Slow Scale Tau-leaping Method.

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Computer Methods in Applied Mechanics and Engineering

• Publication date

  2008-08-01

• Fields of study

  Medicine, Chemistry, Engineering, Computer Science

• Identifiers
  DOI 10.1016/J.CMA.2008.02.024PMID 19794828PMCID PMC2753989
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems

  2008cited by this paper
• Multinomial tau-leaping method for stochastic kinetic simulations.

  2007cited by this paper
• Adaptive explicit-implicit tau-leaping method with automatic tau selection.

  2007cited by this paper
• Feedback regulation of the heat shock response.

  2006cited by this paper
• Efficient step size selection for the tau-leaping simulation method.

  2006cited by this paper
• Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems

  2005cited by this paper
• Avoiding negative populations in explicit Poisson tau-leaping.

  2005cited by this paper
• Binomial distribution based tau-leap accelerated stochastic simulation.

  2005cited by this paper
• The slow-scale stochastic simulation algorithm.

  2005cited by this paper
• Accelerated stochastic simulation of the stiff enzyme-substrate reaction.

  2005cited by this paper
• Consistency and Stability of Tau-Leaping Schemes for Chemical Reaction Systems

  2005influential reference
• Numerical solution of initial value problems in differential - algebraic equations

  2005cited by this paper
• Comment on "Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method" [J. Chem. Phys. 119, 12784 (2003)].

  2004cited by this paper
• Efficient formulation of the stochastic simulation algorithm for chemically reacting systems.

  2004cited by this paper
• Binomial leap methods for simulating stochastic chemical kinetics.

  2004cited by this paper
• Hybrid simulation of cellular behavior

  2004cited by this paper
• Improved leap-size selection for accelerated stochastic simulation

  2003cited by this paper
• Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm

  2003cited by this paper
• Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method

  2003cited by this paper
• Genetic networks. Small numbers of big molecules.

  2002cited by this paper
• Small Numbers of Big Molecules

  2002cited by this paper
• Robustness analysis of the heat shock response in E. coli

  2002cited by this paper
• Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics

  2002cited by this paper
• Approximate accelerated stochastic simulation of chemically reacting systems

  2001cited by this paper
• Feedback regulation of the heat shock response in E. coli

  2001cited by this paper
• Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels

  2000cited by this paper
• Decay of metastable states: Mean relaxation time formulation

  1999cited by this paper
• It's a noisy business! Genetic regulation at the nanomolar scale.

  1999cited by this paper
• Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells.

  1998influential reference
• Stochastic mechanisms in gene expression.

  1997influential reference
• The partial-equilibrium approximation in reacting flows

  1992cited by this paper
• Markov Processes: An Introduction for Physical Scientists

  1991cited by this paper
• The Quasi-Steady-State Assumption: A Case Study in Perturbation

  1989cited by this paper
• Partial chemical equilibrium in fluid dynamics

  1980cited by this paper
• Exact Stochastic Simulation of Coupled Chemical Reactions

  1977cited by this paper
• A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions

  1976cited by this paper

• Flux-Preserving Adaptive Finite State Projection for Multiscale Stochastic Reaction Networks

  2025cites this paper
• Fast Solvers for Discrete Diffusion Models: Theory and Applications of High-Order Algorithms

  2025cites this paper
• Modelling and simulation of lac-operon gene expression using heterogeneous parallel platforms

  2023cites this paper
• Stochastic simulation of hydrogen-oxygen auto-ignition at the microscale.

  2023cites this paper
• A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV

  2020cites this paper
• Stochastic Simulation of Cellular Metabolism

  2020cites this paper
• Modelling the Impact of Drug Resistance on Treatment as Prevention as an HIV Control Strategy

  2019cites this paper
• Dynamic Modeling and Stochastic Simulation of Metabolic Networks

  2018cites this paper
• BioSimulator.jl: Stochastic simulation in Julia

  2018cites this paper
• Stochastic Population Models

  2018cites this paper
• Stochastic Simulation of Pattern Formation in Growing Tissue: A Multilevel Approach

  2018cites this paper
• Slow-scale split-step tau-leap method for stiff stochastic chemical systems

  2017cites this paper
• The best models of metabolism

  2017cites this paper
• Simulation Algorithms for Computational Systems Biology

  2017cites this paper
• Process algebra for located Markovian agents and scalable analysis techniques for the modelling of Collective Adaptive Systems

  2017cites this paper
• The Art of Modeling and Simulation of Multiscale Biochemical Systems

  2015influential citation
• A fast exact simulation algorithm for a class of Markov jump processes

  2015cites this paper
• Structured Projection-Based Model Reduction With Application to Stochastic Biochemical Networks

  2015cites this paper
• A fast exact simulation method for a class of Markov jump processes.

  2015cites this paper
• Self-adaptive simulation time for sensitivity analysis of a stochastic computational model

  2014cites this paper
• On Approximating the Stochastic Behaviour of Markovian Process Algebra Models

  2014cites this paper
• Multi-level modeling and simulation of cell biological systems with ML-Rules - A tutorial

  2014cites this paper
• Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology

  2014influential citation
• Time dependent solution for acceleration of tau-leaping

  2013cites this paper
• Infobiotics : computer-aided synthetic systems biology

  2013cites this paper
• a modular framework for stochastic simulation of reaction-transport processes in

  2012cites this paper
• URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

  2012cites this paper
• Automatic identification of model reductions for discrete stochastic simulation.

  2012cites this paper
• Stochastic simulation of chemically reacting systems using multi-core processors.

  2012cites this paper
• Current challenges in the design and control of multiscale systems

  2011cites this paper
• Current Progress in Static and Dynamic Modeling of Biological Networks

  2010cites this paper
• SSALeaping: efficient leap condition based direct method variant for the stochastic simulation of chemical reacting system

  2010cites this paper
• On Improving Stochastic Simulation for Systems Biology

  2010influential citation
• Stiffness detection and reduction in discrete stochastic simulation of biochemical systems

  2010influential citation
• Exposition and Streamlined Formulation of Adaptive Explicit-Implicit Tau-Leaping ∗

  2009cites this paper
• Streamlined formulation of adaptive explicit-implicit tau-leaping with automatic tau selection

  2009cites this paper
• From Genomic to Functional models

  2009cites this paper
• Exposition and Streamlined Formulation of Adaptive Explicit-Implicit Tau-Leaping

  2009cites this paper
• Numerical simulation of well stirred biochemical reaction networks governed by the master equation

  2008cites this paper
• Hybrid Reactions Modeling for Top-down Design Framework

  2008cites this paper
• Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems

  2008cites this paper
• Numerical simulation of well stirred biochemical reaction networks governed by the master equation

  2008cites this paper
• Numerical Solution Methods in Stochastic Chemical Kinetics

  2008cites this paper
• TR-QC4-2014 Multi-Scale Reductions of Mean-Field and Stochastic Models Tutorial and a survey of the literature

  year unknowncites this paper