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Results: 1 to 20 of 122

Similar articles for PubMed (Select 22697237)

1.

A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling.

Frazier Z, Alber F.

J Comput Biol. 2012 Jun;19(6):606-18. doi: 10.1089/cmb.2012.0027.

2.

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

Morelli MJ, ten Wolde PR.

J Chem Phys. 2008 Aug 7;129(5):054112. doi: 10.1063/1.2958287.

PMID:
18698893
3.

A computational kinetic model of diffusion for molecular systems.

Teo I, Schulten K.

J Chem Phys. 2013 Sep 28;139(12):121929. doi: 10.1063/1.4820876.

4.

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

Drawert B, Engblom S, Hellander A.

BMC Syst Biol. 2012 Jun 22;6:76. doi: 10.1186/1752-0509-6-76.

5.

Stochastic operator-splitting method for reaction-diffusion systems.

Choi T, Maurya MR, Tartakovsky DM, Subramaniam S.

J Chem Phys. 2012 Nov 14;137(18):184102. doi: 10.1063/1.4764108.

6.

Computational methods for diffusion-influenced biochemical reactions.

Dobrzynski M, Rodríguez JV, Kaandorp JA, Blom JG.

Bioinformatics. 2007 Aug 1;23(15):1969-77. Epub 2007 May 30.

7.
8.

Multiresolution stochastic simulations of reaction-diffusion processes.

Bayati B, Chatelain P, Koumoutsakos P.

Phys Chem Chem Phys. 2008 Oct 21;10(39):5963-6. doi: 10.1039/b810795e. Epub 2008 Sep 1.

PMID:
18825283
9.

ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.

Schöneberg J, Noé F.

PLoS One. 2013 Sep 11;8(9):e74261. doi: 10.1371/journal.pone.0074261. eCollection 2013.

10.

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

Dematté L.

IEEE/ACM Trans Comput Biol Bioinform. 2012 May-Jun;9(3):655-67. doi: 10.1109/TCBB.2011.106.

PMID:
21788675
11.

Rule-based modelling and simulation of biochemical systems with molecular finite automata.

Yang J, Meng X, Hlavacek WS.

IET Syst Biol. 2010 Nov;4(6):453-66. doi: 10.1049/iet-syb.2010.0015.

12.
13.

Reaction schemes, escape times and geminate recombinations in particle-based spatial simulations of biochemical reactions.

Klann M, Koeppl H.

Phys Biol. 2013 Aug;10(4):046005. doi: 10.1088/1478-3975/10/4/046005. Epub 2013 Jul 2.

PMID:
23820050
14.

Single-file dynamics with different diffusion constants.

Ambjörnsson T, Lizana L, Lomholt MA, Silbey RJ.

J Chem Phys. 2008 Nov 14;129(18):185106. doi: 10.1063/1.3009853.

PMID:
19045434
15.
16.

Molecular dynamics at low time resolution.

Faccioli P.

J Chem Phys. 2010 Oct 28;133(16):164106. doi: 10.1063/1.3493459.

PMID:
21033774
17.

Studying protein assembly with reversible Brownian dynamics of patchy particles.

Klein HC, Schwarz US.

J Chem Phys. 2014 May 14;140(18):184112. doi: 10.1063/1.4873708.

PMID:
24832258
18.

Brownian dynamics simulations with hard-body interactions: spherical particles.

Behringer H, Eichhorn R.

J Chem Phys. 2012 Oct 28;137(16):164108. doi: 10.1063/1.4761827.

PMID:
23126696
19.

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

Hepburn I, Chen W, Wils S, De Schutter E.

BMC Syst Biol. 2012 May 10;6:36. doi: 10.1186/1752-0509-6-36.

20.
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