Numerical Analysis and Scientific Computing Commons^™

Mechanistic Investigation Of C—C Bond Activation Of Phosphaalkynes With Pt(0) Complexes, Roberto M. Escobar, Abdurrahman C. Ateşin, Christian Müller, William D. Jones, Tülay Ateşin

Research Symposium

Carbon–carbon (C–C) bond activation has gained increased attention as a direct method for the synthesis of pharmaceuticals. Due to the thermodynamic stability and kinetic inaccessibility of the C–C bonds, however, activation of C–C bonds by homogeneous transition-metal catalysts under mild homogeneous conditions is still a challenge. Most of the systems in which the activation occurs either have aromatization or relief of ring strain as the primary driving force. The activation of unstrained C–C bonds of phosphaalkynes does not have this advantage. This study employs Density Functional Theory (DFT) calculations to elucidate Pt(0)-mediated C–CP bond activation mechanisms in phosphaalkynes. Investigating the …

Spectralomics – Towards A Holistic Adaptation Of Label Free Spectroscopy, Hugh Byrne

Articles

Vibrational spectroscopy, largely based on infrared absorption and Raman scattering techniques, is much vaunted as a label free approach, delivering a high content, holistic characterisation of a sample, with demonstrable applications in a broad range of fields, from process analytical technologies and preclinical drug screening, to disease diagnostics, therapeutics, prognostics and personalised medicine. However, in the analysis of such complex systems, a trend has emerged in which spectral analysis is reduced to the identification of individual peaks, based on reference tables of assignments derived from literature, which are then interpreted as biomarkers. More sophisticated analysis attempts to unmix the spectrum …

The Application Of Novel Machine Learning Algorithms To Study Multi-Dimensional Fragmentation Functions Of Hadrons In Jets At Star, Hannah A. Harrison-Smith

Theses and Dissertations--Physics and Astronomy

Hadronization, the process by which colored quarks and gluons shower from high energy collisions and recombine to form stable, experimentally-observable particles, is a fundamental aspect of Quantum Chromodynamics (QCD) that is not yet fully understood. Fragmentation functions, typically measured in electron-positron collisions, encapsulate this hadronization process well for quarks. Studying proton-proton collisions offers direct access to gluon fragmentation that other channels like electron-positron do not. Recent theoretical developments have proposed the study of hadronic showers in groupings called jets, introducing the concept of multi-dimensional jet fragmentation functions. This thesis presents the extraction of collinear and transverse momentum-dependent fragmentation functions for …

Bacterial Motion And Spread In Porous Environments, Yasser Almoteri

Dissertations

Micro-swimmers are ubiquitous in nature from soil and water to mammalian bodies and even many technological processes. Common known examples are microbes such as bacteria, micro-algae and micro-plankton, cells such as spermatozoa and organisms such as nematodes. These swimmers live and have evolved in multiplex environments and complex flows in the presence of other swimmers and types, inert particles and fibers, interfaces and non-trivial confinements and more. Understanding the locomotion and interactions of these individual micro-swimmers in such impure viscous fluids is crucial to understanding the emergent dynamics of such complex systems, and to further enabling us to control and …

Enhanced Quantum Chemistry With Machine Learning, Brock Dyer

Physics and Astronomy Summer Fellows

This file is a catalogue of the relevant quantum mechanical and computer programming topics that I learned during the summer which will be helping me to generate an artificial intelligence that will be able to perform computational chemical calculations at a much faster rate and comparable or better accuracy than current methods.

Optical Response Of 3d Model Topological Nodal-Line Semimetal, Sita Kandel, Godfrey Gumbs, Oleg L. Berman

Publications and Research

Wepresent a semi-analytical expression for both longitudinal and transverse optical conductivities of a model TNLSM employing the Kubo formula with emphasis on the optical spectral weight redistribution, deduced from appropriate Green’s func tions. In this semimetal, the conduction and valence bands cross each other along a one- dimensional curve protected by certain symmetry group in the 3D Brillouin zone. Although the crossing cannot be removed by any perturbations, it can be adjusted by continuous tuning of the Hamiltonian with a parameter α. When α>0, the two bands cross each other near the Γ point in the (kx,ky) plane of …

Monolithic Multiphysics Simulation Of Hypersonic Aerothermoelasticity Using A Hybridized Discontinuous Galerkin Method, William Paul England

Theses and Dissertations

This work presents implementation of a hybridized discontinuous Galerkin (DG) method for robust simulation of the hypersonic aerothermoelastic multiphysics system. Simulation of hypersonic vehicles requires accurate resolution of complex multiphysics interactions including the effects of high-speed turbulent flow, extreme heating, and vehicle deformation due to considerable pressure loads and thermal stresses. However, the state-of-the-art procedures for hypersonic aerothermoelasticity are comprised of low-fidelity approaches and partitioned coupling schemes. These approaches preclude robust design and analysis of hypersonic vehicles for a number of reasons. First, low-fidelity approaches limit their application to simple geometries and lack the ability to capture small scale flow …

Machine Learning-Based Data And Model Driven Bayesian Uncertanity Quantification Of Inverse Problems For Suspended Non-Structural System, Zhiyuan Qin

All Dissertations

Inverse problems involve extracting the internal structure of a physical system from noisy measurement data. In many fields, the Bayesian inference is used to address the ill-conditioned nature of the inverse problem by incorporating prior information through an initial distribution. In the nonparametric Bayesian framework, surrogate models such as Gaussian Processes or Deep Neural Networks are used as flexible and effective probabilistic modeling tools to overcome the high-dimensional curse and reduce computational costs. In practical systems and computer models, uncertainties can be addressed through parameter calibration, sensitivity analysis, and uncertainty quantification, leading to improved reliability and robustness of decision and …

Practical Implementation Of The Immersed Interface Method With Triangular Meshes For 3d Rigid Solids In A Fluid Flow, Norah Hakami

Mathematics Theses and Dissertations

When employing the immersed interface method (IIM) to simulate a fluid flow around a moving rigid object, the immersed object can be replaced by a virtual fluid enclosed by singular forces on the interface between the real and virtual fluids. These forces represent the impact of the rigid motion on the fluid flow and cause jump discontinuities across the interface in the whole flow field. Then, the IIM resolves the fluid flow on a fixed computational domain by directly incorporating the jump conditions across the interface into numerical schemes. Previous development of the method is limited to simple smooth boundaries. …

Phys 275: Intro To Scientific Computing, David Goldberg

Open Educational Resources

No abstract provided.

Probability Distributions Of The Scalar Potential, Candace Mathews

Legacy Theses & Dissertations (2009 - 2024)

In the study of cosmological inflation, string theory and supersymmetry have motivated a wide range of possible inflationary models. These models can be parameterized by a scalar potential V, which is a function of N scalar fields, and determines cosmological parameters such as the vacuum stability and energy density. In principle, we can determine V through high energy physics, such as string theory. In practice, though we may not know the details of V we might have clues about a distribution of plausible V’s, which we can build statistics on to further analyze. The purpose of this thesis defense is …

Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers

Legacy Theses & Dissertations (2009 - 2024)

Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …

Denoising And Deconvolving Sperm Whale Data In The Northern Gulf Of Mexico Using Fourier And Wavelet Techniques, Kendal Mccain Leftwich

LSU New Orleans Theses and Dissertations

The use of underwater acoustics can be an important component in obtaining information from the oceans of the world. It is desirable (but difficult) to compile an acoustic catalog of sounds emitted by various underwater objects to complement optical catalogs. For example, the current visual catalog for whale tail flukes of large marine mammals (whales) can identify even individual whales from their individual fluke characteristics. However, since sperm whales, Physeter microcephalus, do not fluke up when they dive, they cannot be identified in this manner. A corresponding acoustic catalog for sperm whale clicks could be compiled to identify individual …

The Interaction Of Different Primary Producers And Physical And Chemical Dynamics Of An Urban Shallow Lake, Majid Sahin

Dissertations, Theses, and Capstone Projects

An artificial urban shallow lake, Prospect Park Lake (PPL), is situated on a terminal moraine in Brooklyn New York, and supplied with municipal water treated with ortho-phosphates. The constant input of the phosphate nutrient is the primary source of eutrophication in the lake. The numerous pools along the water course houses various aquatic phototrophs, which influence the water quality and the state of the system, driving conditions into favoring the survival of their species. In the first half of the dissertation, the focus of the project is on analyzing how the different primary producers in different regions of PPL affect …

Computational Models To Detect Radiation In Urban Environments: An Application Of Signal Processing Techniques And Neural Networks To Radiation Data Analysis, Jose Nicolas Gachancipa

Beyond: Undergraduate Research Journal

Radioactive sources, such as uranium-235, are nuclides that emit ionizing radiation, and which can be used to build nuclear weapons. In public areas, the presence of a radioactive nuclide can present a risk to the population, and therefore, it is imperative that threats are identified by radiological search and response teams in a timely and effective manner. In urban environments, such as densely populated cities, radioactive sources may be more difficult to detect, since background radiation produced by surrounding objects and structures (e.g., buildings, cars) can hinder the effective detection of unnatural radioactive material. This article presents a computational model …

Fiesta And Shock-Driven Flows, Brian E. Romero

Mechanical Engineering ETDs

In this study, the interaction of a shock with various gas and particle interfaces is analyzed through simulations using a new, GPU capable, multi-species flow solver, FIESTA (Fast, Interface Evolution, Shocks, and Transport in the Atmosphere), de- veloped for this research. The cases studied include the interaction between a shock and i) a two-dimensional (2D), circular cloud of a dense gas; ii) a 2D curtain of a dense gas; iii) a three-dimensional (3D) cylinder of a dense gas, and iv) a 3D curtain of solid particles.

In simulations of a 2D gas curtain and a 3D gas column, the curtain …

Neutron Interferometry Using A Single Modulated Phase Grating, Ivan J. Hidrovo Giler

LSU Master's Theses

Neutron grating interferometry provides information on phase and small-angle scatter in addition to attenuation. Previously, phase grating moiré interferometers (PGMI) with two or three phase gratings have been developed. These phase-grating systems use the moiré far-field technique to avoid the need for high-aspect absorption gratings used in Talbot-Lau interferometers (TLI) which reduce the neutron flux reaching the detector. We demonstrate through simulations a novel phase grating interferometer system for cold neutrons that requires a single modulated phase grating (MPG) for phase-contrast imaging, as opposed to the two or three phase gratings in previously employed PGMI systems. We compare the MPG …

Implementation Of A Least Squares Method To A Navier-Stokes Solver, Jada P. Lytch, Taylor Boatwright, Ja'nya Breeden

Rose-Hulman Undergraduate Mathematics Journal

The Navier-Stokes equations are used to model fluid flow. Examples include fluid structure interactions in the heart, climate and weather modeling, and flow simulations in computer gaming and entertainment. The equations date back to the 1800s, but research and development of numerical approximation algorithms continues to be an active area. To numerically solve the Navier-Stokes equations we implement a least squares finite element algorithm based on work by Roland Glowinski and colleagues. We use the deal.II academic library , the C++ language, and the Linux operating system to implement the solver. We investigate convergence rates and apply the least squares …

Seizure Prediction In Epilepsy Patients, Gary Dean Cravens

NSU REACH and IPE Day

Purpose/Objective: Characterize rigorously the preictal period in epilepsy patients to improve the development of seizure prediction techniques. Background/Rationale: 30% of epilepsy patients are not well-controlled on medications and would benefit immensely from reliable seizure prediction. Methods/Methodology: Computational model consisting of in-silico Hodgkin-Huxley neurons arranged in a small-world topology using the Watts-Strogatz algorithm is used to generate synthetic electrocorticographic (ECoG) signals. ECoG data from 18 epilepsy patients is used to validate the model. Unsupervised machine learning is used with both patient and synthetic data to identify potential electrophysiologic biomarkers of the preictal period. Results/Findings: The model has shown states corresponding to …

Atomistic Simulation Of Na+ And Cl- Ions Binding Mechanisms To Tobermorite 14Å As A Model For Alkali Activated Cements, Ahmed Abdelkawy

Theses and Dissertations

The production of ordinary Portland cement (OPC) is responsible for ~8% of all man-made CO2 emissions. Unfortunately, due to the continuous increase in the number of construction projects, and since virtually all projects depend on hardened cement from the hydration of OPC as the main binding material, the production of OPC is not expected to decrease. Alkali-activated cement produced from the alkaline activation of byproducts of industries, such as iron and coal industries, or processed clays represents a potential substitute for OPC. However, the interaction of the reaction products of AAC with corrosive ions from the environment, such as Cl-, …

Coupled Dynamics Of Spin Qubits In Optical Dipole Microtraps: Application To The Error Analysis Of A Rydberg-Blockade Gate, L. V. Gerasimov, R. R. Yusupov, A. D. Moiseevsky, I. Vybornyi, K. S. Tikhonov, S. P. Kulik, S. S. Straupe, Charles I. Sukenik, D. V. Kupriyanov

Physics Faculty Publications

Single atoms in dipole microtraps or optical tweezers have recently become a promising platform for quantum computing and simulation. Here we report a detailed theoretical analysis of the physics underlying an implementation of a Rydberg two-qubit gate in such a system—a cornerstone protocol in quantum computing with single atoms. We focus on a blockade-type entangling gate and consider various decoherence processes limiting its performance in a real system. We provide numerical estimates for the limits on fidelity of the maximally entangled states and predict the full process matrix corresponding to the noisy two-qubit gate. We consider different excitation geometries and …

High Performance Data Acquisition And Analysis Routines For The Nab Experiment, David Mathews

Theses and Dissertations--Physics and Astronomy

Probes of the Standard Model of particle physics are pushing further and further into the so-called “precision frontier”. In order to reach the precision goals of these experiments, a combination of elegant experimental design and robust data acquisition and analysis is required. Two experiments that embody this philosophy are the Nab and Calcium-45 experiments. These experiments are probing the understanding of the weak interaction by examining the beta decay of the free neutron and Calcium-45 respectively. They both aim to measure correlation parameters in the neutron beta decay alphabet, a and b. The parameter a, the electron-neutrino correlation coefficient, is …

Analysis Of Titan's Fluvial Features Using Numerical Modeling, Jeshurun Horton

Mechanical Engineering Undergraduate Honors Theses

River channels have been observed near the Huygens probe landing site on the surface of Titan, along with evidence of rounded water ice boulders transported through fluid flow. Evidence near the landing site suggests active flow of liquid methane, which has motivated the study of the effects of sediment load and channel sizes on Titan’s fluvial features. A numerical model is used to determine the viscosity, flow velocity, and critical boulder transport diameter based on channel size, slope, and a range of sediment concentrations. This model achieves two ends: first, observed boulder diameters are used to determine the ideal channel …

Acoustic/Gravity Wave Phenomena In Wide-Field Imaging: From Data Analysis To A Modeling Framework For Observability In The Mlt Region And Beyond, Jaime Aguilar Guerrero

Doctoral Dissertations and Master's Theses

Acoustic waves, gravity waves, and larger-scale tidal and planetary waves are significant drivers of the atmosphere’s dynamics and of the local and global circulation that have direct and indirect impacts on our weather and climate. Their measurements and characterization are fundamental challenges in Aeronomy that require a wide range of instrumentation with distinct operational principles. Most measurements share the common features of integrating optical emissions or effects on radio waves through deep layers of the atmosphere. The geometry of these integrations create line-of-sight effects that must be understood, described, and accounted for to properly present the measured data in traditional …

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

The Foundations Of Inference And Its Application To Fundamental Physics, Nicholas Matthew Carrara

Legacy Theses & Dissertations (2009 - 2024)

This thesis concerns the foundations of inference – probability theory,entropic inference, information geometry, etc. – and its application to the Entropic Dynamics (ED) approach to Quantum Mechanics (QM) [21, 22, 41, 53, 56–61, 150–153, 165, 195, 196, 268]. The first half of this thesis, chapters 2-6, concern the development of the inference framework. We begin in chapter 2 by discussing de- ductive inference, which involves formal logic and it’s role in access- ing the truth of propositions. We eventually discover that deductive inference is incomplete, in that it can’t address situations in which we have incomplete information. This necessitates a …

Computational Studies Of Carbon Nanocluster Solidification, Chathuri C. Silva

Dissertations

A subset of micron-size meteoritic carbon particles formed in red giant atmospheres show a core-rim structure, likely condensed from a vapor phase into super-cooled carbon droplets that nucleated graphene sheets (~40Å) on randomly oriented 5-atom loops during solidification, followed by coating with a graphite rim. Similar particles form during slow cooling of carbon vapor in the lab.

Here we investigate the nucleation and growth of carbon rings and graphene sheets using density functional theory (DFT). Our objectives: (1). explore different computational techniques in DFT-VASP for various carbon structures and compare the results with literature, (2). investigate the nucleation and growth …

Knot Theory In Virtual Reality, Donald Lee Price

Masters Theses & Specialist Projects

Throughout the study of Knot Theory, there have been several programmatic solutions to common problems or questions. These solutions have included software to draw knots, software to identify knots, or online databases to look up pre-computed data about knots. We introduce a novel prototype of software used to study knots and links by using Virtual Reality. This software can allow researchers to draw links in 3D, run physics simulations on them, and identify them. This technique has not yet been rigorously explored and we believe it will be of great interest to Knot Theory researchers. The computer code is written …

Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei

Mathematics Faculty Publications

While automated feature extraction has had tremendous success in many deep learning algorithms for image analysis and natural language processing, it does not work well for data involving complex internal structures, such as molecules. Data representations via advanced mathematics, including algebraic topology, differential geometry, and graph theory, have demonstrated superiority in a variety of biomolecular applications, however, their performance is often dependent on manual parametrization. This work introduces the auto-parametrized weighted element-specific graph neural network, dubbed AweGNN, to overcome the obstacle of this tedious parametrization process while also being a suitable technique for automated feature extraction on these internally complex …

Quantum Simulation Of Schrödinger's Equation, Mohamed Eltohfa

Capstone and Graduation Projects

Quantum computing is one of the promising active areas in physics research. This is because of the potential of quantum algorithms to outperform their classical counterparts. Grover’s search algorithm has a quadratic speed-up compared to the classical linear search. The quantum simulation of Schrödinger’s equation has an exponential memory save-up compared to the classical simulation. In this thesis, the ideas and tools of quantum computing are reviewed. Grover’s algorithm is studied and simulated as an example. Using the Qiskit quantum computing library, a code to simulate Schrödinger’s equation for a particle in one dimension is developed, simulated locally, and run …