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Title: Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm

We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajectory is exact by exploiting the rejection-based mechanism. We benchmark tRSSA on different biological systems with varying forms of reaction rates to demonstrate its applicability and efficiency. We reveal that for nontrivial cases, the selection of reaction firings in existing algorithms introduces approximations because the integration of reaction rates is very computationally demanding and simplifying assumptions are introduced. The selection of the next reaction firing by our approach is easier while preserving the exactness.
Authors:
 [1] ;  [1] ;  [2]
  1. The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy)
  2. (Italy)
Publication Date:
OSTI Identifier:
22493481
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 143; Journal Issue: 5; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; ALGORITHMS; BENCHMARKS; BIOCHEMICAL REACTION KINETICS; CHEMICAL REACTIONS; COMPUTERIZED SIMULATION; EFFICIENCY; STOCHASTIC PROCESSES; TIME DEPENDENCE; TRAJECTORIES