Power Spectra of the Total Occupancy in the Totally Asymmetric Simple Exclusion Process

As a solvable and broadly applicable model system, the totally asymmetric exclusion process enjoys iconic status in the theory of non-equilibrium phase transitions. Here, we focus on the time dependence of the total number of particles on a 1-dimensional open lattice, and its power spectrum. Using both Monte Carlo simulations and analytic methods, we explore its behavior in different characteristic regimes. In the maximal current phase and on the coexistence line (between high/low density phases), the power spectrum displays algebraic decay, with exponents -1.62 and -2.00, respectively. Deep within the high/low density phases, we find pronounced \emph{oscillations}, which damp into power laws. This behavior can be understood in terms of driven biased diffusion with conserved noise in the bulk.Comment: 4 pages, 4 figure

Far-from-equilibrium transport with constrained resources

The totally asymmetric simple exclusion process (TASEP) is a well studied example of far-from-equilibrium dynamics. Here, we consider a TASEP with open boundaries but impose a global constraint on the total number of particles. In other words, the boundary reservoirs and the system must share a finite supply of particles. Using simulations and analytic arguments, we obtain the average particle density and current of the system, as a function of the boundary rates and the total number of particles. Our findings are relevant to biological transport problems if the availability of molecular motors becomes a rate-limiting factor.Comment: 14 pages, 7 figures, uses iopart12.clo and iopart.cl

Feedback and Fluctuations in a Totally Asymmetric Simple Exclusion Process with Finite Resources

We revisit a totally asymmetric simple exclusion process (TASEP) with open boundaries and a global constraint on the total number of particles [Adams, et. al. 2008 J. Stat. Mech. P06009]. In this model, the entry rate of particles into the lattice depends on the number available in the reservoir. Thus, the total occupation on the lattice feeds back into its filling process. Although a simple domain wall theory provided reasonably good predictions for Monte Carlo simulation results for certain quantities, it did not account for the fluctuations of this feedback. We generalize the previous study and find dramatically improved predictions for, e.g., the density profile on the lattice and provide a better understanding of the phenomenon of "shock localization."Comment: 11 pages, 3 figures, v2: Minor change

On the Zero-Slope Limit of the Compactified Closed Bosonic String

In the framework of the compactified closed bosonic string theory with the extra spatial coordinates being circular with radius $R$, we perform both the zero-slope limit and the $R \rightarrow 0$ limit of the tree scattering amplitude of four massless scalar particles. We explicitly show that this double limit leads to amplitudes involving scalars which interact through the exchange of a scalar, spin 1 and spin 2 particle. In particular, this latter case reproduces the same result obtained in linearized quantum gravity.Comment: 10 pages, LaTex file, DSF-T-43/9

Matrix Product Ground States for Asymmetric Exclusion Processes with Parallel Dynamics

We show in the example of a one-dimensional asymmetric exclusion process that stationary states of models with parallel dynamics may be written in a matrix product form. The corresponding algebra is quadratic and involves three different matrices. Using this formalism we prove previous conjectures for the equal-time correlation functions of the model.Comment: LaTeX, 8 pages, one postscript figur

Power Spectra of a Constrained Totally Asymmetric Simple Exclusion Process

To synthesize proteins in a cell, an mRNA has to work with a finite pool of ribosomes. When this constraint is included in the modeling by a totally asymmetric simple exclusion process (TASEP), non-trivial consequences emerge. Here, we consider its effects on the power spectrum of the total occupancy, through Monte Carlo simulations and analytical methods. New features, such as dramatic suppressions at low frequencies, are discovered. We formulate a theory based on a linearized Langevin equation with discrete space and time. The good agreement between its predictions and simulation results provides some insight into the effects of finite resoures on a TASEP.Comment: 4 pages, 2 figures v2: formatting change

Gas permeation through a polymer network

We study the diffusion of gas molecules through a two-dimensional network of polymers with the help of Monte Carlo simulations. The polymers are modeled as non-interacting random walks on the bonds of a two-dimensional square lattice, while the gas particles occupy the lattice cells. When a particle attempts to jump to a nearest-neighbor empty cell, it has to overcome an energy barrier which is determined by the number of polymer segments on the bond separating the two cells. We investigate the gas current $J$ as a function of the mean segment density $\rho$, the polymer length $\ell$ and the probability $q^{m}$ for hopping across $m$ segments. Whereas $J$ decreases monotonically with $\rho$ for fixed $\ell$, its behavior for fixed $\rho$ and increasing $\ell$ depends strongly on $q$. For small, non-zero $q$, $J$ appears to increase slowly with $\ell$. In contrast, for $q=0$, it is dominated by the underlying percolation problem and can be non-monotonic. We provide heuristic arguments to put these interesting phenomena into context.Comment: Dedicated to Lothar Schaefer on the occasion of his 60th birthday. 11 pages, 3 figure

Clinical, Radiological, and Molecular Findings of Acute Encephalitis in a COVID-19 Patient: A Rare Case Report.

We report a case of encephalitis in a young male patient with severe coronavirus disease 2019 (COVID-19) who initially presented with typical symptoms of fever, dry cough, and shortness of breath but later on developed acute respiratory distress syndrome and required mechanical ventilation. Two days post-extubation, the patient developed new-onset generalized tonic-clonic seizures and confusion. MRI of the brain was done and it showed an abnormal signal in the bilateral medial cortical frontal region. His cerebral spinal fluid (CSF) analysis revealed a characteristic picture of a viral infection with a high white blood cell count and normal glucose and protein levels. After ruling out all common causes of viral encephalitis such as herpes simplex virus (HSV) and based on the review of available literature regarding the neurological manifestations of COVID-19, this case was labeled as acute viral encephalitis secondary to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection

Zero-range process with long-range interactions at a T-junction

A generalized zero-range process with a limited number of long-range interactions is studied as an example of a transport process in which particles at a T-junction make a choice of which branch to take based on traffic levels on each branch. The system is analysed with a self-consistent mean-field approximation which allows phase diagrams to be constructed. Agreement between the analysis and simulations is found to be very good.Comment: 21 pages, 6 figure

Periodic One-Dimensional Hopping Model with one Mobile Directional Impurity

Analytic solution is given in the steady state limit for the system of Master equations describing a random walk on one-dimensional periodic lattices with arbitrary hopping rates containing one mobile, directional impurity (defect bond). Due to the defect, translational invariance is broken, even if all other rates are identical. The structure of Master equations lead naturally to the introduction of a new entity, associated with the walker-impurity pair which we call the quasi-walker. The velocities and diffusion constants for both the random walker and impurity are given, being simply related to that of the quasi-particle through physically meaningful equations. Applications in driven diffusive systems are shown, and connections with the Duke-Rubinstein reptation models for gel electrophoresis are discussed.Comment: 31 LaTex pages, 5 Postscript figures included, to appear in Journal of Statistical Physic