Physics Commons^™

Transport Of Water And Ions Through Single-Walled Armchair Carbon Nanotubes: A Molecular Dynamics Study, Michelle Patricia Aranha

Doctoral Dissertations

The narrow hydrophobic interior of a carbon nanotube (CNT) poses a barrier to the transport of water and ions, and yet, unexpectedly, numerous experimental and simulation studies have confirmed fast water transport rates comparable to those seen in biological aquaporin channels. These outstanding features of high water permeability and high solute rejection of even dissolved ions that would typically require a lot of energy for separation in commercial processes makes carbon nanotubes an exciting candidate for desalination membranes. Extending ion exclusion beyond simple mechanical sieving by the inclusion of electrostatics via added functionality to the nanotube bears promise to not …

Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega

Doctoral Dissertations

The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes.

In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose …

Study Of Local Structure, Stress And Dynamics In Disordered Materials Using Ab-Initio And Molecular Dynamics Simulation, Madhusudan Ojha

Doctoral Dissertations

Understanding the atomic structure and dynamics in structurally disordered systems has been a long-standing and most challenging problem in physics and material science. To begin with, it is difficult to describe disorder quantitatively and to differentiate the degree of disorder from one system to another. The majorities of experimental and theoretical approaches to the study of disordered systems are either transferred directly from the study of crystals or address the problem in the macroscopic scale where the atomic origin of behavior is obscured. First principle atomic level stresses and dynamic pair distribution functions described in this dissertation represent attempts to …