Perspective: Stochastic algorithms for chemical kinetics (Q36852120)

16 August 2017

Perspective: Stochastic algorithms for chemical kinetics (English)

1 reference

16 August 2017

0 references

2

Andreas Hellander

1 reference

16 August 2017

3

Linda R Petzold

1 reference

16 August 2017

Daniel T Gillespie

1

1 reference

PMCID

3656953

16 August 2017

language of work or name

English

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publication date

1 May 2013

1 reference

Journal of Chemical Physics

16 August 2017

1 reference

16 August 2017

138

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16 August 2017

170901

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16 August 2017

17

1 reference

Spatial stochastic modelling of the Hes1 gene regulatory network: intrinsic noise can explain heterogeneity in embryonic stem cell differentiation

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Reaction-diffusion master equation in the microscopic limit

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

StochKit2: software for discrete stochastic simulation of biochemical systems with events

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

The influence of volume exclusion by chromatin on the time required to find specific DNA binding sites by diffusion

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Automated estimation of rare event probabilities in biochemical systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Stochastic reaction-diffusion kinetics in the microscopic limit

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Spatio-temporal correlations can drastically change the response of a MAPK pathway

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

A diffusional bimolecular propensity function

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Refining the weighted stochastic simulation algorithm

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Effect of excluded volume on 2D discrete stochastic chemical kinetics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Deterministic limit of stochastic chemical kinetics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Stochastic simulation of chemical kinetics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Noise-induced Min phenotypes in E. coli

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Efficient step size selection for the tau-leaping simulation method

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Stochastic model for Soj relocation dynamics in Bacillus subtilis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Stochastic gene expression in a single cell

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Stochastic mechanisms in gene expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

A new method for choosing the computational cell in stochastic reaction-diffusion systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

The two-regime method for optimizing stochastic reaction-diffusion simulations

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Reaction-diffusion master equation, diffusion-limited reactions, and singular potentials

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Linear noise approximation is valid over limited times for any chemical system that is sufficiently large.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Efficient formulations for exact stochastic simulation of chemical systems

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Accurate implementation of leaping in space: the spatial partitioned-leaping algorithm.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

An efficient and exact stochastic simulation method to analyze rare events in biochemical systems.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Incorporating postleap checks in tau-leaping.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

A modified next reaction method for simulating chemical systems with time dependent propensities and delays.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Comment on "nested stochastic simulation algorithm for chemical kinetic systems with disparate rates" [J. Chem. Phys. 123, 194107 (2005)].

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Effect of reactant size on discrete stochastic chemical kinetics

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

R-leaping: accelerating the stochastic simulation algorithm by reaction leaps.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Accelerated stochastic simulation of the stiff enzyme-substrate reaction

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

The slow-scale stochastic simulation algorithm.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Efficient formulation of the stochastic simulation algorithm for chemically reacting systems

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3656953

Ueber das Gesetz, nach welchem die Einwirkung der Säuren auf den Rohrzucker stattfindet

4 September 2018

1 reference

A general method for numerically simulating the stochastic time evolution of coupled chemical reactions

21 January 2018

1 reference

Exact stochastic simulation of coupled chemical reactions

21 January 2018

1 reference

A rigorous derivation of the chemical master equation

21 January 2018

1 reference

Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels

21 January 2018

1 reference

Approximate accelerated stochastic simulation of chemically reacting systems

21 January 2018

1 reference

The multivariate Langevin and Fokker–Planck equations

21 January 2018

1 reference

The chemical Langevin equation

21 January 2018

1 reference

Legitimacy of the stochastic Michaelis-Menten approximation

21 January 2018

1 reference

Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations

21 January 2018

1 reference

The future is noisy: the role of spatial fluctuations in genetic switching

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23656106

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23656106

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.4801941

1 reference

16 August 2017

1 reference

16 August 2017

1 reference

PMCID

3656953