Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation (Q30544055)

18 August 2017

Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation (English)

1 reference

18 August 2017

Zaida Luthey-Schulten

series ordinal

3

object named as

Zaida Luthey-Schulten

1 reference

18 August 2017

Elijah Roberts

1

1 reference

PMCID

3762454

18 August 2017

John E Stone

series ordinal

2

1 reference

18 August 2017

25 September 2012

1 reference

Journal of Computational Chemistry

18 August 2017

1 reference

18 August 2017

34

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18 August 2017

3

1 reference

18 August 2017

245-255

1 reference

Accelerating the Gillespie τ-Leaping Method using graphics processing units

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Using gene expression noise to understand gene regulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Central dogma at the single-molecule level in living cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Decision making in living cells: lessons from a simple system

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Noise contributions in an inducible genetic switch: a whole-cell simulation study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Stochastic reaction-diffusion kinetics in the microscopic limit

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Functional roles for noise in genetic circuits

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Visual proteomics of the human pathogen Leptospira interrogans

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Efficient stochastic simulation of reaction-diffusion processes via direct compilation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Virtual Cell modelling and simulation software environment.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Stochastic simulation of chemical kinetics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

COPASI--a COmplex PAthway SImulator

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Efficient step size selection for the tau-leaping simulation method

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Stochastic reaction-diffusion simulation with MesoRD.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

VMD: visual molecular dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762454

Stochastic mechanisms in gene expression

28 July 2018

1 reference

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

21 January 2018

1 reference

Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli.

21 January 2018

1 reference

Computational methods for diffusion-influenced biochemical reactions.

21 January 2018

1 reference

Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition.

21 January 2018

1 reference

Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon.

21 January 2018

1 reference

Universal architecture of bacterial chemoreceptor arrays

21 January 2018

1 reference

Proteome organization in a genome-reduced bacterium

21 January 2018

1 reference

Anomalous diffusion of proteins due to molecular crowding.

21 January 2018

1 reference

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

21 January 2018

1 reference

Exact stochastic simulation of coupled chemical reactions

21 January 2018

1 reference

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

21 January 2018

1 reference

Binomial leap methods for simulating stochastic chemical kinetics.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Cellular Automata Modeling of Physical Systems

21 January 2018

1 reference

Accelerating reaction-diffusion simulations with general-purpose graphics processing units.

21 January 2018

1 reference

Diffusion of transcription factors can drastically enhance the noise in gene expression

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/JCC.23130

1 reference

18 August 2017

journals/jcc/RobertsSL13

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

18 August 2017

1 reference

PMCID

3762454