<p> Many types of dosimeters are used in the clinic to measure radiation dose for therapy but none of them directly measures the biological effect of this dose. The overall purpose of this work was to develop a dosimeter that measures biological damage in the form of double-strand breaks to deoxyribonucleic acid. This dosimeter could provide a more biologically relevant measure of radiation damage than the currently utilized dosimeters. A pair of oligonucleotides was designed to fabricate this dosimeter. One is labeled with a 5&rsquo;-end biotin and the other with a 5&rsquo;-end 6 Fluorescein amidite (fluorescent dye excited at 495?nanometer, with a peak emission at 520 nanometer). These were designed to adhere to certain locations on the pRS316 vector and serve as the primers for polymerase chain reactions. The end product of this reaction is a 4 kilo-base pair double strands deoxyribonucleic acid fragment with biotin on one end and 6 Fluorescein amidite oligonucleotide on the other attached to streptavidin beads. The biotin end connects the double strands deoxyribonucleic acid to the streptavidin bead. These bead-connected double strands deoxyribonucleic acid were suspended in 50 microliter of phosphate-buffered saline and placed into a tube for irradiation. Following irradiation of the deoxyribonucleic acid dosimeter, we take advantage of the magnetic properties of the streptavidin bead by placing our sample microtube against a magnet. The magnetic field pulls the streptavidin beads against the side of the tube. If a double-strand-break has occurred for a double strands deoxyribonucleic acid, the fluorescein end of the double strands deoxyribonucleic acid becomes free and is no longer attached to the bead or held against the side of the microtube. The free fluorescein following a double-strand-break in double strands deoxyribonucleic acid is referred to here as supernatant. The supernatant is extracted and placed in another microtube, while the unbroken double strands deoxyribonucleic acid remain attached to the beads and stay in the microtube (Fig. 4). Those beads were re-suspended with 50 microliter of phosphate-buffered saline again (called beads), then we placed both supernatant and beads in a reader microplate and we read the fluorescence signal for both with a fluorescence reader (BioTek Synergy 2). These beads and supernatant fluorescence signals are denoted by B and S, respectively. The relative amount of supernatant fluorescence counts is proportional to the probability of a double-strand-break. The probability of double-strand-break was calculated with the following equation: </p><p> (S-BG)/(S+B-2BG) (1) </p><p> where S was the supernatant fluorescence intensity (related to the number of double strands deoxyribonucleic acid with double-strand breaks), B was the re-suspended beads fluorescence intensity (related to the number of double strands deoxyribonucleic acid without double-strand breaks), and BG was the phosphate-buffered saline fluorescence intensity (related to the background signal). There are two advantages that this type of dosimeter has over the gel separation technique. First, it is important to irradiate deoxyribonucleic acid in a solution that has similar osmolarity and ion concentrations to that in a human, such as phosphate-buffered saline. A gel dosimeter would require a transfer to gel to separate deoxyribonucleic acid, whereas our dosimeter can be separated in this solution. Currently, we use pipettes to manually perform this separation, but this step could be automated. Second, the magnetic deoxyribonucleic acid separation technique is much faster than that for gel electrophoresis. Calibration of radiotherapy equipment isn&rsquo;t something that happens in national science laboratories, with only world-leading experts. This is something that happens locally at every cancer clinic, with physicists that do not have the luxury of focusing solely on this one measurement. For this reason, ease of use is critical for this type of technology. (Abstract shortened by ProQuest.)</p><p>

<p> Nuclear fuels with similar aggregate material composition, but with different millimeter and micrometer spatial configurations of the component materials can have very different safety and performance characteristics. This research focuses on modeling and attempting to engineer heterogeneous combinations of nuclear fuels to improve negative prompt temperature feedback in response to reactivity insertion accidents.</p><p> Improvements in negative prompt temperature feedback are proposed by developing a tailored thermal resistance in the nuclear fuel. In the event of a large reactivity insertion, the thermal resistance allows for a faster negative Doppler feedback by temporarily trapping heat in material zones with strong absorption resonances.</p><p> A multi-physics simulation framework was created that could model large reactivity insertions. The framework was then used to model a comparison of a heterogeneous fuel with a tailored thermal resistance and a homogeneous fuel without the tailored thermal resistance. The results from the analysis confirmed the fundamental premise of prompt temperature feedback and provide insights into the neutron spectrum dynamics throughout the transient process. </p><p> A trade study was conducted on infinite lattice fuels to help map a design space to study and improve prompt temperature feedback with many results. A multi-scale fuel pin analysis was also completed to study more realistic geometries.</p><p> The results of this research could someday allow for novel nuclear fuels that would behave differently than current fuels. The idea of having a thermal barrier coating in the fuel is contrary to most current thinking. Inherent resistance to reactivity insertion accidents could enable certain reactor types once considered vulnerable to reactivity insertion accidents to be reevaluated in light of improved negative prompt temperature feedback.</p><p>

Spin plays a key role in the determination of the properties of fundamental particles and their interactions. The spin structure of the proton is one of the most challenging open puzzles in Quantum Chromodynamics (QCD). It was believed that the proton spin was carried by the spin of its three valence quarks. However, The results of the EMC (European Muon Collaboration) experiments in 1987 suggested that the quark intrinsic spin contributes, ∆Σ = 0.12 ± 0.09 ± 0.14 of the proton spin setting off the proton spin crisis. ”Where is the rest of the proton spin is coming from?” remains a major challenge to our understanding of the structure of the proton. The Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory (BNL) delivers the highest energy polarized proton-proton collisions at a center of mass energy up to 510 GeV and provides a unique opportunity to study quark and gluon spin structure of the proton and the QCD dynamics at high energy scale. The production of W −(+) bosons in polarized proton-proton collisions provides an ideal tool to study the spin-flavor structure of the proton sea quark distributions profiting from the parity-violating nature of the weak interactions. W −(+) bosons are produced in u ̄ + d (d ̄ + u) annihilation and can be detected through their leptonic decay mode. The STAR experiment can detect charged leptons e−(+) at mid and forward rapidity regions. In this analysis, the measurement of the longitudinal single-spin asymmetries at forward rapidity for W boson production will be presented based on the data sample collected in 2013 (RUN-13) corresponding to an integrated luminosity 220 pb−1 with an average beam polarization ∼ 56%. / Physics

<p> Patients receiving Intensity Modulated Radiation Therapy (IMRT) for late stage head and neck (HN) cancer often experience anatomical changes due to weight loss, tumor regression, and positional changes of normal anatomy (1). As a result, the actual dose delivered may vary from the original treatment plan. The purpose of this study was (a) to evaluate the dosimetric consequences of the parotid glands during the course of treatment, and (b) to determine if there would be an optimal timeframe for replanning. Nineteen locally advanced HN cancer patients underwent definitive IMRT. Each patient received an initial computerized tomography simulation (CT-SIM) scan and weekly cone beam computerized tomography (CBCT) scans. A Deformable Image Registration (DIR) was performed between the CT-SIM and CBCT of the parotid glands and Planning Target Volumes (PTVs) using the Eclipse treatment planning system (TPS) and the Velocity deformation software. A recalculation of the dose was performed on the weekly CBCTs using the original monitor units. The parameters for evaluation of our method were: the changes in volume of the PTVs and parotid glands, the dose coverage of the PTVs, the lateral displacement in the Center of Mass (COM), the mean dose, and Normal Tissue Complication Probability (NTCP) of the parotid glands. The studies showed a reduction of the volume in the PTVs and parotids, a medial displacement in COM, and alterations of the mean dose to the parotid glands as compared to the initial plans. Differences were observed for the dose volume coverage of the PTVs and NTCP of the parotid gland values between the initial plan and our proposed method utilizing deformable registration-based dose calculations.</p>

<p>This thesis discusses the process of extracting the longitudinal asymmetry, $A_L</p><p>{W\pm}$, describing $W\rightarrow\mu$ production in forward kinematic regimes. This asymmetry is used to constrain our understanding of the polarized parton distribution functions characterizing $\bar{u}$ and $\bar{d}$ sea quarks in the proton. This asymmetry will be used to constrain the overall contribution of the sea-quarks to the total proton spin. The asymmetry is evaluated over the pseudorapidity range of the PHENIX Muon Arms, $2.1 < |\eta|2.6$, for longitudinally polarized proton-proton collisions at 510 GeV $\sqrt{s}$. In particular, I will discuss the statistical methods used to characterize real muonic $W$ decays and the various background processes is presented, including a discussion of likelihood event selection and the Extended Unbinned Maximum Likelihood fit. These statistical methods serve estimate the yields of $W$ muonic decays, which are used to calculate the longitudinal asymmetry.

<p> Fusion in neutron-rich environments is presently a topic of considerable interest. For example, the optical emission spectrum from the neutron star merger GRB170817A clearly establishes this neutron-rich environment as an important nucleosynthetic site. Fusion of neutron-rich light nuclei in the outer crust of an accreting neutron star has also been proposed as responsible for triggering X-ray super-bursts. The underlying hypothesis in this proposition is that the fusion of neutron-rich nuclei is enhanced as compared to stable nuclei. A good approach to understand how fusion proceeds in neutron-rich nuclei is to measure the fusion excitation function for an isotopic chain of nuclei. Modern radioactive beam facilities provide the opportunity to systematically address this question. An experimental program has been established to measure the fusion excitation function for light and mid-mass neutron-rich nuclei using low-intensity radioactive beams. The technique was initially demonstrated by measuring the fusion excitation functions for <i>18</i>O and ¹⁹O nuclei incident on a ¹²C target. The beam of ¹⁹O ions was produced by the <i>18</i>O(d,p) reaction with an intensity of 2-4 x 10⁴ p/s at Florida State University. Evaporation residues resulting from the de-excitation of the fusion product were distinguished by measuring their energy and time-of-flight. To explore mid-mass neutron-rich nuclei much further from stability, the fusion excitation functions for ^39,47K + ²⁸Si were measured using the ReA3 reaccelerator facility at the National Superconducting Cyclotron Laboratory at Michigan State University. Incident ions were identified on a particle-by-particle basis by &Delta;E-TOF just upstream of the target. Fusion products were directly measured and identified by the E-TOF technique with an efficiency of ~70%. The measured fusion excitation functions for both the light and mid-mass systems have been compared to various theoretical models to elucidate how structure and dynamics impact the fusion of neutron-rich nuclei.</p><p>

<p> The anti-matter counterpart to the electron, the positron, can be used for a myriad of different scientific research projects to include materials research, energy storage, and deep space flight propulsion. Currently there is a demand for large numbers of positrons to aid in these mentioned research projects. There are different methods of producing and harvesting positrons but all require radioactive sources or large facilities. Positron beams produced by relatively small accelerators are attractive because they are easily shut down, and small accelerators are readily available. </p><p> A 4MV Van de Graaff accelerator was used to induce the nuclear reaction ¹²C(d,n)¹³N in order to produce an intense beam of positrons. 13N is an isotope of nitrogen that decays with a 10 minute half life into ¹³C, a positron, and an electron neutrino. This radioactive gas is frozen onto a cryogenic freezer where it is then channeled to form an antimatter beam. The beam is then guided using axial magnetic fields into a superconducting magnet with a field strength up to 7 Tesla where it will be stored in a newly designed Micro-Penning-Malmberg trap. </p><p> Several source geometries have been experimented on and found that a maximum antimatter beam with a positron flux of greater than 0.55&times;10⁶ e+s^-1 was achieved. This beam was produced using a solid rare gas moderator composed of krypton. Due to geometric restrictions on this set up, only 0.1-1.0% of the antimatter was being frozen to the desired locations. Simulations and preliminary experiments suggest that a new geometry, currently under testing, will produce a beam of 107 e+s^-1 or more.</p>

<p> Fluctuations are one of the main probes of the physics of the new state of hot and dense nuclear matter called the Quark Gluon Plasma (QGP) which is created in the ultra-relativistic heavy ion collisions. In this dissertation we extend and improve upon the existing descriptions of heavy ion collisions in three different directions: we study the new signatures of initial state fluctuations, the propagation of perturbations in the early stages of the collision, and the effect of thermal fluctuations on the hydrodynamic expansion of the QGP. </p><p> First, in Chapter 3 we study initial state fluctuations by examining the complete statistical information contained in the two-particle correlation measurements in hydrodynamic simulations of Pb+Pb collisions at the CERN Large Hadron Collider (&radic;<i>s_NN</i> = 2.76 TeV). We use Principal Component Analysis (PCA) to decompose the spectrum of harmonic flow, v_n(p_T) for <i>n</i> = 0&ndash;5, into dominant components. The leading component is identified with the standard event plane <i> v_n</i>(<i>p_T</i>), while the subleading component describes additional fluctuations in the two-particle correlation function. We find good geometric predictors for the orientation and the magnitude of the leading and the subleading flows. The subleading <i>v</i>₀, <i>v</i>₁, and <i>v</i>₃ flow harmonics are shown to be a response to the radial excitation of the corresponding eccentricity &epsiv;<i>_n</i>. In contrast, for <i>v</i>₂ the subleading flow in peripheral collisions is dominated by the nonlinear mixing between the leading elliptic flow and radial flow fluctuations. Nonlinear mixing also plays a significant role in generating subleading <i>v</i>₄ and <i>v</i>₅ harmonics. The PCA gives a systematic way of studying the full information of the two-particle correlation matrix and identifying the subleading flows, which we show are responsible for factorization breaking in hydrodynamics. </p><p> Second, in Chapter 4 we study the thermalization and hydrodynamization of fluctuations at the early stages of heavy ion collisions. We use leading order effective kinetic theory, accurate at weak coupling, to simulate the pre-equilibrium evolution of transverse energy and flow perturbations. For the short evolution we can use a linear response theory to construct the pre-equilibrium Green functions. Then the energy-momentum tensor at a time when hydrodynamics becomes applicable can be expressed as a linear convolution of response functions with the initial perturbations. We propose combining effective kinetic theory with weak coupling initial state models, such as IP-Glasma, to model the complete pre-thermal evolution from saturated nuclei to hydrodynamics in a weak coupling framework. </p><p> Last, in Chapter 5 we consider out-of-equilibrium hydrodynamic fluctuations in the expanding QGP. We develop a set of kinetic equations for a correlator of thermal fluctuations which are equivalent to nonlinear hydrodynamics with noise. We first show that the kinetic response precisely reproduces the one-loop renormalization of the shear viscosity for a static fluid. We then use the hydro-kinetic equations to analyze thermal fluctuations for a Bjorken expansion. The steady state solution to the kinetic equations determine the coefficient of the first fractional power of the gradient expansion (&infin; 1/(&tau;<i> T</i>)^3/2), which was computed here for the first time. The formalism of hydro-kinetic equations can be applied to more general background flows and coupled to existing viscous hydrodynamic codes to incorporate the physics of hydrodynamic fluctuations.</p><p>

<p> Cerenkov luminescence (CL) is optical radiation induced by fast, charged, particles. In the biomedical setting, it is produced by all PET radionuclides and by radiotherapy beams.</p><p> The work presented in this dissertation, spanning some five years, has sought to both investigate the utility of Cerenkov luminescence imaging (CLI) in the biomedical setting and to push the boundaries by inventing ultrasound-modulated Cerenkov luminescence imaging (USCLI), a modality that potentially mitigates the scattering limit of resolution for CLI. </p><p> Clinical applications of CLI have focused on evaluating the potential of Cerenkov luminescence as a tool for guidance during brain tumor resection. Monte Carlo simulations of a brain phantom, along with an experimental analysis scheme, were developed to recapitulate a tumor margin assessment task. The brain phantom has optical properties derived from real brain tissues, and the simulation accounts for all physics of nuclear decay, charged particles, and optical photon propagation. The relative merits of the Cerenkov luminescence signal have been compared with other decay signals in the context of an intraoperative detection task. Considering two surgically-feasible implementations, imaging with a sensitive camera or intraoperative probe, CL objectively provides the most sensitive signal when the tumor remnant resides at superficial (&lt;2 mm) depths. </p><p> CL-activated photodynamic therapy (PDT) was quantitatively explored, and progress was made toward resolving the quantitative dissonance between extraordinary published results and expected required dosimetry. Published <i> in vivo</i> results, which purport to positively demonstrate CL-activated PDT, are at least six orders of magnitude below the therapeutic threshold for PDT dosimetry. The results herein suggest that CL is unlikely to be the driver of the observed therapeutic results, and the mechanism behind these surprising results merits further investigation.</p><p> Finally, both the theory and instrumentation for USCLI, a new, high resolution imaging modality, were developed. USCLI uses ultrasound to modulate the CL signal and thereby shift the resolution-dependence from tissue optical properties to those of the ultrasound beam. Monte Carlo simulations were performed and positively demonstrate higher resolution CLI in a scattering media. Instrumentation to experimentally demonstrate and quantify ultrasound modulation of Cerenkov luminescence imaging were developed and characterized.</p><p>

abstract: This work presents analysis and results for the NPDGamma experiment, measuring the spin-correlated photon directional asymmetry in the $\vec{n}p\rightarrow d\gamma$ radiative capture of polarized, cold neutrons on a parahydrogen target. The parity-violating (PV) component of this asymmetry $A_{\gamma,PV}$ is unambiguously related to the $\Delta I = 1$ component of the hadronic weak interaction due to pion exchange. Measurements in the second phase of NPDGamma were taken at the Oak Ridge National Laboratory (ORNL) Spallation Neutron Source (SNS) from late 2012 to early 2014, and then again in the first half of 2016 for an unprecedented level of statistics in order to obtain a measurement that is precise with respect to theoretical predictions of $A_{\gamma,PV}=O(10^{-8})$. Theoretical and experimental background, description of the experimental apparatus, analysis methods, and results for the high-statistics measurements are given. / Dissertation/Thesis / Doctoral Dissertation Physics 2017