Physics Commons^™

Using Protonation Microstates And Hydrogen Bond Networks To Track Proton Transfer Pathways In Complex I, Umesh Khaniya

Dissertations, Theses, and Capstone Projects

Complex I, NADH-ubiquinone oxidoreductase, is the first enzyme in the mitochondrial and bacterial aerobic respiratory chain. It pumps four protons through four transiently open pathways from the high pH, negative, N- side of the membrane to the positive, P-side driven by the exergonic transfer of electrons from NADH to a quinone. Three protons transfer through subunits descended from Mrp antiporters, while the fourth, E-channel is unique. Because of the complex possible paths thorough the many buried polar residues and lack of high-resolution crystal structure, the path for protons through the E-channel is elusive.

In this dissertation, the E-channel proton pumping …

Control Of Nonlinear Properties Of Van Der Waals Materials, Rezlind Bushati

Dissertations, Theses, and Capstone Projects

Van der Waals materials are a broad class of materials that exhibit unique optoelectronic properties. They provide a rich playground for which they can be integrated into current on-chip devices due to their nanometer-scale size, and be utilized for studying fundamental physics. Strong coupling of emitters to microcavities provides many opportunities for new exotic physics through the formation of hybrid quasi-particles exciton-polaritons. This thesis
focuses on exploring and enhancing nonlinearity of van der Waals materials through strongly coupling to microcavities. By taking advantage of the stacking order of TMDs, we show intense second-harmonic generation from bulk, centrosymmetric TMD systems. In …

Electron Transport In Quantum Systems With Interaction, Sara Abedi

Dissertations, Theses, and Capstone Projects

No abstract provided.

Optical Studies Of Wide Bandgap Photonic Materials, Nikesh Maharjan

Dissertations, Theses, and Capstone Projects

In this dissertation work, optical properties of wide bandgap materials such as hexagonal Boron Nitride (h-BN) and Zinc Oxide (ZnO) have been studied. Deep UV photoluminescence spectroscopy was employed to study the optical properties of bulk h-BN and powder crystals using a laser of wavelength 200 nm, which is the fourth harmonic of Ti:Sapphire laser as excitation source. The properties and chemical compositions of annealed and unannealed bulk h-BN were investigated. The PL spectra from h-BN samples annealed at 900 ºC in ambient air, had strong phonon assisted band edge emissions along with a sharp atomic-like emission line at 4.09 …

Collective Behavior Of Dissipatively-Coupled Photonic Oscillator Networks, Jiajie Ding

Dissertations, Theses, and Capstone Projects

This thesis discusses the collective behavior of networks formed by photonic oscillators. The key motivations for doing this research are the interest in developing high power laser arrays on photonic chips and performing optical computing.

Phase Transitions, Critical Phenomena, And Correlation Functions In The 2d Ising Model And Its Applications To Quantum Dynamics: A Tensor Network Approach, Sankhya Basu

Dissertations, Theses, and Capstone Projects

This thesis explores several aspects of the 2D Ising Model at both real and complex temperatures utilizing tensor network algorithms. We briefly discuss the importance of tensor networks in the context of forming efficient representations of wavefunctions and partition functions for quantum and classical many-body systems respectively, followed by a brief review of the tensor network renormalization algorithms to compute the one point and two point correlation functions. We use the Tensor Renormalization Group (TRG) to study critical phenomena and examine feasibility of accurate estimations of universal critical data for three critical points for three critical points in two dimensions …

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …

Symmetries, Zero Modes And Light Transport In Non-Hermitian Photonics, Jose David Hernandez Rivero

Dissertations, Theses, and Capstone Projects

We approach some fundamental aspects of photonic dissipative systems treated by a non-Hermitian theory. Inspired by the possibilities provided by some major non-Hermitian symmetries, we study systematically the properties of the novel pseudochirality, pseudo-anti-Hermiticity, and supersymmetry. We analyze other aspect of photonics, the zero mode, which has a profound connection to non-Hermitian physics. We propose a scheme to realize a zero mode that exists even in the absence of symmetries. Finally, we approach light transport in non-Hermitian photonic systems, where the introduction of gain and loss can modify drastically the propagation speed of wavepackets.

Charge Transport And Spin Dynamics Of Color Centers In Diamond, Damon Daw

Dissertations, Theses, and Capstone Projects

Solid state defects in diamond are promising candidates for room temperature quantum information processors (1, 3, 5). Chief among these defects is the nitrogen vacancy center (‘NV center’ or ‘NV’). The NV has long coherence times (at 300K) and its state is easily initialized, manipulated and read out (5). However, the outstanding issue of entangling NV centers in a scalable fashion, at room temperature remains a challenge. This thesis presents experimental and theoretical work aimed at achieving this goal by developing the ‘flying qubit’ framework in (1). This method for remote entanglement utilizes a charge carrier (initialized into a definite …

Connections Between Atmospheric Blocking, General Circulation, And Weather Extremes In A Hierarchy Of Models And Various Climates, Veeshan Narinesingh

Dissertations, Theses, and Capstone Projects

The field of geophysical fluid dynamics (GFD) includes the study of both the motion and thermodynamic aspects of the atmosphere. These properties are of particular importance because they directly influence both local and large-scale weather and climate and are associated with various phenomena. One phenomena that is particularly influential is atmospheric blocking. Atmospheric blocks are persistent, quasi-stationary anticyclones (a.k.a. high-pressure systems) that occur in the atmosphere and disrupt the flow. Blocks are known to induce heat extremes and cold spells, as well as steer storms and cause numerous types of hazards. Yet despite the hazards associated with blocks, our current …

Topological Classical Wave Systems With Modulations, Interactions, And Higher-Order Topological States, Mengyao Li

Dissertations, Theses, and Capstone Projects

Topological phases in classical wave systems, such as photonic and acoustic, have been actively investigated and applied for wave guiding, lasing, and numerous other novel phenomena and device applications Topological phase transitions enable robust boundary states, and the field has been broadening recently into a vast variety of systems with temporal modulations and interactions. Floquet modulation, for example, is the modulation applied periodically in time which may break symmetries and leads to novel topological phases.

Introducing non-Hermitian Floquet modulation enables more interesting phenomena including bandgap in imaginary part of the spectrum and gainy/lossy topological edge states with complex energy values. …

Wave Excitation And Dynamics In Disordered Systems, Yiming Huang

Dissertations, Theses, and Capstone Projects

This thesis presents studies of the field and energy excited in disordered systems as well as the dynamics of scattering.

Dynamic and steady state aspects of wave propagation are deeply connected in lossless open systems in which the scattering matrix is unitary. There is then an equivalence among the energy excited within the medium through all channels, the Wigner time delay, which is the sum of dwell times in all channels coupled to the medium, and the density of states. But these equivalences fall away in the presence of material loss or gain. In this paper, we use microwave measurements, …

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. …

Monte Carlo, Molecular Dynamics And Network Analysis Of The Gramicidin Water Channel And Proton Transfer Pathways To Qb In Photosynthetic Reaction Centers, Yingying Zhang

Dissertations, Theses, and Capstone Projects

Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields such as used in MCCE (Multi-Conformation Continuum Electrostatics) capture electrostatic interactions in biomolecules with an implicit solvent, to give the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen …

Diffraction-Based Studies Of Magneto- And Baro-Caloric Materials, Steven P. Vallone

Dissertations, Theses, and Capstone Projects

The field of calorics represents a class of materials that offer the potential for solid-state cooling and heating, and, given the global climate crisis, comprise a necessary and active area of research. A clear and thorough understanding of their internal structural interactions and their external response to the environment is necessary for overall progress in the field, as accurate theoretical modeling and efficient materials design for devices both depend on this information. Through analysis of x-ray and neutron diffraction, the atomic order and disorder that drives these interactions is revealed. This dissertation focuses on diffraction studies concerning representative samples from …

Developing Dynamical Probes Of Quantum Spin Liquids Inspired By Techniques From Spintronics, Joshua Aftergood

Dissertations, Theses, and Capstone Projects

We theoretically study low dimensional insulating spin systems using spin fluctuations as a probe of the spin dynamics. In some systems, low dimensionality in conjunction with other quantum fluctuation enhancing effects impedes spontaneous generation of long range magnetic ordering down to zero absolute temperature. In particular, we focus on exotic spin systems hosting mobile, fractionalized spin excitations above their ground state, and ultimately show that techniques already commonplace in spintronics can be utilized in the context of quantum magnetism to develop probes of exotic ground states.

We initially consider quantum spin chains (QSCs), and examine a system of two exchange-coupled …

Nonlinear Optical Studies Of Interfacial Ferroelectricity And Strain Distribution In Perovskite Dielectric Films, Tony Le

Dissertations, Theses, and Capstone Projects

Dielectric and ferroelectric perovskite films have been model energy storage structures for their low-dielectric loss, extremely high charge-discharge speed, and good temperature stability, yet there is still much to understand about the material’s limitations. This dissertation presents a detailed understanding of the strain-induced ferroelectricity at the boundary between a strontium titanate (SrTiO₃) ultrathin film epitaxially grown on a germanium (Ge) substrate through optical second harmonic generation (SHG), and the polydomain distribution in the Zr-doped BaTiO₃ (BZT) films by time-resolved pump-probe spectroscopy.

First, SHG measurements were performed to reveal interfacial ferroelectricity in the epitaxial SrTiO₃/Ge (100) …

Linear And Non Linear Properties Of Two-Dimensional Exciton-Polaritons, Mandeep Khatoniar

Dissertations, Theses, and Capstone Projects

Technology has been accelerating at breakneck speed since the first quantum revolution, an era that ushered transistors and lasers in the late 1940s and early 1960s. Both of these technologies relied on a matured understanding of quantum theories and since their inception has propelled innovation and development in various sectors like communications, metrology, and sensing. Optical technologies were thought to be the game changers in terms of logic and computing operations, with the elevator pitch being "computing at speed of light", a fundamental speed limit imposed by this universe’s legal system (a.k.a physics). However, it was soon realized that that …

Skyrmions And Biskyrmions In Magnetic Films, Daniel Capic

Dissertations, Theses, and Capstone Projects

Skyrmions have garnered significant attention in condensed matter systems in recent years. In principle, they are topologically protected, so there is a large energy barrier preventing their annihilation. Furthermore, they can exist at the nanoscale, be manipulated with very small currents, and be created by a number of different methods. This makes them attractive for use in potential computing applications. This work studies ferromagnetic skyrmions. In particular, it highlights our small contributions to the field of skyrmions in condensed matter systems, specifically in thin-film ferromagnets.

Optimization Of Materials For Magnetic Refrigeration And Thermomagnetic Power Generation, Anthony N. Tantillo

Dissertations, Theses, and Capstone Projects

The magnetocaloric effect, by which a magnetic material experiences a change in temperature due to an applied magnetic field, can be used for refrigeration. The corollary to the magnetocaloric effect -- known as the pyromagnetic effect -- is the phenomenon by which a magnetic material experiences a thermally-induced change in magnetization that can be used to harvest thermal energy. This dissertation has two main parts: one focusing on novel materials for energy harvesting; and another focusing on methods of materials discovery for refrigeration purposes. Thermomagnetic power generation (TMG) is the process by which magnetic flux, which comes from a temperature-driven …

Quantum Transport In Topological Magnets, Haiming Deng

Dissertations, Theses, and Capstone Projects

In the past several years, a new field of symmetry-protected topological materials has emerged in condensed matter physics, based on the wide range of consequences that result from the realization that certain properties of physical systems can be expressed as topological invariants, which are insensitive to local perturbations. This new class of materials hosts unique surface/edge states, such as the first known topological system – quantum Hall insulator with dissipationless chiral edge states, and massless spin-helical Dirac surface states in 3D topological insulators that are unlike any other known 1D or 2D electronic systems. In this thesis, to understand the …

Third Harmonic Generation: A Method For Visualizing Myelin In The Murine Cerebral Cortex, Michael Redlich

Dissertations, Theses, and Capstone Projects

Here we present the use of Third Harmonic Generation (THG) for the label-free imaging of myelinated axons in the murine cerebral cortex. Myelin plays an important role in the processes of learning and disease. However, much of the myelin biology research thus far has focused on white matter tracts where myelin is more visible. Much is still unknown, particularly with regard to myelin in gray matter. First, we engage in THG microscopy using an optical parametric oscillator pumped by a titanium-sapphire laser to demonstrate the utility of the technique for imaging myelin in vivo. Second, we investigate the use of …

Frozen In Time: A Numerical Modeling Approach To The Study Of Ice Bearing Planetesimals Through Carbonaceous Chondrites, Jasmine M. Bayron

Dissertations, Theses, and Capstone Projects

Icy planetesimals are significant objects of study for meteoritics, planetary science, and astrobiology due to their connections to the origins of life and liquid water on Earth. An existing closed system aqueous alteration model was adapted to simulate several scenarios involving early Solar System geologic processes occurring in an icy planetesimal interior. The model described in this work has been developed not only to test the validity of constraints currently thought to apply to CM1 parent bodies, but to directly compare the implications of these constraints for the isotopic composition and the modal mineralogy of carbonaceous chondrites. Isotopic ratios of …

Interactions Of Organic Fluorophores With Plasmonic Surface Lattice Resonances, Robert J. Collison

Dissertations, Theses, and Capstone Projects

It is common knowledge that metals, alloys and pure elements alike, are lustrous and reflective, the more so when a metal surface is flat, polished, and free from oxidation and surface fouling. However, some metals reflect visible light, in the 380 nm to 740 nm range of wavelengths, much more strongly than others. In particular, some metals reflect wavelengths in certain portions of the ultraviolet (UV), visible, and near-infrared (NIR) regime, let us say 200 nm to 2000 nm, while absorbing light strongly in other segments of this range. There are several factors that account for this difference between various …

Mechanism Of Action Of Dihydropteridine Reductase, Gabriela Arias De La Rosa

Dissertations, Theses, and Capstone Projects

Human dihydropteridine reductase is an enzyme that transfers a hydride from NADH to reduce quinonoid 7,8-dihydropterin (qBH₂) to 5,6,7,8-tetrahydropterin (BH₄), which is a cofactor important in the production of neurotransmitters.DHPR deficiency causes a drastic form of the neurological genetic disease phenylketonuria (PKU) that does not benefit from a phenylalanine-free diet.From site-directed mutagenesis studies, mostly on Rat DHPR, we know that certain residues are important for cofactor binding, substrate binding, and hydride transfer; however, there are still some questions about how DHPR works, particularly, because there is not a crystal structure of the tertiary complex: What is …

Role Of Protonation State Changes And Hydrogen Bonding Around The Oxygen Evolving Complex Of Photosystem Ii, Divya Matta

Dissertations, Theses, and Capstone Projects

The mechanism of natural photosynthesis involves the use of solar energy to produce O₂ we breathe and food and fuel we intake. This process results in the biological oxidation of water that takes place at room temperature, neutral pH using earth abundant elements Ca and Mn. Understanding how this challenging chemical reaction occurs in photosynthesis can be useful for designing better artificial photosynthetic complexes that can be used as biofuels. My doctoral work is to study the deprotonation and oxidation events elucidating the mechanistic details of proton coupled electron transfer reaction in a photosynthetic protein.

The O₂ evolution …

Using The Marcus Inverted Region And Artificial Cofactors To Create A Charge Separated State In De Novo Designed Proteins, Eskil Me Andersen

Dissertations, Theses, and Capstone Projects

To create an efficient de novo photosynthetic protein it is important to create long lived charge separated states. Achieving stable charge separation leads to an increase in the efficiency of the photosynthetic reaction which in turn leads to higher yields of end products, such as biofuels, electrical charge, or synthetic chemicals. In an attempt to create charge separated states in de novo proteins we hypothesized that we could engineer the free energy gaps in the proteins from excited primary donor (PD) to acceptor (A), and A back to ground state PD such that the forward electron transfer (ET) would be …

Emulating Condensed Matter Systems In Classical Wave Metamaterials, Matthew Weiner

Dissertations, Theses, and Capstone Projects

One of the best tools we have for the edification of physics is the analogy. When we take our classical set of states and dynamical variables in phase space and treat them as vectors and Hermitian operators respectively in Hilbert space through the canonical quantization, we lose out on a lot of the intuition developed with the previous classical physics. With classical physics, through our own experiences and understanding of how systems should behave, we create easy-to-understand analogies: we compare the Bohr model of the atom to the motion of the planets, we compare electrical circuits to the flow of …

An Accurate Solution Of The Self-Similar Orbit-Averaged Fokker-Planck Equation For Core-Collapsing Isotropic Globular Clusters: Properties And Application, Yuta Ito

Dissertations, Theses, and Capstone Projects

Hundreds of dense star clusters exist in almost all galaxies. Each cluster is composed of approximately ten thousand through ten million stars. The stars orbit in the clusters due to the clusters' self-gravity. Standard stellar dynamics expects that the clusters behave like collisionless self-gravitating systems on short time scales (~ million years) and the stars travel in smooth continuous orbits. Such clusters temporally settle to dynamically stable states or quasi-stationary states (QSS). Two fundamental QSS models are the isothermal- and polytropic- spheres since they have similar structures to the actual core (central part) and halo (outskirt) of the clusters. The …

Particle Dynamics In Anti-De Sitter Space By Eih Method, Jiusi Lei

Dissertations, Theses, and Capstone Projects

Following the work of Einstein, Infeld and Hoffmann, we show that particle dynamics in Anti-de Sitter spacetime can be built up by regarding singularities in spacetime manifold as the source of particles.

Since gauge fields play a foundational role in the action, the singularities are chosen to be point-like instantons. Their winding number, defined by an integration on the spheres surrounding those singularities, will turn out to be related to their masses. And their action, derived from the Chern-Simons forms, will be a co-adjoint orbit action, with group element g ∈ SO(4, 2) describing the collective coordinates of the particle. …