Chemistry & Biochemistry

Permanent URI for this communityhttp://hdl.handle.net/1903/11812

Browse

Subject: search.filters.subject.Monte Carlo simulation

Search Results

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    MODELING AND VALIDATION OF NEUTRON ACTIVATION AND GAMMA-RAY SPECTROSCOPY MEASUREMENTS AS AN EXPLORATORY TOOL FOR NUCLEAR FORENSIC ANALYSIS
    (2018) Goodell, John; Mignerey, Alice C; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The continued success of nuclear forensic analysis relies on the development of new material and process signatures. However, the unique safety hazards and strict controls concerning nuclear materials and operations limit the practicality of experimental scenarios. To bypass these limitations, the nuclear science community is increasingly reliant on simulation-based tools. In this dissertation, neutron activation and gamma-ray spectroscopy measurements are simulated to explore the activation network of stainless steel and its components using two neutron sources. The goal is to identify nuclides or ratios that are indicative of the neutron source and test their measurability in complex samples. The neutron sources are a critical assembly, providing fission spectrum neutrons, and a beryllium (Be) neutron converter, producing neutrons through various deuteron induced reactions. Simulated neutron energy distributions are calculated using the Monte Carlo N-Particle (MCNP) radiation transport code. Neutron activation has an inherent neutron energy dependence, making nuclide production rates contingent on the neutron energy distribution. Activation calculations performed by hand and with the FISPACT-II code are compared against experiments to validate the neutron energy distributions and assess available reaction cross-section data. Additionally, ratios of activation products common to both neutron sources are investigated to determine if they are indicative of the neutron source. Gamma-ray spectroscopy with high-purity germanium (HPGe) detectors is the leading passive assay technique for radioactive samples, providing detailed qualitative and quantitative information while preserving sample integrity. A simple HPGe detector is modeled using MCNP to assess the measurability of different activation product ratios. The HPGe model is validated against its real counterpart to determine if the level of complexity is sufficient for this work. Activation calculations were able to validate the critical assembly neutron energy distribution but showed significant errors in the Be converter model. Additionally, validation of activation calculations identified shortcomings in the 60Ni(n,p)60Co reaction cross section. Absent interferences, HPGe simulation performance was equivalent to the real detector. The HPGe model also showed that decay time can affect measurement accuracy when significant interferences are present. Activation product ratios identified in this work that are indicative of the neutron source are 57Co/54Mn, 51Cr/54Mn, 57Co/59Fe, and 51Cr/59Fe.
  • Thumbnail Image
    Item
    Flexibility and Control of Protein-DNA Loops
    (World Scientific Publishing Company, 2006-10) Kahn, Jason D.; Cheong, Raymond; Edelman, Laurence M.; Mehta, Ruchi A.; Morgan, Michael A.
    Protein-DNA loops are essential for efficient transcriptional repression and activation. The geometry and stability of the archetypal Lac repressor tetramer (LacI)-DNA loop were investigated using designed hyperstable loops containing lac operators bracketing a sequence-directed bend. Electrophoretic mobility shift assays, DNA cyclization, and bulk and single-molecule fluorescence resonance energy transfer (FRET) demonstrate that the DNA sequence controls whether the LacI-DNA loop forms a compact loop with positive writhe or an open loop with little writhe. Monte Carlo methods for simulation of DNA ring closure were extended to DNA loops, including treatment of variable protein hinge angles. The observed distribution of topoisomer products upon cyclization provides a strong constraint on possible models. The experiments and modeling imply that LacI-DNA can adopt a wide range of geometries but has a strong intrinsic preference for an open form. The flexibility of LacI helps explain in vivo observations that DNA looping is less sensitive to DNA length and shape than would be expected from the physical properties of DNA. While DNA cyclization suggests two pools of precursor loops for the 9C14 construct, single-molecule FRET demonstrates a single population. This discrepancy suggests that the LacI-DNA structure is strongly influenced by flanking DNA.