Abstract
Understanding the structural,
mechanical and dynamical properties of lipid self-assembled systems is fundamental to understand the behavior of the cell membrane. This thesis has investigated the equilibrium properties of lipid
systems with edge defects through various molecular simulation techniques. The overall goal of this study is to understand the free energy terms of the edges and to develop efficient methods to
sample equilibrium distributions of mixed-lipid systems. In the first main part of my thesis, an atomistic molecular model is used to study lipid ribbon which has two edges on both sides. Details of the edge
structures, such as area per lipid and tail torsional statistics are presented. Line tension, calculated from pressure tensor in MD simulation has good agreement with result from other sources. To
further investigate edge properties on a longer timescale and larger length scale, we have applied a coarse-grained forcefield on mixed lipid systems and try to interpret the edge fluctuations in
terms of free energy parameters such as line tension and bending modulus. We have identified two regimes with quite different edge behavior: a high line tension regime and a low line tension
regime. The last part of this thesis focuses on a hybrid Molecular dynamics and Configurational-bias Monte Carlo (MCMD) simulation method in which molecules can change their type by growing and
shrinking the terminal acyl united carbon atoms. A two-step extension of the MCMD method has been developed to allow for a larger difference in the components' tail lengths. Results
agreed well with previous one-step mutation results for a mixture with a length difference of four carbons. The current method can efficiently sample mixtures with a length difference of eight
carbons, with a small portion of lipids of intermediate tail length. Preliminary results are obtained for "bicelle"-type (DMPC/DHPC) ribbons.
Table of Contents
TABLE OF CONTENTS
Abstract
List of Figures
List of Tables
Acknowledgments
Chapter 1:
Introduction.................................................................................................... 1
Chapter 2: Atomistic Simulation of lipid Bilayer edge.................................................
15
Introduction.................................................................................................... 16
Methods.......................................................................................................... 19
Results............................................................................................................ 25
Migration of headgroups........................................................................ 25
General morphology of the bilayer......................................................... 26
Tail conformational statistics.................................................................. 30
Line
tension............................................................................................ 34
Equilibrium dynamics............................................................................. 36
Discussion....................................................................................................... 39
Conclusion...................................................................................................... 44
Chapter 3: Coarse-grained MD simulation of mixed bilayer systems: Understanding the in-plane fluctuation of bilayer
edge...................................................... 55
Introduction....................................................................................................
56
Methods......................................................................................................... 59 Theory of
bilayer edge shape fluctuation...................................................... 64 A Monte Carlo model to
simulate bilayer edge fluctuation.......................... 69
Results........................................................................................................... 70
Equilibirum dynamics............................................................................. 71
Line
tension............................................................................................ 71
Partitioning of the short-tail lipids.......................................................... 76
Edge contour
length............................................................................... 76
Position correlation function fourier transform...................................... 78
Discussion...................................................................................................... 82
Conclusions................................................................................................... 86
Chapter 4: Two-step hybrid Configurational-bias Monte Carlo and Molecular dynamics simulations of mixed lipid
bilayer................................................................................................... 92
Introduction.................................................................................................... 93
Methods.......................................................................................................... 96
Results.......................................................................................................... 108
Verification of two-step method............................................................ 108
Simulations on DMPC/DHPC ribbon systems....................................... 109 Discussions...................................................................................................
120
Conclusions.................................................................................................. 123
About this Dissertation
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