Literature DB >> 17693422

Modelling and simulation techniques for membrane biology.

Kevin Burrage1, John Hancock, André Leier, Dan V Nicolau.   

Abstract

One of the most important aspects of Computational Cell Biology is the understanding of the complicated dynamical processes that take place on plasma membranes. These processes are often so complicated that purely temporal models cannot always adequately capture the dynamics. On the other hand, spatial models can have large computational overheads. In this article, we review some of these issues with respect to chemistry, membrane microdomains and anomalous diffusion and discuss how to select appropriate modelling and simulation paradigms based on some or all the following aspects: discrete, continuous, stochastic, delayed and complex spatial processes.

Mesh:

Year:  2007        PMID: 17693422     DOI: 10.1093/bib/bbm033

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  11 in total

Review 1.  Mathematical simulation of membrane protein clustering for efficient signal transduction.

Authors:  Krishnan Radhakrishnan; Ádám Halász; Meghan M McCabe; Jeremy S Edwards; Bridget S Wilson
Journal:  Ann Biomed Eng       Date:  2012-06-06       Impact factor: 3.934

2.  Monte Carlo investigation of diffusion of receptors and ligands that bind across opposing surfaces.

Authors:  Philippos K Tsourkas; Subhadip Raychaudhuri
Journal:  Ann Biomed Eng       Date:  2010-09-02       Impact factor: 3.934

3.  Mathematical modeling of K-Ras nanocluster formation on the plasma membrane.

Authors:  Tianhai Tian; Sarah J Plowman; Robert G Parton; Yoel Kloog; John F Hancock
Journal:  Biophys J       Date:  2010-07-21       Impact factor: 4.033

4.  Biochemical simulations: stochastic, approximate stochastic and hybrid approaches.

Authors:  Jürgen Pahle
Journal:  Brief Bioinform       Date:  2009-01-16       Impact factor: 11.622

5.  Tracing the footsteps of autophagy in computational biology.

Authors:  Dipanka Tanu Sarmah; Nandadulal Bairagi; Samrat Chatterjee
Journal:  Brief Bioinform       Date:  2021-07-20       Impact factor: 11.622

6.  Modeling and simulation of biological systems from image data.

Authors:  Ivo F Sbalzarini
Journal:  Bioessays       Date:  2013-03-27       Impact factor: 4.345

7.  Membrane microdomains emergence through non-homogeneous diffusion.

Authors:  Hédi A Soula; Antoine Coulon; Guillaume Beslon
Journal:  BMC Biophys       Date:  2012-04-30       Impact factor: 4.778

8.  Mathematical modeling and validation of the ergosterol pathway in Saccharomyces cerevisiae.

Authors:  Fernando Alvarez-Vasquez; Howard Riezman; Yusuf A Hannun; Eberhard O Voit
Journal:  PLoS One       Date:  2011-12-14       Impact factor: 3.240

9.  Stochastic modelling of biochemical systems of multi-step reactions using a simplified two-variable model.

Authors:  Qianqian Wu; Kate Smith-Miles; Tianshou Zhou; Tianhai Tian
Journal:  BMC Syst Biol       Date:  2013-10-23

Review 10.  Genome-scale computational biology and bioinformatics in Australia.

Authors:  Mark A Ragan; Tim Littlejohn; Bruce Ross
Journal:  PLoS Comput Biol       Date:  2008-08-29       Impact factor: 4.475

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