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Molecular Dynamics Methodology and Simulations of Phospholipid Bilayers and Liquid Crystals

thesis
posted on 2006-07-18, 00:00 authored by Teng Lin
As a rapidly expanding interdisciplinary science bridging physics, chemistry and biology, the study of soft condensed matter involves the kinetics, dynamics and geometric structures of complex materials like membrane, liquid crystal and polymers. These soft condensed materials are distinguished by the unique physical properties on the mesoscopic scale which can provide useful insights to understand the basic physical principles linking the microscopic structure to the macroscopic properties. Knowledge of the underlying physics is of benefit to a wide range areas, such as the processing of biocompatible materials and development of LCD display technologies. Although the separation of the length scales allows statistical mechanics to be applied, the interesting behavior of these systems usually happens on time scale well beyond current computing power. In order to simulate large soft condensed systems for long times within a reasonable amount of computational time, some new coarse-grained models are presented in this dissertation to describe phospholipids and liquid crystals. Although these models can be described using a small number of physical parameters, it is not trivial to introduce rigid constraints between different molecular fragments correctly and efficiently. Working with colleagues, I developed a new molecular dynamics framework capable of performing simulation on systems with orientational degrees of freedom in a variety of ensembles. Using this new package, I studied the structure, dynamics and transport properties of the biological membranes as well as the the phase behavior of liquid crystals. A new Langevin dynamics algorithm for arbitrary rigid particles is also presented to mimic solvent effects which may eventually expand the time scale of the simulation.

History

Date Modified

2017-06-05

Defense Date

2006-07-13

Research Director(s)

Edward J. Maginn

Committee Members

Steven A. Corcelli S. Alex Kandel J. Daniel Gezelter Dan Meisel

Degree

  • Doctor of Philosophy

Degree Level

  • Doctoral Dissertation

Language

  • English

Alternate Identifier

etd-07182006-152636

Publisher

University of Notre Dame

Program Name

  • Chemistry and Biochemistry

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