The simulation of biomembranes and drug transport therein using a Gay-Berne model
The simulation of biomembranes and drug transport therein using a Gay-Berne model
In this thesis the concepts used to model the liquid crystalline mesophases are applied to the modelling of a lipid membrane. The most popular model for the stimulation of the liquid crystalline mesophase is that developed by Gay and Berne, in which molecules are modelled by ellipsoids of various length and breadth ratios. In this model the individual atoms of the molecule are subsumed into a single ellipsoid that interacts with its neighbours through an anisotropic intermolecular potential. This model has already been applied to model the hydrocarbon region of a lipid bilayer and has proved to give a good fit with experiments. The work in this thesis consists of extending this model to build an entire membrane (tail, glycerol, head group and solvent), and then studying the diffusion of small drugs within this environment. Chapter 4 describes the construction of the model. A new parameterization technique for the Gay-Berne potential is introduced. Chapter 5 presents simulations performed with this model as well as a self aggregation study. Analysis of preassembled bilayer simulated with this model clearly demonstrates the existence of a phase transition, and shows the presence of lipid long-range lateral diffusion. The results obtained have been favourably compared to the available experimental data in most cases. The self aggregation study failed to identify the formation of a bilayer of correct structure. Rather, the formation of a two phases system was observed, water and a low-hydration bilayer. The small molecule permeation study, presented in Chapter 6, shows promising results. However, systematic deficiencies of the membrane model in the interfacial region have been identified.
University of Southampton
Haubertin, David Yan
1c7f79c2-cdef-407a-a698-5e20ea133584
2003
Haubertin, David Yan
1c7f79c2-cdef-407a-a698-5e20ea133584
Haubertin, David Yan
(2003)
The simulation of biomembranes and drug transport therein using a Gay-Berne model.
University of Southampton, Doctoral Thesis.
Record type:
Thesis
(Doctoral)
Abstract
In this thesis the concepts used to model the liquid crystalline mesophases are applied to the modelling of a lipid membrane. The most popular model for the stimulation of the liquid crystalline mesophase is that developed by Gay and Berne, in which molecules are modelled by ellipsoids of various length and breadth ratios. In this model the individual atoms of the molecule are subsumed into a single ellipsoid that interacts with its neighbours through an anisotropic intermolecular potential. This model has already been applied to model the hydrocarbon region of a lipid bilayer and has proved to give a good fit with experiments. The work in this thesis consists of extending this model to build an entire membrane (tail, glycerol, head group and solvent), and then studying the diffusion of small drugs within this environment. Chapter 4 describes the construction of the model. A new parameterization technique for the Gay-Berne potential is introduced. Chapter 5 presents simulations performed with this model as well as a self aggregation study. Analysis of preassembled bilayer simulated with this model clearly demonstrates the existence of a phase transition, and shows the presence of lipid long-range lateral diffusion. The results obtained have been favourably compared to the available experimental data in most cases. The self aggregation study failed to identify the formation of a bilayer of correct structure. Rather, the formation of a two phases system was observed, water and a low-hydration bilayer. The small molecule permeation study, presented in Chapter 6, shows promising results. However, systematic deficiencies of the membrane model in the interfacial region have been identified.
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Published date: 2003
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Local EPrints ID: 465119
URI: http://eprints.soton.ac.uk/id/eprint/465119
PURE UUID: b1c044b8-414d-4edf-b939-a0d4ba4451ee
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Date deposited: 05 Jul 2022 00:24
Last modified: 16 Mar 2024 19:58
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Author:
David Yan Haubertin
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