Literature DB >> 16187129

Implicit solvent simulation models for biomembranes.

Grace Brannigan1, Lawrence C-L Lin, Frank L H Brown.   

Abstract

Fully atomic simulation strategies are infeasible for the study of many processes of interest to membrane biology, biophysics and biochemistry. We review various coarse-grained simulation methodologies with special emphasis on methods and models that do not require the explicit simulation of water. Examples from our own research demonstrate that such models have potential for simulating a variety of biologically relevant phenomena at the membrane surface.

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Year:  2005        PMID: 16187129     DOI: 10.1007/s00249-005-0013-y

Source DB:  PubMed          Journal:  Eur Biophys J        ISSN: 0175-7571            Impact factor:   1.733


  118 in total

1.  Echinocyte shapes: bending, stretching, and shear determine spicule shape and spacing.

Authors:  Ranjan Mukhopadhyay; Gerald Lim H W; Michael Wortis
Journal:  Biophys J       Date:  2002-04       Impact factor: 4.033

2.  Dynamics of pinned membranes with application to protein diffusion on the surface of red blood cells.

Authors:  Lawrence C-L Lin; Frank L H Brown
Journal:  Biophys J       Date:  2004-02       Impact factor: 4.033

3.  Cytoskeleton confinement and tension of red blood cell membranes.

Authors:  N Gov; A G Zilman; S Safran
Journal:  Phys Rev Lett       Date:  2003-06-04       Impact factor: 9.161

4.  Bridging microscopic and mesoscopic simulations of lipid bilayers.

Authors:  Gary Ayton; Gregory A Voth
Journal:  Biophys J       Date:  2002-12       Impact factor: 4.033

5.  Pinning of fluid membranes by periodic harmonic potentials.

Authors:  N Gov; S A Safran
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2004-01-13

6.  The membrane skeleton of erythrocytes. A percolation model.

Authors:  M J Saxton
Journal:  Biophys J       Date:  1990-06       Impact factor: 4.033

Review 7.  Cell surface organization by the membrane skeleton.

Authors:  A Kusumi; Y Sako
Journal:  Curr Opin Cell Biol       Date:  1996-08       Impact factor: 8.382

8.  Spectral analysis of erythrocyte flickering in the 0.3-4- microm-1 regime by microinterferometry combined with fast image processing.

Authors: 
Journal:  Phys Rev A       Date:  1992-12-15       Impact factor: 3.140

9.  Tunable generic model for fluid bilayer membranes.

Authors:  Ira R Cooke; Kurt Kremer; Markus Deserno
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-07-26

10.  Hydrophobic mismatch between helices and lipid bilayers.

Authors:  Thomas M Weiss; Patrick C A van der Wel; J Antoinette Killian; Roger E Koeppe; Huey W Huang
Journal:  Biophys J       Date:  2003-01       Impact factor: 4.033

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  31 in total

1.  Two-component coarse-grained molecular-dynamics model for the human erythrocyte membrane.

Authors:  He Li; George Lykotrafitis
Journal:  Biophys J       Date:  2012-01-03       Impact factor: 4.033

2.  Large-scale simulations of fluctuating biological membranes.

Authors:  Andrea Pasqua; Lutz Maibaum; George Oster; Daniel A Fletcher; Phillip L Geissler
Journal:  J Chem Phys       Date:  2010-04-21       Impact factor: 3.488

3.  An implicit solvent coarse-grained lipid model with correct stress profile.

Authors:  Alex J Sodt; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2010-05-28       Impact factor: 3.488

4.  Multiscale computer simulation of the immature HIV-1 virion.

Authors:  Gary S Ayton; Gregory A Voth
Journal:  Biophys J       Date:  2010-11-03       Impact factor: 4.033

5.  Nonlinearities in tilt and layer displacements of planar lipid bilayers.

Authors:  R De Vita; I W Stewart
Journal:  Eur Phys J E Soft Matter       Date:  2010-07-08       Impact factor: 1.890

6.  Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration.

Authors:  J W Mullinax; W G Noid
Journal:  J Chem Phys       Date:  2010-09-28       Impact factor: 3.488

7.  Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes.

Authors:  Brian A Camley; Michael G Lerner; Richard W Pastor; Frank L H Brown
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

8.  Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation.

Authors:  Gary S Ayton; Philip D Blood; Gregory A Voth
Journal:  Biophys J       Date:  2007-02-26       Impact factor: 4.033

9.  Microseconds dynamics simulations of the outer-membrane protease T.

Authors:  Marilisa Neri; Marc Baaden; Vincenzo Carnevale; Claudio Anselmi; Amos Maritan; Paolo Carloni
Journal:  Biophys J       Date:  2007-09-07       Impact factor: 4.033

10.  Coarse-grained simulation studies of peptide-induced pore formation.

Authors:  Gregoria Illya; Markus Deserno
Journal:  Biophys J       Date:  2008-07-18       Impact factor: 4.033

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