(Q34948910)

5 August 2017

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

1 reference

5 August 2017

Wonryull Koh

1

1 reference

PubMed ID

21513371

5 August 2017

Kim T Blackwell

series ordinal

2

1 reference

PubMed ID

21513371

5 August 2017

language of work or name

English

0 references

publication date

1 April 2011

1 reference

Journal of Chemical Physics

5 August 2017

1 reference

5 August 2017

134

1 reference

5 August 2017

15

1 reference

5 August 2017

154103

1 reference

The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations

5 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Detailed simulations of cell biology with Smoldyn 2.1

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Biphasic synaptic Ca influx arising from compartmentalized electrical signals in dendritic spines

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Subcellular dynamics of type II PKA in neurons

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Activation of CaMKII in single dendritic spines during long-term potentiation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

The spread of Ras activity triggered by activation of a single dendritic spine

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

PKA-I holoenzyme structure reveals a mechanism for cAMP-dependent activation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Protein kinase signaling in synaptic plasticity and memory

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

cAMP activation of PKA defines an ancient signaling mechanism.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Dynamics of single-cell gene expression

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Stochastic simulation of chemical kinetics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

An efficient stochastic diffusion algorithm for modeling second messengers in dendrites and spines

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

The fluorescent toolbox for assessing protein location and function

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Fluctuations in nonequilibrium systems

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Efficient step size selection for the tau-leaping simulation method

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Molecules into cells: specifying spatial architecture

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Noise in gene expression: origins, consequences, and control

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Avoiding negative populations in explicit Poisson tau-leaping

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Automatic generation of cellular reaction networks with Moleculizer 1.0.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Microtubule self-organisation by reaction-diffusion processes causes collective transport and organisation of cellular particles

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Noise in eukaryotic gene expression

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Stochastic gene expression in a single cell

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Regulation of noise in the expression of a single gene

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Dynamic spatial regulation in the bacterial cell

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

It's a noisy business! Genetic regulation at the nanomolar scale

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

A free-energy-based stochastic simulation of the Tar receptor complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

The chemical basis of morphogenesis

8 July 2018

1 reference

Pattern Formation inside Bacteria: Fluctuations due to the Low Copy Number of Proteins

21 January 2018

1 reference

Associative pairing enhances action potential back-propagation in radial oblique branches of CA1 pyramidal neurons.

21 January 2018

1 reference

From form to function: calcium compartmentalization in dendritic spines

21 January 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

Stochastic simulation of chemical reactions with spatial resolution and single molecule detail.

21 January 2018

1 reference

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.

21 January 2018

1 reference

First-passage kinetic Monte Carlo method

21 January 2018

1 reference

Reactive boundary conditions for stochastic simulations of reaction-diffusion processes.

21 January 2018

1 reference

Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations

21 January 2018

1 reference

Reaction-diffusion master equation: A comparison with microscopic simulations.

21 January 2018

1 reference

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

21 January 2018

1 reference

Efficient formulation of the stochastic simulation algorithm for chemically reacting systems

21 January 2018

1 reference

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

21 January 2018

1 reference

Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method.

21 January 2018

1 reference

Binomial leap methods for simulating stochastic chemical kinetics.

21 January 2018

1 reference

Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm.

21 January 2018

1 reference

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

21 January 2018

1 reference

The chemical Langevin equation

21 January 2018

1 reference

Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems.

21 January 2018

1 reference

On the origins of approximations for stochastic chemical kinetics

21 January 2018

1 reference

The slow-scale stochastic simulation algorithm.

21 January 2018

1 reference

Incorporating postleap checks in tau-leaping.

21 January 2018

1 reference

Multinomial tau-leaping method for stochastic kinetic simulations.

21 January 2018

1 reference

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

21 January 2018

1 reference

Hybrid simulations of stochastic reaction-diffusion processes for modeling intracellular signaling pathways.

21 January 2018

1 reference

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

21 January 2018

1 reference

Approximate accelerated stochastic simulation of chemically reacting systems

21 January 2018

1 reference

Mechanisms of calcium decay kinetics in hippocampal spines: role of spine calcium pumps and calcium diffusion through the spine neck in biochemical compartmentalization.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089647

Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm

26 October 2018

1 reference

Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.3572335

1 reference

5 August 2017

1 reference

5 August 2017

1 reference

PubMed ID

21513371