Physical Sciences and Mathematics Commons^™

Block Copolymer Directed Self-Assembly: Exploring The Efficacy Of Applications In Semiconductor Fabrication, Jakin Bryce Delony

USF Tampa Graduate Theses and Dissertations

Over the course of the past 80 years, semiconductor devices have become increasingly ubiquitous in everyday life.From constructing mainframes that encompassed entire rooms during the 1940s, to inventing personal computers in the 1980s, to developing progressively faster smartphones and wearable technology in the 2010s, the primary driving force behind the Digital Revolution has been increasing transistor counts, and thus computing power, via incremental improvements in optical lithography. In 1965, Intel co-founder Gordon Moore boldly predicted that the transistor density of semiconductor devices would double approximately every 18-24 months. While this prediction -- now colloquially referred to as Moore's Law -- …

Msspark: Implementation Of Molecular Simulation Queries Using Apache Spark, Parneet Kaur

USF Tampa Graduate Theses and Dissertations

Huge amount of data is being generated in almost every field and it cannot be avoided, rather is essential for the advancement of the field. Analysis of this data requires intensive computing power. Molecular Simulation is a powerful tool for understanding the behavior of natural systems. The simulation generates large amount data while observing the spatial and temporal relationships. The challenge is to handle the analytical queries that are often compute intensive.

Although various tools exist to tackle this problem, but in this paper we have tried an alternate approach that uses Apache Spark- a modern big data platform – …

Application And Development Of Computational Methods In Conformational Studies Of Bio-Molecules, Aleksandra Karolak

USF Tampa Graduate Theses and Dissertations

The work presented in my dissertation focuses on the conformational studies of bio-molecules including proteins and DNA using computational approaches. Conformational changes are important in numerous molecular bioprocesses such as recognition, transcription, replication and repair, etc. Proteins recognize specific DNA sequences and upon binding undergo partial or complete folding or partial unfolding in order to find the optimal conformational fit between molecules involved in the complex. In addition to sequence specific recognition, proteins are able to distinguish between subtle differences in local geometry and flexibility associated with DNA that may further affect their binding affinities. Experimental techniques provide high-resolution details …

Dcms: A Data Analytics And Management System For Molecular Simulation, Meryem Berrada

USF Tampa Graduate Theses and Dissertations

Despite the fact that Molecular Simulation systems represent a major research tool in multiple scientific and engineering fields, there is still a lack of systems for effective data management and fast data retrieval and processing. This is mainly due to the nature of MS which generate a very large amount of data - a system usually encompass millions of data information, and one query usually runs for tens of thousands of time frames. For this purpose, we designed and developed a new application, DCMS (A data Analytics and Management System for molecular Simulation), that intends to speed up the process …

Non-Equilibrium Melting And Sublimation Of Graphene Simulated With Two Interatomic Potentials, Brad Steele

USF Tampa Graduate Theses and Dissertations

The mechanisms of the sublimation of graphene at zero pressure and the condensation of carbon vapor is investigated by molecular dynamics (MD) simulations. The interatomic interactions are described by the Reactive Empirical Bond Order potential (REBO). It is found that graphene sublimates at a temperature of 5,200 K. At the onset of sublimation, defects that contain several pentagons and heptagons are formed, that are shown to evolve from double vacancies and stone wales defects. These defects consisting of pentagons and heptagons act as nucleation sites for the gaseous phase. The influence of the interatomic interactions on the sublimation process are …

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 …

Atomistic Studies Of Shock-Wave And Detonation Phenomena In Energetic Materials, Mikalai Budzevich

USF Tampa Graduate Theses and Dissertations

The major goal of this PhD project is to investigate the fundamental properties of energetic materials, including their atomic and electronic structures, as well as mechanical properties, and relate these to the fundamental mechanisms of shock wave and detonation propagation using state-of-the-art simulation methods. The first part of this PhD project was aimed at the investigation of static properties of energetic materials (EMs) with specific focus on 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). The major goal was to calculate the isotropic and anisotropic equations of state for TATB within a range of compressions not accessible to experiment, and to make predictions of anisotropic sensitivity …