Parallelising the finite state projection method

Vikram Sunkara, Markus Hegland

Abstract


Many realistic mathematical models of biological and chemical systems, such as enzyme cascades and gene regulatory networks, need to include stochasticity. These systems are described as Markov processes and are modelled using the Chemical Master Equation. The Chemical Master Equation is a differential-difference equation (continuous in time and discrete in the state space) for the probability of a certain state at a given time. The state space is the population count of species in the system. A successful method for computing the Chemical Master Equation is the Finite State Projection Method. We give a new algorithm to distribute the Finite State Projection Method method onto multi-core systems. This method is called the Parallel Finite State Projection method. This article also analyses the theory needed for parallelisation of the Chemical Master Equation.

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Keywords


Chemical Master Equation, Finite State Projection Method, Computational Biology

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DOI: http://dx.doi.org/10.21914/anziamj.v52i0.3958



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