Physical Sciences and Mathematics Commons^™

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

The Role Of Conformational Changes In Viral And Bacterial Protein Functions, Md Lokman Hossen

FIU Electronic Theses and Dissertations

Proteins do versatile work in cells. They require a cascade of structural changes to perform different tasks like binding to the other neighboring biomolecules, transporting small chemicals, activating a chemical reaction, etc. The structural conformations of proteins can be critical in changing their working ability. In this dissertation, I investigated the role of conformational changes of viral protein, e.g., spike and envelope protein of SARS-CoV-2, and bacterial protein, e.g., multidrug transporter and toxic extrusion protein- PfMATE from Pyrococcus furiosus. Also, I performed molecular docking-based drug screening targeting the E protein to suggest a set of drugs that can be repurposed …

Tri-Molybdenum Phosphide (Mo3P) And Multi-Walled Carbon Nanotube Junctions For Volatile Organic Compounds (Vocs) Detection, Baleeswaraiah Muchharla, Praveen Malali, Brenna Daniel, Alireza Kondori, Mohammad Asadi, Wei Cao, Hani E. Elsayed-Ali, Mickaël Castro, Mehran Elahi, Adetayo Adedeji, Kishor Kumar Sadasivuni, Muni Raj Mauya, Kapil Kumar, Abdennaceur Karoui, Bijandra Kumar

Electrical & Computer Engineering Faculty Publications

Detection and analysis of volatile organic compounds’ (VOCs) biomarkers lead to improvement in healthcare diagnosis and other applications such as chemical threat detection and food quality control. Here, we report on tri-molybdenum phosphide (Mo₃P) and multi- walled carbon nanotube (MWCNT) junction-based vapor quantum resistive sensors (vQRSs), which exhibit more than one order of magni- tude higher sensitivity and superior selectivity for biomarkers in comparison to pristine MWCNT junctions based vQRSs. Transmission electron microscope/scanning tunneling electron microscope with energy dispersive x-ray spectroscopy, x-ray diffraction, and x-ray photo- electron spectroscopy studies reveal the crystallinity and the presence of Mo and …

Quantifying Complex Systems Via Computational Fly Swarms, Troy Taylor

Senior Theses

Complexity is prevalent both in natural and in human-made systems, yet is not well understood quantitatively. Qualitatively, complexity describes a phenomena in which a system composed of individual pieces, each having simple interactions with one another, results in interesting bulk properties that would otherwise not exist. One example of a complex biological system is the bird flock, in particular, a starling murmuration. Starlings are known to move in the direction of their neighbors and avoid collisions with fellow starlings, but as a result of these simple movement choices, the flock as a whole tends to exhibit fluid-like movements and form …

The Computational Study Of Fly Swarms & Complexity, Austin Bebee

Senior Theses

A system is considered complex if it is composed of individual parts that abide by their own set of rules, while the system, as a whole, will produce non-deterministic properties. This prevents the behavior of such systems from being accurately predicted. The motivation for studying complexity spurs from the fact that it is a fundamental aspect of innumerable systems. Among complex systems, fly swarms are relatively simple, but even so they are still not well understood. In this research, several computational models were developed to assist with the understanding of fly swarms. These models were primarily analyzed by using the …

Thin Film Thermal Deposition At Various Pressures, James Kela Yee Keen Grace

Senior Theses

This research was to verify the hypothesis that resistivity of metal's thin film deposited in a low-pressure environment is the same as its solid material. Thermal Evaporation is a thin film deposition technique in which metal inside a vacuum is evaporated, then deposited onto a surface. Higher quality metal films are deposited when the vacuum pressure is lower. At higher pressures, more air molecules are trapped within the layers of metal, thus increasing scattering sites and increasing the resistance. However, reaching a lower pressure requires more time and effort. In this research, films were deposited at various pressures and resistivities …

Competing Theories Of Pitch Perception: Frequency And Time Domain Analysis, Nowell Thacher Stoddard

Senior Projects Spring 2017

Pitch perception is a phenomenon that has been the subject of much debate within the psychoacoustics community. It is at once a psychological, physiological and mathematical issue that has divided scientists for the last 200 years. My project aims to investigate the benefits and shortcomings of both the place theory and time theory approaches. This is done first by a model consistent with the long-standing focus on the frequency domain, and then by expanding to a more modern approach that functions in the time domain.

A First-Principles Computational Study Of Structural And Elastic Properties Of Zno, Jeevake Attapattu, Changfeng Chen

McNair Poster Presentations

The purpose of this study is to determine structural and mechanical properties of zinc oxide (ZnO) using first-principles computational methods. ZnO is a semiconductor widely used in many electronic and optical applications. ZnO is also economically and environmentally desirable – first, both the constituent elements are abundant on Earth and therefore inexpensive for large-scale applications; second, it is non- toxic. The most significant contribution of this study is the simulations of the high-pressure phases. These high-pressure simulations are important because the rock salt phase of ZnO obtained at high pressure can be recovered at ambient pressure, and this new structural …

An Ethnographic Study: Becoming A Physics Expert In A Biophysics Research Group, Idaykis Rodriguez

FIU Electronic Theses and Dissertations

Expertise in physics has been traditionally studied in cognitive science, where physics expertise is understood through the difference between novice and expert problem solving skills. The cognitive perspective of physics experts only create a partial model of physics expertise and does not take into account the development of physics experts in the natural context of research. This dissertation takes a social and cultural perspective of learning through apprenticeship to model the development of physics expertise of physics graduate students in a research group. I use a qualitative methodological approach of an ethnographic case study to observe and video record the …

Self-Assembly Of Helical Ribbons, Yevgeniya V. Zastavker, Neer Asherie, Aleksey Lomakin, Jayanti Pande, Joanne M. Donovan, Joel M. Schnur, George B. Benedek

Yevgeniya V. Zastavker

The self-assembly of helical ribbons is examined in a variety of multicomponent enantiomerically pure systems that contain a bile salt or a nonionic detergent, a phosphatidylcholine or a fatty acid, and a steroid analog of cholesterol. In almost all systems, two different pitch types of helical ribbons are observed: high pitch, with a pitch angle of 54 ± 2°, and low pitch, with a pitch angle of 11 ± 2°. Although the majority of these helices are right-handed, a small proportion of left-handed helices is observed. Additionally, a third type of helical ribbon, with a pitch angle in the range …

Relativistic Transformation Of Phase-Space Distributions, R A. Treumann, R Nakamura, W Baumjohann

Dartmouth Scholarship

We investigate the transformation of the distri- bution function in the relativistic case, a problem of interest in plasma when particles with high (relativistic) velocities come into play as for instance in radiation belt physics, in the electron-cyclotron maser radiation theory, in the vicin- ity of high-Mach number shocks where particles are acceler- ated to high speeds, and generally in solar and astrophysical plasmas. We show that the phase-space volume element is a Lorentz constant and construct the general particle distri- bution function from first principles. Application to thermal equilibrium lets us derive a modified version of the isotropic relativisticthermaldistribution,themodifiedJu …

The Economics Of The Atomic Bomb: Cost And Utilization, Jonathan M. Davis Mr.

Senior Honors Theses

Few moments in human history can be compared to the culmination of events that brought the atomic bomb into creation. It is incredible to contemplate that while a nation was fighting a two front war that spanned from Europe into the Pacific, that the United States was able to utilize the time, energy, brains, materials, manpower, and capital to complete a project in four years. That under any other circumstances would have taken greater than half a century to complete.

First, this thesis will discuss breakthroughs in research that led scientists to believe that the atomic weapons could be built, …