The IP3R calcium release channel has been simulated using a stochastic simulation algorithm (SSA;Gillespie algorithm) and De young-Keiser model. A set of different concentration for Cat' and IP3 havebeen used. Considering the Number of molecules in each state, a non linear behavior of the system can beseen clearly. The inhibiting role of the Ca+2 on the open state (X110) has been studied. The d...

the ip3r calcium release channel has been simulated using a stochastic simulation algorithm (ssa;gillespie algorithm) and de young-keiser model. a set of different concentration for cat' and ip3 havebeen used. considering the number of molecules in each state, a non linear behavior of the system can beseen clearly. the inhibiting role of the ca+2 on the open state (x110) has been studied. the d...

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can ...

A discrete-time conversion is applied to the continuous-time Markov process that describes the dynamics of biochemically reacting systems within the discrete-state stochastic modeling approach (chemical master equation approach). This yields a stochastically identical discrete-time Markov chain and an according formulation of the chemical master equation. Simulating the resulting chain is equiv...

We propose a faster algorithm for individual based simulations for adaptive dynamics based on a simple modification to the standard Gillespie Algorithm for simulating stochastic birth death processes. We provide an analytical explanation that shows that simulations based on the modified algorithm, in the deterministic limit, lead to the same equations of adaptive dynamics as well as same condit...

Problem statement: The evolution rules of membrane computing have been applied in a nondeterministic and maximally parallel way. In order to capture these characteristics, Gillespie’s algorithm has been used as simulation strategy of membrane computing in simulating biological systems. Approach: This study was carried to discuss the simulation strategy of membrane computing with Gillespie algor...

We present a simple and general framework to simulate statistically correct realizations of a system of non-Markovian discrete stochastic processes. We give the exact analytical solution and a practical and efficient algorithm like the Gillespie algorithm for Markovian processes, with the difference being that now the occurrence rates of the events depend on the time elapsed since the event las...