Molecular Detailed Simulations of Lipid Bilayers

Berkowitz, Max L.; Kindt, James T.

doi:10.1002/9780470890905.ch5

Cited by 5 publications

(3 citation statements)

References 100 publications

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“…The principles behind MD are so simple and general that since its first appearance in the 70s, it has been applied to a wide range of systems, at very different scales. For example, MD is the dominant theoretical tool of investigation in the field of biophysics, where structural changes in proteins [3,4,5,6] and lipid bilayers [7,8] interacting with drugs can be studied, ultimately providing a better understanding of drug delivery mechanisms.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Computational Physics on Graphics Processing Units

Harju

Siro

Canova

et al. 2013

Applied Parallel and Scientific Computing

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The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing on classical molecular dynamics, and on quantum simulations for electronic structure calculations using the density functional theory, wave function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012, Helsinki, Finland, June 10-13, 201

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Section: Molecular Dynamicsmentioning

confidence: 99%

Computational Physics on Graphics Processing Units

Harju

Siro

Canova

et al. 2013

Applied Parallel and Scientific Computing

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“…Several recent reviews [9][10][11] give an excellent introduction to the field. Atomistic simulations are, in principle, capable of calculating all the properties and effects in membranes at all length-and time-scales [12] . When combined with experiment, they have shed some light on the various features affecting membrane-mediated protein interactions [13].…”

Section: Introductionmentioning

confidence: 99%

Coarse-grained simulation of transmembrane peptides in the gel phase

Al-Lehyani

Grime

Bano

et al. 2013

Journal of Computational Physics

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We use Dissipative Particle Dynamics simulations, combined with parallel tempering and umbrella sampling, to investigate the potential of mean force between model transmembrane peptides in the various phases of a lipid bilayer, including the low-temperature gel phase. The observed oscillations in the effective interaction between peptides are consistent with the different structures of the surrounding lipid phases.

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“…There have been some efforts in using MC to accelerate conformational equilibration [23,24] of lipid tails and to explore hydration of the bilayer interior [25]; a general discussion of the relative strengths and complementarity of molecular dynamics (MD) and MC methods applied to lipid bilayers has been given in a recent review [26]. In simulations of mixed-lipid bilayers, the use of the configuration-bias MC (CBMC) [27] method to allow lipids to change their structure in a constant Dm ensemble was inspired by the successful application of this method to monolayers [28] and to bulk mixtures of alkanes [29], whose packing density is similar to the bilayer interior.…”

Section: Introductionmentioning

confidence: 99%

Atomistic simulation of mixed-lipid bilayers: mixed methods for mixed membranes

Kindt

2011

Molecular Simulation

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Biomembranes are characterised by diversity in the composition of the lipids they contain and the local environments these lipids occupy. The principles that govern the lateral distribution of lipids in a heterogeneous system have important implications for membrane structure and function. Modelling equilibrium lateral distributions with atomistic detail using molecular dynamics (MD) simulation is challenging due to the very long trajectories needed for lipid lateral diffusion. A mixed MD/Monte Carlo (MC) approach relying on configuration-bias MC mutation moves allows fluctuations in local composition to occur without diffusion and has been applied to several simple mixtures. Mixtures of saturated-tail lipids differing in tail length by four carbons per tail showed lateral distribution in the fluid phase indistinguishable from random mixing, but with a distinct tendency for short-tailed lipids to cluster together within the gel phase. Local environment influenced local composition strongly at edge defects, weakly in the neighbourhood of a transmembrane helical peptide under conditions of hydrophobic mismatch and to no measurable extent in a curved bilayer. The use of an isomolar semigrand canonical ensemble also enables insight into the phase coexistence between the gel and fluid phases in a binary mixture and between the liquid-ordered and liquid-disordered systems in ternary, cholesterol-containing system.

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Molecular Detailed Simulations of Lipid Bilayers

Cited by 5 publications

References 100 publications

Computational Physics on Graphics Processing Units

Computational Physics on Graphics Processing Units

Coarse-grained simulation of transmembrane peptides in the gel phase

Atomistic simulation of mixed-lipid bilayers: mixed methods for mixed membranes

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