Stochastic simulation of signal transduction: impact of the cellular architecture on diffusion (Q42536834)

1 November 2017

Stochastic simulation of signal transduction: impact of the cellular architecture on diffusion (English)

1 reference

1 November 2017

Michael T Klann

1 reference

1 November 2017

Alexei Lapin

series ordinal

1 reference

1 November 2017

Matthias Reuss

series ordinal

1 reference

1 November 2017

language of work or name

English

0 references

publication date

1 June 2009

1 reference

1 November 2017

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

1 November 2017

1 reference

1 November 2017

1 reference

1 November 2017

5122-5129

1 reference

Introducing spatial information into predictive NF-kappaB modelling--an agent-based approach

1 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

A biological interpretation of transient anomalous subdiffusion. I. Qualitative model

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Accommodating space, time and randomness in network simulation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

A comprehensive pathway map of epidermal growth factor receptor signaling

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Anomalous diffusion of proteins due to molecular crowding.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Stochastic approaches for modelling in vivo reactions.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Size effects on diffusion processes within agarose gels

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Of JAKs, STATs, blind watchmakers, jeeps and trains

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Anomalous protein diffusion in living cells as seen by fluorescence correlation spectroscopy

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Trafficking of signaling modules by kinesin motors

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Solute and macromolecule diffusion in cellular aqueous compartments

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Reduced protein diffusion rate by cytoskeleton in vegetative and polarized dictyostelium cells

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Diffusion of macromolecules in agarose gels: comparison of linear and globular configurations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Monte Carlo analysis of obstructed diffusion in three dimensions: application to molecular diffusion in organelles

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Translational Diffusion of Macromolecule-sized Solutes in Cytoplasm and Nucleus

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Determinants of the translational mobility of a small solute in cell cytoplasm

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

The translational mobility of substances within the cytoplasmic matrix

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

The cytoplasmic matrix: its volume and surface area and the diffusion of molecules through it.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

The submicroscopic properties of cytoplasm as a determinant of cellular function

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Tracer diffusion of globular proteins in concentrated protein solutions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Effect of cytoskeletal geometry on intracellular diffusion

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Tracer diffusion in F-actin and Ficoll mixtures. Toward a model for cytoplasm

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Toward realistic modeling of dynamic processes in cell signaling: quantification of macromolecular crowding effects

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Mass fluctuation kinetics: capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Actin cytoskeleton as the principal determinant of size-dependent DNA mobility in cytoplasm: a new barrier for non-viral gene delivery

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Role of the cytoskeleton in signaling networks

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Trafficking and signaling through the cytoskeleton: a specific mechanism.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Macromolecular diffusion in crowded solutions

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Macromolecular Architecture in Eukaryotic Cells Visualized by Cryoelectron Tomography

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712048

Diffusion of hard sphere fluids in disordered media: a molecular dynamics simulation study

1 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19527672

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2009.03.049

1 reference

1 November 2017

1 reference

1 November 2017

PubMed publication ID

19527672

1 reference