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Combined approach to the inverse protein folding problem. Final report

Description: The main scientific contribution of the project ''Combined approach to the inverse protein folding problem'' submitted in 1996 and funded by the Department of Energy in 1997 is the formulation and development of the idea of the multilink recognition method for identification of functional and structural homologues of newly discovered genes. This idea became very popular after they first announced it and used it in prediction of the threading targets for the CASP2 competition (Critical Assessment of Structure Prediction).
Date: June 1, 2000
Creator: Abagyan, Ruben A.
Partner: UNT Libraries Government Documents Department
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The Migration and Entrapment of DNAPLs in Physically and Chemically Heterogeneous Porous Media

Description: This document summarizes EMSP funded research designed to improve our understanding of and ability to simulate the influence of subsurface chemical heterogeneities on DNAPL flow and entrapment in the saturated zone. Specific project objectives include: (i) the quantification of DNAPL interfacial and hydraulic properties; (ii) development and assessment of constitutive hydraulic property and continuum based multiphase flow models; (iii) exploration of DNAPL migration and entrapment in heterogeneous systems at larger scales; and (iv) development of innovative remediation schemes.
Date: June 1, 2000
Creator: Abriola, Linda M. & Demond, Avery H.
Partner: UNT Libraries Government Documents Department
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Verification survey of the hot cell facility site, General Atomics, San Diego, California

Description: From 1958, General Atomics maintain a hot cell facility in support of government-funded research into reactor fuels. As the use of the facility declined, General Atomics entered into an agreement with DOE to dismantle the facility and decontaminate and decommission (D&D) the site so that it could made available for unrestricted use. The Environmental Survey and Site Assessment Program (ESSAP) was requested to verify the final radiological status of the D&D effort. This is the report of ESSAP survey and verification activities conducted at the San Diego site from November 1999 through March 2000.
Date: June 30, 2000
Creator: Adams, W. C.
Partner: UNT Libraries Government Documents Department
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Contaminant-Organic Complexes, Their Structure and Energetics in Surface Decontamination Processes

Description: There are many compounds that are naturally occurring biodegradable organic chelates (siderophores) and appear to be more effective at oxide dissolution and actinide complexation than ethylenediaminetetraacetic acid (EDTA) or other organic acids currently used in decontamination processes. These chelates bind hard acids [Fe(III) and actinides(IV)] with extraordinarily high affinities. For example, the binding constant for the siderophore enterobactin with iron is about 1050, and its binding constant for Pu(IV) is estimated to be as high. Hence, this project is investigating the efficacy of using siderophores (or siderophore-like chelates) as decontamination agents of metal surfaces. The specific goals of this project are as follows: (1) To develop an understanding of the interactions between siderophores (and their functional moieties), Fe and actinide oxides, their surface chemical properties that foster their dissolution and the conditions that maximize that dissolution. (2) To develop the computational tools necessary to predict the reactivity of different siderophore functional groups toward oxide dissolution and actinide (IV) solubilization. (3) To identify likely candidate chelates for use in decontamination processes. To meet these objectives, the project combines x-ray absorption spectroscopy (XAS) and computational chemistry to provide basic information on the structure and bonding of siderophore functional groups to metal (Fe and U) oxide specimens common to corrosion products and scales on carbon steel and stainless steel encountered in DOE facilities. The project explores fundamental scientific aspects of oxide mineral surface chemistry and dissolution related to chelate-induced solubilization. The spectroscopic and computational aspects of this project are complemented by macroscopic dissolution and solubilization studies of oxides and associated contaminants. From this combination of molecular, macroscopic, and computational studies, structure-function and structure-reactivity relationships will be developed. These tasks are centered on investigative themes: (1) macroscopic dissolution studies (C. Ainsworth, PNNL), (2) optical spectroscopy (C. Ainsworth [PNNL]), (3) x-ray absorption spectroscopy (XAS) (S. …
Date: June 2000
Creator: Ainsworth, Calvin C.; Hay, Benjamin P.; Traina, Samuel J. & Myneni, Satish C. B.
Partner: UNT Libraries Government Documents Department
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The dynamics of combustion fronts in porous media

Description: In this report, a method for solving this problem by treating the reaction region as a place of discontinuities in the appropriate variables, which include, for example, fluxes of heat and mass was proposed. Using a rigorous perturbation approach, similar to that used in the propagation of flames and smoldering combustion, appropriate jump conditions that relate the change in these variables across the front was derived. These conditions account for the kinetics of the reaction between the oxidant and the fuel, the changes in the morphology of the pore space and the heat and mass transfer in the reaction zone. The modeling of the problem reduces to the modeling of the dynamics of a combustion front, on the regions of either side of which transport of momentum (fluids), heat and mass, but not chemical reactions, must be considered. Properties of the two regions are coupled using the derived jump conditions. This methodology allows one to explicitly incorporate permeability heterogeneity effects in the process description, without the undue complexity of the coupled chemical reactions.
Date: June 15, 2000
Creator: Akkutlu, I. Yucel & Yortsos, Yannis C.
Partner: UNT Libraries Government Documents Department
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A Hydrologic-Geophysical Method for Characterizing Flow and Transport Processes within the Vadose Zone

Description: The objective of this study is to analyze flow within the vadose zone during a mid-scale hydrologic test to and to characterize transport processes in-situ. This project will employ numerical and experimental tools that have been developed under a previously funded EMSP proposal (project number 55332). Geophysical imaging techniques will be employed to image the changes produced by the transport experiments in-situ as they occur. Results will help to better understand flow and transport modes within the vadose zone at DOE sites, including the influence of natural heterogeneities and man-made structures. In addition the data will provide checks against which numerical flow and transport simulations can be compared.
Date: June 1, 2000
Creator: Alumbaugh, David L. & Brainard, James R.
Partner: UNT Libraries Government Documents Department
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A Hybrid Hydrologic-Geophysical Inverse Technique for the Assessment and Monitoring of Leachates in the Vadose Zone

Description: The objective of this study is to develop and field test a new, integrated Hybrid Hydrologic- Geophysical Inverse Technique (HHGIT) for characterization of the vadose zone at contaminated sites. This new approach to site characterization and monitoring can provide detailed maps of hydrogeologic heterogeneity and the extent of contamination by combining information from 3D electric resistivity tomography (ERT) and/or 2D cross-borehole ground penetrating radar (XBGPR) surveys, statistical information about heterogeneity and hydrologic processes, and sparse hydrologic data. Because the electrical conductivity and dielectric constant of the vadose zone (from the ERT and XBGPR measurements, respectively) can be correlated to the fluid saturation and/or contaminant concentration, the hydrologic and geophysical measurements are related.
Date: June 1, 2000
Creator: Alumbaugh, David L.; Yeh, Jim; LaBrecque, Doug & Glass, Robert J.
Partner: UNT Libraries Government Documents Department
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Analysis, tuning and comparison of two general sparse solvers for distributed memory computers

Description: We describe the work performed in the context of a Franco-Berkeley funded project between NERSC-LBNL located in Berkeley (USA) and CERFACS-ENSEEIHT located in Toulouse (France). We discuss both the tuning and performance analysis of two distributed memory sparse solvers (superlu from Berkeley and mumps from Toulouse) on the 512 processor Cray T3E from NERSC (Lawrence Berkeley National Laboratory). This project gave us the opportunity to improve the algorithms and add new features to the codes. We then quite extensively analyze and compare the two approaches on a set of large problems from real applications. We further explain the main differences in the behavior of the approaches on artificial regular grid problems. As a conclusion to this activity report, we mention a set of parallel sparse solvers on which this type of study should be extended.
Date: June 30, 2000
Creator: Amestoy, P. R.; Duff, I. S.; L'Excellent, J. Y. & Li, X. S.
Partner: UNT Libraries Government Documents Department
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Complexants fsro Actinide Element Coordination & Immobilization

Description: The goal of this project is to develop inorganic metal oxide clusters known as polyoxoanions (POAs) as complexants for the immobilization of actinide (An) ions from high-level waste (HLW). A diverse array of rugged isopolyoxoanions, [MxOy]z- , and heteropolyoxoanions, [XaMbOc]d-, comprised of M = V, Nb, Mo, W and X = Si, P polyhedra are under investigation for their ability to incarcerate An ions. The research combines two objectives-An-POA coordination and An-POA containment. The first involves the synthesis, isolation, and characterization of POAs that can selectively bind An ions to form stable An-POA complexes in alkaline and acidic solutions. The second involves investigations of the thermochemistry of the An-POA complexes under vitrification conditions germane to the formation of proposed HLW forms, such as borosilicate glass. The approach is envisioned to provide two levels of An encapsulation for maximum stability and durability as well as the potential to incorporate higher levels of An ions (particularly Pu) in waste forms than now possible. Such versatility bodes well for prospective applications of POAs as An complexants in technology of significance to the environmental management of HLW.
Date: June 1, 2000
Creator: Antonio, Mark R. & Soderholm, L.
Partner: UNT Libraries Government Documents Department
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Strong Earthquake Motion Estimates for the UCSB Campus, and Related Response of the Engineering 1 Building

Description: This is the second report on the UC/CLC Campus Earthquake Program (CEP), concerning the estimation of exposure of the U.C. Santa Barbara campus to strong earthquake motions (Phase 2 study). The main results of Phase 1 are summarized in the current report. This document describes the studies which resulted in site-specific strong motion estimates for the Engineering I site, and discusses the potential impact of these motions on the building. The main elements of Phase 2 are: (1) determining that a M 6.8 earthquake on the North Channel-Pitas Point (NCPP) fault is the largest threat to the campus. Its recurrence interval is estimated at 350 to 525 years; (2) recording earthquakes from that fault on March 23, 1998 (M 3.2) and May 14, 1999 (M 3.2) at the new UCSB seismic station; (3) using these recordings as empirical Green's functions (EGF) in scenario earthquake simulations which provided strong motion estimates (seismic syntheses) at a depth of 74 m under the Engineering I site; 240 such simulations were performed, each with the same seismic moment, but giving a broad range of motions that were analyzed for their mean and standard deviation; (4) laboratory testing, at U.C. Berkeley and U.C. Los Angeles, of soil samples obtained from drilling at the UCSB station site, to determine their response to earthquake-type loading; (5) performing nonlinear soil dynamic calculations, using the soil properties determined in-situ and in the laboratory, to calculate the surface strong motions resulting from the seismic syntheses at depth; (6) comparing these CEP-generated strong motion estimates to acceleration spectra based on the application of state-of-practice methods - the IBC 2000 code, UBC 97 code and Probabilistic Seismic Hazard Analysis (PSHA), this comparison will be used to formulate design-basis spectra for future buildings and retrofits at UCSB; and (7) comparing the response of …
Date: June 6, 2000
Creator: Archuleta, R.; Bonilla, F.; Doroudian, M.; Elgamal, A. & Hueze, F.
Partner: UNT Libraries Government Documents Department
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Savannah River Site Environmental Data for 1999

Description: This document presents data from Savannah River Site routine effluent monitoring and environmental surveillance programs.
Date: June 30, 2000
Creator: Arnett, M.
Partner: UNT Libraries Government Documents Department
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Savannah River Site Environmental Report for 1999

Description: The purpose of this report is to present summary environmental data that characterize site environmental management performance, confirm compliance with environmental standards and requirements, highlight significant programs and efforts, and assess the impact of SRS operations on the public and the environment.
Date: June 30, 2000
Creator: Arnett, M.
Partner: UNT Libraries Government Documents Department
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Processing High Level Waste: Spectroscopic Characterization of Redox Reactions in Supercritical Water

Description: We are engaged in a collaborative research effort with Los Alamos staff scientists Steven Buelow and Jeanne Robinson, staff members in group CST-6. The work proposed by these LANL staff scientists is directed towards the destruction of complexants and oxidation of chromium and technetium by hydrothermal processing in near critical or supercritical aqueous solutions. Our own work has been focused on a careful kinetic study of oxidation reactions of hydrogen peroxide with chromium hydroxide. This reaction occurs readily at ambient temperatures.
Date: June 1, 2000
Creator: Arrington, Charles A., (Jr.)
Partner: UNT Libraries Government Documents Department
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Development of Novel, Simple, Multianalyte Sensors for Remote Environmental Analysis

Description: We will develop simple, inexpensive new chemical sensing materials which can be used as visual color test strips to sensitively and selectively report on the concentration and identity of environmental pollutants such as cations of Pb, U, Pu, Sr, Hg, Cs, Co as well as other species. We will develop inexpensive chemical test strips which can be immersed in water to determine these analytes in the field. We will also develop arrays of these chemical sensing materials which will be attached to fiber optic bundles to be used as rugged multichannel optrodes to simultaneously monitor numerous analytes remotely in hostile environments. These sensing materials are based on the intelligent polymerized crystalline colloidal array (PCCA) technology we recently developed. This sensing motif utilizes a mesoscopically periodic array of colloidal particles polymerized into an acrylamide hydrogel. This array Bragg diffracts light in the visible spectral region due to the periodic array of colloidal particles. This material also contains chelating agents for the analytes of interest. When an analyte binds, its charge is immobilized within the acrylamide hydrogel. The resulting Donnan potential causes an osmotic pressure which swells the array proportional to the concentration of analyte bound. The diffracted wavelength shifts and the color changes. The change in the wavelength diffracted reports on the identity and concentration of the target analyte. Our successful development of these simple, inexpensive highly sensitive chemical sensing optrodes, which are easily coupled to simple optical instrumentation, could revolutionize environmental monitoring. In addition, we will develop highly rugged versions, which can be attached to core penetrometers and which can be used to determine analytes in buried core samples. Research Progress and Implications This report summarizes work after 21 months of a three year project. We have developed a new method to crosslink our PCCA sensing materials with disulfide bridges. …
Date: June 1, 2000
Creator: Asher, Sanford A.
Partner: UNT Libraries Government Documents Department
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Tank Monitoring and Control System (TMACS) Acceptance Test Procedure

Description: The purpose of this document is to describe tests performed to validate Revision 12.0 of the TMACS Monitor and Control System (TMACS) and verify that the software functions as intended by design. This document is intended to test the software portion of TMACS. The tests will be performed on the development system. The software to be tested is the TMACS knowledge bases (KB) and the I/O driver/services. The development system will not be communicating to field equipment; instead, the field equipment is simulated using emulators or multiplexers in the lab.
Date: June 1, 2000
Creator: BARNES, D.A.
Partner: UNT Libraries Government Documents Department
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Energy Storage Systems Program Report for FY99

Description: Sandia National Laboratories, New Mexico, conducts the Energy Storage Systems Program, which is sponsored by the US Department of Energy's Office of Power Technologies. The goal of this program is to develop cost-effective electric energy storage systems for many high-value stationary applications in collaboration with academia and industry. Sandia National Laboratories is responsible for the engineering analyses, contracted development, and testing of energy storage components and systems. This report details the technical achievements realized during fiscal year 1999.
Date: June 1, 2000
Creator: BOYES,JOHN D.
Partner: UNT Libraries Government Documents Department
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Hanford Waste Tank Bump Accident and Consequence Analysis

Description: This report provides a new evaluation of the Hanford tank bump accident analysis and consequences for incorporation into the Authorization Basis. The analysis scope is for the safe storage of waste in its current configuration in single-shell and double-shell tanks.
Date: June 20, 2000
Creator: BRATZEL, D.R.
Partner: UNT Libraries Government Documents Department
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Performance testing of elastomeric seal materials under low and high temperature conditions: Final report

Description: The US Department of Energy Offices of Defense Programs and Civilian Radioactive Waste Management jointly sponsored a program to evaluate elastomeric O-ring seal materials for radioactive material shipping containers. The report presents the results of low- and high-temperature tests conducted on 27 common elastomeric compounds.
Date: June 1, 2000
Creator: BRONOWSKI,DAVID R.
Partner: UNT Libraries Government Documents Department
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The Case for a 500 GEV E+E - Linear Collider

Description: There are now several proposals that have been put forward from around the world for an e{sup +}e{sup {minus}} linear collider with an initial center of mass energy of 500 GeV. In this paper, the authors discuss why a project of this type deserves priority as the next, major initiative in high energy physics.
Date: June 30, 2000
Creator: Bagger, J.; Baltay, C.; AL, ET; Marciano, W.; Paige, F.; Turcot, A. S. et al.
Partner: UNT Libraries Government Documents Department
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Broadening and shifting of the methanol 119 {mu}m gain line of linear and circular polarization by collision with chiral molecules

Description: Evidence of circular dichroism has been observed in the spectral properties of a gas of left-right symmetric molecules. This dichroism comes about as the result of collisions of the symmetric molecules with left-right asymmetric molecules introduced as a buffer gas. In this sense, the dichroism can be said to have been transferred from the chiral buffer molecules to the symmetric, non-chiral molecules of the background vapor. This transferred dichroism appears as broadening in the gain line of the symmetric molecule which is asymmetric with respect to the right or left handedness of a circularly polarized probe. The broadening of the 119 {mu}m line of the methanol molecule was observed using infrared-far infrared double resonance spectroscopy.
Date: June 21, 2000
Creator: Bakos, J.S.; Djotyan, G.; Soerlei, Zsuzsa; Szigeti, J.; Mansfield, D. K. & Sarkozi, J.
Partner: UNT Libraries Government Documents Department
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Studies of Dynamic Properties of Shock Compressed Solids by In-Situ Transient X-Ray Diffraction

Description: In the transient diffraction NLYF proposal we set forward a program of work to investigate the response of crystals to shock compression in regions of strain rates previously unexplored, in a coordinated experimental, computational, and analytical program. Time resolved x-ray diffraction was used to directly determine the lattice parameters of crystals during shock loading previously on the Nova and Trident laser facilities. Under this proposal we extended this work to exploit the multi-beam direct drive capability of the Omega laser facility to allow more extensive diagnostic access for measuring the lattice parameters both parallel and perpendicular to the shock front. Under the NLUF Program in FY 99, we transitioned the dynamic diffraction experiments to the OMEGA facility. We developed a direct drive target configuration that uses a single beam to direct irradiate the surface of a thin crystal and 4 beams to irradiate a separate metal backlighter foil. Experiments were done with single crystal Si to demonstrate that the target design worked and that simultaneous measurements of compression both parallel and perpendicular to the shock propagation direction could be performed. We obtained simultaneous measurements of the (400) and (040) lattice planes during the period when a shock traveled through the crystal in the (100) direction. Follow-up experiments were done to demonstrate that this technique would work with thin metal crystals such as Cu. Simultaneous measurements were made of the (200) and (020) lattice planes of Cu shocked along the (100) direction. Future experiments (FY 00 and beyond) will be focused on further studying the time resolved lattice response in Cu at a range of shock pressures. Additional techniques such as introducing a knife edge near the x-ray source are expected to provide information about the density of lattice dislocations created by the shock front. Results from these experiments will enable …
Date: June 26, 2000
Creator: Baldis, H; Kalantar, D H; Remington, B A; Weber, S V; Meyers, M A; Wark, J S et al.
Partner: UNT Libraries Government Documents Department
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