Recent experimental studies elucidating the importance of noise in gene regulation have ignited widespread interest in Gillespie's stochastic simulation technique for biochemical networks. We formulate modifications to the Gillespie algorithm which are necessary to correctly simulate chemical reactions with time-dependent reaction rates. We concentrate on time dependence of kinetic rates arisin...

We show how the Gillespie algorithm, originally developed to describe coupled chemical reactions, can be used to perform numerical simulations of a granular intruder particle colliding with thermalized bath particles. The algorithm generates a sequence of collision " events " separated by variable time intervals. As input, it requires the position-dependent flux of bath particles at each point ...

Several discrete, as well as continuous, stochastic approaches have been developed for the time-series simulation of biochemical systems. Stochastic approaches, in general, are needed because chemical reactions involve discrete, random collisions between individual chemical species. One of the well-known discrete stochastic approaches is the computationally demanding Gillespie stochastic simula...

Spatial stochastic simulation is a valuable method for studying processes of reaction and diffusion in biological systems. This technique requires significant computational efforts, but the availability of high-performance computing made it possible to develop coherent computational models of cells [1]. Several approaches were introduced in order to utilize parallel execution to speed up simula...

In this study we present simulation system based on Gillespie algorithm for generating evolutionary events in the evolution scenario of microbial population. We adjusted to reproducing experimental data obtained barcoding studies – techniques microbiology allowing tracing populations with very high resolution. engine is constructed by defining its state vector and rules modifications. order eff...

The Gillespie Algorithm is used to simulate a prion model so that the kinetics of the prions may be observed. The model is purely autocatalytic, that is, there is no fusion or fission of the infectious units. There is only conversion of PrP C into prions through a mechanism comprised of attaching PrP C to a PrP Sc p-mer, domain swapping, and splitting. It is well known that any model of an infe...

In this study we have predominantly used a set of ordinary differential equations (ode) to describe the behavior of transposons and host control. However, it is well known that for small numbers of molecules intrinsic noise may play an important role in the dynamics. In order to verify our results with respect to small numbers of transposons, vlp levels and other molecules we also design and st...