimental work on zebrafish has shown the activity of photoreceptors and horizontal cells (HCs) as a function of the stimulus spectrum, highlighting the appearance of chromatic-opponent signals at their first synaptic connection. Altogether with the observed lack of excitatory intercone connections, these findings suggest that the mechanism yielding early color opponency in zebrafish is dominated by inhibitory feedback. We propose a neuronal population model based on zebrafish retinal circuitry to investigate whether networks with predominantly inhibitory feedback are more advantageous in encoding chromatic information than networks with mixed excitatory and inhibitory mechanisms.

Microemulsions in the driven Widom-Rowlinson lattice gas.

An investigation of the two-dimensional Widom-Rowlinson lattice gas under an applied drive uncovered a remarkable nonequilibrium steady state in which uniform stripes (reminiscent of an equilibrium lamellar phase) form perpendicular to the drive direction [R. Dickman and R. K.

Hidden role of mutations in the evolutionary process.

Mutations not only alter allele frequencies in a genetic pool but may also determine the fate of an evolutionary process. Here we study which allele fixes in a one-step, one-way model including the wild type and two adaptive mutations. We study the effect of the four basic evolutionary mechanisms-genetic drift, natural selection, mutation, and gene flow-on mutant fixation and its kinetics.

Multirange Ising model on the square lattice.

We study the Ising model on the square lattice (Z^{2}) and show, via numerical simulation, that allowing interactions between spins separated by distances 1 and m (two ranges), the critical temperature, T_{c}(m), converges monotonically to the critical temperature of the Ising model on Z^{4} as m→∞. Only interactions between spins located in directions parallel to each coordinate axis are considered. We also simulated the model with interactions between spins at distances of 1, m, and u (three ranges), with u a multiple of m; in this case our results indicate that T_{c}(m,u) converges to the critical temperature of the model on Z^{6}.

Order-disorder transition in a two-dimensional associating lattice gas.

We study an associating lattice gas (ALG) using Monte Carlo simulation on the triangular lattice and semianalytical solutions on Husimi lattices. In this model, the molecules have an orientational degree of freedom and the interactions depend on the relative orientations of nearest-neighbor molecules, mimicking the formation of hydrogen bonds. We focus on the transition between the high-density liquid (HDL) phase and the isotropic phase in the limit of full occupancy, corresponding to chemical potential μ→∞, which has not yet been studied systematically.

Steady-state entropy: A proposal based on thermodynamic integration.

Defining an entropy function out of equilibrium is an outstanding challenge. For stochastic lattice models in spatially uniform nonequilibrium steady states, definitions of temperature T and chemical potential μ have been verified using coexistence with heat and particle reservoirs. For an appropriate choice of exchange rates, T and μ satisfy the zeroth law, marking an important step in the development of steady-state thermodynamics.

Driven Widom-Rowlinson lattice gas.

In the Widom-Rowlinson lattice gas, two particle species (A, B) diffuse freely via particle-hole exchange, subject to both on-site exclusion and prohibition of A-B nearest-neighbor pairs. As an athermal system, the overall densities are the only control parameters. As the densities increase, an entropically driven phase transition occurs, leading to ordered states with A- and B-rich domains separated by hole-rich interfaces.

The advantage of being slow: The quasi-neutral contact process.

According to the competitive exclusion principle, in a finite ecosystem, extinction occurs naturally when two or more species compete for the same resources. An important question that arises is: when coexistence is not possible, which mechanisms confer an advantage to a given species against the other(s)? In general, it is expected that the species with the higher reproductive/death ratio will win the competition, but other mechanisms, such as asymmetry in interspecific competition or unequal diffusion rates, have been found to change this scenario dramatically. In this work, we examine competitive advantage in the context of quasi-neutral population models, including stochastic models with spatial structure as well as macroscopic (mean-field) descriptions.

Traffic model with an absorbing-state phase transition.

We consider a modified Nagel-Schreckenberg (NS) model in which drivers do not decelerate if their speed is smaller than the headway (number of empty sites to the car ahead). (In the original NS model, such a reduction in speed occurs with probability p, independent of the headway, as long as the current speed is greater than zero.) In the modified model the free-flow state (with all vehicles traveling at the maximum speed, v_{max}) is absorbing for densities ρ smaller than a critical value ρ_{c}=1/(v_{max}+2).

Spatiotemporal generalization of the Harris criterion and its application to diffusive disorder.

We investigate how a clean continuous phase transition is affected by spatiotemporal disorder, i.e., by an external perturbation that fluctuates in both space and time.

Griffiths phases and localization in hierarchical modular networks.

We study variants of hierarchical modular network models suggested by Kaiser and Hilgetag [ Front. in Neuroinform., 4 (2010) 8] to model functional brain connectivity, using extensive simulations and quenched mean-field theory (QMF), focusing on structures with a connection probability that decays exponentially with the level index.

Particle-density fluctuations and universality in the conserved stochastic sandpile.

We examine fluctuations in particle density in the restricted-height, conserved stochastic sandpile (CSS). In this and related models, the global particle density is a temperaturelike control parameter. Thus local fluctuations in this density correspond to disorder; if this disorder is a relevant perturbation of directed percolation (DP), then the CSS should exhibit non-DP critical behavior.

Computational model of a vector-mediated epidemic.

We discuss a lattice model of vector-mediated transmission of a disease to illustrate how simulations can be applied in epidemiology. The population consists of two species, human hosts and vectors, which contract the disease from one another. Hosts are sedentary, while vectors (mosquitoes) diffuse in space.

Failure of steady-state thermodynamics in nonuniform driven lattice gases.

To be useful, steady-state thermodynamics (SST) must be self-consistent and have predictive value. Consistency of SST was recently verified for driven lattice gases under global weak exchange. Here I verify consistency of SST under local (pointwise) exchange, but only in the limit of a vanishing exchange rate; for a finite exchange rate the coexisting systems have different chemical potentials.

Phase diagram of the symbiotic two-species contact process.

We study the two-species symbiotic contact process, recently proposed by de Oliveira, Santos, and Dickman [Phys. Rev. E 86, 011121 (2012)].

Inconsistencies in steady-state thermodynamics.

We address the issue of extending thermodynamics to nonequilibrium steady states. Using driven stochastic lattice gases, we ask whether consistent definitions of an effective chemical potential μ, and an effective temperature Te, are possible. μ and Te are determined via coexistence, i.

Symbiotic two-species contact process.

We study a contact process (CP) with two species that interact in a symbiotic manner. In our model, each site of a lattice may be vacant or host individuals of species A and/or B; multiple occupancy by the same species is prohibited. Symbiosis is represented by a reduced death rate μ<1 for individuals at sites with both species present.

Models of the radiation-induced bystander effect.

Purpose: To implement quantitative models of the Radiation-Induced Bystander Effects (RIBE) based on cellular excitation at a rate proportional to the concentration of signal molecules (called signals here) released by irradiated cells. Clonogenic cell survival and transformation frequency as a function of rescue time and dose were considered.

Materials And Methods: Our first stochastic model was based on the hypothesis that chemical signals are released into the extracellular medium by irradiated cells.

Discontinuous phase transition in a dimer lattice gas.

I study a dimer model on the square lattice with nearest neighbor exclusion as the only interaction. Detailed simulations using tomographic entropic sampling show that as the chemical potential is varied, there is a strongly discontinuous phase transition, at which the particle density jumps by about 18% of its maximum value, 1/4. The transition is accompanied by the onset of orientational order, to an arrangement corresponding to the {1/2, 0, 1/2} structure identified by Phares et al.

Complete high-precision entropic sampling.

Monte Carlo simulations using entropic sampling to estimate the number of configurations of a given energy are a valuable alternative to traditional methods. We introduce tomographic entropic sampling, a scheme which uses multiple studies, starting from different regions of configuration space, to yield precise estimates of the number of configurations over the full range of energies, without dividing the latter into subsets or windows. Applied to the Ising model on the square lattice, the method yields the critical temperature to an accuracy of about 0.

Glassy dynamics and hysteresis in a linear system of orientable hard rods.

We study the dynamics of a one-dimensional fluid of orientable hard rectangles with a non-coarse-grained microscopic mechanism of facilitation. The length occupied by a rectangle depends on its orientation, which is a discrete variable coupled to an external field. The equilibrium properties of our model are essentially those of the Tonks gas, but at high densities the orientational degrees of freedom become effectively frozen due to jamming.

Contact process with sublattice symmetry breaking.

We study a contact process with creation at first- and second-neighbor sites and inhibition at first neighbors, in the form of an annihilation rate that increases with the number of occupied first neighbors. Mean-field theory predicts three phases: inactive (absorbing), active symmetric, and active asymmetric, the latter exhibiting distinct sublattice densities on a bipartite lattice. These phases are separated by continuous transitions; the phase diagram is re-entrant.