Seeking an upper limit of the Neutron Electric Dipole Moment (nEDM) is a test of charge-parity (CP) violation beyond the Standard Model. The present experimentally tested nEDM upper limit is 3x10^(26) e cm. An experiment to be performed at the Oak Ridge National Lab Spallation Neutron Source (SNS) facility seeks to reach the 3x10^(28) e cm limit. The experiment is designed to probe for a dependence of the neutron's Larmor precession frequency on an applied electric eld. The experiment will use polarized helium-3

(3He) as a comagnetometer, polarization analyzer, and detector.

Systematic influences on the nEDM measurement investigated in this thesis include (a) room temperature measurements on polarized 3He in a measurement cell made from the same materials as the nEDM experiment, (b) research and development of the Superconducting QUantum Interference Devices (SQUID) which will be used in the nEDM experiment, (c) design contributions for an experiment with nearly all the same conditions as will be present in the nEDM experiment, and (d) scintillation studies in superfluid helium II generated from alpha particles which are fundamentally similar to the nEDM scintillation process. The result of this work are steps toward achievement of a new upper limit for the nEDM experiment at the SNS facility.

The challenge of radiation therapy is to maximize the dose to the tumor while simultaneously minimizing the dose elsewhere. Proton therapy is well suited to this challenge due to the way protons slow down in matter. As the proton slows down, the rate of energy loss per unit path length continuously increases leading to a sharp dose near the end of range. Unlike conventional radiation therapy, protons stop inside the patient, sparing tissue beyond the tumor. Proton therapy should be superior to existing modalities, however, because protons stop inside the patient, there is uncertainty in the range. “Range uncertainty” causes doctors to take a conservative approach in treatment planning, counteracting the advantages offered by proton therapy. Range uncertainty prevents proton therapy from reaching its full potential.

A new method of delivering protons, pencil-beam scanning (PBS), has become the new standard for treatment over the past few years. PBS utilizes magnets to raster scan a thin proton beam across the tumor at discrete locations and using many discrete pulses of typically 10 ms duration each. The depth is controlled by changing the beam energy. The discretization in time of the proton delivery allows for new methods of dose verification, however few devices have been developed which can meet the bandwidth demands of PBS.

In this work, two devices have been developed to perform dose verification and monitoring with an emphasis placed on fast response times. Measurements were performed at the Mayo Clinic. One detector addresses range uncertainty by measuring prompt gamma-rays emitted during treatment. The range detector presented in this work is able to measure the proton range in-vivo to within 1.1 mm at depths up to 11 cm in less than 500 ms and up to 7.5 cm in less than 200 ms. A beam fluence detector presented in this work is able to measure the position and shape of each beam spot. It is hoped that this work may lead to a further maturation of detection techniques in proton therapy, helping the treatment to reach its full potential to improve the outcomes in patients.

Measurements of the response of superconducting nanowire single photon detector (SNSPD) devices to changes in various forms of input power can be used for characterization of the devices and for probing device-level physics. Two niobium nitride (NbN) superconducting nanowires developed for use as SNSPD devices are embedded as the inductive (L) component in resonant inductor/capacitor (LC) circuits coupled to a microwave transmission line. The capacitors are low loss commercial chip capacitors which limit the internal quality factor of the resonators to approximately $Qi = 170$. The resonator quality factor, approximately $Qr = 23$, is dominated by the coupling to the feedline and limits the detection bandwidth to on the order of 1MHz. In our experiments with this first generation device, we measure the response of the SNSPD devices to changes in thermal and optical power in both the time domain and the frequency domain. Additionally, we explore the non-linear response of the devices to an applied bias current. For these nanowires, we find that the band-gap energy is $\Delta_0 \approx 1.1$meV and that the density of states at the Fermi energy is $N_0 \sim 10^{10}$/eV/$\mu$m$^3$.

We present the results of experimentation with a superconducting nanowire that can be operated in two detection modes: i) as a kinetic inductance detector (KID) or ii) as a single photon detector (SPD). When operated as a KID mode in linear mode, the detectors are AC-biased with tones at their resonant frequencies of 45.85 and 91.81MHz. When operated as an SPD in Geiger mode, the resonators are DC biased through cryogenic bias tees and each photon produces a sharp voltage step followed by a ringdown signal at the resonant frequency of the detector. We show that a high AC bias in KID mode is inferior for photon counting experiments compared to operation in a DC-biased SPD mode due to the small fraction of time spent near the critical current with an AC bias. We find a photon count rate of $\Gamma_{KID} = 150~$photons/s/mA in a critically biased KID mode and a photon count rate of $\Gamma_{SPD} = 10^6~$photons/s/mA in SPD mode.

This dissertation additionally presents simulations of a DC-biased, frequency-multiplexed readout of SNSPD devices in Advanced Design System (ADS), LTspice, and Sonnet. A multiplexing factor of 100 is achievable with a total count rate of $>5$MHz. This readout could enable a 10000-pixel array for astronomy or quantum communications. Finally, we present a prototype array design based on lumped element components. An early implementation of the array is presented with 16 pixels in the frequency range of 74.9 to 161MHz. We find good agreement between simulation and experimental data in both the time domain and the frequency domain and present modifications for future versions of the array.

This research has studied remote plasma enhanced atomic layer deposited Ga2O3 thin films with gallium acetylacetonate (Ga(acac)3) as Ga precursor and remote inductively coupled oxygen plasma as oxidizer. The Ga2O3 thin films were mainly considered as passivation layers on GaN. Growth conditions including Ga(acac)3 precursor pulse time, O2 plasma pulse time, N2 purge time and deposition temperature were investigated and optimized on phosphorus doped Si (100) wafer to achieve a saturated self-limiting growth. A temperature growth window was observed between 150 ℃ and 320 ℃. Ga precursor molecules can saturate on the substrate surface in 0.6 s in one cycle and the plasma power saturates at 150 W. A growth rate of 0.31 Å/cycle was observed for PEALD Ga2O3. Since the study is devoted towards Ga2O3 working as passivation layer on GaN, the band alignment of Ga2O3 on GaN were further determined with X-ray Photoemission Spectroscopy and Ultraviolet Photoemission Spectroscopy. Two models are often used to decide the band alignment of a heterojunction: the electron affinity model assumes the heterojunction aligns at the vacuum level, and the charge neutrality level model (CNL) which considers the presence of an interface dipole. The conduction band offset (CBO), valence band offset (VBO) and band bending (BB) of PEALD Ga2O3 thin films on GaN were 0.1 ±0.2 eV, 1.0±0.2 eV and 0.3 eV respectively. Type-I band alignments were determined. Further study including using PEALD Ga2O3 as passivation layer on GaN MOS gate and applying atomic layer etching to GaN was described.

The Cosmic Microwave Background (CMB) has provided precise information on the evolution of the Universe and the current cosmological paradigm. The CMB has not yet provided definitive information on the origin and strength of any primordial magnetic fields or how they affect the presence of magnetic fields observed throughout the cosmos. This work outlines an alternative method to investigating and identifying the presence of cosmic magnetic fields. This method searches for Faraday Rotation (FR) and specifically uses polarized CMB photons as back-light. I find that current generation CMB experiments may be not sensitive enough to detect FR but next generation experiments should be able to make highly significant detections. Identifying FR with the CMB will provide information on the component of magnetic fields along the line of sight of observation.

The 21cm emission from the hyperfine splitting of neutral Hydrogen in the early universe is predicted to provide precise information about the formation and evolution of cosmic structure, complementing the wealth of knowledge gained from the CMB.

21cm cosmology is a relatively new field, and precise measurements of the Epoch of Reionization (EoR) have not yet been achieved. In this work I present 2σ upper limits on the power spectrum of 21cm fluctuations (Δ²(k)) probed at the cosmological wave number k from the Donald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER) 64 element deployment. I find upper limits on Δ²(k) in the range 0.3 < k < 0.6 h/Mpc to be (650 mK)², (450 mK)², (390 mK)², (250 mK)², (280mK)², (250 mK)² at redshifts z = 10.87, 9.93, 8.91, 8.37, 8.13 and 7.48 respectively

Building on the power spectrum analysis, I identify a major limiting factor in detecting the 21cm power spectrum.

This work is concluded by outlining a metric to evaluate the predisposition of redshifted 21cm interferometers to foreground contamination in power spectrum estimation. This will help inform the construction of future arrays and enable high fidelity imaging and

cross-correlation analysis with other high redshift cosmic probes like the CMB and other upcoming all sky surveys. I find future

arrays with uniform (u,v) coverage and small spectral evolution of their response in the (u,v,f) cube can minimize foreground leakage while pursuing 21cm imaging.

In a typical living cell, millions to billions of proteins—nanomachines that fluctuate and cycle among many conformational states—convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible.

Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.

The exceptional mechanical properties of polymers with heterogeneous structure, such as the high toughness of polyethylene and the excellent blast-protection capability of polyurea, are strongly related to their morphology and nanoscale structure. Different polymer microstructures, such as semicrystalline morphology and segregated nanophases, lead to coordinated molecular motions during deformation in order to preserve compatibility between the different material phases. To study molecular relaxation in polyethylene, a coarse-grained model of polyethylene was calibrated to match the local structural variable distributions sampled from supercooled atomistic melts. The coarse-grained model accurately reproduces structural properties, e.g., the local structure of both the amorphous and crystalline phases, and thermal properties, e.g., glass transition and melt temperatures, and dynamic properties: including the vastly different relaxation time scales of the amorphous and crystalline phases. A hybrid Monte Carlo routine was developed to generate realistic semicrystalline configurations of polyethylene. The generated systems accurately predict the activation energy of the alpha relaxation process within the crystalline phase. Furthermore, the models show that connectivity to long chain segments in the amorphous phase increases the energy barrier for chain slip within crystalline phase. This prediction can guide the development of tougher semicrystalline polymers by providing a fundamental understanding of how nanoscale morphology contributes to chain mobility. In a different study, the macroscopic shock response of polyurea, a phase segregated copolymer, was analyzed using density functional theory (DFT) molecular dynamics (MD) simulations and classical MD simulations. The two models predict the shock response consistently up to shock pressures of 15 GPa, beyond which the DFT-based simulations predict a softer response. From the DFT simulations, an analysis of bond scission was performed as a first step in developing a more fundamental understanding of how shock induced material transformations effect the shock response and pressure dependent strength of polyurea subjected to extreme shocks.

Improved knowledge connecting the chemistry, structure, and properties of polymers is necessary to develop advanced materials in a materials-by-design approach. Molecular dynamics (MD) simulations can provide tremendous insight into how the fine details of chemistry, molecular architecture, and microstructure affect many physical properties; however, they face well-known restrictions in their applicable temporal and spatial scales. These limitations have motivated the development of computationally-efficient, coarse-grained methods to investigate how microstructural details affect thermophysical properties. In this dissertation, I summarize my research work in structure-based coarse-graining methods to establish the link between molecular-scale structure and macroscopic properties of two different polymers. Systematically coarse-grained models were developed to study the viscoelastic stress response of polyurea, a copolymer that segregates into rigid and viscous phases, at time scales characteristic of blast and impact loading. With the application of appropriate scaling parameters, the coarse-grained models can predict viscoelastic properties with a speed up of 5-6 orders of magnitude relative to the atomistic MD models. Coarse-grained models of polyethylene were also created to investigate the thermomechanical material response under shock loading. As structure-based coarse-grained methods are generally not transferable to states different from which they were calibrated at, their applicability for modeling non-equilibrium processes such as shock and impact is highly limited. To address this problem, a new model is developed that incorporates many-body interactions and is calibrated across a range of different thermodynamic states using a least square minimization scheme. The new model is validated by comparing shock Hugoniot properties with atomistic and experimental data for polyethylene. Lastly, a high fidelity coarse-grained model of polyethylene was constructed that reproduces the joint-probability distributions of structural variables such as the distributions of bond lengths and bond angles between sequential coarse-grained sites along polymer chains. This new model accurately represents the structure of both the amorphous and crystal phases of polyethylene and enabling investigation of how polymer processing such as cold-drawing and bulk crystallization affect material structure at significantly larger time and length scales than traditional molecular simulations.

Richard Feynman said “There’s plenty of room at the bottom”. This inspired the techniques to improve the single molecule measurements. Since the first single molecule study was in 1961, it has been developed in various field and evolved into powerful tools to understand chemical and biological property of molecules. This thesis demonstrates electronic single molecule measurement with Scanning Tunneling Microscopy (STM) and two of applications of STM; Break Junction (BJ) and Recognition Tunneling (RT). First, the two series of carotenoid molecules with four different substituents were investigated to show how substituents relate to the conductance and molecular structure. The measured conductance by STM-BJ shows that Nitrogen induces molecular twist of phenyl distal substituents and conductivity increasing rather than Carbon. Also, the conductivity is adjustable by replacing the sort of residues at phenyl substituents. Next, amino acids and peptides were identified through STM-RT. The distribution of the intuitive features (such as amplitude or width) are mostly overlapped and gives only a little bit higher separation probability than random separation. By generating some features in frequency and cepstrum domain, the classification accuracy was dramatically increased. Because of large data size and many features, supporting vector machine (machine learning algorithm for big data) was used to identify the analyte from a data pool of all analytes RT data. The STM-RT opens a possibility of molecular sequencing in single molecule level. Similarly, carbohydrates were studied by STM-RT. Carbohydrates are difficult to read the sequence, due to their huge number of possible isomeric configurations. This study shows that STM-RT can identify not only isomers of mono-saccharides and disaccharides, but also various mono-saccharides from a data pool of eleven analytes. In addition, the binding affinity between recognition molecule and analyte was investigated by comparing with surface plasmon resonance. In present, the RT technique is applying to chip type sequencing device onto solid-state nanopore to read out glycosaminoglycans which is ubiquitous to all mammalian cells and controls biological activities.

Cubic boron nitride (c-BN) has potential for electronic applications as an electron emitter and serving as a base material for diodes, transistors, etc. However, there has been limited research on c-BN reported, and many of the electronic properties of c-BN and c-BN interfaces have yet to be reported. This dissertation focused on probing thin film c-BN deposited via plasma enhanced chemical vapor deposition (PECVD) with in situ photoelectron spectroscopy (PES). PES measurements were used to characterize the electronic properties of c-BN films and interfaces with vacuum and diamond. First, the interface between c-BN and vacuum were characterized with ultraviolet PES (UPS). UPS measurements indicated that as-deposited c-BN, H2 plasma treated c-BN, and annealed c-BN post H2 plasma treatment exhibited negative electron affinity surfaces. A dipole model suggested dipoles from H-terminated N surface sites were found to be responsible for the NEA surface. Then, Si was introduced into c-BN films to realize n-type doped c-BN. The valence structure and work function of c-BN:Si films were characterized with XPS and UPS measurements. Measurements were unable to confirm n-type character, and it is concluded that silicon nitride formation was the primary effect for the observations. Finally, XPS measurements were employed to measure the band offsets at the c-BN/diamond interface. Measurements indicated the valence band maximum (VBM) of c-BN was positioned ~0.8 eV above the VBM of diamond.