(Q33899218)

English

Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants

scientific article

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scholarly article

1 reference

Europe PubMed Central

29 July 2017

Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants (English)

1 reference

Europe PubMed Central

29 July 2017

author name string

Michael T Klann

1

1 reference

Europe PubMed Central

29 July 2017

Alexei Lapin

2

1 reference

Europe PubMed Central

29 July 2017

Matthias Reuss

3

1 reference

Europe PubMed Central

29 July 2017

publication date

14 May 2011

1 reference

Europe PubMed Central

29 July 2017

BMC Systems Biology

1 reference

Europe PubMed Central

29 July 2017

5

1 reference

Europe PubMed Central

29 July 2017

71

1 reference

Europe PubMed Central

29 July 2017

https://scigraph.springernature.com/pub.10.1186/1752-0509-5-71

0 references

Effects of macromolecular crowding on intracellular diffusion from a single particle perspective.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Assessment of in silico models for fraction of unbound drug in human liver microsomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Multi-scale spatio-temporal modeling: lifelines of microorganisms in bioreactors and tracking molecules in cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Signaling dynamics of the KSR1 scaffold complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

The 'fuzzy' interactome.

1 reference

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5 July 2018

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

1 reference

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5 July 2018

Prediction of the pharmacokinetics of atorvastatin, cerivastatin, and indomethacin using kinetic models applied to isolated rat hepatocytes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Molecular scaffolds regulate bidirectional crosstalk between Wnt and classical seven-transmembrane-domain receptor signaling pathways.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Mathematical modeling of intracellular signaling pathways

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

How can biochemical reactions within cells differ from those in test tubes?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

A systematic investigation of the rate laws valid in intracellular environments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

The p65/RelA subunit of NF-kappaB interacts with actin-containing structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Macromolecular compartmentation and channeling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Implications of macromolecular crowding for signal transduction and metabolite channeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Metabolic channeling versus free diffusion: transition-time analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Microcompartmentation, metabolic channelling and carbohydrate metabolism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Interactions between glycolytic enzymes and components of the cytomatrix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Diffusion-controlled macromolecular interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

Old pathway--new concept: control of glycolysis by metabolite-modulated dynamic enzyme associations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

The 6-phosphogluconate dehydrogenase reaction in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3123599

5 July 2018

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

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-71

21 January 2018

Analysis of reaction-diffusion systems with anomalous subdiffusion

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-71

21 January 2018

Subcellular localization determines MAP kinase signal output.

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-71

21 January 2018

Insight or illusion? Seeing inside the cell with mesoscopic simulations

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-71

21 January 2018

Formal agent-based modelling of intracellular chemical interactions.

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-71

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-71

21 January 2018

Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network.

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-71

21 January 2018

Quantification of statin effects on hepatic cholesterol synthesis by transient (13)C-flux analysis.

1 reference

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29 October 2018

Macromolecular Architecture in Eukaryotic Cells Visualized by Cryoelectron Tomography

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-71

21 January 2018

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/21569565

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/21569565

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1752-0509-5-71

1 reference

Europe PubMed Central

29 July 2017

DBLP publication ID

journals/bmcsb/KlannLR11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

1 reference

Europe PubMed Central

29 July 2017

1 reference

Europe PubMed Central

29 July 2017

ResearchGate publication ID

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