Parallelization of Stochastic Simulation of Biochemical Reaction Systems on Multi-Core Processors

The Gillespie’s Stochastic Simulation Algorithm (SSA) is a compact, computer-oriented Monte Carlo simulation procedure that is useful for modeling simulation of well-stirred biochemical systems. This thesis describes different sequential methods of SSA such as Direct Method, Next Reaction Method, Rejection based SSA and different methodologies of parallelization of these methods on CPUs. The thesis investigates different parallelization strategies and discusses experimental results on two states of the art multicore architectures