ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments (Q34989921)

5 August 2017

ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments (English)

1 reference

5 August 2017

0 references

Johannes Schöneberg

1

1 reference

PubMed ID

24040218

5 August 2017

Frank Noé

series ordinal

2

1 reference

PubMed ID

24040218

5 August 2017

language of work or name

English

0 references

publication date

11 September 2013

1 reference

5 August 2017

1 reference

5 August 2017

8

1 reference

5 August 2017

e74261

1 reference

5 August 2017

9

1 reference

Creative Commons Attribution 4.0 International

5 August 2017

start time

11 September 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate

8 July 2018

1 reference

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A physiological role for the supramolecular organization of rhodopsin and transducin in rod photoreceptors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Spatial simulations in systems biology: from molecules to cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Super-resolution imaging reveals the internal architecture of nano-sized syntaxin clusters

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Modelling complex biological systems using an agent-based approach

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Diffusion in crowded biological environments: applications of Brownian dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Diffusion of hydrophobin proteins in solution and interactions with a graphite surface

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Noise contributions in an inducible genetic switch: a whole-cell simulation study

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Ultrasensitivity in multisite phosphorylation of membrane-anchored proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Protein scaffolds in the coupling of synaptic exocytosis and endocytosis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Browndye: A Software Package for Brownian Dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Syntaxin clusters assemble reversibly at sites of secretory granules in live cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Single secretory granules of live cells recruit syntaxin-1 and synaptosomal associated protein 25 (SNAP-25) in large copy numbers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

THE VIRTUAL INSTRUMENT: SUPPORT FOR GRID-ENABLED MCELL SIMULATIONS

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

A metabolic model of human erythrocytes: practical application of the E-Cell Simulation Environment.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Detailed simulations of cell biology with Smoldyn 2.1

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Lateral diffusion of rhodopsin in photoreceptor membrane: a reappraisal.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Maturation of active zone assembly by Drosophila Bruchpilot

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

GridCell: a stochastic particle-based biological system simulator

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Filling in the gaps: artistic license in education and outreach

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Ultra-high resolution imaging by fluorescence photoactivation localization microscopy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Accommodating space, time and randomness in network simulation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Imaging intracellular fluorescent proteins at nanometer resolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Scalable molecular dynamics with NAMD

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Stochastic reaction-diffusion simulation with MesoRD.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Visual methods from atoms to cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Quantitative cell biology with the Virtual Cell

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Escaping free-energy minima

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Phospholipids undergo hop diffusion in compartmentalized cell membrane

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Atomistic simulations of competition between substrates binding to an enzyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Solute and macromolecule diffusion in cellular aqueous compartments

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Macromolecular crowding: obvious but underappreciated

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Protein mobility in the cytoplasm of Escherichia coli.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

VMD: visual molecular dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Macromolecular crowding: biochemical, biophysical, and physiological consequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Molecular anatomy of a trafficking organelle

8 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Cell++--simulating biochemical pathways.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Anatomy and dynamics of a supramolecular membrane protein cluster.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Coarse-grained Brownian dynamics simulations of protein translocation through nanopores.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

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://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

OpenMM: A Hardware Independent Framework for Molecular Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Brownian dynamics simulations on CPU and GPU with BD_BOX.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Smoldyn on graphics processing units: massively parallel Brownian dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Mesoscopic Monte Carlo simulations of stochastic encounters between photoactivated rhodopsin and transducin in disc membranes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Molecular crowding reduces to a similar extent the diffusion of small solutes and macromolecules: measurement by fluorescence correlation spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Anomalous diffusion of proteins due to molecular crowding.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

Long time-scale simulations of in vivo diffusion using GPU hardware

26 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Rhodopsin dimers in native disc membranes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074261

Cycling of Synaptic Vesicles: How Far? How Fast!

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3770580

A dynamic scaffolding mechanism for rhodopsin and transducin interaction in vertebrate vision

9 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24040218

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Rhodopsin is spatially heterogeneously distributed in rod outer segment disk membranes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24040218

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0074261

1 reference

5 August 2017

0 references

1 reference

5 August 2017

1 reference

PubMed ID

24040218