Literature DB >> 17951742

Modeling 2D and 3D diffusion.

Michael J Saxton1.   

Abstract

Modeling obstructed diffusion is essential to the understanding of diffusion-mediated processes in the crowded cellular environment. Simple Monte Carlo techniques for modeling obstructed random walks are explained and related to Brownian dynamics and more complicated Monte Carlo methods. Random number generation is reviewed in the context of random walk simulations. Programming techniques and event-driven algorithms are discussed as ways to speed simulations.

Mesh:

Year:  2007        PMID: 17951742     DOI: 10.1007/978-1-59745-519-0_20

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  19 in total

Review 1.  Use of virtual cell in studies of cellular dynamics.

Authors:  Boris M Slepchenko; Leslie M Loew
Journal:  Int Rev Cell Mol Biol       Date:  2010       Impact factor: 6.813

Review 2.  Systems biology in immunology: a computational modeling perspective.

Authors:  Ronald N Germain; Martin Meier-Schellersheim; Aleksandra Nita-Lazar; Iain D C Fraser
Journal:  Annu Rev Immunol       Date:  2011       Impact factor: 28.527

3.  A biological interpretation of transient anomalous subdiffusion. II. Reaction kinetics.

Authors:  Michael J Saxton
Journal:  Biophys J       Date:  2007-09-28       Impact factor: 4.033

4.  Evidence for a DNA-relay mechanism in ParABS-mediated chromosome segregation.

Authors:  Hoong Chuin Lim; Ivan Vladimirovich Surovtsev; Bruno Gabriel Beltran; Fang Huang; Jörg Bewersdorf; Christine Jacobs-Wagner
Journal:  Elife       Date:  2014-05-23       Impact factor: 8.140

5.  Residence times of receptors in dendritic spines analyzed by stochastic simulations in empirical domains.

Authors:  Nathanael Hoze; David Holcman
Journal:  Biophys J       Date:  2014-12-16       Impact factor: 4.033

6.  Real-time dynamics of carbon nanotube porins in supported lipid membranes visualized by high-speed atomic force microscopy.

Authors:  Yuliang Zhang; Ramya H Tunuguntla; Pyung-On Choi; Aleksandr Noy
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-08-05       Impact factor: 6.237

7.  Diffusion of DNA-Binding Species in the Nucleus: A Transient Anomalous Subdiffusion Model.

Authors:  Michael J Saxton
Journal:  Biophys J       Date:  2020-04-04       Impact factor: 4.033

8.  Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores.

Authors:  Kyu Il Lee; Sunhwan Jo; Huan Rui; Bernhard Egwolf; Benoît Roux; Richard W Pastor; Wonpil Im
Journal:  J Comput Chem       Date:  2011-11-21       Impact factor: 3.376

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

Authors:  Damien Hall; Masaru Hoshino
Journal:  Biophys Rev       Date:  2010-02-06

10.  Simplified equation to extract diffusion coefficients from confocal FRAP data.

Authors:  Minchul Kang; Charles A Day; Anne K Kenworthy; Emmanuele DiBenedetto
Journal:  Traffic       Date:  2012-10-10       Impact factor: 6.215

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