Name
Abstract | ||
|---|---|---|
We compare stochastic computational methods accounting for space and discrete nature of reactants in biochemical systems. Implementations based on Brownian dynamics (BD) and the reaction-diffusion master equation are applied to a simplified gene expression model and to a signal transduction pathway in Escherichia coli.In the regime where the number of molecules is small and reactions are diffusion-limited predicted fluctuations in the product number vary between the methods, while the average is the same. Computational approaches at the level of the reaction-diffusion master equation compute the same fluctuations as the reference result obtained from the particle-based method if the size of the sub-volumes is comparable to the diameter of reactants. Using numerical simulations of reversible binding of a pair of molecules we argue that the disagreement in predicted fluctuations is due to different modeling of inter-arrival times between reaction events. Simulations for a more complex biological study show that the different approaches lead to different results due to modeling issues. Finally, we present the physical assumptions behind the mesoscopic models for the reaction-diffusion systems.Input files for the simulations and the source code of GMP can be found under the following address: http://www.cwi.nl/projects/sic/bioinformatics2007/ |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1093/bioinformatics/btm278 | Bioinformatics |
Keywords | Field | DocType |
different approach,different modeling,computational approach,bioinformatics online,diffusion-influenced biochemical reaction,stochastic computational methods accounting,reaction-diffusion system,nl supplementary information,reaction-diffusion master equation,product number,different result,gene expression,escherichia coli,reaction diffusion,brownian dynamics,master equation,signal transduction pathway,source code,numerical simulation | Source code,Mesoscopic physics,Brownian dynamics,Biochemical reactions,Bioinformatics,Master equation,Mathematics,Particle | Journal |
Volume | Issue | ISSN |
23 | 15 | 1367-4811 |
Citations | PageRank | References |
17 | 1.62 | 4 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Maciej Dobrzyński | 1 | 50 | 5.89 |
| Jordi Vidal Rodríguez | 2 | 17 | 1.62 |
| Jaap A. Kaandorp | 3 | 110 | 19.07 |
| Joke G Blom | 4 | 161 | 23.43 |