Department of Computer Science | Institute of Theoretical Computer Science | CADMO

Theory of Combinatorial Algorithms

Prof. Emo Welzl and Prof. Bernd Gärtner

Mittagsseminar (in cooperation with A. Steger, D. Steurer and B. Sudakov)

Mittagsseminar Talk Information

Date and Time: Tuesday, March 31, 2009, 12:15 pm

Duration: This information is not available in the database

Location: OAT S15/S16/S17

Speaker: Rajesh Ramaswamy (Mosaic Group)

A new class of highly efficient exact stochastic simulation algorithm for chemical reaction networks

Stochastic chemical kinetics is modeled by the chemical master equation (CME), a Markov-chain model that incorporates thermal fluctuations accurately. The trajectories of the CME are sampled using the stochastic simulation algorithm (SSA), a kinetic Monte-Carlo scheme proposed by Gillespie. The computational complexity of the current exact SSA formulations scales with the number of reactions. Using factored-out reaction propensities, coined the partial-propensity, we propose a new class of SSA formulations whose computational complexity scales with the number of species. Since, the number of reactions in a chemical reaction network grows faster than the number of species when the latter is increased, our SSA formulation is orders of magnitude faster than the current exact SSA formulations.

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