Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Algorithms and software for stochastic simulation of biochemical reacting systems.

Literature DB >> 17894470

Algorithms and software for stochastic simulation of biochemical reacting systems.

Hong Li¹, Yang Cao, Linda R Petzold, Daniel T Gillespie.

Abstract

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. In this manuscript, we briefly review the state of the art in discrete stochastic and multiscale algorithms for simulation of biochemical systems and we present the StochKit software toolkit.

Entities: Disease

Mesh：

Year: 2007 PMID： 17894470 PMCID： PMC2664303 DOI： 10.1021/bp070255h

Source DB: PubMed Journal: Biotechnol Prog ISSN： 1520-6033

25 in total

1. Kinetic Monte Carlo simulations with minimal searching.

Authors: T P Schulze
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2002-02-13

2. Comment on "Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method" [J. Chem. Phys. 119, 12784 (2003)].

Authors: Katrien De Cock; Xueying Zhang; Mónica F Bugallo; Petar M Djurić
Journal: J Chem Phys Date: 2004-08-15 Impact factor: 3.488

Algorithms and software for stochastic simulation of biochemical reacting systems.

1. Kinetic Monte Carlo simulations with minimal searching.

2. Comment on "Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method" [J. Chem. Phys. 119, 12784 (2003)].

3. The numerical stability of leaping methods for stochastic simulation of chemically reacting systems.

4. Sensitivity analysis of discrete stochastic systems.

5. Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates.

6. Accelerated stochastic simulation of the stiff enzyme-substrate reaction.

7. Adaptive explicit-implicit tau-leaping method with automatic tau selection.

8. The finite state projection algorithm for the solution of the chemical master equation.

9. Efficient step size selection for the tau-leaping simulation method.

10. Stochastic mechanisms in gene expression.

Review 1. Mathematical simulation of membrane protein clustering for efficient signal transduction.

2. Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression.

3. Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda.

4. Simulation of large-scale rule-based models.

5. Bistable switches control memory and plasticity in cellular differentiation.

6. Biochemical simulations: stochastic, approximate stochastic and hybrid approaches.

Review 7. Stochastic modelling for quantitative description of heterogeneous biological systems.

8. Stiffness detection and reduction in discrete stochastic simulation of biochemical systems.

9. Kinetic Monte Carlo method for rule-based modeling of biochemical networks.

10. Discrete stochastic simulation methods for chemically reacting systems.