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Open AccessJournal ArticleDOI

Under the Influence of Alcohol: The Effect of Ethanol and Methanol on Lipid Bilayers

TLDR
In this article, the effects of short-chain alcohols, methanol and ethanol, on two different fully hydrated lipid bilayer systems (POPC and DPPC) in the fluid phase at 323 K were investigated.
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This article is published in Biophysical Journal.The article was published on 2006-02-15 and is currently open access. It has received 318 citations till now. The article focuses on the topics: Lipid bilayer & Methanol.

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Cryoprotectant Toxicity: Facts, Issues, and Questions

TL;DR: This review attempts to describe what is known about CPA toxicity, theories of CPA Toxicology, and strategies to reduce CPAoxicity.
Journal ArticleDOI

Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments.

TL;DR: An overview of the literature in which experimental order parameters from 2H NMR are compared to those calculated from MD simulations is given and a case study of cholesterol in a DMPC bilayer is presented.
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Assessing the nature of lipid raft membranes.

TL;DR: The results propose that the functioning of certain classes of membrane proteins is regulated by changes in the lateral pressure profile, which can be altered by a change in lipid content.
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Biomolecular simulations of membranes: physical properties from different force fields

TL;DR: This work compares the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all- atom generalized AMBER force field (GAFF) for dioleoylphosphatidylcholine molecules.
References
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Journal ArticleDOI

Molecular dynamics with coupling to an external bath.

TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
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A smooth particle mesh Ewald method

TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Journal ArticleDOI

LINCS : A linear constraint solver for molecular simulations

TL;DR: Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules.
Book

Physical chemistry of surfaces

TL;DR: In this paper, the authors discuss the nature and properties of liquid interfaces, including the formation of a new phase, nucleation and crystal growth, and the contact angle of surfaces of solids.
Journal ArticleDOI

GROMACS 3.0: a package for molecular simulation and trajectory analysis

TL;DR: The design includes an extraction of virial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x–1/2.
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