Biomedical subjects

R K P Zia

Publications and source records attributed to R K P Zia.

5 recordsLinked to original sources

PubMed2005

Exact dynamics of a reaction-diffusion model with spatially alternating rates.

We present the exact solution for the full dynamics of a nonequilibrium spin chain and its dual reaction-diffusion model, for arbitrary initial conditions. The spin chain is driven out of equilibrium by coupling alternating spins to two thermal baths at different temperatures. In the reaction-diffusion model, this translates into spatially alternating rates for particle creation and annihilation, and even negative "temperatures" have a perfectly natural interpretation. Observables of interest include the magnetization, the particle density, and all correlation functions for both models. Two generic types of time dependence are found: if both temperatures are positive, the magnetization, density, and correlation functions decay exponentially to their steady-state values. In contrast, if one of the temperatures is negative, damped oscillations are observed in all quantities. They can be traced to a subtle competition of pair creation and annihilation on the two sublattices. We comment on the limitations of mean-field theory and propose an experimental realization of our model in certain conjugated polymers and linear chain compounds.

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PubMed2005

Nature of the condensate in mass transport models.

We study the phenomenon of real space condensation in the steady state of a class of one-dimensional mass transport models. We derive the criterion for the occurrence of a condensation transition and analyze the precise nature of the shape and the size of the condensate in the condensed phase. We find two distinct condensate regimes: one where the condensate is Gaussian distributed and the particle number fluctuations scale normally as L(1/2) where L is the system size, and the second regime where the particle number fluctuations become anomalously large and the condensate peak is non-Gaussian. We interpret these results within the framework of sums of random variables.

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PubMed2005

Anomalous nucleation far from equilibrium.

We present precision Monte Carlo data and analytic arguments for an asymmetric exclusion process, involving two species of particles driven in opposite directions on a 2xL lattice. To resolve a stark discrepancy between earlier simulation data and an analytic conjecture, we argue that the presence of a single macroscopic cluster is an intermediate stage of a complex nucleation process: in smaller systems, this cluster is destabilized while larger systems form multiple clusters. Both limits lead to exponential cluster size distributions, controlled by very different length scales.

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PubMed2003

Punctuated equilibria and 1/f noise in a biological coevolution model with individual-based dynamics.

We present a study by linear stability analysis and large-scale Monte Carlo simulations of a simple model of biological coevolution. Selection is provided through a reproduction probability that contains quenched, random interspecies interactions, while genetic variation is provided through a low mutation rate. Both selection and mutation act on individual organisms. Consistent with some current theories of macroevolutionary dynamics, the model displays intermittent, statistically self-similar behavior with punctuated equilibria. The probability density for the lifetimes of ecological communities is well approximated by a power law with exponent near -2, and the corresponding power spectral densities show 1/f noise (flicker noise) over several decades. The long-lived communities (quasisteady states) consist of a relatively small number of mutualistically interacting species, and they are surrounded by a "protection zone" of closely related genotypes that have a very low probability of invading the resident community. The extent of the protection zone affects the stability of the community in a way analogous to the height of the free-energy barrier surrounding a metastable state in a physical system. Measures of biological diversity are on average stationary with no discernible trends, even over our very long simulation runs of approximately 3.4 x 10(7) generations.

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PubMed2003

Totally asymmetric exclusion process with extended objects: a model for protein synthesis.

The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied totally asymmetric exclusion process, in which particles typically cover a single lattice site, to include cases with extended objects. Exact solutions can be determined for a uniform closed system. We analyze the uniform open system through two approaches. First, a continuum limit produces a modified diffusion equation for particle density profiles. Second, an extremal principle based on domain wall theory accurately predicts the phase diagram and currents in each phase. Finally, we briefly consider approximate approaches to a nonuniform open system with quenched disorder in the particle hopping rates and compare these approaches with Monte Carlo simulations.

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