(Q31011555)

6 November 2017

1 reference

title

Diffusion in crowded biological environments: applications of Brownian dynamics (English)

1 reference

6 November 2017

2

Joanna Trylska

1 reference

6 November 2017

Maciej Długosz

1

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publication date

2 March 2011

1 reference

6 November 2017

1 reference

6 November 2017

4

1 reference

6 November 2017

3

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Creative Commons Attribution 2.0 Generic

6 November 2017

start time

2 March 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

exact match

https://scigraph.springernature.com/pub.10.1186/2046-1682-4-3

0 references

cites work

Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association

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Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

28 July 2018

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Volume exclusion and soft interaction effects on protein stability under crowded conditions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Crowding effects on association reactions at membranes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Diffusion of alpha-chymotrypsin in solution-crowded media. A fluorescence recovery after photobleaching study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Protein (19)F NMR in Escherichia coli

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Effect of macromolecular crowding on reaction rates: a computational and theoretical study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Single-molecule approach to molecular biology in living bacterial cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Crowding effects on diffusion in solutions and cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Crowding and confinement effects on protein diffusion in vivo

28 July 2018

1 reference

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Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

28 July 2018

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

28 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Brownian dynamics simulation of rigid particles of arbitrary shape in external fields

28 July 2018

1 reference

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

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

28 July 2018

1 reference

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Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Brownian dynamics simulation of the lateral distribution of charged membrane components.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Brownian dynamics simulations of probe and self-diffusion in concentrated protein and DNA solutions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Energetics of charge-charge interactions in proteins.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

A bioreactor for in-cell protein NMR.

28 July 2018

1 reference

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Single particle tracking of complex diffusion in membranes: simulation and detection of barrier, raft, and interaction phenomena

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

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

21 January 2018

1 reference

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Probing the interior of living cells with fluorescence correlation spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

Long-time dynamics of concentrated charge-stabilized colloids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

Short-time transport properties in dense suspensions: from neutral to charge-stabilized colloidal spheres

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

Brownian dynamics simulation of protein-protein diffusional encounter

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

Calculation of NMR relaxation, covolume, and scattering-related properties of bead models using the SOLPRO computer program.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

Influence of macromolecular crowding on protein-protein association rates--a Brownian dynamics study

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

On the Contributions of Diffusion and Thermal Activation to Electron Transfer betweenPhormidium laminosumPlastocyanin and Cytochromef: Brownian Dynamics Simulations with Explicit Modeling of Nonpolar Desolvation Interactions and Electron Transfer Eve

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-4-3

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

A simple patchy colloid model for the phase behavior of lysozyme dispersions.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Brownian dynamics simulation of probe diffusion in DNA: effects of probe size, charge and DNA concentration

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Diffusion in cells measured by fluorescence recovery after photobleaching

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Protein mobility in the cytoplasm of Escherichia coli.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093676

Average hydrodynamic correction for the Brownian dynamics calculation of flocculation rates in concentrated dispersions

25 November 2018

1 reference

12 December 2020

Generic behavior of the hydrodynamic function of charged colloidal suspensions

1 reference

12 December 2020

Dynamics of hard-sphere suspensions

1 reference

12 December 2020

An Expression for the Dispersion Force between Colloidal Particles

1 reference

12 December 2020

Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems

1 reference

12 December 2020

Description of nonspecific DNA-protein interaction and facilitated diffusion with a dynamical model

1 reference

12 December 2020

Role of anisotropy for protein-protein encounter

1 reference

12 December 2020

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins

1 reference

12 December 2020

Identifiers

DOI

10.1186/2046-1682-4-3

1 reference

PMCID

3093676

Dimensions Publication ID

6 November 2017

0 references

0 references

1 reference

6 November 2017

1 reference

PMCID

3093676