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Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics
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10.1063/1.2771548
/content/aip/journal/jcp/127/10/10.1063/1.2771548
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/10/10.1063/1.2771548

Figures

Image of FIG. 1.
FIG. 1.

Trade-off between simulation time and resolution.

Image of FIG. 2.
FIG. 2.

Illustration of events within a time step in -SSSA as compared with NSM ( stands for reaction event and for diffusion event).

Image of FIG. 3.
FIG. 3.

Relative difference in time to reach a chemical steady state: Different numbers of subvolumes, with and without time scaling.

Image of FIG. 4.
FIG. 4.

Solutions of the bistable system. (a) Deterministic solutions for molecular species and . (b) Sample single run using the NSM in 64 subvolumes, portraying the case where . (c) Sample single run using the NSM in 64 subvolumes, portraying the case where .

Image of FIG. 5.
FIG. 5.

Average over ten independent runs in which after , for both NSM and -SSSA in 64 subvolumes (with ).

Tables

Generic image for table
Table I.

Description of the matrices and vectors used in the NSM method and .

Generic image for table
Table II.

Reaction propensities (diffusion propensities are calculated the same way as unary reaction propensities).

Generic image for table
Table III.

Comparison of CPU times in NSM and -SSSA, first reaction set, uniform distribution of molecules as initial condition.

Generic image for table
Table IV.

Comparison of CPU times in NSM and -SSSA, second reaction set, clusters of molecules (“hotspots”) as initial condition.

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/content/aip/journal/jcp/127/10/10.1063/1.2771548
2007-09-10
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/10/10.1063/1.2771548
10.1063/1.2771548
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