(Q34315353)

1 August 2017

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

1 reference

1 August 2017

3

Andreas Hellander

1 reference

1 August 2017

Stefan Engblom

2

0 references

author name string

Brian Drawert

series ordinal

1

1 reference

1 August 2017

22 June 2012

1 reference

1 August 2017

1 reference

1 August 2017

6

1 reference

1 August 2017

76

1 reference

https://scigraph.springernature.com/pub.10.1186/1752-0509-6-76

1 August 2017

0 references

cites work

Reaction-diffusion master equation in the microscopic limit

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Michaelis-Menten speeds up tau-leaping under a wide range of conditions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Stable kinesin and dynein assemblies drive the axonal transport of mammalian prion protein vesicles

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Stochastic reaction-diffusion kinetics in the microscopic limit

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Detailed simulations of cell biology with Smoldyn 2.1

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Slow Scale Tau-leaping Method

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Basic mechanisms for recognition and transport of synaptic cargos

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Imaging individual mRNA molecules using multiple singly labeled probes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Differential regulation of dynein and kinesin motor proteins by tau

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Cargo transport: two motors are sometimes better than one.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Probing transcription factor dynamics at the single-molecule level in a living cell

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Noise-induced Min phenotypes in E. coli

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

RNA trafficking and local protein synthesis in dendrites: an overview.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Noise in gene expression: origins, consequences, and control

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Stochastic reaction-diffusion simulation with MesoRD.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Molecular motors and mechanisms of directional transport in neurons

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Molecular motors: strategies to get along

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Bidirectional transport along microtubules.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Dynamic structures inEscherichia coli: Spontaneous formation of MinE rings and MinD polar zones

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

The molecular motor toolbox for intracellular transport

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Intrinsic and extrinsic contributions to stochasticity in gene expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Stochastic gene expression in a single cell

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Intrinsic noise in gene regulatory networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Microtubule-based transport systems in neurons: the roles of kinesins and dyneins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

The movement of kinesin along microtubules

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Analysis of intracellular receptor/ligand sorting. Calculation of mean surface and bulk diffusion times within a sphere

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Diffusion-controlled reactions on spherical surfaces. Application to bacteriophage tail fiber attachment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

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

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1752-0509-6-76

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1752-0509-6-76

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

The slow-scale stochastic simulation algorithm.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439286

Circadian clocks limited by noise

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22727185

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22727185

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/22727185

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1752-0509-6-76

1 reference

journals/bmcsb/DrawertEH12

1 August 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

1 August 2017

1 reference

PubMed ID

22727185