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- Daniel T. Gillespie
- Annual review of physical chemistry
- 2007

Stochastic chemical kinetics describes the time evolution of a well-stirred chemically reacting system in a way that takes into account the fact that molecules come in whole numbers and exhibit someâ€¦ (More)

- Yang Cao, Daniel T. Gillespie, Linda R. Petzold
- The Journal of chemical physics
- 2006

The tau-leaping method of simulating the stochastic time evolution of a well-stirred chemically reacting system uses a Poisson approximation to take time steps that leap over many reaction events.â€¦ (More)

- Daniel T. Gillespie, Andreas Hellander, Linda R. Petzold
- The Journal of chemical physics
- 2013

We outline our perspective on stochastic chemical kinetics, paying particular attention to numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose description usingâ€¦ (More)

In this paper, we introduce a multiscale stochastic simulation algorithm (MSSA) which makes use of Gillespie s stochastic simulation algorithm (SSA) together with a new stochastic formulation of theâ€¦ (More)

- Muruhan Rathinam, Linda R. Petzold, Yang Cao, Daniel T. Gillespie
- Multiscale Modeling & Simulation
- 2005

We develop a theory of local errors for the explicit and implicit tau-leaping methods for simulating stochastic chemical systems, and we prove that these methods are first-order consistent. Ourâ€¦ (More)

- Yang Cao, Daniel T. Gillespie, Linda R. Petzold
- The Journal of chemical physics
- 2005

The explicit tau-leaping procedure attempts to speed up the stochastic simulation of a chemically reacting system by approximating the number of firings of each reaction channel during a chosen timeâ€¦ (More)

- Hong Li, Yang Cao, Linda R. Petzold, Daniel T. Gillespie
- Biotechnology progress
- 2008

Traditional deterministic approaches for simulation of chemically reacting systems fail to capture the randomness inherent in such systems at scales common in intracellular biochemical processes. Inâ€¦ (More)

- Bernie J. Daigle, Min K. Roh, Daniel T. Gillespie, Linda R. Petzold
- The Journal of chemical physics
- 2011

In biochemical systems, the occurrence of a rare event can be accompanied by catastrophic consequences. Precise characterization of these events using Monte Carlo simulation methods is oftenâ€¦ (More)

- Daniel T. Gillespie, Min K. Roh, Linda R. Petzold
- The Journal of chemical physics
- 2009

The weighted stochastic simulation algorithm (wSSA) recently introduced by Kuwahara and Mura [J. Chem. Phys. 129, 165101 (2008)] is an innovative variation on the stochastic simulation algorithmâ€¦ (More)

- Kevin R. Sanft, Daniel T. Gillespie, Licda R. Petzold
- IET systems biology
- 2011

Michaelis-Menten kinetics are commonly used to represent enzyme-catalysed reactions in biochemical models. The Michaelis-Menten approximation has been thoroughly studied in the context of traditionalâ€¦ (More)