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Improved Accuracy and Performance of Lennard-Jones Lattice Summation in Gromacs
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-4591-9809
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-7498-7763
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-2734-2794
(English)Manuscript (preprint) (Other academic)
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-146176OAI: oai:DiVA.org:kth-146176DiVA: diva2:722588
Note

QS 2014

Available from: 2014-06-09 Created: 2014-06-09 Last updated: 2014-06-09Bibliographically approved
In thesis
1. Exploring the Interactive Landscape of Lipid Bilayers
Open this publication in new window or tab >>Exploring the Interactive Landscape of Lipid Bilayers
2014 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

One of the most important aspects for all life on this planet is theact to keep their cellular processes in a state where they do notreach equilibrium. One part in the upholding of this imbalanced stateis the barrier between the cells and their surroundings, created bythe cell membrane. In addition to experiments, the investigation ofprocesses occuring in the cell membrane can be performed by usingmolecular dynamics simulations. Through this method we can obtain anatomistic description of the dynamics associated with events that arenot accessible to experimental setups. Molecular dynamics relies onthe integration of Newton's equations of motion in order to sample therelevant parts of phase-space for the system, and therefore it isdependent on a correct description of the interactions between all thesimulated particles. In this thesis I first present an improved methodfor the calculation of long-range interactions in molecular dynamicssimulations, followed by a study of cholesterol's impact on thepermeation of small solutes across a lipid bilayer.

The first paper presents a previously derived modification to theparticle-mesh Ewald method, which makes it possible to apply thisto long-range Lennard-Jones interactions. Old implementations of themethod have been haunted by an extreme performance degradation andhere I propose a solution to this problem by applying a modifiedinteraction potential. I further show that the historical treatmentof long-range interactions in simulations of lipid bilayers hasnon-negligible effects on their structural properties.In the second paper, this modification is improved such that the smallerrors introduced by the modified interaction potential becomenegligible. Furthermore, I demonstrate that I have also improved theimplementation of the method so that it now only incurs a performanceloss of roughly 15% compared to conventional simulations using theGromacs simulation package.The third paper presents a simulation study of cholesterol's effect onthe permeation of six different solutes across a variety of lipidbilayers. I analyze the effect of different head groups, tail lengths,and tail saturation by performing simulations of the solutes in fourdifferent bilayers, with cholesterol contents between 0% and50%. Analysis of the simulations shows that the impact of the surfacearea per lipid on the partitioning of the solute could be lower thanpreviously thought. Furthermore, a model with a laterallyinhomogeneous permeability in cholesterol-containing membranes isproposed, which could explain the large differences betweenpermeabilities from experiments and calculated partition coefficientsin simulations.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2014. xi, 38 p.
Series
TRITA-FYS, ISSN 0280-316X ; 2014:24
Keyword
Molecular Dynamics, lipid bilayer, cholesterol, permeability, long-range interactions, Lennard-Jones, dispersion, particle-mesh Ewald
National Category
Biophysics
Research subject
Biological Physics
Identifiers
urn:nbn:se:kth:diva-145559 (URN)978-91-7595-174-4 (ISBN)
Presentation
2014-06-13, FB54, Roslagstullsbacken 21, AlbaNova, Stockholm, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

QC 20140609

Available from: 2014-06-09 Created: 2014-05-22 Last updated: 2014-06-09Bibliographically approved

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Wennberg, Christian L.Hess, BerkLindahl, Erik

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