Discrete nondeterministic modeling of biochemical networks

The ideas expressed in this work pertain to biochemical modeling. We explore our technique, the Nondeterministic Waiting Time algorithm, for modeling molecular signaling cascades. The algorithm is presented with pseudocode along with an explanation of its implementation. The entire source code can be found in the Appendices. This algorithm builds on earlier work from the lab of Dr. Andrei Nun, the advisor for this dissertation. We discuss several important extensions including: (i) a heap with special maintenance functions for sorting reaction waiting times, (ii) a nondeterministic component for handling reaction competition, and (iii) a memory enhancement allowing slower reactions to compete with faster reactions. Several example systems are provided for comparisons between modeling with systems of ordinary differential equations, the Gillespie Algorithm, and our Nondeterministic Waiting Time algorithm. Our algorithm has a unique ability to exhibit behavior similar to the solutions to systems of ordinary differential equations for certain models and parameter choices, but it also has the nondeterministic component which yields results similar stochastic methods (e.g., the Gillespie Algorithm). Next, we turn our attention to the Fas-mediated apoptotic signaling cascade. Fas signaling has important implications in the research of cancer, autoimmune and neurodegenerative disorders. We provide an exhaustive account of results from the Nondeterministic Waiting Time algorithm in comparison to solutions to the system of ordinary differential equations described by another modeling group. Our work with the Fas pathway led us to explore a new model, focusing on the effects of HIV-1 proteins on the Fas signaling cascade. There is extensive information in the literature on the effects of the HIV-1 proteins on this pathway. The model described in this work represents the first attempt ever made in modeling Fas-induced apoptosis in latently infected T cells. There are several extensions for the Fas model discussed at the end of the work. Calcium signaling would be an interesting avenue to investigate, building on some recent results reported in the literature. For the HIV model, there are several extensions discussed. We also suggest a new direction for the Nondeterministic Waiting Time algorithm exploring parallelization options

Recent laboratory tests of a hard x-ray solar flare polarimeter

We report on the development of a Compton scatter polarimeter for measuring the linear polarization of hard X-rays (50 - 300 keV) from solar flares. Such measurements would be useful for studying the directivity (or beaming) of the electrons that are accelerated in solar flares. We initially used a simple prototype polarimeter to successfully demonstrate the reliability of our Monte Carlo simulation code and to demonstrate our ability to generate a polarized photon source in the lab. We have recently fabricated a science model based on a modular design concept that places a self-contained polarimeter module on the front-end of a 5-inch position- sensitive PMT (PSPMT). The PSPMT is used to determine the Compton interaction location within an annular array of small plastic scintillator elements. Some of the photons that scatter within the plastic scintillator array are subsequently absorbed by a small centrally-located array of CsI(Tl) crystals that is read out by an independent multi-anode PMT. The independence of the two PMT readout schemes provides appropriate timing information for event triggering. We are currently testing this new polarimeter design in the laboratory to evaluate the performance characteristics of this design. Here we present the initial results from these laboratory tests. The modular nature of this design lends itself toward its accommodation on a balloon or spacecraft platform. A small array of such modules can provide a minimum detectable polarization (MDP) of less than 1% in the integrated 50 - 300 keV energy range for X-class solar flares

Understanding Caribou Population Cycles

The complex population dynamics of caribou (Rangifer tarandus) were studied to determine the patterns of their population cycles and the processes driving them. It is well established, via previous archaeological research and Indigenous knowledge, that large migrating caribou herds found in and around the tundra at northern latitudes experience population boom and busts roughly every several decades. However, the processes driving the dynamics of these cycles are relatively unknown, which makes managing caribou herds for recreational and subsistence harvests difficult. It has been hypothesized that a combination of intrinsic and extrinsic factors shape these cycles, with density-dependence, predation, harvest, climate, and others likely all playing a role. I aimed to determine whether caribou herds experience population cycling and, if so, estimate the period and amplitude of their cycles and determine which factors drive them. I collected population data on 43 caribou herds throughout the world, and in doing so, assembled the largest caribou population database to date. I used statistical interpolation to fill in the gaps between available data due to low sampling frequency. I quantified whether herds were cycling by fitting populations to sine waves and using periodograms to distinguish cycling tendencies from white-noise stochasticity. I collected additional information on other factors hypothesized to affect caribou cycles, including predator presence data, climate oscillation data, subspecies and ecotype data, and the latitudes of each herd. I used the interpolated data for each herd to determine the variables influencing the periods and amplitudes of caribou population cycles. The median period length was 40.5 years and the amplitude, standardized about the mean population size, was .871; period length and amplitude were also positively correlated. In addition, cycle amplitude was best predicted by period length, subspecies, biome, and average winter minimum temperature. Period length was best predicted by amplitude, latitude, subspecies, biome, NDVI, and average winter minimums. A better understanding of caribou population dynamics could help wildlife professionals and policymakers adapt their caribou management strategies. Climate appears to be a strong driver of these cycles, and with climate change becoming an increasingly apparent reality in the Arctic, cyclic tendencies may prove to disappear, or become amplified and spell disaster for caribou populations. Caribou management strategies will need to adapt to an ever-changing world if we want to preserve natural caribou population cycles—but what that entails remains to be seen

Aerodynamic Characteristics of a Slender Cone-cylinder Body of Revolution at a Mach Number of 3.85

An experimental investigation of the aerodynamics of a slender cone-cylinder body of revolution was conducted at a Mach number of 3.85 for angles of attack of 0 degree to 10 degrees and a Reynolds number of 3.85x10(exp 6). Boundary-layer measurements at zero angle of attack are compared with the compressible-flow formulations for predicting laminar boundary-layer characteristics. Comparison of experimental pressure and force values with theoretical values showed relatively good agreement for small angles of attack. The measured mean skin-friction coefficients agreed well with theoretical values obtained for laminar flow over cones

Theoretical pressure distribution and wave drags for conical boattails

Afterbody pressure distributions and wave drag were calculated using a second-order theory for a variety of conical boattails at zero angle of attack. Results are presented for Mach numbers from 1.5 to 4.5, area ratios from 0.200 to 0.800, and boattail angle from 3 degrees to 11 degrees. The results indicate that for a given boattail angle, the wave drag decreases with increasing Mach number and area ratio. The wave drag, for a constant area ratio, increases with increasing boattail angle. For a specific Mach number, area ratio, and fineness ratio, a comparison of the wave-drag coefficients for conical, tangent-parabolic, and secant-parabolic boattails showed the conical boattail to have the smallest wave drag

Aerodynamic characteristics of two flat-bottomed bodies at Mach number of 3.12

The aerodynamic characteristics of two flat-bottomed bodies having a semicircular and a semielliptical cross section have been determined at a Mach number of 3.12 for a range of angles of attack from -10 degrees to 10 degrees and for Reynolds numbers of 8 x 10 (superscript)6 and 14 x 10 (superscript)6 (based on model length). A comparison of the flat-bottomed body characteristics with those previously determined for an equivalent cone-cylinder body of revolution shows that significant increases in lift and lift-drag ratio are obtained with a flat bottom. Additional improvement in lift and lift-drag ratio was achieved at positive angles of attack by expanding the plan form in the spanwise direction