In this article we consider a new derivation mode for generalized communicating P systems (GCPS) corresponding to the functioning of population protocols (PP) and based on the sequential derivation mode and a fairness condition. We show that PP can be seen as a particular variant of GCPS. We also consider a particular stochastic evolution satisfying the fairness condition and obtain that it cor...

Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algor...

CURRENT SCIENCE, VOL. 110, NO. 10, 25 MAY 2016 1916 Thomas W. Gillespie, Scott Barron and Corey Rovzar are in the Department of Geography and Monica L. Smith and Kanika Kalra are in the Cotsen Institute of Archaeology and Department of Anthropology, University of California, Los Angeles, CA 90095-1553, USA *For correspondence. (e-mail: [email protected]) Predictive modelling for archaeological s...

Many physical and biological processes are stochastic in nature. Computational models and simulations of such processes are a mathematical and computational challenge. The basic stochastic simulation algorithm was published by Gillespie about three decades ago [J. Phys. Chem. 81, 2340 (1977)]. Since then, intensive work has been done to make the algorithm more efficient in terms of running time...

Subdiffusion is an important physical phenomenon observed in many systems. However, numerical techniques to study it, especially when coupled to reactions, are lacking. In this paper, we develop an efficient Monte Carlo algorithm based on the Gillespie algorithm and the continuous-time random walk to simulate reaction-subdiffusion systems. Using this algorithm, we investigate Turing pattern for...

tIHE Council begs to present the seventy-second anntual report of the Society. Tlhe roll of the Society now stands as follows T'his 1Year Last Year Honorary Fellows 7 9 Life Fellows 13 11 Life MNem-nbers (under o0l regtulationis) 2 2 Fellowxs 274 243 Members 39 During the sessioni the Societv has lost by (leath Sir WN'illiam \Vhitla, M.A., MI.D., LL.D., Honorary Fellow, Presi(lent 1886-7, 1901-...

The stochastic simulation algorithm ~SSA! is an essentially exact procedure for numerically simulating the time evolution of a well-stirred chemically reacting system. Despite recent major improvements in the efficiency of the SSA, its drawback remains the great amount of computer time that is often required to simulate a desired amount of system time. Presented here is the ‘‘t-leap’’ method, a...

In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate constants, it is necessary to investigate how one can simulate such a biochemical system. To do this, we will take the Gillespie’s stochastic simulation algorithm f...