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Computational methods for molecular docking

Description: This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Recently, it has been demonstrated that the knowledge of the three-dimensional structure of the protein can be used to derive new protein ligands with improved binding properties. This tutorial focuses on the following questions: What is its binding affinity toward a particular receptor? What are putative conformations of a ligand at the binding site? What are the similarities of different ligands in terms of their recognition capabilities? Where and in which orientation will a ligand bind to the active site? How is a new putative protein ligand selected? An overview is presented of the algorithms which are presently used to handle and predict protein-ligand interactions and to dock small molecule ligands into proteins.
Date: December 31, 1995
Creator: Klebe, G. & Lengauer, T.
Partner: UNT Libraries Government Documents Department

CT imaging techniques for two-phase and three-phase in-situ saturation measurements

Description: The aim of this research is to use the SUPRI 3D steam injection laboratory model to establish a reliable method for 3-phase in-situ saturation measurements, and thereafter investigate the mechanism of steamflood at residual oil saturation. Demiral et al. designed and constructed a three dimensional laboratory model that can be used to measure temperature, pressure and heat loss data. The model is also designed so that its construction materials are not a limiting factor for CT scanning. We have used this model for our study. In this study, we saturated the model with mineral oil, and carried out waterflood until residual oil saturation. Steamflood was then carried out. A leak appeared at the bottom of the model. Despite this problem, the saturation results, obtained by using 2-phase and 3-phase saturation equations and obtained from the Cat scanner, were compared with the saturations obtained from material balance. The errors thus obtained were compared with those obtained by an error analysis carried out on the saturation equations. This report gives details of the experimental procedures, the data acquisition and data processing computer programs, and the analysis of a steamflood experiment carried out at residual oil saturation.
Date: June 1, 1997
Creator: Sharma, B. C.; Brigham, W. E. & Castanier, L. M.
Partner: UNT Libraries Government Documents Department

Human Genome Education Program

Description: The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final ...
Date: May 1, 2000
Creator: Myers, Richard & Conn, Lane
Partner: UNT Libraries Government Documents Department

Final Report on the Construction of the HERS Endstation, September 1, 1996 - October 31, 1998

Description: The construction of the HERS endstation was successfully completed. The resolution of the photoemission apparatus is better than 7meV. The angular resolution is +0.15 degrees. The system has a high precision sample manipulator w/ five-degrees of freedom and a temperature range from 10 - 450 degrees K. The sample transfer system allows transfer of a sample from atmosphere onto the crystal @ 5x10 in less than 2 hrs.
Date: April 3, 2000
Creator: Kellar, S.A. Dr. & Shen, Z.X.
Partner: UNT Libraries Government Documents Department

K-Edge Subtraction Angiography with Synchrotron X-Rays

Description: The purpose of this project was to utilize dual energy, monochromatic X-rays produced from synchrotrons radiation in order to obtain noninvasive medical imaging. The application of synchrotrons radiation to medical imaging is based on the principle of iodine dichromography, first described by Bertil Jacobson of the Karolinska Institute in 1953. Medical imaging using synchrotrons radiation and K-edge dichromography was pioneered at Stanford University under the leadership of Dr. Ed Rubenstein, and the late Nobel Laureate in Physics, Dr. Robert Hofstadter. With progressive refinements in hardware, clinical-quality images were obtained of human coronary arteries utilizing peripheral injections of iodinated contrast agent. These images even now are far superior to those being presented by investigators using MRI as an imaging tool for coronary arteries. However, new supplies and instruments in the cardiac catheterization laboratory have served to transform coronary angiography into an outpatient procedure, with relatively little morbidity. We extended the principles learned with coronary angiography to noninvasive imaging of the human bronchial tree. For these images, we utilized xenon as the contrast agent, as it has a K-edge very similar to that of iodine. In this case, there is no true competing diagnostic test, and pulmonary neoplasm is an enormous public health concern. In early experiments, we demonstrated remarkably clear images of the human bronchial tree. These images have been shown internationally; however, funding difficulties primarily with the Department of Energy have not allowed for progression of this promising avenue of research. One potential criticism of the project is that in order to obtain these images, we utilized national laboratories. Some have questioned whether this would lead to a practical imaging modality. However, we have shown that the technology exists to allow for construction of a miniature storage ring, with a superconducting wiggler magnet, which would occupy minimal space, and would ...
Date: December 31, 1996
Creator: Giacomini, John C.
Partner: UNT Libraries Government Documents Department

Mechanisms, Chemistry, and Kinetics of Anaerobic Biodegradation of cis-Dichloroethene and Vinyl Chloride

Description: Anaerobic biological processes can result in PCE and TCE destruction through conversion to cis-dichloroethene (cDCE) then to vinyl chloride (VC), and finally to ethene. Here, the chlorinated aliphatic hydrocarbons (CAHs) serve as electron acceptors in energy metabolism, requiring electron donors such as hydrogen from an external source. The purpose of this study was to learn more about the biochemistry of cDCE and VC conversion to ethene, to better understand the requirements for electron donors, and to determine factors affecting the rates of CAH degradation and organism growth. The biochemistry of reductive dehalogenation of VC was studied with an anaerobic mixed culture enriched on VC. In other studies on electron donor needs for dehalogenation of cDCE and VC, competition for hydrogen was found to occur between the dehalogenators and other microorganisms such as methanogens and homoacetogens in a benzoate-acclimated dehalogenating methanogenic mixed culture. Factors affecting the relative rates of destruction of the solvents and their intermediate products were evaluated. Studies using a mixed PCE-dehalogenating culture as well as the VC enrichment for biochemical studies suggested that the same species was involved in both cDCE and VC dechlorination, and that cDCE and VC competitively inhibited each other's dechlorination rate.
Date: December 1, 2000
Creator: McCarty, P.L. & Spormann, A.M.
Partner: UNT Libraries Government Documents Department

Method for Sampling Alpha-Helical Protein Backbones

Description: We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible 3-D arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case the method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for 4 of the 25 proteins. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (0.02%--82%) within 6A of the native structure. The method's speed and efficiency make it a valuable contribution towards the goal of predicting protein structure.
Date: February 22, 2000
Creator: Fain, Boris & Levitt, Michael
Partner: UNT Libraries Government Documents Department

Molecular-Level Processes Governing the Interaction of Contaminants with Iron and Manganese Oxides - Final Report

Description: Many of the inorganic and organic contaminants present in sediments at DOE sites can be altered or destroyed by reduction and oxidation (redox) reactions occurring at mineral surfaces. A fundamental understanding of such redox processes provided by molecular-level studies on structurally and compositionally well-defined mineral surfaces will lead to: (i) improved models of contaminant fate and transport in geochemical systems, and (ii) optimized manipulation of these processes for remediation purposes. To contribute to this understanding, we will study, both experimentally and theoretically, redox processes involving three important contaminants - chromate ion, carbon tetrachloride, and trichloroethene TCE, on the following iron and manganese oxides - hematite, magnetite, maghemite, and pyrolusite. These oxides and their hydroxylated analogs commonly occur as coatings on minerals or as interfaces in the subsurface environment. Single-crystal surfaces of these oxides will be synthesized in carefully controlled fashion by molecular beam epitaxy. These surfaces, as well as high surface are powdered samples of these oxides, will be used in spectroscopic and kinetic experiments in both aqueous and gas phases. Our goal is to identify products and to determine the kinetics and mechanisms of surface-catalyzed redox reaction of Cr(VI) and CR(III), and the reductive dechlorination of carbon tetrachloride and TCE. The combination of theory and experiment will provide the base information needed to scale from the molecular level to the microscopic grain level minerals.
Date: October 31, 1999
Creator: Brown Jr., G. E. & Chambers, S. A.
Partner: UNT Libraries Government Documents Department

CT measurements of two-phase flow in fractured porous media

Description: The simulation of flow in naturally fractured reservoirs commonly divides the reservoir into two continua - the matrix system and the fracture system. Flow equations are written presuming that the primary flow between grid blocks occurs through the fracture system and that the primary fluid storage is in the matrix system. The dual porosity formulation of the equations assumes that there is no flow between matrix blocks while the dual permeability formulation allows fluid movement between matrix blocks. Since most of the fluid storage is contained in the matrix, recovery is dominated by the transfer of fluid from the matrix to the high conductivity fractures. The physical mechanisms influencing this transfer have been evaluated primarily through numerical studies. Relatively few experimental studies have investigated the transfer mechanisms. Early studies focused on the prediction of reservoir recoveries from the results of scaled experiments on single reservoir blocks. Recent experiments have investigated some of the mechanisms that are dominant in gravity drainage situations and in small block imbibition displacements. The mechanisms active in multiphase flow in fractured media need to be further illuminated, since some of the experimental results appear to be contradictory. This report describes the design, construction, and preliminary results of an experiment that studies imbibition displacement in two fracture blocks. Multiphase (oil/water) displacements will be conducted at the same rate on three core configurations. The configurations are a compact core, a two-block system with a 1 mm spacer between the blocks, and a two-block system with no spacer. The blocks are sealed in epoxy so that saturation measurements can be made throughout the displacement experiments using a Computed Tomography (CT) scanner.
Date: June 1, 1997
Creator: Hughes, R. G.; Brigham, W. E. & Castanier, L. M.
Partner: UNT Libraries Government Documents Department

Stanford geothermal program. Final report, July 1990--June 1996

Description: This report discusses the following: (1) improving models of vapor-dominated geothermal fields: the effects of adsorption; (2) adsorption characteristics of rocks from vapor-dominated geothermal reservoir at the Geysers, CA; (3) optimizing reinjection strategy at Palinpinon, Philippines based on chloride data; (4) optimization of water injection into vapor-dominated geothermal reservoirs; and (5) steam-water relative permeability.
Date: March 1, 1998
Partner: UNT Libraries Government Documents Department

Two-Mile Accelerator Project: Quarterly Status Report, 1 October to 30 December 1962

Description: Introduction: This is the third Quarterly Status Report of work under AEC Contract AT(04-3)-400, held by Stanford University. This contract provides for the construction of the Stanford Linear Accelerator Center (SLAC), a laboratory that will have as its chief instrument a two-mile-long linear electron accelerator.
Date: March 1963
Creator: Chu, E. L.; Ballam, J.; Neal, R. B.; Loew, G.; Eldredge, A. & DeStaebler, H.
Partner: UNT Libraries Government Documents Department

Two-Mile Accelerator Project: Quarterly Status Report, 1 January to 31 March 1963

Description: Introduction: This is the fourth Quarterly Status Report of work under AEC Contract AT(04-3)-400, held by Stanford University. This contract provides for the construction of the Stanford Linear Accelerator Center (SLAC), a laboratory that will have as its chief instrument a two-mile-long linear electron accelerator.
Date: May 1963
Partner: UNT Libraries Government Documents Department

Growth of high T{sub c} superconducting fibers using a miniaturized laser-heated float zone process. Annual progress report, October 15, 1989--November 5, 1990

Description: This report covers the research accomplished on the program entitled {open_quotes}Growth of High Tc Superconducting Fibers using a Miniaturized Laser-Heated Float Zone Process{close_quotes} during the 12.5 month period from Oct. 15, 1989 to Nov. 5, 1990. Research was done in four areas: phase relationships, preparation of starting materials, growth studies and the advanced fiber growth apparatus. The phase relationship studies built on the work published by Ono. Comparison studies with the well known compound Ca{sub 3}Al{sub 2}O{sub 6} confirmed that the Bi{sub 2+x}(Sr,Ca){sub 3-x}Cu{sub 2}O{sub y} is incongruently melting and that cuprous oxide, calcium oxide and (strontium, calcium) cuprate are the higher melting compounds which coexist with the melt and the superconducting phase. The preparation of the starting materials is crucial to the stable growth of the fibers. Non-uniform distribution of second phase particles, gaseous inclusions or porosity can lead to instabilities. A process was developed to ensure uniform starting materials. `Ibis process involves grinding the individual starting materials to a uniform size (44 {mu}m). The resulting powders are mixed and calcined three times with regrinding between each calcining step. The calcined powder is then cold pressed and sintered, reground, re-pressed and sintered. Ibis final material is then cut into bars for feed material for fiber growth. Growth rate studies showed a relationship between the growth rate and the regions of stability for single and multiphase fibers. This was traced to changes in the Bi and Cu levels in the melt related to changes in the growth rate. It was also shown that fluctuation in laser power lead to CaO inclusions in the fibers. The necessary components for the Advanced Fiber Growth Apparatus have been determined. Some of the components have been ordered and others are being designed.
Date: November 1, 1990
Creator: Feigelson, R.S.
Partner: UNT Libraries Government Documents Department

Growth of high T{sub c} superconducting fibers using a minaturized laser-heated float zone process. Annual progress report, January 1, 1993--December 31, 1993

Description: This report covers the research done on {open_quotes}Growth of High Tc Superconducting Fibers using a Miniaturized Laser-Heated Float Zone Process{close_quotes} during the 12 months from Jan. 1, 1993 until Dec. 31, 1993. The effort during this period were directed into two areas; the influence of growth conditions on the properties of the superconducting fibers and the construction of the advanced fiber growth station. In the first area of emphasis, studies were done on constitutional super cooling effect, the influence of processing parameters on Tc, the correlation between Tc and growth parameters and the mechanical properties of 2212 fibers. These studies showed that there are two types of interfacial breakdowns; one type that involves low temperature inclusions caused by excessive solute buildup and another involving high temperature inclusions which require two conditions to be met. These condition are: (1) significant compositional gradients in the melt and (2) an interface melt temperature near the peritectic decomposition temperature. Analysis of the experimental data lead to the hypothesis that fibers with the highest crystallinity are grown from SrO-rich 2212 melts. Evaluation of the constitutional supercooling responsible for the high temperature inclusions suggested that growth under these conditions was most vulnerable to disruption by HT inclusions. Tc increased with growth temperature for as-grown fibers. The concentration of SrO in the fibers had a parabolic relationship with temperature. The same parabolic relationship was observed between composition and Tc. The thermal history of 2212 crystals has been shown to influence their oxygen content which played a significant role in determining their Tc`s. Fiber heat treatment and the ambient gaseous atmosphere were found to dominate the Tc variations measured in this study.
Date: December 1, 1993
Creator: Feigelson, R.S.
Partner: UNT Libraries Government Documents Department

Energy changes in transforming solids. Continuation proposal for the period January 1--December 31, 1990

Description: This report describes work completed, work in progress, and work planned during the continuation of funding. Research is being carried out on the following: bonded inclusions are being treated as problems of a homogeneous body; the problem of two cavities or inclusions is being studied; the examination of non-classical transformations is leading to conservation laws in statics and dynamics with applications in fracture and defect mechanics; mathematical and physical modeling of damage in brittle solids is being performed; a theoretical and numerical study of subsonic interfacial waves in bonded piezoelectric dissimilar half-spaces has been completed; the study of which crystal classes are capable of admitting the so-called Type 3 transonic state in anisotropic elasticity is also complete; and wave studies will be extended into the supersonic regime. The authors also intend to complete a study of the general self-force on a 3-dimensional dislocation loop element in an elastic medium of arbitrary anisotropy, as this is currently a needed ingredient in modern fracture and damage mechanics and in the study of defects in integrated circuit materials.
Date: September 15, 1989
Creator: Herrmann, G. & Barnett, D.M.
Partner: UNT Libraries Government Documents Department

A precise measurement of the left-right cross section asymmetry in Z boson production

Description: The thesis presents a measurement of the left-right asymmetry, A{sub LR}, n the production cross section of Z Bosons produced by e{sup +}e{sup -} annihilations, using polarized electrons, at a center of mass energy of 91.26 Gev. The data presented was recorded by the SLD detector at the SLAC Linear Collider during the 1993 run. The mean luminosity-weighted polarization of the electron beam was {rho}{sup lum} = (63.0{+-}1.1)%. Using a sample of 49,392 Z events, we measure A{sub LR} to be 0.1626{+-}0.0071(stat){+-}0.0030(sys.), which determined the effective weak mixing angle to be sin{sup 2} {theta}{sub W}{sup eff} = 0.2292{+-}0.0009(stat.){+-}0.0004(sys.). This result differs from that expected by the Standard Model of Particles and Fields by 2.5 standard deviations.
Date: September 1, 1994
Creator: Lath, A.
Partner: UNT Libraries Government Documents Department

SUPRI heavy oil research program. Annual report, February 8, 1995--February 7, 1996

Description: The goal of the Stanford University Petroleum Research Institute (SUPRI) is to conduct research directed toward increasing the recovery of heavy oils. Presently SUPRI is working in five main directions: (1) flow properties studies to assess the influence of different reservoir conditions (temperature and pressure) on the absolute and relative permeability to oil and water and on capillary pressure; (2) in-situ combustion to evaluate the effect of different reservoir parameters on the in-situ combustion process; (3) steam with additives to develop and understand the mechanisms of the process using commercially available surfactants for reduction of gravity override and channeling of steam; (4) formation evaluation to develop and improve techniques of formation evaluation such as tracer tests and pressure transient tests; and (5) field support services to provide technical support for design and monitoring of DOE sponsored or industry initiated field projects. This report consists of abstracts of reports and copies of technical papers presented or published.
Date: June 1, 1996
Creator: Brigham, W.E. & Castanier, L.M.
Partner: UNT Libraries Government Documents Department

Growth of high T{sub c} superconducting fibers using a miniaturized laser-heated float zone process. Annual progress report, January 1, 1992--December 31, 1992

Description: This report covers the research done on {open_quotes}Growth of High Tc Superconducting Fibers using a Miniaturized Laser-Heated Float Zone Process{close_quotes} during the 12 months from Jan. 1, 1992 until Dec. 31, 1992. The major part of the work focused on phase relations and kinetics in the Bi{sub 2}O{sub 3}-SrO-CaO-CuO (BSCCO) system. By analyzing the crystal and melt composition, and the growth temperature of the float-zone samples, new data was obtained on the phase relationships. These results were shown to form a subset of solid solubility ranges reported by other investigators and was typical of the data available from other flux growth experiments. These experiments resulted in the development of a technique for the growth of long, single-phase 2212 samples. This was highly depended on starting material composition with Bi{sub 2.1}Sr{sub 1.8}Ca{sub 1.1}Cu{sub 2}O{sub y} being the most successful. Examination of the single phase 2212 growth interfaces was used to characterize the crystal/melt equilibrium conditions. These studies showed that 2212 crystal solidify from Bi{sub 2}O{sub 3}-rich and SrO-poor melts. Increasing melt concentrations of bismuth and cooper oxide increased the growth temperature. The sum of the bismuth and copper oxide in the crystals was invariant leading to the conclusion that the segregation of bismuth and copper oxide is interdependent. Work also proceeded on the new LHPG growth station.
Date: December 1, 1992
Creator: Feigelson, R.S.
Partner: UNT Libraries Government Documents Department

A study of steam injection in fractured media

Description: Steam injection is the most widely used thermal recovery technique for unfractured reservoirs containing heavy oil. There have been numerous studies on theoretical and experimental aspects of steam injection for such systems. Fractured reservoirs contain a large fraction of the world supply of oil, and field tests indicate that steam injection is feasible for such reservoirs. Unfortunately there has been little laboratory work done on steam injection in such systems. The experimental system in this work was designed to understand the mechanisms involved in the transfer of fluids and heat between matrix rocks and fractures under steam injection.
Date: February 1, 1996
Creator: Dindoruk, M.D.S.; Aziz, K.; Brigham, W. & Castanier, L.
Partner: UNT Libraries Government Documents Department

Scale-up of miscible flood processes for heterogeneous reservoirs. Final report

Description: Results of a wide-ranging investigation of the scaling of gas injection processes are reported. The research examines how the physical mechanisms at work during a gas injection project interact to determine process performance. In particular, the authors examine: the interactions of equilibrium phase behavior and two-phase flow that determine local displacement efficiency and minimum miscibility pressure, the combined effects of viscous fingering, gravity segregation and heterogeneity that control sweep efficiency in 2- and 3-dimensional porous media, the use of streamtube/streamline methods to create very efficient simulation technique for multiphase compositional displacements, the scaling of viscous, capillary and gravity forces for heterogeneous reservoirs, and the effects of the thin films and spreading behavior on three-phase flow. The following key results are documented: rigorous procedures for determination of minimum miscibility pressure (MMP) or minimum miscibility enrichment (MME) for miscibility have been developed for multicomponent systems; the complex dependence of MMP`s for nitrogen/methane floods on oil and injection gas composition observed experimentally is explained for the first time; the presence of layer-like heterogeneities strongly influences the interplay of gravity segregation and viscous fingering, as viscous fingers adapt to preferential flow paths and low permeability layers restrict vertical flow; streamtube/streamline simulation techniques are demonstrated for a variety of injection processes in 2 and 3 dimensions; quantitative scaling estimates for the transitions from capillary-dominated to gravity-dominated to viscous-dominated flows are reported; experimental results are given that demonstrate that high pressure CO{sub 2} can be used to generate low IFT gravity drainage in fractured reservoirs if fractures are suitably connected; and the effect of wetting and spreading behavior on three-phase flow is described. 209 refs.
Date: April 1, 1996
Creator: Orr, F.M. Jr.
Partner: UNT Libraries Government Documents Department

A precise measurement of the left-right asymmetry of Z Boson production at the SLAC linear collider

Description: We present a precise measurement of the left-right cross section asymmetry of Z boson production (A{sub LR}) observed in 1993 data at the SLAC linear collider. The A{sub LR} experiment provides a direct measure of the effective weak mixing angle through the initial state couplings of the electron to the Z. During the 1993 run of the SLC, the SLD detector recorded 49,392 Z events produced by the collision of longitudinally polarized electrons on unpolarized positrons at a center-of-mass energy of 91.26 GeV. A Compton polarimeter measured the luminosity-weighted electron polarization to be (63.4{+-}1.3)%. ALR was measured to be 0.1617{+-}0.0071(stat.){+-}0.0033(syst.), which determines the effective weak mixing angle to be sin {sup 2}{theta}{sub W}{sup eff} = 0.2292{+-}0.0009(stat.){+-}0.0004(syst.). This measurement of A{sub LR} is incompatible at the level of two standard deviations with the value predicted by a fit of several other electroweak measurements to the Standard Model.
Date: September 1, 1994
Partner: UNT Libraries Government Documents Department

Anomalous charm production at large x{sub F}

Description: We show that the new QCD production mechanisms which were proposed by S.J. Brodsky, P. Hoyer, A.H. Mueller and the author can explain at least some of the anomalous behavior of open and/or closed charm production at large x{sub F}.
Date: October 1, 1995
Creator: Tang, W. K.
Partner: UNT Libraries Government Documents Department