Independent yield distributions of high-energy neutron-induced fission are of importance to achieve a good understanding of fission. Even though the mass and charge yield distributions of thermal neutron-induced fission are well known, there are few experimental data for high-energy neutron-induced fission. In addition to basic research on the fission process, independent yield distributions of high-energy neutron-induced fission play a key role in the development of Generation IV fast nuclear reactors. To facilitate measurements of independent fission yields of high-energy neutron-induced fission, a dedicated ion guide and a proton-neutron converter were developed and put to use in experiments at the isotope separator facility IGISOL in Jyväskylä. In parallel, a simulation model of the system was developed in order to optimize the collecting efficiency of fission products in the ion guide. The model uses the Monte Carlo code MCNPX to simulate the neutron production, the fission model code GEF to simulate the fission process, and GEANT4 for ion transportation. In order to benchmark the simulation model, metal foils were inserted in the ion guide with the purpose of collecting fission products. At the same time, nickel, cobalt and indium foils were located between the pn-converter and the ion guide to record the neutron flux from the pn-converter. After the beam was turned off, and after several days of cooling, g-ray spectroscopy measurements of the foils were conducted using a well shielded HPGe detector. Based on the identified g-ray transitions in the spectroscopy data, the productions of corresponding fission products and neutron activation products were calculated, and then used to benchmark the transportation and collection of fission products, as well as neutron production, in the simulations. The conclusion from the benchmark is that the transportation of fission products in the helium gas, as simulated by GEANT4, agrees very well with the measurement, while the transportation of fission products in the uranium targets agrees with the measurement within 10%. The neutron flux at the high-energy part of the neutron spectrum is overestimated by about 40%.Thanks to the benchmark it has been shown that the predictive power of the model is satisfactory and sufficient for the purpose of modeling the ion guide. Furthermore, the parameters involved in the simulations, such as neutron production, distance between the neutron source and the ion guide, volume of the ion guide and so on, play an important role in the optimization of the setup. However, the lower than expected fission rate suggests that the optimization on these parameters may not be enough to achieve a sufficiently high intensity of fission products, especially for nuclei far from the stability line. To achieve a sufficiently high intensity, an electric field guidance, similar to the RF structure of the CARIBU gas catcher presented in G.Savard et al. Nucl. Inst. Meth. B, 376: 246, 2016, to collect fission products is considered.

<p>Orthology identification is central to comparative and evolutionary genomics and is an active area of research. Despite a recent shift towards tree reconciliation and other phylogenetic methods, previous comparisons between different algorithms relied on real datasets where true orthology relationships are unknown and did not conclusively show whether phylogenetic methods truly outperform sequence similarity-based methods. Using simulated datasets generated from programs we developed, we show that tree reconciliation does perform better than similarity-based methods when the true species phylogeny is known. Even slight deviations in the species phylogeny can have adverse effects on the performance of reconciliation algorithms and in those cases similarity-based methods may perform better. Fusion and fission complicate orthology identification and are not explicitly considered in most existing algorithms. Programs designed specifically to investigate fusion and fission events are either unavailable or are not specific enough to identify events affecting orthologous genes. We developed a pipeline of programs called FusionFinder that perform this task, gaining new insights to the contributions of fusion and fission to bacterial protein evolution and uncover an unexpected abundance of fissions in <em>Bacillus anthracis</em> that to our knowledge yet to be reported.</p> / Master of Science (MS)

In this dissertation, the laser spectroscopic methods, second harmonic generation (SHG) and ultrafast transient absorption, have been employed to study the reactions and dynamics in two different types of materials, namely, silver nanoparticles and micro-sized ultrathin crystalline oligoacenes. These two materials, although both are in small dimensions, represent two distinct types of systems with divergent characteristics: 1) systems in which interactions at the surface/interface are dominant, and 2) systems in which bulk interactions are dominant. Silver nanoparticles are an important member of the class of noble metal nanoparticles, and possess unique optical and chemical properties due to their ultrafine size and high surface-to-volume ratio. Strong SHG signal has been observed from silver nanoparticles dispersed in aqueous colloidal solution, in which the SHG signal is enhanced due to a resonance with the localized surface plasmon of silver nanoparticles. Further experiments proved that the SHG signal predominantly originates from the particle surface, in full agreement with the intrinsically interface-sensitive properties of SHG. With the surface origin of the signal now well established, SHG can be used to probe the adsorption and reactions of thiol molecules at the nanoparticle surface in situ and in real time. It is experimentally demonstrated that the free energy change, activation energy, as well as adsorption density of the reactions of a variety of neutral and anionic thiols at the particle surface can be measured by means of SHG. The reaction mechanisms at the molecular level have been deduced, and the neutral vs anionic thiols are found to exhibit qualitatively different reaction mechanisms that reflect the effect of their molecular interactions with the particle surface. Oligoacenes, such as pentacene and hexacene, constitute a family of organic semiconductors that exhibit remarkable optoelectronic properties. In contrast to the nanoparticles in which surface interactions are dominant, as the sizes of materials become larger, the bulk characteristics become more deterministic. Therefore, polarized linear absorption and transient absorption spectroscopies have been applied to study the excitonic properties of crystalline pentacene and the mechanism of singlet fission in crystalline hexacene, respectively. The polarized absorption spectra of crystalline pentacene have been obtained by measuring transmitted light normal to the ab herringbone plane of micro-sized ultrathin single crystals. The significant deviations between the spectral line shapes polarized along the b-axis and orthogonal to the b-axis provide detailed information on the anisotropic mixing nature of the Frenkel/charge-transfer excitons responsible for the pronounced Davydov splitting between the lowest-energy singlet states. Additionally, both singlet and triplet Davydov splittings were also observed from the linear and transient absorption experiments in micrometer-sized ultrathin hexacene single crystals. A two-step process of anisotropic singlet fission was uncovered from the kinetic data, in which singlet fission at different rates were deduced along the a- and b-axes. Both the spectral and kinetic features indicate that singlet fission in crystalline hexacene is an anisotropic and charge-transfer mediated many-molecule process. / Chemistry

The relative fission yields of the isotopes of krypton and xenon have been determined mass spectrometrically. Abnormal fission yields, resulting in fine structure in the mass fission yield curve, have been found in both mass ranges. A shift of the fine structure to lower masses has been observed in going from U^235 + n fission to U^238 + n fission. From this shift in fine structure, it has been possible to determine the proportion of U^235 and U^236 neutron fission that have occurred in the sample. Evidence is presented to show that the observed fine structure and the shift in this fine structure is the result of a combination of two effects involved the extra stability of closed neutron shells of 50 and 82 neutrons which fall in the Kr and Xe ranges respectively. The capture of thermal neutrons by Xe^135, which modifies the fission yields in the 135 and 136 mass chains, has been studied so that the observed fission yields at these masses may be suitably corrected. Finally, the branching ratio between the isomeric states of Kr^85 and the half-life of the long-lived isomer have been re-determined and found to be 0.29 and 10.27 ± 0.18 yrs. respectively. / Thesis / Doctor of Philosophy (PhD)

Mild blast-induced traumatic brain injury (bTBI) is a modality of injury that has been of major concern considering a large number of military personnel exposed to the blast wave from explosives. bTBI results from the propagation of high-pressure static blast forces and their subsequent energy transmission within brain tissue. Current literature presents a neuro-centric approach to the role of mitochondria dynamics dysfunction in bTBI; however, changes in astrocyte-specific mitochondrial dynamics have not been characterized. As a result of fission and fusion, the mitochondrial structure is constantly altering shape to respond to physiological stimuli or stress insults by adapting structure and function, which are intimately connected. Dysregulation of the protein regulator of mitochondrial fission, DRP1, and upregulation in the phosphorylation of DRP1 at the serine 616 site is reported to play a crucial role in astrocytic mitochondrial dysfunction, favoring fission over fusion post-TBI. Astrocytic mitochondria are starting to be recognized to play an essential role in overall brain metabolism, synaptic transmission, and neuron protection. Mitochondria are vulnerable to injury insults leading to the worsening of mitochondrial fission and increased mitochondrial fragmentation. In this study, a combination of in vitro and in vivo bTBI models were used to examine the effect of blast on astrocytic mitochondrial dynamics. Acute differential remodeling of the astrocytic mitochondrial network was observed, accompanied by an acute (4hr) and sub-acute (7 days) activation of the GTP-protein DRP1. Further, results showed a time-dependent reactive astrocyte phenotype transition in the rat hippocampus. This discovery can lead to innovative therapeutics targets to help prevent secondary injury cascades that involve mitochondria dysfunction. / Doctor of Philosophy / Blast-induced traumatic brain injury (bTBI) is a modality of injury that has become prominent considering a large number of military personnel exposed to a blast wave caused by explosives. Blast injury results from the energy transmission of the blast wave to the brain. Within the brain, there are specialized cells, called astrocytes, that help maintain a healthy environment. This work investigates the role that astrocytes play during the injury recovery process. Within the astrocytes, there are organelles called mitochondria, that help maintain the energy for the cell. The number and function of mitochondria can change in response to the brain injury. They can increase in number by a process called fission and they can decrease in number by a process called fusion. These events effect the function of the mitochondria. Researchers have methods that can identify changes in the number and function of the mitochondria. In this work, astrocyte mitochondrial dynamics were examined and compared using models of bTBI. We found significant changes in the mitochondria of astrocytes, which could lead to an unhealthy environment in the brain. This discovery can lead to new treatments for patients that may improve their quality of life following bTBI.

MtDNA mutations in mammalian cells are implicated in cellular ageing and encephalomyopathies, although mechanisms involved are not completely understood. The mitochondrial genetic bottleneck has puzzled biologists for a long time. Approximate models of genetic bottleneck proposed in the literature do not accurately model underlying biology. Recent studies indicate mitochondrial morphology changes during cellular aging in culture. In particular, the rates of mitochondrial fission and fusion are shown to be in tight balance, though this rate decreases with age. Some proteins involved in mitochondrial morphology maintenance are implicated in apoptosis. Hence, mitochondrial genetic and morphologic dynamics are critical to the life and death of cells. By working closely with experimental collaborators and by utilizing data derived from literature, we have developed stochastic simulation models of mitochondrial genetic and morphologic dynamics. Hypotheses from the mitochondrial genetic dynamics model include: (1) the decay of mtDNA heteroplasmy in blood is exponential and not linear as reported in literature. (2) Blood heteroplasmy measurements are a good proxy for the blood stem cell heteroplasmy. (3) By analyzing our simulation results in tandem with published longitudinal clinical data, we propose for the first time, a way to correct for the patient's age in the analysis of heteroplasmy data. (4) We develop a direct model of the genetic bottleneck process during mouse embryogenesis. (5) Partitioning of mtDNA into daughter cells during blastocyst formation and relaxed replication of mtDNA during the exponential growth phase of primordial germ cells leads to the variation in heteroplasmy inherited by offspring from the same mother. (6) We develop a “simulation control” for experimental studies on mtDNA heteroplasmy variation in cell cultures. Hypothesis from the mitochondrial morphologic dynamics model: (7) A cell adjusts the mitochondrial fusion rate to compensate for the fluctuations in the fission rate, but not vice versa. A deterministic model for this control is proposed. Contributions: extensible simulation models of mitochondrial genetic and morphologic dynamics to aide in the powerful analysis of published and new experimental data. Our results have direct relevance to cell biology and clinical diagnosis. The work also illustrates scientific success by tight integration of theory with practice. / Ph. D.

This thesis presents a detailed analysis of the bRAPID (burnup for RAPID – Real Time Analysis for Particle transport and In-situ Detection) code system, and the implementation and validation of two new algorithms for improved burnup simulation. bRAPID is a fuel burnup algorithm capable of performing full core 3D assembly-wise burnup calculations in real time, through its use of the RAPID Fission Matrix methodology. A study into the effect of time step resolution on isotopic composition in Monte Carlo burnup calculations is presented to provide recommendations for time step scheme development in bRAPID. Two novel algorithms are implemented into bRAPID, which address: i) the generation of time-dependent correction factors for the fission density distribution in boundary nuclear fuel assemblies within a reactor core; ii) the calculation of pin-wise burnup distributions and isotopic concentrations. Time step resolution analysis shows that a variable time step scheme, developed to accurately characterize important isotope evolution, can be used to optimize burnup calculations and minimize computation time. The two new algorithms have been benchmarked against the Monte Carlo code system Serpent. Results indicate that the time-dependent boundary correction algorithm improves fission density distribution calculations by including a more detailed representation of boundary physics. The pin-wise burnup algorithm expands bRAPID capabilities to provide material composition data at the pin level, with accuracy comparable to the reference calculation. In addition, wall-clock time analyses show that burnup calculations performed using bRAPID with these novel algorithms require a fraction of the time of Serpent. / Master of Science / Fuel burnup modeling is an important aspect of nuclear reactor design that provides information about the energy extracted (called burnup) and isotopes created or used in the fuel of a reactor over time. A reactor core is a collection of fuel assemblies, and assemblies are simply a bundle of fuel pins, which contain nuclear fuel such as Uranium. The desire for accurate and fast computer codes to calculate fuel burnup rises each year as engineers working in reactor core design seek to arrange fuel assemblies in an optimal pattern to extract the most energy. State of the art burnup codes exist, however they have certain limitations due to their underlying methodologies. To satisfy this need, the bRAPID algorithm was developed by the Virginia Tech Transport Theory Group (VT³G). bRAPID is a new methodology capable of performing full core fuel burnup calculations in real time. bRAPID is able to calculate the criticality and burnup distribution of a reactor orders of magnitude faster than comparable algorithms, while addressing many of the shortcomings seen in other burnup codes. In this thesis, studies of standard burnup codes are conducted in order to aid in bRAPID analysis: first in the form of a detailed study of the reference Monte Carlo model used in this thesis, and secondly in an investigation of the effect of time step selection – or the time intervals used in burnup calculations – on isotope concentration. Both of these studies are conducted using the benchmark code system, Serpent, with the latter study providing useful insight that can be used for bRAPID database development. This thesis then presents two new algorithms for bRAPID that expand its capability and improve performance. First, an algorithm to more accurately simulate the boundary regions of the core – called the time dependent boundary correction algorithm – is presented and benchmarked. Next, an algorithm to expand bRAPID capability from assembly-wise to pin-wise burnup calculations is implemented and tested. These two algorithms are benchmarked against the Serpent Monte Carlo based burnup code.

When a pressurized water reactor is operated for a sufficiently long period of time, a small number of fuel rods will develop ruptures in their claddings. These defects will leak volatile fission products into the primary coolant, including radioactive iodine. During steady-state operation of the reactor a low level iodine activity is thus present in the coolant. Initiation of a down-power or up-power transient will result in a rapid climb in the activity of the iodine which peaks at a level much higher than the initial activity. After this time the activity levels out and then slowly begins to decay back to a new steady-state level. This phenomenon is termed "iodine spiking.” A physical model of this process is sought for explanatory and predictive purposes. A FORTRAN code is developed that solves a system of differential equations which describe the production and removal of iodine in the fuel, gap region, and primary coolant. As much physics as possible is employed but some complicated diffusion processes have led to the utilization of certain parametric results obtained from empirical data. Actual PWR spiking data is also employed for comparison and adjustment of the model. It is the goal of this project to be able to utilize the model for predictive analysis· during actual PWR operation so that a better understanding of iodine spiking behavior can be obtained. / Master of Science

The absolute cumulative yields of forty-one light and heavy fragments farmed in the thermal neutron fission of Pu239 have been measured with a mass spectrometer twins the isotope dilution technique. These include the yields of isotopes of rubidium, strontium, zirconium, molybdenum, ruthenium, cesium, cerium, neodymium and samarium. The yields of twelve light fragments formed in the thermal neutron fission of U235 have also been reported. A comprehensive study of fission yields requires a knowledge of carrier-free separation techniques, accurate half-lives and neutron capture crocs sections of the various fission nuclides. Lew procedures for the carrier—free analysis of the elements of zirconium, molybdenum and ruthenium have been developed. Also the half-lives of Sr89 and Zr95 and the thermal neutron capture cross sections of Xe135 and Sm149 were determined. A comparison of the yields of the light and heavy mass fission products of Pu239 has made possible a more detailed understanding of neutron emission from the primary fragments of fission. / Thesis / Doctor of Philosophy (PhD)

The interplay of nuclear fuel with fission products is key for safe and efficient nuclear power operation. The diffusion of volatile fission products in very heavy reactor fuel matrices was investigated by analysing Zirconium Dioxide and Uranium Nitride, implanted with different ions. The samples were implanted using the 350kV Ion Implanter available at Uppsala University. Zirconium Dioxide was implanted with Xenon, Krypton and Iron, and Uranium Nitride was implanted with Krypton and Zirconium. The samples were then analysed using Time of Flight Elastic Recoil Detection Analysis (ToF-ERDA), Rutherford Backscattering Spectrometry (RBS), Scanning Electron Microscopy (SEM), and X-Ray Diffraction (XRD). After the implantation and analysis, the samples were annealed at different times and temperatures. The annealing times were predicted by solving Fick’s second law with numerical methods and using Stopping and Range of Ions in Matter (SRIM) as an initial guess. The results show that annealing times can be predicted by solving Fick’s second law, to first order, and that ion implantation effects the stoichiometry of the samples. Future improvements could include improvement of underlying physics in the annealing predictions, and more extensive measurements performed on a wider range of samples.