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Title: Molecular dynamics simulation study of lipid membranes using coarse-grained models
Author: Zhang, Yawen
ISNI:       0000 0004 5918 0501
Awarding Body: Imperial College London
Current Institution: Imperial College London
Date of Award: 2014
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In this work we use coarse-grained molecular dynamics simulations to investigate how lipid composition affects the phase transition of phospholipid bilayers. We consider a fully hydrated membrane consisting of saturated 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and cholesterol or unsaturated 1,2-dioleoyol-sn-glycero-3-phosphocholine (DOPC). We report structural, dynamic changes occurring in the model bilayer mixtures with varying temperature and composition. Firstly we study the effect of cholesterol on the properties of a DPPC bilayer. We have combined the computations of area per lipid, radial distribution function, chain order parameter and Voronoi construction to quantify the phase transitions, and the coarse-grained (CG) model is found to quantitatively reproduce most of the experimental observations. Based on the changes in the structural and dynamic properties, a temperature-composition phase diagram of DPPC/cholesterol is proposed and compared with the experiments. 'Thread-like' cholesterol clusters in the bilayer at high cholesterol concentrations are observed and the origin of this specific lateral organisation is discussed. To explore the role of the CG bead size, a series of simulations varying the cholesterol cross sectional areas were performed. Parameters obtained from simulation of the different cholesterol isomorphs provide important insight into the microscopic degrees of freedom determining the cholesterol arrangement in the bilayer. The results for the modified cholesterols are further discussed in relation to naturally occurring sterols. Finally, the effect of a mono-unsaturated phospholipid (DOPC) on the main melting phase transition is investigated. This analysis is performed by simulating bilayer systems which were constructed by combining a gel phase DPPC bilayer and a fluid phase DOPC bilayer. The visual observations of the bilayers show that the gel and fluid phases coexist within a wide range of temperature and composition. A temperature-composition phase diagram with phase coexistences is proposed using the information extracted from structural and local composition analysis.
Supervisor: Bresme, Fernando ; Seddon, John Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available