title: Fast adaptive uniformisation of the chemical master equation.
abstract: Within systems biology there is an increasing interest in the stochastic behaviour of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). The uniformisation technique is an efficient method to compute probability distributions of a CTMC if the number of states is manageable. However, the size of a CTMC that represents a biochemical reaction network is usually far beyond what is feasible. In this study, the authors present an on-the-fly variant of uniformisation, where they improve the original algorithm at the cost of a small approximation error. By means of several examples, the authors show that their approach is particularly well-suited for biochemical reaction networks.
authors.affiliation: EPFL, School of Computer and Communication Sciences, Lausanne, Switzerland.
authors.forename: M
authors.initials: M
authors.lastname: Mateescu
authors.forename: V
authors.initials: V
authors.lastname: Wolf
authors.forename: F
authors.initials: F
authors.lastname: Didier
authors.forename: T A
authors.initials: TA
authors.lastname: Henzinger
mesh_terms: D000465:Algorithms; D001669:Biochemical Phenomena; D003460:Crystallization; D008390:Markov Chains; D009010:Monte Carlo Method; D009696:Nucleic Acids; D049490:Systems Biology
chemical_list: D009696:Nucleic Acids