(Q30525666)

13 August 2017

STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies (English)

1 reference

13 August 2017

4

Erik De Schutter

1 reference

13 August 2017

Iain Hepburn

1

1 reference

PMCID

3472240

13 August 2017

Weiliang Chen

series ordinal

2

1 reference

PMCID

3472240

13 August 2017

Stefan Wils

series ordinal

3

1 reference

13 August 2017

10 May 2012

1 reference

13 August 2017

1 reference

13 August 2017

6

1 reference

13 August 2017

36

1 reference

https://scigraph.springernature.com/pub.10.1186/1752-0509-6-36

13 August 2017

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Detailed simulations of cell biology with Smoldyn 2.1

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Run-time interoperability between neuronal network simulators based on the MUSIC framework

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

The effect of noise on CaMKII activation in a dendritic spine during LTP induction

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

A diffusional bimolecular propensity function

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Effect of excluded volume on 2D discrete stochastic chemical kinetics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

GridCell: a stochastic particle-based biological system simulator

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Spine expansion and stabilization associated with long-term potentiation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Particle simulation approach for subcellular dynamics and interactions of biological molecules

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

DARPP-32 is a robust integrator of dopamine and glutamate signals

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Anomalous diffusion in Purkinje cell dendrites caused by spines

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Stochastic simulation of chemical kinetics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Microdomains of intracellular Ca2+: molecular determinants and functional consequences.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Stochastic reaction-diffusion simulation with MesoRD.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Correct diffusion coefficients of proteins in fluorescence correlation spectroscopy. Application to tubulin oligomers induced by Mg2+ and Paclitaxel

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Structural basis of long-term potentiation in single dendritic spines

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Local calcium signaling in neurons.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

The versatility and universality of calcium signalling

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Macromolecular crowding: an important but neglected aspect of the intracellular environment

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Translational diffusion of globular proteins in the cytoplasm of cultured muscle cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

From calcium blips to calcium puffs: theoretical analysis of the requirements for interchannel communication

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Single-channel kinetics, inactivation, and spatial distribution of inositol trisphosphate (IP3) receptors in Xenopus oocyte nucleus.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Fluorescence photobleaching with spatial Fourier analysis: measurement of diffusion in light-scattering media

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Rallpacks: a set of benchmarks for neuronal simulators

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

The life cycle of Ca(2+) ions in dendritic spines.

14 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-36

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-36

A mathematical model of spontaneous calcium(II) oscillations in astrocytes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-36

Effect of reactant size on discrete stochastic chemical kinetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-36

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-36

Efficient formulation of the stochastic simulation algorithm for chemically reacting systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-36

Reconstruct: a free editor for serial section microscopy

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472240

Exponential temporal asymptotics of the A+B-->0 reaction-diffusion process with initially separated reactants

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22574658

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dendritic spines of rat cerebellar Purkinje cells: serial electron microscopy with reference to their biophysical characteristics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22574658

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Macromolecular crowding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22574658

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1752-0509-6-36

1 reference

journals/bmcsb/HepburnCWS12

13 August 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

13 August 2017

1 reference

PMCID

3472240