Molecular Dynamics Methodology and Simulations of Phospholipid Bilayers and Liquid Crystals

Doctoral Dissertation
Thumbnail

Abstract

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.

Attributes

Attribute NameValues
URN
  • etd-07182006-152636

Author Teng Lin
Advisor Edward J. Maginn
Contributor Edward J. Maginn, Committee Chair
Contributor Steven A. Corcelli, Committee Member
Contributor S. Alex Kandel, Committee Member
Contributor J. Daniel Gezelter, Committee Member
Contributor Dan Meisel, Committee Member
Degree Level Doctoral Dissertation
Degree Discipline Chemistry and Biochemistry
Degree Name PhD
Defense Date
  • 2006-07-13

Submission Date 2006-07-18
Country
  • United States of America

Subject
  • phospholipid bilayers

  • Langevin dynamics

  • liquid crystals

  • hydrodynamics

  • molecular dynamics

  • rigid body

Publisher
  • University of Notre Dame

Language
  • English

Record Visibility and Access Public
Content License
  • All rights reserved

Departments and Units

Files

Please Note: You may encounter a delay before a download begins. Large or infrequently accessed files can take several minutes to retrieve from our archival storage system.