Literature DB >> 19050734

Simulations of Biomembranes and Water: Important Technical Aspects.

Sandra V Bennun1, Allison N Dickey, Chenyue Xing, Roland Faller.   

Abstract

In this contribution, we discuss several important technical aspects which are relevant for the molecular modeling of biomembranes in aqueous environments. We study the effect of coarse-grained water models on free and supported systems and show that the choice of water model has dramatic repercussions on the phase behavior. We characterize the phase behavior of a widely used water model and discuss the technical implications of modeling solid supports for biomembrane simulations. Finally, we compare the effect of anisotropic pressure coupling with surface tension coupling in atomistic bilayer simulations including alcohols.

Entities:  

Year:  2007        PMID: 19050734      PMCID: PMC2151735          DOI: 10.1016/j.fluid.2007.07.056

Source DB:  PubMed          Journal:  Fluid Phase Equilib        ISSN: 0378-3812            Impact factor:   2.775


  26 in total

Review 1.  Modeling the lipid component of membranes.

Authors:  H Larry Scott
Journal:  Curr Opin Struct Biol       Date:  2002-08       Impact factor: 6.809

2.  Simulation of domain formation in DLPC-DSPC mixed bilayers.

Authors:  Roland Faller; Siewert-Jan Marrink
Journal:  Langmuir       Date:  2004-08-31       Impact factor: 3.882

3.  Thermodynamics, structure, and dynamics of water confined between hydrophobic plates.

Authors:  Pradeep Kumar; Sergey V Buldyrev; Francis W Starr; Nicolas Giovambattista; H Eugene Stanley
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-11-11

4.  Karhunen-Loeve analysis for pattern description in phase separated lipid bilayer systems.

Authors:  Jeff M Switzer; Sandra V Bennun; Marjorie L Longo; Ahmet Palazoglu; Roland Faller
Journal:  J Chem Phys       Date:  2006-06-21       Impact factor: 3.488

5.  How alcohol chain-length and concentration modulate hydrogen bond formation in a lipid bilayer.

Authors:  Allison N Dickey; Roland Faller
Journal:  Biophys J       Date:  2007-01-11       Impact factor: 4.033

6.  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

7.  Simulations of zwitterionic and anionic phospholipid monolayers.

Authors:  Yiannis N Kaznessis; Sangtae Kim; Ronald G Larson
Journal:  Biophys J       Date:  2002-04       Impact factor: 4.033

Review 8.  Supported membranes: scientific and practical applications.

Authors:  E Sackmann
Journal:  Science       Date:  1996-01-05       Impact factor: 47.728

9.  Restatement of order parameters in biomembranes: calculation of C-C bond order parameters from C-D quadrupolar splittings.

Authors:  J P Douliez; A Léonard; E J Dufourc
Journal:  Biophys J       Date:  1995-05       Impact factor: 4.033

10.  Simulating induced interdigitation in membranes.

Authors:  Marieke Kranenburg; Martin Vlaar; Berend Smit
Journal:  Biophys J       Date:  2004-09       Impact factor: 4.033

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  1 in total

1.  Structure of Mycobacterium tuberculosis cytochrome bcc in complex with Q203 and TB47, two anti-TB drug candidates.

Authors:  Shan Zhou; Weiwei Wang; Xiaoting Zhou; Yuying Zhang; Yuezheng Lai; Yanting Tang; Jinxu Xu; Dongmei Li; Jianping Lin; Xiaolin Yang; Ting Ran; Hongming Chen; Luke W Guddat; Quan Wang; Yan Gao; Zihe Rao; Hongri Gong
Journal:  Elife       Date:  2021-11-25       Impact factor: 8.140

  1 in total

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