Thesis M.S. Michigan State University. Physics 2015.

Charge balance functions have been proposed to study the quark-gluon plasma hypothesized to form in relativistic heavy-ion collisions. Motivated by previous work, a microscopic model is developed that considers the evolution of thermal quark-antiquark pairs in the quark-gluon plasma to calculate hadronic balance functions based on the chemical properties of the plasma. This involves modeling the generation of the quarks given the hydrodynamic properties of the quark-gluon plasma combined with what we know about its chemistry from lattice quantum chromodynamics, as well as modeling the separation of these quarks and their hadronization. After feeding the resulting hadrons into a cascade where they scatter and decay, the balance function for any combination of hadrons species can be calculated.

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Thesis Ph. D. Michigan State University. Physics 2014.

Certain light nuclei are known to have inherent cluster structuring, and the nature of the triple-α structure of carbon isotopes is a subject of active discussion in nuclear physics. Clustering in neutron-rich nuclei is of particular interest as such work could shed light on how neutrons affect α clustering, making ¹⁴C a logical candidate for such a study. Cluster structure in ¹⁴C was investigated at the University of Notre Dame with the prototype Active Target-Time Projection Chamber (AT-TPC). A 38.2 MeV secondary beam of ¹⁰Be was incident on an active target volume containing He:CO₂ 90:10 gas at 1 atm, in which trajectories of beam particles and reaction products were measured using the tracking capabilities of the prototype AT-TPC. Angular correlations of ¹⁰Be and α particles were used to reconstruct kinematics of scattering. Excitation functions and angular distributions were measured in both elastic and inelastic channels, which unraveled a number of resonances in ¹⁴C. Spin-parity assignments have been made for the elastic resonances by R-matrix analysis. Evidence of a positive-parity rotational band has been indicated by the ¹⁴C resonances. The proposed level scheme and the strong resonance strength observed in the inelastic channel are in line with the prediction by the antisymmetrized molecular dynamics (AMD) method indicating linear-chain structure in ¹⁴C. The results also demonstrate unique and powerful potentials of active-target technology in radioactive-beam experiments and are an important step toward the construction of the full-scale AT-TPC for the ReA3 facility at NSCL

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Thesis Ph. D. Michigan State University. Physics 2015

Transcription Factor binding to DNA binding sites is one of the primary causes of generegulation. A common representation of transcription factor binding sites is at the DNAsequence level, partly due to reoccurring patterns at the sequence level that occur throughoutthe genome for a given factor. The first chapter of this dissertation introduces gene regulationfrom the perspective of development. In addition the mathematical-physics foundation forperforming calculations and for representations of the transcription factor binding sites atthe sequence level is discussed in Chapter 1. In Chapter 2 I explore the possibility thattwo distinct sub-types of binding sites may co-exist within a population of functional sites.This leads to a model that can be used for prediction of transcription factor binding sites.In Chapter 3 I explore modelling of Dorsal Ventral early development Gene RegulatoryNetwork, using the tools built up in Chapter 1 and 2, namely 'Position Weight Matrices'that allow for prediction of binding energies for genomic segments of DNA.

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Thesis Ph. D. Michigan State University. Physics - Doctor of Philosophy 2015.

The superconducting fluctuation effect, due to droplets of preformed Cooper pairs above the critical temperature Tc, governs the temperature dependence of kinetic coefficients in superconductors at the onset of the phase transition. The transverse thermoelectric response - Nernst effect - is particularly sensitive to the fluctuations, and the large Nernst signal found in the various superconducting materials has raised much debate on its connection to the origin of unconventional superconductivity. In this thesis, we present a systematic study of the electrical and thermomagnetic transport phenomena in mesoscopic and paramagnetically (Pauli) limited superconductors.In the first chapter of this thesis we concentrate on the study of mesoscopic effects on transport in superconductors. We find that long-range phase coherence developing close to Tc triggers a great amplification of mesoscopic fluctuations due to strong pairing correlations. As a result, mesoscopic conductance fluctuations cease to be universal and exhibit pronounced dependence on temperature. Despite the lack of universality, in the sense of random matrix theory classification, we have discovered a different kind of universality in terms of temperature dependence of fluctuating characteristics. We find that mesoscopic fluctuations of conductivity, transversal thermoelectric coefficient and diamagnetic susceptibility consistently display the same scaling with temperature close to Tc. We connect our results to the existing experimental measurements of conductance fluctuations in superconducting films. Experimental verification of the temperature scaling and the overall magnitude ofthe mesoscopic fluctuations of Nernst coefficient will provide a powerful tool for a better understanding of thermomagnetic transport phenomena in correlated systems.In the second chapter of this thesis we examine the electrical and thermal transport anomalies in the ultra-thin superconducting films in an external in-plane magnetic field. We concentrate on the Clogston-Chandrasekhar phase transition, i.e., the destruction of superconductivity by a magnetic field by virtue of the Zeeman splitting. Near the quantum critical point of the supercooling line in the phase diagram, we discover highly non-monotonic magnetoresistance. The most remarkable feature of this effect is that fluctuation-induced transport is dominated by the virtual excitations rather than real preformed Cooper pairs. We also carefully study how spin-orbit scattering and other pair-breaking effects modify the fluctuation transport. In the strong spin-orbit scattering regime, we find that the scaling of the thermomagnetic coefficient is the same as conductivity within the classical region of transition, however they are drastically different near the quantum critical point. Even though we primarily focus on the conventional superconductors our result for the Nernst effect may have important implications to the other systems, such as…

Thesis Ph. D. Michigan State University. Physics 2015

Nanostructured materials have brought an unprecedented opportunity for advancement in many fields of human endeavor and in applications. Nanostructures are a new research field which may revolutionize people's everyday life. In the Thesis, I have usedtheoretical methods including density functional theory (DFT), molecular dynamic simulations (MD) and tight-binding methods to explore the structural, mechanical and electronic properties of various nanomaterials. In all this, I also paid attention topotential applications of these findings.First, I will briefly introduce the scientific background of this Thesis, including the motivation for the study of a boron enriched aluminum surface, novel carbon foam structures and my research interest in 2D electronics. Then I will review the computational techniques I used in the study, mostly DFT methods.In Chapter 3, I introduce an effective way to enhance surface hardness of aluminum by boron nanoparticle implantation. Using boron dimers to represent the nanoparticles, the process of boron implantation is modeled in a molecular dynamics simulation ofbombarding the aluminum surface by energetic B₂ molecules. Possible metastable structures of boron-coated aluminum surface are identified. Within these structures, I find that boron atoms prefer to stay in the subsurface region of aluminum. By modeling the Rockwell indentation process, boron enriched aluminum surface is found to be harder than the pristine aluminum surface by at least 15%.In Chapter 4, I discuss novel carbon structures, including 3D carbon foam and related 2D slab structures. Carbon foam contains both sp² and sp³ hybridized carbon atoms. It forms a 3D honeycomb lattice with a comparable stability to fullerenes, suggesting possible existence of such carbon foam structures. Although the bulk 3D foam structure is semiconducting, an sp² terminated carbon surface could maintain a conducting channel even when passivated by hydrogen. To promote the experimental realization of this novel foam structure, I also propose a growth model. I postulate that preferred growth should occur near the grain boundary of a carbon saturated polycrystal of transition metal. These findings are supported by a calculation of carbon diffusion in the solid.2D semiconductors of group V elements are discussed in Chapters 5, 6, 7, and 8, including different phosphorus and arsenic structural phases. Structural and electronicproperties of bulk and few-layer black phosphorus, so-called phosphorene, are studiedin Chapter 5. In Chapter 6, I propose a new 2D structural phase of phosphorus,with the name blue phosphorus related to its wide predicted fundamental band gap. Then I move down in the periodic table and investigate the properties of grey arsenic in Chapter 7. Finally, I propose a tiling model to identify and categorize these structural phases in Chapter 8.

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"This dissertation describes a search for a new particle using the largest detector in the world at the highest energy particle collider ever built and is part of an international research program in collaboration with a multinational research group, specifically the search for W′ → t⁻b using the ATLAS detector at CERN."  – Introduction, page 1.

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Thesis Ph. D. Michigan State University. Physics 2016

We study the spectra of fluctuations in linear and nonlinear vibrational systems. Fluctuations play a major role in mesoscopic systems explored in nanomechanics, cavity and circuit quantum electrodynamics, and Josephson junction based systems to mention but a few. We find that important insights into the nature of the fluctuations can be gained by investigating the system dynamics in the presence of periodic driving. This is because the interplay of the driving and fluctuations leads to specific pronounced spectral features. Our predictions are corrobarated by measurements on a carbon nanotube resonator which show that the theory allows one both to reveal and to characterize frequency fluctuations in a vibrational system, as well as to determine the decay rate without ring-down measurements. Our results bear on the general area of decoherence of mesoscopic oscillators and also on the classical problems of resonance fluorescence and light scattering by oscillators. An important and poorly understood mechanism of fluctuations in mesoscopic systems is the dispersive mode coupling. This coupling is inherent essentially to all mesoscopic systems. It comes from the nonlinear interaction between vibrational modes with non-resonating frequencies. We consider the power spectrum of one of these modes. Thermal fluctuations of the modes nonlinearly coupled to it lead to fluctuations of the mode frequency and thus to the broadening of its spectrum. However, the coupling-induced broadening is partly masked by the spectral broadening due to the mode decay. We show that the effect of the mode coupling can be identified and characterized using the change of the spectrum by resonant driving. The theoretical analysis is complicated by the fact that the dispersive-coupling induced fluctuations are non-Gaussian. We develop a path-integral method of averaging over the fluctuations and obtain the power spectrum in an explicit form. The shape of the spectrum depends on the interrelation between the coupling strength and the decay rates of the modes involved, providing a means of characterizing these modes even where they cannot be directly accessed. The analysis is extended to the case of coupling to many modes which, because of the cumulative effect, can become effectively strong. We also find the power spectrum of a driven mode where the mode has internal nonlinearity. Unexpectedly, for a driven mode, the power spectra dominated by the intra- and inter-mode nonlinearities are qualitatively different. The analytical results are in excellent agreement with the numerical simulations.Of significant interest for physics and biophysics are overdamped mesoscopic and microscopic systems. Inertial effects play no role in their dynamics. We show that where such systems are periodically driven, along with the conventional delta-peak at the driving frequency their power spectra display extra features. These can be peaks or dips with height quadratic in the driving amplitude, for weak driving.…

Thesis Ph. D. Michigan State University. Physics 2015.

The nuclear symmetry energy, which is important for asymmetric nuclear systems including rare isotopes and neutron stars, has been studied through both experimental and theoretical approaches, spanning a range of densities from below and above normal nuclear matter density. In the past decade, significant constraints on the density dependence have been obtained in the subsaturation density region, from Heavy Ion Collision (HIC) experiments as well as experiments probing nuclear structure. On the other hand, very little has been determined about the symmetry energy at suprasaturation densities; experimentally, this density region is only accessible in HICs. It is therefore important to understand how to extract nuclear symmetry energy information from HIC at high energies where high density nuclear matter is created in a very brief instant.Symmetry energy constraints from HICs are determined by comparing experimental observables with those calculated using transport models. The goals of this dissertation are to identify the observables most sensitive to the symmetry energy strength, the effective mass splitting, and the in-medium nucleon-nucleon cross sections, σ_NN, at the region just above saturation density which can be created with heavy ion beams available at NSCL. With better constraints in place, the predictive power of transport models will improve. Recent constraints from HIC experiments have relied on symmetric systems, which are predicted to be sensitive to both the density- and the momentum-dependence of the symmetry potentials. In the study of the nuclear equation of state, asymmetric systems have proven to be more effective at low energy in exploring sensitivities to nucleon-nucleon collisions, which is an important input to any transport model.In this work, particles that were emitted from Ca+Sn systems, with a ⁴⁸Ca beam impinging on ¹¹²Sn or ¹²⁴Sn targets are measured. The experimental data were compared to predictions from the Improved Molecular Dynamics model with Skyrme interactions (ImQMD-Sky). Four Skyrme parameter sets were chosen that span current constraints on the density dependence of the symmetry energy and on the nucleon effective mass splitting, m^*_n \neq m^*_p, which results from the momentum dependent interaction potentials. ImQMD-Sky calculations were repeated using an alternate form for σ_NN.The yields and ratios of both free and coalescence invariant experimental spectra, constructed as a function of the transverse momentum, were contrasted to those simulated by ImQMD-Sky. To select the overlap region between beam and target nuclei, a mid-rapidity cut was taken in the analysis. The parameter sets included in this analysis did not show a significant sensitivity to the symmetry energy strength, but do suggest that the neutron-to-proton ratio bears a large sensitivity both to the nucleon effective mass splitting and the σ_NN forms used in the calculations.Comparison to the measured…

The main focus of this dissertation is centered around the study of structural dynamics and phase transition in charge-density waves (CDW) materials. Due to their quasi-reduced dimensionality, a CDW presents a unique system to study the interplay between electron and lattice, effect of symmetry breaking, and electronic condensates. Femtosecond time-resolved pump-probe technique with electron crystallography offers the perfect tool to disentangle the two main players in CDW: electrons and ions. By illumination with intense femtosecond optical pulses to increase the electron energy, we monitor how the energy flows to other subsystems, and explore regions of the energy landscape that are not accessible through conventional methods. Taking advantages of the uniaxial CDW formation of CeTe3 allows us to differentiate non-CDW-related contributions to the lattice response and isolate the CDW-related structural response from the thermal effects on lattice. From the two-component structural dynamics, we examine how strongly the electron and lattice couple to each other, and further distinguish the internal energy transfer between each charge and lattice subsystems. From this CeTe3 experiment, we provide an explanation to a signature phenomena belonging to "classical Peierls" CDW systems. Compared to the classical CDW in CeTe3, 1T-TaS2 is at the other end of spectrum with its well decorated phase diagram including almost all flavors of CDW, Mott insulating, and superconducting states. Utilizing femtosecond photo-doping, we explore the energy landscape for states or phases that are not accessible by other conventional means, like chemical doping and pressure induced modification. The remaining part of this dissertation presents the journey we embarked on when trying to unveil the mystery of water, the ubiquitous molecule that sustains life on earth. Utilizing water delivery system designed specifically for our ultra-high-vacuum chamber, we explore the structural change near the water phase boundary and carrier redistribution or diffusion at the water/nanoparticle/silicon interface.

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