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Physical properties of mixed membranes explored using atomistic and coarse grained molecular dynamic simulations with enhanced sampling techniques

Physical properties of mixed membranes explored using atomistic and coarse grained molecular dynamic simulations with enhanced sampling techniques
Physical properties of mixed membranes explored using atomistic and coarse grained molecular dynamic simulations with enhanced sampling techniques
Studies of three different, but interlinked, aspects of membrane properties are presented here. First an analysis of both the lyotropic and thermotropic phase transitions of a phospholipid bilayer using the ELBA1.0 forcefield. This is believed to be the first time such transitions (including the rippled gel phase) have been observed using a coarse grained (CG) forcefield not specifically parameterised to do so. Further, analysis via enhanced sampling methods of the relative free energies of the phases is presented. These analyses confirm the enormous effects comparatively small changes to a forcefield can have on the aggregate behaviour of lipids modelled with it. Molecular dynamics studies on the bending rigidity of bilayers are also presented, including a comparison of 4 different computational methods for calculating the bending rigidity of bilayers. The system size dependency of such methods is compared, as well as their ability to reproduce trends in bending rigidity across lipid species already measured experimentally. The methods are compared across two different atomistic and one CG method for the first time and, despite quite different theoretical bases, are shown to produce surprisingly consistent results both with each other and with previously published experiment.
Finally, two new parameterisations of cholesterol using the ELBA forcefield are explored. Their ability to induce the ordering and structure seen in atomistic simulations is measured and compared with another widely using coarse grained forcefield. ELBA's unique (amongst CG forcefields) direct compatibility with atomistic forcefields also allowed dual-resolution simulations of binary bilayers to be analysed. Results from such dual-resolution simulations are consistent with those resulting from atomistic simulation.
University of Southampton
Wheeler, Sophia
18e8bbfc-7c05-4b01-9963-93a11c2142c9
Wheeler, Sophia
18e8bbfc-7c05-4b01-9963-93a11c2142c9
Essex, Jonathan
1f409cfe-6ba4-42e2-a0ab-a931826314b5

Wheeler, Sophia (2018) Physical properties of mixed membranes explored using atomistic and coarse grained molecular dynamic simulations with enhanced sampling techniques. University of Southampton, Doctoral Thesis, 215pp.

Record type: Thesis (Doctoral)

Abstract

Studies of three different, but interlinked, aspects of membrane properties are presented here. First an analysis of both the lyotropic and thermotropic phase transitions of a phospholipid bilayer using the ELBA1.0 forcefield. This is believed to be the first time such transitions (including the rippled gel phase) have been observed using a coarse grained (CG) forcefield not specifically parameterised to do so. Further, analysis via enhanced sampling methods of the relative free energies of the phases is presented. These analyses confirm the enormous effects comparatively small changes to a forcefield can have on the aggregate behaviour of lipids modelled with it. Molecular dynamics studies on the bending rigidity of bilayers are also presented, including a comparison of 4 different computational methods for calculating the bending rigidity of bilayers. The system size dependency of such methods is compared, as well as their ability to reproduce trends in bending rigidity across lipid species already measured experimentally. The methods are compared across two different atomistic and one CG method for the first time and, despite quite different theoretical bases, are shown to produce surprisingly consistent results both with each other and with previously published experiment.
Finally, two new parameterisations of cholesterol using the ELBA forcefield are explored. Their ability to induce the ordering and structure seen in atomistic simulations is measured and compared with another widely using coarse grained forcefield. ELBA's unique (amongst CG forcefields) direct compatibility with atomistic forcefields also allowed dual-resolution simulations of binary bilayers to be analysed. Results from such dual-resolution simulations are consistent with those resulting from atomistic simulation.

Text
Wheler thesis final - Version of Record
Restricted to Repository staff only until 30 September 2021.
Available under License University of Southampton Thesis Licence.

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Published date: October 2018

Identifiers

Local EPrints ID: 425867
URI: http://eprints.soton.ac.uk/id/eprint/425867
PURE UUID: 20d43b35-2ad6-4fd8-80a6-935a424f5905
ORCID for Jonathan Essex: ORCID iD orcid.org/0000-0003-2639-2746

Catalogue record

Date deposited: 05 Nov 2018 17:30
Last modified: 14 Mar 2019 01:52

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