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Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation
KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.ORCID-id: 0000-0002-4591-9809
KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.ORCID-id: 0000-0003-0603-5514
KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.ORCID-id: 0000-0001-6363-2521
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2015 (Engelska)Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 12, s. 5737-5746Artikel i tidskrift (Refereegranskat) Published
Resurstyp
Text
Abstract [en]

Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for electrostatics have been revolutionary to the precision and accuracy of molecular simulations in general. Despite the performance penalty associated with lattice summation electrostatics, few biomolecular simulations today are performed without it. There are increasingly strong arguments for moving in the same direction for Lennard-Jones (LJ) interactions, and by using geometric approximations of the combination rules in reciprocal space, we have been able to make a very high-performance implementation available in GROMACS. Here, we present a new way to correct for these approximations to achieve exact treatment of Lorentz-Berthelot combination rules within the cutoff, and only a very small approximation error remains outside the cutoff (a part that would be completely ignored without LJ-PME). This not only improves accuracy by almost an order of magnitude but also achieves absolute biomolecular simulation performance that is an order of magnitude faster than any other available lattice summation technique for LJ interactions. The implementation includes both CPU and GPU acceleration, and its combination with improved scaling LJ-PME simulations now provides performance close to the truncated potential methods in GROMACS but with much higher accuracy.

Ort, förlag, år, upplaga, sidor
American Chemical Society (ACS), 2015. Vol. 11, nr 12, s. 5737-5746
Nationell ämneskategori
Fysik
Identifikatorer
URN: urn:nbn:se:kth:diva-180232DOI: 10.1021/acs.jctc.5b00726ISI: 000366223400017PubMedID: 26587968Scopus ID: 2-s2.0-84949640540OAI: oai:DiVA.org:kth-180232DiVA, id: diva2:895418
Anmärkning

QC 20160119

Tillgänglig från: 2016-01-19 Skapad: 2016-01-08 Senast uppdaterad: 2017-11-30Bibliografiskt granskad
Ingår i avhandling
1. Computational modeling of biological barriers
Öppna denna publikation i ny flik eller fönster >>Computational modeling of biological barriers
2016 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

One of the most important aspects for all life on this planet is the act to keep their biological processes in a state where they do not reach equilibrium. One part in the upholding of this imbalanced state is the barrier between the cells and their surroundings, created by the cell membrane. Additionally, terrestrial animal life often requires a barrier that protects the organism's body from external hazards and water loss. As an alternative to experiments, the investigation of the processes occurring at these barriers can be performed by using molecular dynamics simulations. Through this method we can obtain an atomistic description of the dynamics associated with events that are not accessible to experimental setups.

 In this thesis the first paper presents an improved particle-mesh Ewald method for the calculation of long-range Lennard-Jones interactions in molecular dynamics simulations, which solves the historical performance problem of the method. The second paper demonstrate an improved implementation, with a higher accuracy, that only incurs a performance loss of roughly 15% compared to conventional simulations using the Gromacs simulation package. Furthermore, the third paper presents a study of cholesterol's effect on the permeation of six different solutes across a variety of lipid bilayers. A laterally inhomogeneous permeability in cholesterol-containing membranes is proposed as an explanation for the large differences between experimental permeabilities and calculated partition coefficients in simulations. The fourth paper contains a coarse-grained simulation study of a proposed structural transformation in ceramide bilayer structures, during the formation of the stratum corneum. The simulations show that glycosylceramides are able to stabilize a three-dimensionally folded bilayer structure, while simulations with ceramides collapse into a lamellar bilayer structure.

Ort, förlag, år, upplaga, sidor
Stockholm: KTH Royal Institute of Technology, 2016. s. xii, 49
Serie
TRITA-FYS, ISSN 0280-316X ; 2016:10
Nyckelord
Molecular dynamics, cholesterol, lipid bilayer, permeability, long-range interactions, Lennard-Jones, dispersion, particle-mesh Ewald, stratum corneum, skin formation
Nationell ämneskategori
Biofysik
Forskningsämne
Biologisk fysik
Identifikatorer
urn:nbn:se:kth:diva-183362 (URN)978-91-7595-884-2 (ISBN)
Disputation
2016-04-15, sal F3, Lindstedtsvägen 26, KTH, Stockholm, 10:00 (Engelska)
Opponent
Handledare
Anmärkning

QC 20160308

Tillgänglig från: 2016-03-08 Skapad: 2016-03-08 Senast uppdaterad: 2016-03-09Bibliografiskt granskad

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