Physical Sciences and Mathematics Commons^™

Development Of Interatomic Potentials For Large Scale Molecular Dynamics Simulations Of Carbon Materials Under Extreme Conditions, Romain Perriot

USF Tampa Graduate Theses and Dissertations

The goal of this PhD research project is to devise a robust interatomic potential for large scale molecular dynamics simulations of carbon materials under extreme conditions. This screened-environment dependent reactive empirical bond order potential (SED-REBO) is specifically designed to describe carbon materials under extreme compressive or tensile stresses. Based on the original REBO potential by Brenner and co workers, SED-REBO includes reparametrized pairwise interaction terms and a new screening term, which serves the role of a variable cutoff. The SED-REBO potential overcomes the deficiencies found with the most commonly used interatomic potentials for carbon: the appearance of artificial forces due …

Design Of Novel Inhibitors For Infectious Diseases Using Structure-Based Drug Design: Virtual Screening, Homology Modeling And Molecular Dynamics, Divya Ramamoorthy

USF Tampa Graduate Theses and Dissertations

The main aim of the study in this thesis was to use structure-based protocols to design new drugs for enzymes, DXS and DXR in the non mevalonate pathway. Another aim of this study was to identify the dimer interface in E.coli FabH as an allosteric binding site for designing new class of anti-infective drugs. We have attempted to identify potential inhibitors for DXS by docking the NCI Diversity set compounds, compound libraries available from GSK-MMV and St. Jude's Children's research center. FabH dimer interface has been identified as a potential target using SiteMap, Alanine mutagenesis and docking studies.

The first …

Properties Of Ferroelectric Perovskite Structures Under Non-Equilibrium Conditions, Qingteng Zhang

USF Tampa Graduate Theses and Dissertations

Ferroelectric materials have received lots of attention thanks to their intriguing properties such as the piezoelectric and pyroelectric effects, as well as the large dielectric constants and the spontaneous polarization which can potentially be used for information storage. In particular, perovskite crystal has a very simple unit cell structure yet a very rich phase transition diagram, which makes it one of the most intensively studied ferroelectric materials. In this dissertation, we use effective Hamiltonian, a first-principles-based computational technique to study the finite-temperature properties of ferroelectric perovskites. We studied temperature-graded

(BaxSr1-x )TiO3 (BST) bulk alloys as well as the dynamics of …