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Type of Document Dissertation Author Lin, Teng Author's Email Address tlin@nd.edu URN etd-07182006-152636 Title Molecular Dynamics Methodology and Simulations of Phospholipid Bilayers and Liquid Crystals Degree Doctor of Philosophy Department Chemistry and Biochemistry Advisory Committee
Advisor Name Title Edward J. Maginn Committee Chair Dan Meisel Committee Member J. Daniel Gezelter Committee Member S. Alex Kandel Committee Member Steven A. Corcelli Committee Member Keywords
- hydrodynamics
- liquid crystals
- phospholipid bilayers
- molecular dynamics
- rigid body
- Langevin dynamics
Date of Defense 2006-07-13 Availability restricted 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 studiedthe 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.
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