Time-Based Risk-Informed Safety Margins: Concepts and Application to Heterogeneous Systems

A model to quantify the temporal failure probability for a nuclear power station’s fleet of multiple, redundant, emergency diesel generators (EDGs) is developed and demonstrated in this thesis. The initiating event for this problem is Loss of Offsite Power (LOOP). This model calculates the probability that the load on the system overcomes (LOOP duration) the capacity of the system (time until the EDGs fail), as a means to quantify system safety margin; this concept comes from The United States Department of Energy (DOE), the Idaho National Laboratory (INL) and the Electric Power Research Institute (EPRI) collaboration on the “Risk-Informed Safety Margin Characterization” (RISMC) approach. The ultimate application of this model is to quantify improved safety margin for an originally two-EDG system that has been upgraded with an additional, reinforced, FLEX diesel generator (DG). Some unique features of the Non-Recovery Integral (NRI) (main model of this thesis) are that it can account for dynamic timing of the EDG failures, model both hot and cold standby EDG arrangements, and accept time-dependent hazard function inputs for hot standby cases (when the hazard functions meet certain conditions). Nuclear industry and Standardized Plant Analysis Risk (SPAR) model data are used as inputs to the NRI to create six specific system model cases. The results from these cases are compared to see how different EDG arrangements affect the overall system reliability. The three main conclusions drawn from the various result comparisons are the following: (1) adding a FLEX DG to an originally two-EDG system makes the system three times less likely to fail for LOOP durations of 24 hours (further improvement in system reliability is seen for longer LOOP durations); (2) the specific model of load placed on the system has a major impact on the system failure probability quantification; and (3) the most effective way to increase safety margin (for the most likely LOOP duration scenarios) is to reduce the likelihood of common-cause failure events

Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase

Methylation of the five position of cytosine in DNA plays important roles in epigenetic regulation in diverse organisms including humans. The transfer of methyl groups from the cofactor S-adenosyl-l-methionine is carried out by methyltransferase enzymes. Using the paradigm bacterial methyltransferase M.HhaI we demonstrate, in a chemically unperturbed system, the first direct real-time analysis of the key mechanistic events—the flipping of the target cytosine base and its covalent activation; these changes were followed by monitoring the hyperchromicity in the DNA and the loss of the cytosine chromophore in the target nucleotide, respectively. Combined with studies of M.HhaI variants containing redesigned tryptophan fluorophores, we find that the target base flipping and the closure of the mobile catalytic loop occur simultaneously, and the rate of this concerted motion inversely correlates with the stability of the target base pair. Subsequently, the covalent activation of the target cytosine is closely followed by but is not coincident with the methyl group transfer from the bound cofactor. These findings provide new insights into the temporal mechanism of this physiologically important reaction and pave the way to in-depth studies of other base-flipping systems

Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes

The Type I restriction-modification enzymes comprise three protein subunits; HsdS and HsdM that form a methyltransferase (MTase) and HsdR that associates with the MTase and catalyses Adenosine-5′-triphosphate (ATP)-dependent DNA translocation and cleavage. Here, we examine whether the MTase and HsdR components can ‘turnover’ in vitro, i.e. whether they can catalyse translocation and cleavage events on one DNA molecule, dissociate and then re-bind a second DNA molecule. Translocation termination by both EcoKI and EcoR124I leads to HsdR dissociation from linear DNA but not from circular DNA. Following DNA cleavage, the HsdR subunits appear unable to dissociate even though the DNA is linear, suggesting a tight interaction with the cleaved product. The MTases of EcoKI and EcoAI can dissociate from DNA following either translocation or cleavage and can initiate reactions on new DNA molecules as long as free HsdR molecules are available. In contrast, the MTase of EcoR124I does not turnover and additional cleavage of circular DNA is not observed by inclusion of RecBCD, a helicase–nuclease that degrades the linear DNA product resulting from Type I cleavage. Roles for Type I restriction endonuclease subunit dynamics in restriction alleviation in the cell are discussed

Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies

To investigate nucleic acid base pairing and stacking via atom-specific mutagenesis and crystallography, we have synthesized for the first time the 6-Se-deoxyguanosine phosphoramidite and incorporated it into DNAs via solid-phase synthesis with a coupling yield over 97%. We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm (ε = 2.3 × 104 M−1 cm−1), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature. Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H. The crystal structure determination and analysis reveal that the overall structures of the native and Se-modified nucleic acid duplexes are very similar, the selenium atom participates in a Se-mediated hydrogen bond (Se … H–N), and the SeG and C form a base pair similar to the natural G–C pair though the Se-modification causes the base-pair to shift (approximately 0.3 Å). Our biophysical and structural studies provide new insights into the nucleic acid flexibility, duplex recognition and stability. Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes

The structure of SgrAI bound to DNA; recognition of an 8 base pair target

The three-dimensional X-ray crystal structure of the ‘rare cutting’ type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca2+ bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn2+, with strong binding at the protein–DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI

Development and Implementation of Systems-Level RCIC Models in RELAP-7

The Reactor Core Isolation Cooling (RCIC) system is a standby system for safe plant shutdown used in over 20 US BWRs. The coupled system can cool the core without AC power, and is composed of a Terry steam turbine, a pump, and the containment wetwell. The 2011 accident at Fukushima Daiichi highlighted the importance of the RCIC system which provided core cooling to Unit 2 for 70 hours during an extended Station Blackout (SBO). This dissertation details development and implementation of new component models in RELAP-7 so that long-term operation of a complete RCIC system can be easily and accurately simulated. The original wetwell model captures buoyancy-induced thermal stratification effects due to injection of the Terry turbine exhaust steam. This phenomenon is not accounted for in current systems-level analysis codes, yet the pressure suppression capacity of the wetwell is largely influenced by the energy redistribution due to RCIC turbine steam exhaust. The stratified wetwell model has been benchmarked against three sets of experimental data for the possible RCIC turbine exhaust condensation regimes. The two-phase turbine component was designed to degrade performance as a function of incoming liquid water content; the two-phase turbine was coupled to the one-phase pump to demonstrate the “self-regulating” mode that was observed at Fukushima Daiichi Unit 2. A full-scale coupled RCIC demonstration problem is presented which shows how wetwell stratification increases wetwell pressure which then has a direct influence on both turbine and pump performance. The new RELAP-7 modeling capabilities developed in this dissertation will enable users to simulate RCIC system operation more accurately and investigate RCIC system capacity for enhanced reactor safety

Migration and maturation: The acculturation of women in Naguib Mahfouz's Zuqaq Al-Midaqq and Yusuf Idris' "Al-Naddaha"

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