Physics Commons^™

Interdisciplinary Studies Of Complex Network And Machine Learning And Its Applications, Shaojun Luo

Dissertations, Theses, and Capstone Projects

In this dissertation, we introduce the concept of network-based statistical inference methods of two types: network structure inference and variable inference. For network structure inference, we introduce correlation matrix, graphical Lasso, network clustering and identify the influencer in the network. For variable inference, we also introduce from Bayesian network, to Random Markov Field and Ising Model, Boltzmann and Restricted Boltzmann machine and the algorithm of Belief Propagation. Last but not the least, we introduce the most widely used neural network family and its two main types: Convolutional Neural Network and Recurrent Neural Network.

In Chapter 3 we provide an example …

Baryons And Interactions In Magnetic Fields, Amol Deshmukh

Dissertations, Theses, and Capstone Projects

The QCD external field problem allows one to probe the rich behavior of strongly interacting systems under external conditions, including the modification of hadron structure and interactions due to external electromagnetic fields. These dynamics, moreover, are likely relevant to describe the physics in the interiors of magnetars and in non-central heavy-ion collisions, for which large magnetic fields upwards of $10^{19}$ Gauss are conceivable. Additionally motivated by lattice QCD calculations in external fields, we study the behavior of single- and two-baryon (specifically, two-nucleon) systems in large magnetic fields. The dependence of single-baryon energies on magnetic fields is explored using chiral dynamics. …

Nmr Characterizations Of Candidate Battery Electrolytes, Stephen A. Munoz

Dissertations, Theses, and Capstone Projects

Enormous strides have been made in next-generation power sources to build a more sustainable society. Energy storage has become a limiting factor in our progress, and there are huge environmental and financial incentives to find the next step forward in battery technology. This work discusses NMR methods for characterizing materials for use in battery application, with a special focus on relaxometry and diffusometry. Examples are provided of various recent investigations involving novel candidate electrolyte materials with different collaborators. Works discussed in this thesis include: the characterization of a new disruptive solid polymer electrolyte technology, investigations of the dynamics of super …

Quantum And Classical Transport Of 2d Electrons In The Presence Of Long And Short Range Disorder, Jesse Kanter

Dissertations, Theses, and Capstone Projects

This work focuses on the study of electron transport of 2-D electron gas systems in relation to both fundamental properties of the systems such as disorder and scattering mechanisms, as well as unique magnetoresistance (MR) effects. A large portion of the discussion is built around the use of an in plane magnetic field to vary the ratio between the Zeeman energy between electrons of different spins and the Landau level spacing, creating a tool to control the quantization of the density of states (DOS).

This tool is first used to isolate Quantum Positive Magnetoresistance (QPMR), which grants insight to the …

Supercharged Models Of Intrinsically Disordered Proteins And Their Utility In Sensing, Peter J. Schnatz

Dissertations, Theses, and Capstone Projects

In this thesis I show that greatly increasing the magnitude of a protein’s net charge using surface supercharging transforms that protein into a ligand-gated or counterion-gated conformational molecular switch. To demonstrate this I first modified the designed helical bundle hemoprotein H4 using simple molecular modeling, creating a highly charged protein which both unfolds reversibly at low ionic strength and undergoes the ligand-induced folding transition commonly observed in signal transduction by intrinsically disordered proteins in biology. Due to the high surface charge density, ligand binding to this protein is allosterically activated by low concentrations of divalent cations and the polyamine spermine. …

Charge State Dynamics And Quantum Sensing With Defects In Diamond, Jacob D. Henshaw

Dissertations, Theses, and Capstone Projects

In recent years, defect centers in wide band gap semiconductors such as diamond, have received significant attention. Defects offer great utility as single photon emitters, nanoscale sensors, and quantum memories and registers for quantum computation. Critical to the utility of these defects, is their charge state.

In this dissertation, experiments surrounding the charge state dynamics and the carrier dynamics are performed and analyzed. Extensive studies of the ionization and recombination processes of defects in diamond, specifically, the Nitrogen Vacancy (NV) center, have been performed. Diffusion of ionized charge carriers has been imaged indirectly through the recapture of said carriers by …

A Network Theoretical Approach To Real-World Problems: Application Of The K-Core Algorithm To Various Systems, Kate Burleson-Lesser

Dissertations, Theses, and Capstone Projects

The study of complex networks is, at its core, an exploration of the mechanisms that control the world in which we live at every scale, from particles no bigger than a grain of sand and amino acids that comprise proteins, to social networks, ecosystems, and even countries. Indeed, we find that, regardless of the physical size of the network's components, we may apply principles of complex network theory, thermodynamics, and statistical mechanics to not only better understand these specific networks, but to formulate theories which may be applied to problems on a more general level. This thesis explores several networks …

Direct Experimental Evidence Of Toroidal Symmetry In A Lanthanide-Based Molecular Magnet, Qing Zhang

Dissertations, Theses, and Capstone Projects

Molecular magnets (MM) are finite clusters of identical exchange-coupled magnetic systems arranged within a crystalline array such that interactions between neighboring MMs are negligible. Their small size has proven them amenable test beds for the investigation of a wide range of fundamental quantum phenomena such as spin frustration quantum tunneling (QT) of magnetization and Neel vector quantum coherence and Berry phase interference.

Cases where MMs have been found to exhibit quantum wave-functions that evolve coherently are particularly interesting due to their potential for use in quantum information processing. Toroidal magnetic moments, a kind of MM, have fascinating properties that could …

N-Representability In The Quantum Kernel Energy Method, Walter Polkosnik

Dissertations, Theses, and Capstone Projects

The Kernel Energy Method (KEM) delivers accurate full molecule energies using less computational resources than standard ab-initio quantum chemical approaches. KEM achieves this efficiency by decomposing a system of atoms into disjoint subsets called kernels. The results of full ab-initio calculations on each individual single kernel and on each double kernel formed by the union of each pair of single kernels are combined in an equation of a form that is specific to KEM to provide an approximation to the full molecule energy. KEM has been demonstrated to give accurate molecular energies over a wide range of systems, chemical methods …

Optimization Of Cuinxga1-Xse2 Solar Cells With Post Selenization, Zehra Cevher

Dissertations, Theses, and Capstone Projects

The chalcopyrite semiconductor CuIn_xGa_1-xSe₂ is considered as the most promising material for high efficiency thin film solar cells due to its exceptional radiation stability, tunable direct bandgap, high light absorption coefficient and low cost preparation methods. In this thesis, we present the systematic investigation of the deposition conditions to optimize the CuIn_xGa_1-xSe₂ device performance using the two-step deposition method. Further, we utilized nonlinear optical methods to investigate the deposition parameters to optimize the bulk and interface properties of photovoltaic devices.

First, we investigated the deposition parameters to optimize the structural, …

Standard And Anomalous Wave Transport Inside Random Media, Xujun Ma

Dissertations, Theses, and Capstone Projects

This thesis is a study of wave transport inside random media using random matrix theory. Anderson localization plays a central role in wave transport in random media. As a consequence of destructive interference in multiple scattering, the wave function decays exponentially inside random systems. Anderson localization is a wave effect that applies to both classical waves and quantum waves. Random matrix theory has been successfully applied to study the statistical properties of transport and localization of waves. Particularly, the solution of the Dorokhov-Mello-Pereyra-Kumar (DMPK) equation gives the distribution of transmission.

For wave transport in standard one dimensional random systems in …

Finding Paths Via Quantum Systems And Its Application For Quantum Algorithms, Daniel S. Koch

Dissertations, Theses, and Capstone Projects

The field of Quantum Information Theory provides the theoretical foundation for the pursuit of quantum computers. The ongoing questions of how quantum computers will be realized and what they will achieve, are both very uncertain. However, worldwide efforts are beginning to converge on some answers, and the future of quantum computers is looking brighter than ever. In contribution to the grand goal that is quantum computing, this thesis serves as a demonstration to the usefulness of quantum over classical computing. The central theme of my work, and my collaborators, is the exploration of using quantum systems as a tool for …

The Advection-Diffusion Equation And The Enhanced Dissipation Effect For Flows Generated By Hamiltonians, Michael Kumaresan

Dissertations, Theses, and Capstone Projects

We study the Cauchy problem for the advection-diffusion equation when the diffusive parameter is vanishingly small. We consider two cases - when the underlying flow is a shear flow, and when the underlying flow is generated by a Hamiltonian. For the former, we examine the problem on a bounded domain in two spatial variables with Dirichlet boundary conditions. After quantizing the system via the Fourier transform in the first spatial variable, we establish the enhanced-dissipation effect for each mode. For the latter, we allow for non-degenerate critical points and represent the orbits by points on a Reeb graph, with vertices …

Pregnancy Induced Alterations Of Reproductive Tract Collagen And Elastin In A Murine Model, Basant K. Dhital

Dissertations, Theses, and Capstone Projects

This thesis reports on structural and dynamical modifications of reproductive tract elastin and collagen as a function of parity. Pelvic floor dysfunction, including pelvic organ prolapse (POP) is a major concern affecting female health worldwide, leading to surgeries costing billions of dollars annually. Collagen, elastic fibers, and proteoglycans are major extracellular matrix (ECM) components found in connective tissues. Vaginal child birth, advancing age, and disruption or dysfunction of connective tissue are major risk factors of POP. In the female reproductive tract, the assembly of elastic fibers is crucial for the pelvic floor support. Any disturbance in the synthesis, assembly, and …

Physical Applications Of The Geometric Minimum Action Method, George L. Poppe Jr.

Dissertations, Theses, and Capstone Projects

This thesis extends the landscape of rare events problems solved on stochastic systems by means of the \textit{geometric minimum action method} (gMAM). These include partial differential equations (PDEs) such as the real Ginzburg-Landau equation (RGLE), the linear Schroedinger equation, along with various forms of the nonlinear Schroedinger equation (NLSE) including an application towards an ultra-short pulse mode-locked laser system (MLL).

Additionally we develop analytical tools that can be used alongside numerics to validate those solutions. This includes the use of instanton methods in deriving state transitions for the linear Schroedinger equation and the cubic diffusive NLSE.

These analytical solutions are …

Information Content, Charge Transport Properties, And Computational Capacities Of Proteins, Joseph Murphy Brisendine Jr.

Dissertations, Theses, and Capstone Projects

This thesis is the beginning of an attempt to build a coherent theory of the properties of proteins based in information theory and the duality of information theory and nonequilibrium thermodynamics. Throughout, we will adopt the viewpoint that information can act as a thermodynamic potential, which is necessary to understand how biological processes are both enabled and constrained by the laws of thermodynamics. Understanding information as a form of thermodynamic potential also clarifies the description of proteins and other biological macromolecules as “molecular machines”: meso-scale structures with emergent causal powers which perform work on their environments by irreversibly dissipating energy …

Investigation Of Novel Electrolytes For Use In Lithium-Ion Batteries And Direct Methanol Fuel Cells, Kartik Pilar

Dissertations, Theses, and Capstone Projects

Energy storage and conversion plays a critical role in the efficient use of available energy and is crucial for the utilization of renewable energy sources. To achieve maximum efficiency of renewable energy sources, improvements to energy storage materials must be developed. In this work, novel electrolytes for secondary batteries and fuel cells have been studied using nuclear magnetic resonance and high pressure x-ray scattering techniques to form a better understanding of dynamic and structural properties of these materials. Ionic liquids have been studied due to their potential as a safer alternative to organic solvent-based electrolytes in lithium-ion batteries and composite …

Effects Of Structural And Electronic Disorder In Topological Insulator Sb2te3 Thin Films, Inna Korzhovska

Dissertations, Theses, and Capstone Projects

Topological quantum matter is a unique and potentially transformative protectorate against disorder-induced backscattering. The ultimate disorder limits to the topological state, however, are still not known - understanding these limits is critical to potential applications in the fields of spintronics and information processing. In topological insulators spin-orbit interaction and time-reversal-symmetry invariance guarantees - at least up to a certain disorder strength - that charge transport through 2D gapless Dirac surface states is robust against backscattering by non-magnetic disorder. Strong disorder may destroy topological protection and gap out Dirac surface states, although recent theories predict that under severe electronic disorder a …

Developing A 3d In Vitro Model By Microfluidics, Hung-Ta Chien

Dissertations and Theses

In vitro tissue models play an important role in providing a platform that mimics the realistic tissue microenvironment for stimulating and characterizing the cellular behavior. In particular, the hydrogel-based 3D in vitro models allow the cells to grow and interact with their surroundings in all directions, thus better mimicking in vivo than their 2D counterparts. The objective of this thesis is to establish a 3D in vitro model that mimics the anatomical and functional complexity of the realistic cancer microenvironment for conveniently studying the transport coupling in porous tissue structures. We pack uniform-sized PEGDA-GelMA microgels in a microfluidic chip to …