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Biomolecular Simulation of Base Excision Repair and Protein Signaling

Description: The goal of the Biomolecular Simulation of Base Excision Repair and Protein Signaling project is to enhance our understanding of the mechanism of human polymerase-, one of the key enzymes in base excision repair (BER) and the cell-signaling enzymes cyclic-AMP-dependent protein kinase. This work used molecular modeling and simulation studies to specifically focus on the • dynamics of DNA and damaged DNA • dynamics and energetics of base flipping in DNA • mechanism and fidelity of nucleotide insertion by BER enzyme human polymerase-β • mechanism and inhibitor design for cyclic-AMP-dependent protein kinase. Molecular dynamics simulations and electronic structure calculations have been performed using the computer resources at the Molecular Science Computing Facility at the Environmental Molecular Sciences Laboratory.
Date: March 3, 2006
Creator: Straatsma, TP; McCammon, J. A.; Miller, John H.; Smith, Paul E.; Vorpagel, Erich R.; Wong, Chung F. et al.
Partner: UNT Libraries Government Documents Department

Theory, Modeling and Simulation Annual Report 2000

Description: This annual report describes the 2000 research accomplishments for the Theory, Modeling, and Simulation (TM&S) directorate, one of the six research organizations in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). EMSL is a U.S. Department of Energy (DOE) national scientific user facility and is the centerpiece of the DOE commitment to providing world-class experimental, theoretical, and computational capabilities for solving the nation's environmental problems.
Date: November 1, 2001
Creator: Dixon, David A.; Garrett, Bruce C.; Straatsma, Tp; Jones, Donald R.; Studham, Ronald S.; Harrison, Robert J. et al.
Partner: UNT Libraries Government Documents Department

Theory, Modeling and Simulation Annual Report 2000

Description: This annual report describes the 2000 research accomplishments for the Theory, Modeling, and Simulation (TM and S) directorate, one of the six research organizations in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). EMSL is a U.S. Department of Energy (DOE) national scientific user facility and is the centerpiece of the DOE commitment to providing world-class experimental, theoretical, and computational capabilities for solving the nation's environmental problems.
Date: November 1, 2001
Creator: Dixon, David A; Garrett, Bruce C; Straatsma, TP; Jones, Donald R; Studham, Scott; Harrison, Robert J et al.
Partner: UNT Libraries Government Documents Department

Chemical Fate of Contaminants in the Environment: Chlorinated Hydrocarbons in the Groundwater

Description: Chlorinated hydrocarbons (CHCs) are the most common contaminant found at hazardous waste sites and are the most prevalent contaminants on U.S. Department of Energy (DOE) weapons production sites. Many of the CHCs are either known or suspected carcinogens and thus pose health risks to the public and/or site workers. Unlike simple hydrocarbons, CHCs are resistant to biodegradation, but can degrade by abiotic processes such as hydrolysis, nucleophilic substitution, and dehydrochlorination. Unfortunately, few studies of the reactions of chlorinated hydrocarbons have been reported in literature, and disagreement still exists about the mechanisms and rates of many of the key reactions. In this work, we modeled the reactions involved in the degradation of CHCs in the groundwater. The goals of the research proposed are: • development of a computational approach that will allow reaction pathways and rate constants to be accurately calculated • development of more approximate approaches, evaluated against the more accurate approach, which will lay the groundwork for exploratory studies of more complex CHCs • application of these approaches to study the degradation pathways of CHCs in aqueous liquids • application of the more approximate approaches to study the mechanism of forming complex CHC polychlorinated benzene compounds and dioxins. We examined elementary reactions involved in the aqueous-phase chemistry of chlorinated methanes and ethylenes in an attempt to obtain a detailed understanding of the abiotic processes involved in the degradation of this important class of contaminants. We began by studying the reactions of CHnCl(4-n) and C2HnCl(4-n) with OH¯, as these are thought to be the dominant processes involved in the degradation of these chlorinated species. We used state-of-the-art theoretical techniques to model the elementary reactions of CHCs important in the groundwater. We employed high-accuracy electronic structure methods (e.g., perturbation theory and coupled cluster methods with correlation-consistent basis sets) to determine the ...
Date: September 21, 2006
Creator: Truhlar, Donald G.; Cramer, Christopher; Gao, Jiali; Garrett, Bruce C.; Dupuis, Michel; Straatsma, TP et al.
Partner: UNT Libraries Government Documents Department

Computational Studies in Molecular Geochemistry and Biogeochemistry

Description: The ability to predict the transport and transformations of contaminants within the subsurface is critical for decisions on virtually every waste disposal option facing the Department of Energy (DOE), from remediation technologies such as in situ bioremediation to evaluations of the safety of nuclear waste repositories. With this fact in mind, the DOE has recently sponsored a series of workshops on the development of a Strategic Simulation Plan on applications of high perform-ance computing to national problems of significance to the DOE. One of the areas selected for application was in the area of subsurface transport and environmental chemistry. Within the SSP on subsurface transport and environmental chemistry several areas were identified where applications of high performance computing could potentially significantly advance our knowledge of contaminant fate and transport. Within each of these areas molecular level simulations were specifically identified as a key capability necessary for the development of a fundamental mechanistic understanding of complex biogeochemical processes. This effort consists of a series of specific molecular level simulations and program development in four key areas of geochemistry/biogeochemistry (i.e., aqueous hydrolysis, redox chemistry, mineral surface interactions, and microbial surface properties). By addressing these four differ-ent, but computationally related, areas it becomes possible to assemble a team of investigators with the necessary expertise in high performance computing, molecular simulation, and geochemistry/biogeochemistry to make significant progress in each area. The specific targeted geochemical/biogeochemical issues include: Microbial surface mediated processes: the effects of lipopolysacchardies present on gram-negative bacteria. Environmental redox chemistry: Dechlorination pathways of carbon tetrachloride and other polychlorinated compounds in the subsurface. Mineral surface interactions: Describing surfaces at multiple scales with realistic surface functional groups Aqueous Hydrolysis Reactions and Solvation of Highly Charged Species: Understanding the formation of polymerized species and ore formation under extreme (Hanford Vadose Zone and geothermo) conditions. By understanding ...
Date: April 18, 2006
Creator: Felmy, Andrew R.; Bylaska, Eric J.; Dixon, David A.; Dupuis, Michel; Halley, James W.; Kawai, R. et al.
Partner: UNT Libraries Government Documents Department