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Sample records for macromolecular crystallography mx

  1. Instrumentation upgrades for the Macromolecular Crystallography...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    322 Martin Fuchs, MX Group, Swiss Light Source; Paul Scherrer Institute (Villigen, Switzerland) A new unified diffractometer - the D3 - has been developed for the three MX...

  2. The macromolecular crystallography station at beamline BM16 at the ESRF

    SciTech Connect (OSTI)

    Juanhuix, Jordi; Labrador, Ana; Beltran, David; Herranz, Juan F.; Carpentier, Philippe; Bordas, Joan [CELLS, Campus UAB, 08193 Bellaterra, Barcelona (Spain)

    2005-08-15

    A beamline previously used for powder diffraction (BM16) at the European Synchrotron Radiation Facility has been redesigned and rebuilt to carry out both mcromolecular crystallography (MX) and noncrystalline diffraction/scattering (NCD/S) experiments. The MX station has become available for routine user experiments since September 2003 and the NCD/S station is currently being commissioned. The optics are designed so that both the focal spot and flux are good in the 6-17 keV energy range (2.1-0.73 A), while the performance is optimal at the selenium K-edge (12.658 keV,0.98 A). The MX facility is fully equipped to carry out multiwavelength anomalous dispersion experiments, in particular at the Se K-edge. Moreover, experiments using lower energies such as those of the Mn and Fe K-edges are also possible. Here we describe the optical configuration and the setup for MX experiments, as well as a typical example of the experiments carried out so far.

  3. [18] improving structures using all-atom contacts 385 The methodology of macromolecular crystallography is mature, powerful,

    E-Print Network [OSTI]

    Richardson, David

    [18] improving structures using all-atom contacts 385 The methodology of macromolecular crystallography is mature, powerful, and effective, and it has transformed our understanding of biology at the mo.2 Much of the sensitivity and the power of those tools derives from their independence of the target

  4. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

    SciTech Connect (OSTI)

    Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

    2013-05-01

    New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.

  5. SMB, Macromolecular Crystallography

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

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  6. Macromolecular Crystallography - Beamline facilities

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

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  7. In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF

    SciTech Connect (OSTI)

    Stetten, David von; Giraud, Thierry; Carpentier, Philippe; Sever, Franc; Terrien, Maxime; Dobias, Fabien; Juers, Douglas H.; Flot, David; Mueller-Dieckmann, Christoph; Leonard, Gordon A.; Sanctis, Daniele de; Royant, Antoine

    2015-01-01

    The current version of the Cryobench in crystallo optical spectroscopy facility of the ESRF is presented. The diverse experiments that can be performed at the Cryobench are also reviewed. The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for ‘spectroscopy’). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.

  8. Automated macromolecular crystallization screening

    DOE Patents [OSTI]

    Segelke, Brent W.; Rupp, Bernhard; Krupka, Heike I.

    2005-03-01

    An automated macromolecular crystallization screening system wherein a multiplicity of reagent mixes are produced. A multiplicity of analysis plates is produced utilizing the reagent mixes combined with a sample. The analysis plates are incubated to promote growth of crystals. Images of the crystals are made. The images are analyzed with regard to suitability of the crystals for analysis by x-ray crystallography. A design of reagent mixes is produced based upon the expected suitability of the crystals for analysis by x-ray crystallography. A second multiplicity of mixes of the reagent components is produced utilizing the design and a second multiplicity of reagent mixes is used for a second round of automated macromolecular crystallization screening. In one embodiment the multiplicity of reagent mixes are produced by a random selection of reagent components.

  9. The MX Factor

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    MX Factor Test films played a strategic-planning role in the debates of the late 1970s and early 1980s about where and how to deploy the MX intercontinental ballistic missile...

  10. Goniometer-based Femtosecond Macromolecular Crystallography ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    on XPP until the MFX station is fully operational in 2016. References: 1. A. E. Cohen, et al., Proc. Natl. Acad. Sci. USA 111, 17122 (2014). 2. Q. Zhou, et al., Nature 525,...

  11. Goniometer-based Femtosecond Macromolecular Crystallography | Stanford

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

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  12. Instrumentation upgrades for the Macromolecular Crystallography beamlines

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

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  13. Resources for Macromolecular Crystallography | Advanced Photon Source

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

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  14. Systems Biology in Prokaryote - Eukaryote Symbiosis | Stanford...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Frontier challenges for macromolecular crystallography (MX) now include determining structures of trapped reactive intermediates, large macromolecules and viruses, membrane...

  15. Deformable elastic network refinement for low-resolution macromolecular crystallography

    SciTech Connect (OSTI)

    Schröder, Gunnar F.; Levitt, Michael; Brunger, Axel T.

    2014-09-01

    An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations for its optimal usage. Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  16. Operation of the Australian Store.Synchrotron for macromolecular crystallography

    SciTech Connect (OSTI)

    Meyer, Grischa R. [Monash University, Clayton, Victoria 3800 (Australia); Aragão, David; Mudie, Nathan J.; Caradoc-Davies, Tom T. [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia); McGowan, Sheena; Bertling, Philip J.; Groenewegen, David; Quenette, Stevan M. [Monash University, Clayton, Victoria 3800 (Australia); Bond, Charles S. [The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia (Australia); Buckle, Ashley M. [Monash University, Clayton, Victoria 3800 (Australia); Androulakis, Steve, E-mail: steve.androulakis@monash.edu [Monash Bioinformatics Platform, Monash University, Clayton, Victoria 3800 (Australia)

    2014-10-01

    The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (?1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

  17. Method for removing atomic-model bias in macromolecular crystallography

    DOE Patents [OSTI]

    Terwilliger, Thomas C. (Santa Fe, NM)

    2006-08-01

    Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

  18. Introduction to Bayesian methods in macromolecular crystallography (Journal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

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  19. Freescale i. MX Feb 15, 2011

    E-Print Network [OSTI]

    Huang, Wei

    Freescale i. MX Shuai Che Feb 15, 2011 #12;i. MX Market Segmentation · Automotive · Smart Mobile Temperature Compensation "DPTC mechanism measures delays of reference circuits that are dependent, smartbooks, automotive infotainment and eReaders #12;Thank you! #12;Power Management Features for i

  20. Cryogenic Neutron Protein Crystallography: routine methods and potential benefits

    SciTech Connect (OSTI)

    Weiss, Kevin L [ORNL; Tomanicek, Stephen J [ORNL; NG, Joseph D [ORNL

    2014-01-01

    The use of cryocooling in neutron diffraction has been hampered by several technical challenges such as the need for specialized equipment and techniques. Recently we have developed and deployed equipment and strategies that allow for routine neutron data collection on cryocooled crystals using off the shelf components. This system has several advantages, compared to a closed displex cooling system such as fast cooling coupled with easier crystal mounting and centering. The ability to routinely collect cryogenic neutron data for analysis will significantly broaden the range of scientific questions that can be examined by neutron protein crystallography. Cryogenic neutron data collection for macromolecules has recently become available at the new Biological Diffractometer BIODIFF at FRM II and the Macromolecular Diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge National Laboratory. To evaluate the benefits of a cryocooled neutron structure we collected a full neutron data set on the BIODIFF instrument on a Toho-1 lactamase structure at 100K.

  1. SIBYLS - A SAXS and protein crystallography beamline at the ALS

    SciTech Connect (OSTI)

    Trame, Christine; MacDowell, Alastair A.; Celestre, Richard S.; Padmore, Howard A.; Cambie, Daniella; Domning, Edward E.; Duarte, Robert M.; Kelez, Nicholas; Plate, David W.; Holton, James M.; Frankel, Kenneth; Tsutakawa, Susan; Tsuruta, Hiro; Tainer, John A.; Cooper, Priscilla K.

    2003-08-22

    The new Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the Advanced Light Source will be dedicated to Macromolecular Crystallography (PX) and Small Angle X-ray Scattering (SAXS). SAXS will provide structural information of macromolecules in solutions and will complement high resolution PX studies on the same systems but in a crystalline state. The x-ray source is one of the 5 Tesla superbend dipoles recently installed at the ALS that allows for a hard x-ray program to be developed on the relatively low energy Advanced Light Source (ALS) ring (1.9 GeV). The beamline is equipped with fast interchangeable monochromator elements, consisting of either a pair of single Si(111) crystals for crystallography, or a pair of multilayers for the SAXS mode data collection (E/{Delta}E {approx} 1/110). Flux rates with Si(111) crystals for PX are measured as 2 x 10{sup 11} hv/sec/400 mA through a 100 {micro}m pinhole at 12.4 KeV. For SAXS the flux is up to 3 x 10{sup 13} photons/sec at 10 KeV with all apertures open when using the multilayer monochromator elements. The performance characteristics of this unique beamline will be described.

  2. Microbial Electrochemical Technology (MxCs): Challenges and Opportunit...

    Broader source: Energy.gov (indexed) [DOE]

    and Bioproduct Precursors from Wastewaters Workshop held March 18-19, 2015. Microbial Electrochemical Technology (MxCs): Challenges and Opportunities More Documents &...

  3. Nanostructure, Chemistry and Crystallography of Iron Nitride...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic Materials by Ultra-High-Resolution Electron Microscopy and Related Methods Nanostructure, Chemistry and...

  4. Timely deposition of macromolecular structures is necessary for peer review

    SciTech Connect (OSTI)

    Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Soueidan, Hayssam; Wessels, Lodewyk F. A. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam (Netherlands); Perrakis, Anastassis, E-mail: a.perrakis@nki.nl [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)

    2013-12-01

    Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature.

  5. Phenix - a comprehensive python-based system for macromolecular structure solution

    SciTech Connect (OSTI)

    Terwilliger, Thomas C [Los Alamos National Laboratory; Hung, Li - Wei [Los Alamos National Laboratory; Adams, Paul D [UC BERKELEY; Afonine, Pavel V [UC BERKELEY; Bunkoczi, Gabor [UNIV OF CAMBRIDGE; Chen, Vincent B [DUKE UNIV; Davis, Ian [DUKE UNIV; Echols, Nathaniel [LBNL; Headd, Jeffrey J [DUKE UNIV; Grosse Kunstleve, Ralf W [LBNL; Mccoy, Airlie J [UNIV OF CAMBRIDGE; Moriarty, Nigel W [LBNL; Oeffner, Robert [UNIV OF CAMBRIDGE; Read, Randy J [UNIV OF CAMBRIDGE; Richardson, David C [DUKE UNIV; Richardson, Jane S [DUKE UNIV; Zwarta, Peter H [LBNL

    2009-01-01

    Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages, and the repeated use of interactive three-dimensional graphics. Phenix has been developed to provide a comprehensive system for crystallographic structure solution with an emphasis on automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand, and finally the development of a framework that allows a tight integration between the algorithms.

  6. Using Two-Dimensional Colloidal Crystals to Understand Crystallography

    E-Print Network [OSTI]

    Loening, Niko

    Using Two-Dimensional Colloidal Crystals to Understand Crystallography Instructor Notes Geometric). #12;Using Two-Dimensional Colloidal Crystals to Understand Crystallography Instructions for Students the patterns that result from the diffraction of electromagnetic radiation by a crystal provides structural

  7. Serial Femtosecond Crystallography of G Protein-Coupled Receptors

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Liu, Liu

    2013-10-23

    Serial femtosecond crystallography data on microcrystals of 5-HT2B receptor bound to ergotamine grown in lipidic cubic phase.

  8. MICROFLUIDICS-BASED STRATEGIES FOR PROTEIN CRYSTALLOGRAPHY

    E-Print Network [OSTI]

    Quake, Stephen R.

    MICROFLUIDICS-BASED STRATEGIES FOR PROTEIN CRYSTALLOGRAPHY Thesis by Megan J. Anderson In Partial of this project. #12;iv I would also like to thank all of the microfluidic foundry technicians who provided me laboratories to produce high-quality protein crystals, the use of microfluidic technology for structural

  9. MX Group SpA | Open Energy Information

    Open Energy Info (EERE)

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  10. MxEnergy Electric, Inc. (Massachusetts) | Open Energy Information

    Open Energy Info (EERE)

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  11. MxEnergy Electric, Inc. (Pennsylvania) | Open Energy Information

    Open Energy Info (EERE)

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  12. MxEnergy Electric, Inc. (New York) | Open Energy Information

    Open Energy Info (EERE)

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  13. Resilient data staging through MxN distributed transactions.

    SciTech Connect (OSTI)

    Schwan, Karsten (Georgia Institute of Technology, Atlanta, GA); Oldfield, Ron A.; Lofstead, Gerald Fredrick, II; Dayal, Jai (Georgia Institute of Technology, Atlanta, GA)

    2011-11-01

    Scientific computing-driven discoveries are frequently driven from workflows that use persistent storage as a staging area for data between operations. With the bad and progressively worse bandwidth vs. data size issues as we continue towards exascale, eliminating persistent storage through techniques like data staging will both enable these workflows to continue online, but also enable more interactive workflows reducing the time to scientific discoveries. Data staging has shown to be an effective way for applications running on high-end computing platforms to offload expensive I/O operations and to manage the tremendous amounts of data they produce. This data staging approach, however, lacks the ACID style guarantees traditional straight-to-disk methods provide. Distributed transactions are a proven way to add ACID properties to data movements, however distributed transactions follow 1xN data movement semantics, where our highly parallel HPC environments employ MxN data movement semantics. In this paper we present a novel protocol that extends distributed transaction terminology to include MxN semantics which allows our data staging areas to benefit from ACID properties. We show that with our protocol we can provide resilient data staging with a limited performance penalty over current data staging implementations.

  14. Automated High Throughput Drug Target Crystallography

    SciTech Connect (OSTI)

    Rupp, B

    2005-02-18

    The molecular structures of drug target proteins and receptors form the basis for 'rational' or structure guided drug design. The majority of target structures are experimentally determined by protein X-ray crystallography, which as evolved into a highly automated, high throughput drug discovery and screening tool. Process automation has accelerated tasks from parallel protein expression, fully automated crystallization, and rapid data collection to highly efficient structure determination methods. A thoroughly designed automation technology platform supported by a powerful informatics infrastructure forms the basis for optimal workflow implementation and the data mining and analysis tools to generate new leads from experimental protein drug target structures.

  15. Constructing Irregular Surfaces to Enclose Macromolecular Complexes for Mesoscale Modeling Using the Discrete

    E-Print Network [OSTI]

    Schlick, Tamar

    Constructing Irregular Surfaces to Enclose Macromolecular Complexes for Mesoscale Modeling Using proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale

  16. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; Hattne, Johan; Brewster, Aaron S.; Sauter, Nicholas K.; Brunger, Axel T.; Weis, William I.

    2015-03-17

    There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore »resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

  17. Biological Macromolecular Structures Data from the RCSB Protein Data Bank (RCSB PDB)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium that works to improve understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. The RCSB PDB is one of three sites serving as deposition, data processing, and distribution sites of the Protein Data Bank Archive. Each site provides its own view of the primary data, thus providing a variety of tools and resources for the global community. RCSB is also the official keeper for the PDB archive, with sole access authority to the PDB archive directory structure and contents. The RCSB PDB Information Portal for Biological Macromolecular Structures offers online tools for search and retrieval, for visualizing structures, for depositing, validating, or downloading data, news and highlights, a discussion forum, and links to other areas of related research. The PDB archive is a repository of atomic coordinates and other information describing proteins and other important biological macromolecules. Structural biologists use methods such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each atom relative to each other in the molecule. They then deposit this information, which is then annotated and publicly released into the archive by the wwPDB. Results can be viewed as 3-D images or models.

  18. Theoretical crystallography with the Advanced Visualization System

    SciTech Connect (OSTI)

    Younkin, C.R.; Thornton, E.N.; Nicholas, J.B.; Jones, D.R.; Hess, A.C.

    1993-05-01

    Space is an Application Visualization System (AVS) graphics module designed for crystallographic and molecular research. The program can handle molecules, two-dimensional periodic systems, and three-dimensional periodic systems, all referred to in the paper as models. Using several methods, the user can select atoms, groups of atoms, or entire molecules. Selections can be moved, copied, deleted, and merged. An important feature of Space is the crystallography component. The program allows the user to generate the unit cell from the asymmetric unit, manipulate the unit cell, and replicate it in three dimensions. Space includes the Buerger reduction algorithm which determines the asymmetric unit and the space group of highest symmetry of an input unit cell. Space also allows the user to display planes in the lattice based on Miller indices, and to cleave the crystal to expose the surface. The user can display important precalculated volumetric data in Space, such as electron densities and electrostatic surfaces. With a variety of methods, Space can compute the electrostatic potential of any chemical system based on input point charges.

  19. Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

    SciTech Connect (OSTI)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545 (United States); Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.; Adams, Paul D.; Moriarty, Nigel W.; Zwart, Peter [Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720 (United States); Read, Randy J. [Department of Haematology, University of Cambridge, Cambridge CB2 0XY (United Kingdom); Turk, Dusan [Jozef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia); Hung, Li-Wei [Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545 (United States)

    2007-05-01

    Heterogeneity in ensembles generated by independent model rebuilding principally reflects the limitations of the data and of the model-building process rather than the diversity of structures in the crystal. Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ‘perfect’ structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models.

  20. Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin

    E-Print Network [OSTI]

    Ramakrishnan, Venki

    determined by x-ray crystallography except at very high resolution. The scattering of neutrons by hydrogenEnhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin Fong and structurally, direct visu- alization of them by using crystallography is difficult. Neutron crys- tallography

  1. Optical properties of MX chain materials: An extended Peierls-Hubbard model

    SciTech Connect (OSTI)

    Bishop, A.R.; Batistic, I.; Gammel, J.T.; Saxena, A.

    1991-01-01

    We describe theoretical modeling of both pure (MX) and mixed-halide (MX{sub x}X{prime}{sub 1-x}) halogen (X)-bridged transition metal (M) linear chain complexes in terms of an extended Peierls-Hubbard, tight-binding Hamiltonian with 3/4-filling of two-bands. Both inter- and intra-site electron-phonon coupling are included. Electronic (optical absorption), lattice dynamic (IR, Raman) and spin (ESR) signatures are obtained for the ground states, localized excited states produced by impurities, doping or photo-excitation -- excitons, polarons, bipolarons, solitons; and the edge states (which occur in mixed-halide crystals, e.g. PtCl{sub x}Br{sub 1-x}). Adiabatic molecular dynamics is used to explore photodecay channels in pure and impure systems for ground states as well as in the presence of pre-existing polaronic states. 12 refs., 3 figs., 1 tab.

  2. Improved ambient-pressure organic superconductor. [Bis(ethylenedithio)TTF-MX/sub 2/

    DOE Patents [OSTI]

    Williams, J.M.; Wang, Hsien-Hau; Beno, M.A.

    1985-05-29

    Disclosed is a new class of organic superconductors having the formula (ET)/sub 2/MX/sub 2/ wherein ET represents bis(ethylenedithio)-tetrathiafulvalene, M is a metal such as Au, Ag, In, Tl, Rb, Pd and the like and X is a halide. The superconductor (ET)/sub 2/AuI/sub 2/ exhibits a transition temperature of 5/sup 0/K which is high for organic superconductors.

  3. Workshop on algorithms for macromolecular modeling. Final project report, June 1, 1994--May 31, 1995

    SciTech Connect (OSTI)

    Leimkuhler, B.; Hermans, J.; Skeel, R.D.

    1995-07-01

    A workshop was held on algorithms and parallel implementations for macromolecular dynamics, protein folding, and structural refinement. This document contains abstracts and brief reports from that workshop.

  4. Identifying, studying and making good use of macromolecular crystals

    SciTech Connect (OSTI)

    Calero, Guillermo; Cohen, Aina E.; Luft, Joseph R.; Newman, Janet; Snell, Edward H.

    2014-07-25

    As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.

  5. Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability

    E-Print Network [OSTI]

    Weston, Ken

    Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how on the effects of macro- molecular crowding on protein folding and binding stability has been reached. Crowders

  6. A novel inert crystal delivery medium for serial femtosecond crystallography

    SciTech Connect (OSTI)

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; Wang, Dingjie; Schaffer, Alexander; Roy-Chowdhury, Shatabdi; Zatsepin, Nadia A.; Aquila, Andrew; Coe, Jesse; Gati, Cornelius; Hunter, Mark S.; Koglin, Jason E.; Kupitz, Christopher; Nelson, Garrett; Subramanian, Ganesh; White, Thomas A.; Zhao, Yun; Zook, James; Boutet, Sébastien; Cherezov, Vadim; Spence, John C. H.; Fromme, Raimund; Weierstall, Uwe; Fromme, Petra

    2015-06-30

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.

  7. A novel inert crystal delivery medium for serial femtosecond crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; Wang, Dingjie; Schaffer, Alexander; Roy-Chowdhury, Shatabdi; Zatsepin, Nadia A.; Aquila, Andrew; Coe, Jesse; Gati, Cornelius; et al

    2015-06-30

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, themore »structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.« less

  8. Macromolecular Crystallization with Microfluidic Free-Interface Diffusion

    SciTech Connect (OSTI)

    Segelke, B

    2005-02-24

    Fluidigm released the Topaz 1.96 and 4.96 crystallization chips in the fall of 2004. Topaz 1.96 and 4.96 are the latest evolution of Fluidigm's microfluidics crystallization technologies that enable ultra low volume rapid screening for macromolecular crystallization. Topaz 1.96 and 4.96 are similar to each other but represent a major redesign of the Topaz system and have of substantially improved ease of automation and ease of use, improved efficiency and even further reduced amount of material needed. With the release of the new Topaz system, Fluidigm continues to set the standard in low volume crystallization screening which is having an increasing impact in the field of structural genomics, and structural biology more generally. In to the future we are likely to see further optimization and increased utility of the Topaz crystallization system, but we are also likely to see further innovation and the emergence of competing technologies.

  9. Feedback on the use of the MX6 Mox Fuel transport cask: reduction of the dose uptake during operations

    SciTech Connect (OSTI)

    Blachet, L.; Lallemant, Th. [TN International, AREVA Group, 78 - Montigny le Bretonneux (France)

    2007-07-01

    In the framework of the quality, safety and environment policy of AREVA, TN International has implemented a global management system according to ISO 9001, OHSAS 18001 and ISO 14001 requirements with certification obtained from third part organization (1). The design of the MX6 cask is an example of the implementation of this system in order to guarantee safety and the health of everyone involved and the protection of the environment. The MX6 design has allowed ALARA dose rates for the workers during all the phases of use of the cask, to be significantly reduced compared to previous design. The MX6 cask was developed by TN International for the transport of either BWR or PWR fresh MOX fuel assemblies. Replacing the previous SIEMENS type III and SIEMENS BWR packaging, the MX6 has been firstly used in the German Nuclear Power Plants. Complying with the TS-R-1 (IAEA 1996) regulations, the MX6 cask is based on innovative solutions implemented at each step of the design and the manufacturing. Its design includes an efficient neutron shielding for high Plutonium content and an easy use content restraining system. The large payload of the MX6 cask, 6 PWR MOX fuel assemblies or 16 BWR MOX fuel assemblies, minimizes the doses uptake during its unloading at the NPP. Moreover, new sequences of loading and unloading operations were proposed for testing and implementation in each Nuclear Facility. Concurrently, total dose uptakes by the operators were assessed in order to prove the efficiency of the packaging and the proposed sequences. In this paper, the main contributors to the transports to Germany with the MX6 cask will present their involvement and feedback for the reduction of the dose uptakes by the operators during the loading and unloading operations. Presently in use at GUNDREMMINGEN and ISAR Nuclear Power Plants (NPPs), the MX6 cask use will be extended to other German and Swiss NPPs from 2006 onwards. (1) AFAQ-AFNOR Certification for ISO 9001, OHSAS 18001 and ISO 14001, and CEFRI (Comite francais de certification des Entreprises pour la formation et le suivi du personnel travaillant sous Rayonnements Ionisants) certification in the health physics field according to its E specification. (authors)

  10. Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Fromme, Raimund; Ishchenko, Andrii; Metz, Markus; Chowdhury, Shatabdi Roy; Basu, Shibom; Boutet, Sébastien; Fromme, Petra; White, Thomas A.; Barty, Anton; Spence, John C. H.; et al

    2015-08-04

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is shown enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals deliveredmore »by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.« less

  11. The evaluation of melamine dendrimers as potential macromolecular vehicles for anticancer drug delivery 

    E-Print Network [OSTI]

    Neerman, Michael Frederick

    2005-08-29

    Often associated with chemotherapy are the dangerous and sometimes lifethreatening side effects towards non-cancerous tissue that can occur while on such drug regimens. The design and utilization of macromolecular drug delivery vehicles is gaining...

  12. Automated identification of elemental ions in macromolecular crystal structures

    SciTech Connect (OSTI)

    Echols, Nathaniel, E-mail: nechols@lbl.gov; Morshed, Nader; Afonine, Pavel V. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235 (United States); McCoy, Airlie J. [University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY (United Kingdom); Miller, Mitchell D. [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Joint Center for Structural Genomics, (United States); Read, Randy J. [University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY (United Kingdom); Richardson, Jane S. [Duke University Medical Center, Durham, NC 27710 (United States); Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545-0001 (United States); Adams, Paul D. [University of California at Berkeley, Berkeley, CA 94720-1762 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235 (United States)

    2014-04-01

    The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.

  13. Effective tight-binding model for MX2 under electric and magnetic fields

    SciTech Connect (OSTI)

    Kavungal Veedu, Shanavas [ORNL; Satpathy, S [University of Missouri, Columbia

    2015-01-01

    We present a systematic method for developing a five band Hamiltonian for the metal d orbitals that can be used to study the effect of electric and magnetic fields on multilayer MX2 (M=Mo,W and X=S,Se) systems. On a hexagonal lattice of d orbitals, the broken inversion symmetry of the monolayers is incorporated via fictitious s orbitals at the chalcogenide sites. A tight-binding Hamiltonian is constructed and then downfolded to get effective d orbital overlap parameters using quasidegenerate perturbation theory. The steps to incorporate the effects of multiple layers, external electric and magnetic fields are also detailed. We find that an electric field produces a linear-k Rashba splitting around the point, while a magnetic field removes the valley pseudospin degeneracy at the K points. Our model provides a simple tool to understand the recent experiments on electric and magnetic control of valley pseudospin in monolayer dichalcogendies.

  14. John Pendry: His Contributions to the Development of LEED Surface Crystallography

    E-Print Network [OSTI]

    Rous, P.J.

    2008-01-01

    of Surface Structure by LEED (IBM Research Symposia Series)Surface Crystallography by LEED. M.A. Van Hove and S.Y.Surface Science 300(1-3), LEED Analysis of Acetylene and

  15. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; et al

    2015-08-18

    We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore »Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

  16. APPENDIX 6 --X-Ray Crystallography Reports Relevant to Chapter 3 861 X-Ray Crystallography Reports Relevant to Chapter 3

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Compound 262 (NBB04) Contents Table A6.1. Crystal data. Table A6.2. Atomic coordinates. Table A6.3. Full coordinates and isotropic displacement parameters. Table A6.6. Hydrogen bond distances and angles. Figure A6-Ray Crystallography Reports Relevant to Chapter 3 865 Table A6.2. Atomic coordinates (x 104 ) and equivalent isotropic

  17. APPENDIX 3 --X-Ray Crystallography Reports Relevant to Chapter 2 686 X-Ray Crystallography Reports Relevant to Chapter 2

    E-Print Network [OSTI]

    Stoltz, Brian M.

    ) Contents Table A3.1. Crystal data Table A3.2. Atomic coordinates Table A3.3. Full bond distances and angles Table A3.4. Anisotropic displacement parameters Table A3.5. Hydrogen bond distances and angles #12.ccdc.cam.ac.uk/data_request/cif. #12;APPENDIX 3 -- X-Ray Crystallography Reports Relevant to Chapter 2 689 Table A3.1. Crystal data

  18. Kinesin Motor Transport is Altered by Macromolecular Crowding and Transiently Associated Microtubule-Associated Proteins

    E-Print Network [OSTI]

    Ross, Jennifer

    01 Kinesin Motor Transport is Altered by Macromolecular Crowding and Transiently Associated of crowding and an increasingly complex cellular environment on the transport of individual motor proteins, we have performed in vitro reconstitution experiments with single kinesin-1 motors walking on microtubules

  19. Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level

    E-Print Network [OSTI]

    Shorter, James

    Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level coupled to the process of protein folding in vivo. While previous studies have provided invaluable insight into the effect of crowding on the stability and folding rate of protein tertiary structures, very little is known

  20. Adaptive Multiscale Molecular Dynamics of Macromolecular Fluids Steven O. Nielsen,1

    E-Print Network [OSTI]

    Nielsen, Steven O.

    diffusion in polymer electrolytes, signal transduction be- tween proteins, nanostructure formationAdaptive Multiscale Molecular Dynamics of Macromolecular Fluids Steven O. Nielsen,1 Preston B 2010; published 3 December 2010) Until now, adaptive atomistic­coarse-grain (A/CG) molecular dynamics

  1. between the nucleus and cytoplasm occurs through large macromolecular structures, the nuclear pores. Quantitative

    E-Print Network [OSTI]

    Forbes, Douglass

    363 between the nucleus and cytoplasm occurs through large macromolecular structures, the nuclear pores. Quantitative scanning transmission electron microscopy has estimated the mass of a nuclear pore noteworthy in that they saw: 1) the purification of both the yeast and vertebrate nuclear pores, 2

  2. Modulation of the Toxicity and Macromolecular Binding of Benzene Metabolites by NAD(P)H:Quinone

    E-Print Network [OSTI]

    California at Berkeley, University of

    Articles Modulation of the Toxicity and Macromolecular Binding of Benzene Metabolites by NAD, San Francisco, California 94143-0560 Received April 17, 1998 Benzene is oxidized in the liver of benzene metabolite toxicity. NQO1 expression reduced a class of hydroquinone- and benzenetriol-induced DNA

  3. Materials Science/Crystallography 30m SANS Measurements on Intercalated and Delaminated Phenolic

    E-Print Network [OSTI]

    Materials Science/Crystallography 30m SANS Measurements on Intercalated and Delaminated Phenolic Resin/Clay Dispersions and Nanocomposites Yoonessi, M.725 , Toghiani, H.725 , Pittman, C.725 A SANS on AOT Reverse Micelle Dynamics in Liquid, Compressed and Supercritical Alkanes Measured by SANS Kitchens

  4. First-principles codes for computational crystallography in the Quantum-ESPRESSO package

    E-Print Network [OSTI]

    Giannozzi, Paolo

    crystallography Abstract. The Quantum-ESPRESSO package is a multi- purpose and multi-platform software for ab-purpose and multi-platform package, called Quantum-ESPRESSO (standing for Quan- tum-opEn-Source Package for Research and others (Baroni, de Gironcoli, Dal Corso, Giannozzi, 2001); CP (Car-Parrinello), developed by A

  5. Weighting Features to Recognize 3D Patterns of Electron Density in X-ray Protein Crystallography

    E-Print Network [OSTI]

    Ioerger, Thomas R.

    Weighting Features to Recognize 3D Patterns of Electron Density in X-ray Protein Crystallography features to recognize 3D patterns of electron density to determine protein structures. We present SLIDER, Texas A&M University 2 Department of Biochemistry & Biophysics, Texas A&M University 1 {kgopal

  6. ?{sup 2}{sub R}, a reciprocal-space measure of the quality of macromolecular electron-density maps

    SciTech Connect (OSTI)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    1999-06-01

    A reciprocal-space measure of the quality of macromolecular crystallographic phases based on the variance of the local roughness of the map is presented. It has previously been shown that the presence of distinct regions of solvent and protein in macromolecular crystals leads to a high value of the standard deviation of local r.m.s. electron density and that this can in turn be used as a reliable measure of the quality of macromolecular electron-density maps [Terwilliger & Berendzen (1999a ?). Acta Cryst. D55, 501–505]. Here, it is demonstrated that a similar measure, ?{sub R}{sup 2}, the variance of the local roughness of the electron density, can be calculated in reciprocal space. The formulation is suitable for rapid evaluation of macromolecular crystallographic phases, for phase improvement and for ab initio phasing procedures.

  7. Effects of Macromolecular Crowding on the Structure of a Protein Complex

    SciTech Connect (OSTI)

    Rajapaksha Mudalige, Ajith Rathnaweera [ORNL; Stanley, Christopher B [ORNL; Todd, Brian [ORNL

    2015-01-01

    Macromolecular crowding can alter the structure and function of biological macromolecules. We used small angle scattering (SAS) to measure the change in size of a protein complex, superoxide dismutase (SOD), induced by macromolecular crowding. Crowding was induced using 400 MW polyethylene glycol (PEG), triethylene glycol (TEG), methyl- -glucoside ( -MG) and trimethylamine N-oxide (TMAO). Parallel small angle neutron scattering (SANS) and small angle x-ray scattering (SAXS) allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. Considering the osmotic pressure due to PEG, this deformation corresponds to a highly compressible structure. SAXS done in the presence of TEG suggests that for further deformation beyond a 9% decrease in volume the resistance to deformation may increase dramatically.

  8. Pi sampling: a methodical and flexible approach to initial macromolecular crystallization screening

    SciTech Connect (OSTI)

    Gorrec, Fabrice, E-mail: fgorrec@mrc-lmb.cam.ac.uk; Palmer, Colin M.; Lebon, Guillaume; Warne, Tony [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom)

    2011-05-01

    Pi sampling, derived from the incomplete factorial approach, is an effort to maximize the diversity of macromolecular crystallization conditions and to facilitate the preparation of 96-condition initial screens. The Pi sampling method is derived from the incomplete factorial approach to macromolecular crystallization screen design. The resulting ‘Pi screens’ have a modular distribution of a given set of up to 36 stock solutions. Maximally diverse conditions can be produced by taking into account the properties of the chemicals used in the formulation and the concentrations of the corresponding solutions. The Pi sampling method has been implemented in a web-based application that generates screen formulations and recipes. It is particularly adapted to screens consisting of 96 different conditions. The flexibility and efficiency of Pi sampling is demonstrated by the crystallization of soluble proteins and of an integral membrane-protein sample.

  9. Description and procedures for synchrotron radiation, small molecule, single crystal crystallography of plutonium complexes at ALS beamline 11.3.1

    E-Print Network [OSTI]

    Gorden, A.E.V.; Raymond, K.N.; Shuh, D.K.

    2008-01-01

    Crystallography of Plutonium Complexes at ALS Beamlineof the Structural Parameters of Plutonium Complexes by Smallpreparation and growth of the plutonium complexes (crystals)

  10. Combining Electron Crystallography and X-ray Crystallography to Study the MlotiK1 Cyclic Nucleotide-Regulated Potassium Channel

    SciTech Connect (OSTI)

    Clayton, G.; Aller, S; Wang, J; Unger, V; Morais-Cabral, J

    2009-01-01

    We have recently reported the X-ray structure of the cyclic nucleotide-regulated potassium channel, MlotiK1. Here we describe the application of both electron and X-ray crystallography to obtain high quality crystals. We suggest that the combined application of these techniques provides a useful strategy for membrane protein structure determination. We also present negative stain projection and cryo-data projection maps. These maps provide new insights about the properties of the MlotiK1 channel. In particular, a comparison of a 9 {angstrom} cryo-data projection with calculated model maps strongly suggests that there is a very weak interaction between the pore and the S1-S4 domains of this 6 TM tetrameric cation channel and that the S1-S4 domains can adopt multiple orientations relative to the pore.

  11. Suite of three protein crystallography beamlines with single superconducting bend magnet as the source

    SciTech Connect (OSTI)

    MacDowell, Alastair A.; Celestre, Richard S.; Howells, Malcolm; McKinney, Wayne; Krupnick, James; Cambie, Daniella; Domning, Edward E; Duarte, Robert M.; Kelez, Nicholas; Plate, David W.; Cork, Carl W.; Earnest, Thomas N.; Dickert, Jeffery; Meigs, George; Ralston, Corie; Holton, James M.; Alber, Thomas; Berger, James M.; Agard, David A.; Padmore, Howard A.

    2004-08-01

    At the Advanced Light Source (ALS), three protein crystallography (PX) beamlines have been built that use as a source one of the three 6 Tesla single pole superconducting bending magnets (superbends) that were recently installed in the ring. The use of such single pole superconducting bend magnets enables the development of a hard x-ray program on a relatively low energy 1.9 GeV ring without taking up insertion device straight sections. The source is of relatively low power, but due to the small electron beam emittance, it has high brightness. X-ray optics are required to preserve the brightness and to match the illumination requirements for protein crystallography. This was achieved by means of a collimating premirror bent to a plane parabola, a double crystal monochromator followed by a toroidal mirror that focuses in the horizontal direction with a 2:1 demagnification. This optical arrangement partially balances aberrations from the collimating and toroidal mirrors such that a tight focused spot size is achieved. The optical properties of the beamline are an excellent match to those required by the small protein crystals that are typically measured. The design and performance of these new beamlines are described.

  12. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques -Philippe

    2015-04-25

    High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore »resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

  13. Administered activity and metastatic cure probability during radioimmunotherapy of ovarian cancer in nude mice with {sup 211}At-MX35 F(ab'){sub 2}

    SciTech Connect (OSTI)

    Elgqvist, Joergen . E-mail: jorgen.elgqvist@radfys.gu.se; Andersson, Hakan; Bernhardt, Peter; Baeck, Tom; Claesson, Ingela; Hultborn, Ragnar; Jensen, Holger; Johansson, Bengt R.; Lindegren, Sture; Olsson, Marita; Palm, Stig; Warnhammar, Elisabet; Jacobsson, Lars

    2006-11-15

    Purpose: To elucidate the therapeutic efficacy of {alpha}-radioimmunotherapy of ovarian cancer in mice. This study: (i) estimated the minimum required activity (MRA), giving a reasonable high therapeutic efficacy; and (ii) calculated the specific energy to tumor cell nuclei and the metastatic cure probability (MCP) using various assumptions regarding monoclonal-antibody (mAb) distribution in measured tumors. The study was performed using the {alpha}-particle emitter Astatine-211 ({sup 211}At) labeled to the mAb MX35 F(ab'){sub 2}. Methods and Materials: Animals were inoculated intraperitoneally with {approx}1 x 10{sup 7} cells of the cell line NIH:OVCAR-3. Four weeks later animals were treated with 25, 50, 100, or 200 kBq {sup 211}At-MX35 F(ab'){sub 2} (n = 74). Another group of animals was treated with a nonspecific mAb: 100 kBq {sup 211}At-Rituximab F(ab'){sub 2} (n = 18). Eight weeks after treatment the animals were sacrificed and presence of macro- and microscopic tumors and ascites was determined. An MCP model was developed and compared with the experimentally determined tumor-free fraction (TFF). Results: When treatment was given 4 weeks after cell inoculation, the TFFs were 25%, 22%, 50%, and 61% after treatment with 25, 50, 100, or 200 kBq {sup 211}At-MX35 F(ab'){sub 2}, respectively, the specific energy to irradiated cell nuclei varying between {approx}2 and {approx}400 Gy. Conclusion: As a significant increase in the therapeutic efficacy was observed between the activity levels of 50 and 100 kBq (TFF increase from 22% to 50%), the conclusion was that the MRA is {approx}100 kBq {sup 211}At-MX35 F(ab'){sub 2}. MCP was most consistent with the TFF when assuming a diffusion depth of 30 {mu}m of the mAbs in the tumors.

  14. Theory and simulation of macromolecular crowding effects on protein folding stability and kinetics

    E-Print Network [OSTI]

    Jeetain Mittal; Robert B. Best

    2009-02-26

    We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta- and alpha/beta-proteins are well described by an adaptation of the scaled particle theory (SPT). In this approach, the native state, transition state, and the unfolded protein are treated as effective hard spheres with radii approximately independent of the size and concentration of the crowders. The same model predicts the effect of crowding on the folding barrier and therefore refolding rates with no adjustable parameters. A simple extension of the SPT model, assuming additivity, can also describe the behavior of mixtures of crowding particles.

  15. JBLULCE

    Energy Science and Technology Software Center (OSTI)

    002719MLTPL00 JBlulce Data Acquisition Software for Macromolecular Crystallography  http://www.gmca.anl.gov/jbluice-epics/ 

  16. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

    SciTech Connect (OSTI)

    Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; Pai, E. F.; Pearson, A. R.; Olson, J. S.; Anfinrud, P. A.; Ernst, O. P.; Miller, R. J. Dwayne

    2015-08-18

    We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.

  17. Subangstrom Crystallography Reveals that Short Ionic Hydrogen Bonds, and Not a His-Asp Low-Barrier Hydrogen

    E-Print Network [OSTI]

    Agard, David

    Subangstrom Crystallography Reveals that Short Ionic Hydrogen Bonds, and Not a His-Asp Low-Barrier Hydrogen Bond, Stabilize the Transition State in Serine Protease Catalysis Cynthia N. Fuhrmann, Matthew D that destabilizes the His57-Ser195 hydrogen bond, preventing the back-reaction. In both structures the His57-Asp102

  18. Geothermal assessment of the MX deployment area in Nevada. Final report, April 1, 1981-April 30, 1982

    SciTech Connect (OSTI)

    Trexler, D.T.; Bruce, J.L.; Cates, D.; Dolan, H.H.; Covington, C.H.

    1982-06-01

    A preliminary geothermal resource assessment of the MX deployment area in Nevada focused on Coyote Spring Valley in southeastern Nevada. Initially, an extensive literature search was conducted and a bibliography consisting of 750 entries was compiled covering all aspects of geology pertaining to the study area. A structural study indicates that Coyote Spring Valley lies in a tectonically active area which is favorable for the discovery of geothermal resources. Hot water may be funneled to the near-surface along an extensive fracture and fault system which appears to underlie the valley, according to information gathered during the literature search and aerial photo survey. A total of 101 shallow temperature probes were emplanted in Coyote Spring Valley. Three anomalous temperature points all lying within the same vicinity were identified in the north-central portion of the valley near a fault. A soil-mercury study also identified one zone of anomalous mercury concentrations around the north end of the Arrow Canyon Range. A literature search covering regional fluid geochemistry indicated that the three fluid samples taken from Coyote Spring Valley have a higher concentration of Na + K. During field work, seven fluid samples were collected in Coyote Spring Valley which also appear to be derived from volcanic units due to the presence of Ca-Mg or Na-K carbonate-bicarbonate. A temperature gradient study of six test water wells indicates that only one geothermal well with a temperature of 35.5/sup 0/C (96/sup 0/F) exists in the central portion of the valley at the north end of Arrow Canyon Range near the zone of anomalous soil-mercury points. A cultural assessment of Coyote Spring Valley was performed prior to field work.

  19. Crystallography Without Crystals: Determining the Structure of Individual Biological Molecules and Nanoparticles

    ScienceCinema (OSTI)

    Ourmazd, Abbas [University of Wisconsin, Milwaukee, Wisconsin, USA

    2010-01-08

    Ever shattered a valuable vase into 10 to the 6th power pieces and tried to reassemble it under a light providing a mean photon count of 10 minus 2 per detector pixel with shot noise? If you can do that, you can do single-molecule crystallography. This talk will outline how this can be done in principle. In more technical terms, the talk will describe how the combination of scattering physics and Bayesian algorithms can be used to reconstruct the 3-D diffracted intensity distribution from a collection of individual 2-D diffiraction patterns down to a mean photon count of 10 minus 2 per pixel, the signal level anticipated from the Linac Coherent Light Source, and hence determine the structure of individual macromolecules and nanoparticles.

  20. A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bunker, Richard D.; Mandal, Kalyaneswar; Bashiri, Ghader; Chaston, Jessica J.; Pentelute, Bradley L.; Lott, J. Shaun; Kent, Stephen B. H.; Baker, Edward N.

    2015-04-07

    Racemic protein crystallography was used to determine the X-ray structure of the predicted Mycobacterium tuberculosis protein Rv1738, which had been completely recalcitrant to crystallization in its natural L-form. Native chemical ligation was used to synthesize both L-protein and D-protein enantiomers of Rv1738. Crystallization of the racemic {D-protein + L-protein} mixture was immediately successful. The resulting crystals diffracted to high resolution and also enabled facile structure determination because of the quantized phases of the data from centrosymmetric crystals. The X-ray structure of Rv1738 revealed striking similarity with bacterial hibernation factors, despite minimal sequence similarity. As a result, we predict that Rv1738,more »which is highly up-regulated in conditions that mimic the onset of persistence, helps trigger dormancy by association with the bacterial ribosome.« less

  1. The MX Factor

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservationBio-Inspired Solar FuelTechnologyTel: Name:Department of Energy TheThe LifeThe

  2. DOE F 740-MX

    Broader source: Energy.gov (indexed) [DOE]

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of Natural GasAdjustmentsShirleyEnergyTher i n c i pState Efficiency,EnergyProgrammaticFEDERAL(09/2012) Replaces

  3. The MX Factor

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effectWorking With U.S.Week Day Year(activeInforum LIFTMEMS Technology Revolution

  4. Polydimethylsiloxane as a Macromolecular Additive for Enhanced Performance of Molecular Bulk Heterojunction Organic Solar Cells

    SciTech Connect (OSTI)

    Graham, Kenneth R.; Mei, Jianguo; Stalder, Romain; Shim, Jae Won; Cheun, Hyeunseok; Steffy, Fred; So, Franky; Kippelen, Bernard; Reynolds, John R.

    2011-03-15

    The effect of the macromolecular additive, polydimethylsiloxane (PDMS), on the performance of solution processed molecular bulk heterojunction solar cells is investigated, and the addition of PDMS is shown to improve device power conversion efficiency by ~70% and significantly reduce cell-to-cell variation, from a power conversion efficiency of 1.25 ± 0.37% with no PDMS to 2.16 ± 0.09% upon the addition of 0.1 mg/mL PDMS to the casting solution. The cells are based on a thiophene and isoindigo containing oligomer as the electron donor and [6,6]-phenyl-C61 butyric acid methyl ester (PC61BM) as the electron acceptor. PDMS is shown to have a strong influence on film morphology, with a significant decrease in film roughness and feature size observed. The morphology change leads to improved performance parameters, most notably an increase in the short circuit current density from 4.3 to 6.8 mA/cm2 upon addition of 0.1 mg/mL PDMS. The use of PDMS is of particular interest, as this additive appears frequently as a lubricant in plastic syringes commonly used in device fabrication; therefore, PDMS may unintentionally be incorporated into device active layers.

  5. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-04-25

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore »diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

  6. Protein crystallography: From X-ray diffraction spots to a three dimensional image

    SciTech Connect (OSTI)

    Terwilliger, T.C.; Berendzen, J.

    1998-02-25

    Proteins are remarkable molecular machines that are essential for life. They can do many things ranging from the precise control of blood clotting to synthesizing complex organic compounds. Pictures of protein molecules are in high demand in biotechnology because they are important for applications such as drug discovery and for engineering enzymes for commercial use. X-ray crystallography is the most common method for determining the three-dimensional structures of protein molecules. When a crystal of a protein is placed in an X-ray beam, scattering of X-rays off the ordered molecules produces a diffraction pattern that can be measured on a position-sensitive CCD or image-plate detector. Protein crystals typically contain thousands of atoms and the diffraction data are generally measured to relatively low resolution. Consequently the direct methods approaches generally cannot be applied. Instead, if the crystal is modified by adding metal atoms at specific sites or by tuning the wavelength of the X-rays to cross an absorption edge of a metal atom in the crystal, then the information from these additional measurements is sufficient to first identify the /locations of the metal atoms. This information is then used along with the diffraction data to make a three-dimensional picture of electron densities. This picture can be used to determine the position of most or all of the atoms in the protein.

  7. Goniometer-based femtosecond crystallography with X-ray free electron lasers

    SciTech Connect (OSTI)

    Cohen, Aina E.; Soltis, S. Michael; González, Ana; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Baxter, Elizabeth L.; Brehmer, Winnie; Brewster, Aaron S.; Brunger, Axel T.; Calero, Guillermo; Chang, Joseph F.; Chollet, Matthieu; Ehrensberger, Paul; Eriksson, Thomas L.; Feng, Yiping; Hattne, Johan; Hedman, Britt; Hollenbeck, Michael; Holton, James M.; Keable, Stephen; Kobilka, Brian K.; Kovaleva, Elena G.; Kruse, Andrew C.; Lemke, Henrik T.; Lin, Guowu; Lyubimov, Artem Y.; Manglik, Aashish; Mathews, Irimpan I.; McPhillips, Scott E.; Nelson, Silke; Peters, John W.; Sauter, Nicholas K.; Smith, Clyde A.; Song, Jinhu; Stevenson, Hilary P.; Tsai, Yingssu; Uervirojnangkoorn, Monarin; Vinetsky, Vladimir; Wakatsuki, Soichi; Weis, William I.; Zadvornyy, Oleg A.; Zeldin, Oliver B.; Zhu, Diling; Hodgson, Keith O.

    2014-10-31

    The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. With smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of ?2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.

  8. Goniometer-based femtosecond crystallography with X-ray free electron lasers

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Cohen, Aina E.; Soltis, S. Michael; González, Ana; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Baxter, Elizabeth L.; Brehmer, Winnie; Brewster, Aaron S.; Brunger, Axel T.; et al

    2014-10-31

    The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. With smaller crystals, high-density grids were usedmore »to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of ?2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.« less

  9. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-01-23

    Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patternsmore »with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less

  10. Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

    SciTech Connect (OSTI)

    Pražnikar, Jure [Institute Jožef Stefan, Jamova 39, 1000 Ljubljana (Slovenia); University of Primorska, (Slovenia); Turk, Dušan, E-mail: dusan.turk@ijs.si [Institute Jožef Stefan, Jamova 39, 1000 Ljubljana (Slovenia); Center of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, (Slovenia)

    2014-12-01

    The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of R{sub free} or may leave it out completely.

  11. Prospects for Simulating Macromolecular Surfactant Chemistry at the Ocean-Atmosphere Boundary

    SciTech Connect (OSTI)

    Elliott, S.; Burrows, Susannah M.; Deal, C.; Liu, Xiaohong; Long, M.; Ogunro, O.; Russell, Lynn M.; Wingenter, O.

    2014-05-01

    Biogenic lipids and polymers are surveyed for their ability to adsorb at the water-air interfaces associated with bubbles, marine microlayers and particles in the overlying boundary layer. Representative ocean biogeochemical regimes are defined in order to estimate local concentrations for the major macromolecular classes. Surfactant equilibria and maximum excess are then derived based on a network of model compounds. Relative local coverage and upward mass transport follow directly, and specific chemical structures can be placed into regional rank order. Lipids and denatured protein-like polymers dominate at the selected locations. The assigned monolayer phase states are variable, whether assessed along bubbles or at the atmospheric spray droplet perimeter. Since oceanic film compositions prove to be irregular, effects on gas and organic transfer are expected to exhibit geographic dependence as well. Moreover, the core arguments extend across the sea-air interface into aerosol-cloud systems. Fundamental nascent chemical properties including mass to carbon ratio and density depend strongly on the geochemical state of source waters. High surface pressures may suppress the Kelvin effect, and marine organic hygroscopicities are almost entirely unconstrained. While bubble adsorption provides a well-known means for transporting lipidic or proteinaceous material into sea spray, the same cannot be said of polysaccharides. Carbohydrates tend to be strongly hydrophilic so that their excess carbon mass is low despite stacked polymeric geometries. Since sugars are abundant in the marine aerosol, gel-based mechanisms may be required to achieve uplift. Uncertainties in the surfactant logic distill to a global scale dearth of information regarding two dimensional kinetics and equilibria. Nonetheless simulations are recommended, to initiate the process of systems level quantification.

  12. Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density

    SciTech Connect (OSTI)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Berendzen, Joel [Biophysics Group, Mail Stop D454, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    1999-11-01

    The correlation of local r.m.s. density is shown to be a good measure of the presence of distinct solvent and macromolecule regions in macromolecular electron-density maps. It has recently been shown that the standard deviation of local r.m.s. electron density is a good indicator of the presence of distinct regions of solvent and protein in macromolecular electron-density maps [Terwilliger & Berendzen (1999 ?). Acta Cryst. D55, 501–505]. Here, it is demonstrated that a complementary measure, the correlation of local r.m.s. density in adjacent regions on the unit cell, is also a good measure of the presence of distinct solvent and protein regions. The correlation of local r.m.s. density is essentially a measure of how contiguous the solvent (and protein) regions are in the electron-density map. This statistic can be calculated in real space or in reciprocal space and has potential uses in evaluation of heavy-atom solutions in the MIR and MAD methods as well as for evaluation of trial phase sets in ab initio phasing procedures.

  13. Mechanical and thermal properties of h-MX{sub 2} (M?=?Cr, Mo, W; X?=?O, S, Se, Te) monolayers: A comparative study

    SciTech Connect (OSTI)

    Çak?r, Deniz, E-mail: deniz.cakir@uantwerpen.be; Peeters, François M., E-mail: francois.peeters@uantwerpen.be [Department of Physics, University of Antwerp, 2610 Antwerpen (Belgium); Sevik, Cem, E-mail: csevik@anadolu.edu.tr [Department of Mechanical Engineering, Faculty of Engineering, Anadolu University, Eskisehir TR 26555 (Turkey)

    2014-05-19

    Using density functional theory, we obtain the mechanical and thermal properties of MX{sub 2} monolayers (where M?=?Cr, Mo, W and X?=?O, S, Se, Te). The ?-centered phonon frequencies (i.e., A{sub 1}, A{sub 2}{sup ?}, E?, and E?), relative frequency values of A{sub 1}, and E? modes, and mechanical properties (i.e., elastic constants, Young modulus, and Poisson's ratio) display a strong dependence on the type of metal and chalcogenide atoms. In each chalcogenide (metal) group, transition-metal dichalcogenides (TMDCs) with W (O) atom are found to be much stiffer. Consistent with their stability, the thermal expansion of lattice constants for TMDCs with O (Te) is much slower (faster). Furthermore, in a heterostructure of these materials, the difference of the thermal expansion of lattice constants between the individual components becomes quite tiny over the whole temperature range. The calculated mechanical and thermal properties show that TMDCs are promising materials for heterostructures.

  14. Systematics of the temperature-dependent interplane resistivity in Ba(Fe1-xMx)?As? (M=Co, Rh, Ni, and Pd)

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tanatar, M. A.; Ni, N.; Thaler, A.; Bud’ko, S. L.; Canfield, P. C.; Prozorov, R.

    2011-07-27

    Temperature-dependent interplane resistivity ?c(T) was measured systematically as a function of transition-metal substitution in the iron-arsenide superconductors Ba(Fe1-xMx)?As?, M=Ni, Pd, Rh. The data are compared with the behavior found in Ba(Fe1-xCox)?As?, revealing resistive signatures of pseudogap. In all compounds we find resistivity crossover at a characteristic pseudogap temperature T* from nonmetallic to metallic temperature dependence on cooling. Suppression of T* proceeds very similarly in cases of Ni and Pd doping and much faster than in similar cases of Co and Rh doping. In cases of Co and Rh doping an additional minimum in the temperature-dependent ?c emerges for high dopings,more »when superconductivity is completely suppressed. These features are consistent with the existence of a charge gap covering part of the Fermi surface. The part of the Fermi surface affected by this gap is notably larger for Ni- and Pd-doped compositions than in Co- and Rh-doped compounds.« less

  15. A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    van Thor, Jasper J.; Madsen, Anders

    2015-01-01

    In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/?I) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ?F,more »in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

  16. A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

    SciTech Connect (OSTI)

    van Thor, Jasper J.; Madsen, Anders

    2015-01-01

    In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/?I) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ?F, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.

  17. CCD(charge-coupled device)-based synchrotron x-ray detector for protein crystallography: Performance projected from an experiment

    SciTech Connect (OSTI)

    Strauss, M.G.; Naday, I.; Sherman, I.S.; Kraimer, M.R.; Westbrook, E.M.

    1986-01-01

    The intense x radiation from a synchrotron source could, with a suitable detector, provide a complete set of diffraction images from a protein crystal before the crystal is damaged by radiation (2 to 3 min). An area detector consisting of a 40 mm dia. x-ray fluorescing phosphor, coupled with an image intensifier and lens to a CCD image sensor, was developed to determine the effectiveness of such a detector in protein crystallography. The detector was used in an experiment with a rotating anode x-ray generator. Diffraction patterns from a lysozyme crystal obtained with this detector are compared to those obtained with film. The two images appear to be virtually identical. The flux of 10/sup 4/ x-ray photons/s was observed on the detector at the rotating anode generator. At the 6-GeV synchrotron being designed at Argonne, the flux on an 80 x 80 mm/sup 2/ detector is expected to be >10/sup 9/ photons/s. The projected design of such a synchrotron detector shows that a diffraction-peak count >10/sup 6/ could be obtained in approx.0.5 s. With an additional approx.0.5 s readout time of a 512 x 512 pixel CCD, the data acquisition time per frame would be approx.1 s so that ninety 1/sup 0/ diffraction images could be obtained, with approximately 1% precision, in less than 3 min.

  18. Bent Diamond Crystals and Multilayer Based Optics at the new 5-Station Protein Crystallography Beamline 'Cassiopeia' at MAX-lab

    SciTech Connect (OSTI)

    Mammen, Christian B.; Als-Nielsen, Jens; Ursby, Thomas; Thunnissen, Marjolein

    2004-05-12

    A new 5-station beamline for protein crystallography is being commissioned at the Swedish synchrotron light source MAX-II at Lund University. Of the 2K/{gamma} = 14 mrad horizontal wiggler fan, the central 2 mrad are used and split in three parts. The central 1 mrad will be used for a station optimized for MAD experiments and on each side of the central fan, from 0.5 mrad to 1 mrad, there are two fixed energy stations using different energies of the same part of the beam. These, in total five stations, can be used simultaneously and independently for diffraction data collection. The two upstream monochromators for the side stations are meridionally bent asymmetric diamond(111) crystals in Laue transmission geometry. The monochromators for the downstream side stations are bent Ge(111) crystals in asymmetric Bragg reflection geometry. Curved multilayer mirrors inserted in the monochromatic beams provide focusing in the vertical plane. The first side station is under commissioning, and a preliminary test protein data set has been collected.

  19. Automatic recovery of missing amplitudes and phases in tilt-limited electron crystallography of two-dimensional crystals

    SciTech Connect (OSTI)

    Gipson, Bryant R.; Stahlberg, Henning [Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum, University Basel, WRO-1058 Mattenstrasse 26, CH-4058 Basel (Switzerland); Masiel, Daniel J.; Browning, Nigel D. [Department of Chemical Engineering and Materials Sciences, University of California at Davis, Davis, California 95616 (United States); Spence, John [Department of Physics, Arizona State University, Tempe, Arizona 85287 (United States); Mitsuoka, Kaoru [Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064 (Japan)

    2011-07-15

    Electron crystallography of 2D protein crystals provides a powerful tool for the determination of membrane protein structure. In this method, data is acquired in the Fourier domain as randomly sampled, uncoupled, amplitudes and phases. Due to physical constraints on specimen tilting, those Fourier data show a vast un-sampled ''missing cone'' of information, producing resolution loss in the direction perpendicular to the membrane plane. Based on the flexible language of projection onto sets, we provide a full solution for these problems with a projective constraint optimization algorithm that, for sufficiently oversampled data, produces complete recovery of unmeasured data in the missing cone. We apply this method to an experimental data set of Bacteriorhodopsin and show that, in addition to producing superior results compared to traditional reconstruction methods, full, reproducible, recovery of the missing cone from noisy data is possible. Finally, we present an automatic implementation of the refinement routine as open source, freely distributed, software that will be included in our 2dx software package.

  20. HIGH PERFORMANCE MACROMOLECULAR MATERIALS

    E-Print Network [OSTI]

    M. Gregory Forest. Department of Mathematics. Institute for Advanced Materials, Nanoscience & Technology. University of North Carolina at Chapel Hill.

  1. electronic reprint Crystallography

    E-Print Network [OSTI]

    Read, Randy J.

    for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK, b Lawrence Berkeley was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from, to the crystallographic community. 1. Introduction Improved crystallographic methods rely on both improved automation

  2. electronic reprint Crystallography

    E-Print Network [OSTI]

    Meagher, Mary

    remarkable progress in X-ray and neutron scattering instrumentation (see e.g. Pedersen, 2002, for a review-based system for small-angle scattering data analysis Petr V. Konarev, Vladimir V. Volkov, Anna V. Sokolova-based system for small- angle scattering data analysis Petr V. Konarev,a,b Vladimir V. Volkov,a,b Anna V

  3. electronic reprint Crystallography

    E-Print Network [OSTI]

    Gruner, Sol M.

    , PEG 400 and glycerol necessary for complete vitrification under pressure cryocooling were determined et al., 2006; Manjasetty et al., 2008). These developments substantially reduce the costs

  4. Protein crystallography prescreen kit

    DOE Patents [OSTI]

    Segelke, Brent W. (San Ramon, CA); Krupka, Heike I. (Livermore, CA); Rupp, Bernhard (Livermore, CA)

    2007-10-02

    A kit for prescreening protein concentration for crystallization includes a multiplicity of vials, a multiplicity of pre-selected reagents, and a multiplicity of sample plates. The reagents and a corresponding multiplicity of samples of the protein in solutions of varying concentrations are placed on sample plates. The sample plates containing the reagents and samples are incubated. After incubation the sample plates are examined to determine which of the sample concentrations are too low and which the sample concentrations are too high. The sample concentrations that are optimal for protein crystallization are selected and used.

  5. electronic reprint Crystallography

    E-Print Network [OSTI]

    topics in condensed matter research, materials science and the life sci- ences make use University and Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy

  6. electronic reprint Crystallography

    E-Print Network [OSTI]

    Winter, Rudolf

    SAXS studies of the morphological changes of an alumina­zirconia­silicate ceramic during its formation et al. ¯ Alumina­zirconia­silicate ceramic #12;research papers J. Appl. Cryst. (2006). 39, 589 ­ all rights reserved In situ SAXS studies of the morphological changes of an alumina­zirconia

  7. electronic reprint Crystallography

    E-Print Network [OSTI]

    Gruner, Sol M.

    include SAXS characterization of hydrogen storage materials, solid oxide fuel cells, chalcogenide glasses etc. In most SAXS applications the samples are enclosed in a sample cell with X-ray windows, DC 20015, USA, and d Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA

  8. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    SciTech Connect (OSTI)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States); Bricogne, Gerard, E-mail: terwilliger@lanl.gov [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom); Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States)

    2014-10-01

    Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  9. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when itmore »was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.« less

  10. PHASE DIAGRAMS and MACROMOLECULAR STABILITY

    E-Print Network [OSTI]

    Middaugh, C. Russell

    2006-10-26

    #0;? 0.41mg/ml; #0;{ 350mg/ml #0;? A.ii. Intensity at 335nm #0;? B.i. ?max Fibrinogen #0;? 0.17mg/ml; #0;{ 59mg/ml #0;? B.ii. Intensity at 336nm #0;? C.i. ?max BSA #0;? 0.55mg/ml; #0;{ 399mg/ml #0;? C.ii. Intensity at 339nm....1 Temperature (?C) ABC DEF Tryptophan emission fluorescence of NV-VLPs as a function of pH and temperature 0 2040608010 0 20 40 60 80 100 Fl u o res cenc e i n ten s i t y at 330 nm (AU ) pH3 332 334 336 338 0 2040608010 0 20 40 60 80 100 pH5 328 330 332...

  11. Johann Deisenhofer, Crystallography, and Proteins

    Office of Scientific and Technical Information (OSTI)

    2011. with acknowledgment of APS at ANL Crystal Structure of the Catalytic Portion of Human HMG-CoA Reductase with acknowledgment of APS at ANL and NSLS at BNL Crystal...

  12. Powder Diffraction Crystallography Instructional Materials

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass mapSpeedingProgram Guidelines This document outlinesPotential partnerships andSoftware

  13. Johann Deisenhofer, Crystallography, and Proteins

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverseIMPACT EVALUATIONIntroducingJobs Human Resources andAbout »Joe W. Gray,Johann

  14. Neutron crystallography aids drug design

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJessework usesofPublications TheScience4.21Reviews

  15. A national facility for biological cryo-electron microscopy

    SciTech Connect (OSTI)

    Saibil, Helen R.; Grünewald, Kay; Stuart, David I.

    2015-01-01

    This review provides a brief update on the use of cryo-electron microscopy for integrated structural biology, along with an overview of the plans for the UK national facility for electron microscopy being built at the Diamond synchrotron. Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback.

  16. Continuous mutual improvement of macromolecular structure models...

    Office of Scientific and Technical Information (OSTI)

    software: The dual role of deposited experimental data Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields....

  17. Proposal Submittal and Scheduling Procedures for Macromolecular...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    single derivative), either several different unrelated research problems or several experiments or projects intellectually and scientifically strongly linked together. Extension...

  18. Center for Nanophase Materials Sciences (CNMS) - Macromolecular

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room News PublicationsAudits &BradburyMay 1,CenterJohn PriceNEWSSubmitting a Proposal to

  19. Improving the accuracy of macromolecular structure refinement

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation CurrentHenry Bellamy,Impact AssessmentsImproving ReactorElectricImproving the

  20. Proposal Submittal and Scheduling Procedures for Macromolecular

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) by Carbon-Rich MatricesstudentsProjectsProperty - THERE

  1. EA-279_UNS__MX.pdf | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of Natural GasAdjustmentsShirleyEnergy A plug-inPPL EnergyPlus, LLC to export electric energySvcs to3 UBSrescinding

  2. MxEnergy Electric, Inc. (Connecticut) | Open Energy Information

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QA J-E-1 SECTION J APPENDIX ECoop Inc Jump to: navigation,Mereg GmbHMontebalitoMt

  3. Microbial Electrochemical Technology (MxCs): Challenges and Opportunities |

    Broader source: Energy.gov (indexed) [DOE]

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of Natural GasAdjustmentsShirleyEnergyTher i nAand DOE Safetyof Methane Hydrate Program AnnualEnergy Photo

  4. PHASE RETRIEVAL METHODS FOR SURFACE CRYSTALLOGRAPHY

    E-Print Network [OSTI]

    Saldin, Dilano

    of current through a transistor in an integrated circuit, to the function of the catalyst in a car the method will be described in detail. The second is the case of low energy electron diffraction (LEED-time post-doc Valentin Shneerson. New topics and ideas often mystify each of us in the same way. I've had

  5. Microcrystallization techniques for serial femtosecond crystallography

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory ofDid you notHeatMaRIEdioxide capture | Center forDioxideFirst Neutrino

  6. Lipidic phase membrane protein serial femtosecond crystallography

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJesse BergkampCenter (LMI-EFRC) ProximityCenterLee Facultya A B C D

  7. Crystal Structure of Crataeva tapia Bark Protein (CrataBL) and Its Effect in Human Prostate Cancer Cell Lines

    E-Print Network [OSTI]

    Federal de Sa~o Paulo, Sa~o Paulo, Sa~o Paulo, Brazil, 2 Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America, 3 Centro de Engenharias e Cie^ncias Exatas, Universidade Estadual do Oeste do Parana´, Toledo, Parana´, Brazil, 4

  8. Structural Characterization of B and non-B Subtypes of HIV-Protease: Insights into the Natural Susceptibility

    E-Print Network [OSTI]

    , Brazil 2 Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA Although a majority of HIV-1 infections in Brazil are caused by the subtype B virus (also prevalent in the United States and Western Europe), viral subtypes F and C are also

  9. Structural Basis for p300 Taz2-p53 TAD1 Binding and Modulation by Phosphorylation

    E-Print Network [OSTI]

    Laboratory of Biochemistry and Molecular Biology 2Laboratory of Cell Biology National Cancer Institute, NIH, Bethesda, MD 20892, USA 3Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick. Among those domains are two transcriptional adaptor zinc-binding (Taz) domains, Taz1 (C/H1) and Taz2 (C

  10. Insights into assembly of the macromolecular inflammasome complex

    E-Print Network [OSTI]

    Monie, Tom P.; Boyle, Joseph P.

    2014-12-23

    underpinning the different appearances of the inflammasome specks visualised to date. This may well require application of various technologies to multiple systems to look for consistency. Certainly applying the high- resolution techniques used to visualise... inflammasome NLRP3 inflammasome AIM2 inflammasome NLRC4 inflammasome Figure 1: General architecture and organisation of the inflammasome. (A) Domain architecture of the major inflammasome forming pattern recognition receptors and apoptosome forming proteins...

  11. Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations

    E-Print Network [OSTI]

    Vajda, Sandor

    mechanics and molecular dynamics simulations is the calculation of the nonbonded terms in the energy based cutoff approximations for faster computation of pairwise van der Waals and electrostatic energy, which slows computation for large distance cutoffs. Also, the high cost of updates means that one cannot

  12. Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform

    E-Print Network [OSTI]

    Xu, Dong; Zhang, Yang

    2009-12-02

    are called VVW , VSAand VMS separately. Step I. Translate and scale the coordinates of all the atoms in the molecular structure in order to fit them in the bounding box. After scaling, the van der Waals radius ri and the probe radius rp become sri and srp... surface, set the radius to be the summation of sri and srp. Use the space-filling method to get the scaled volumetric solid VSA. Step III. To get the van der Waals surface and the solvent- accessible surface, go to step IV directly. To get the molecular...

  13. Perspective Research in Macromolecular Science: Challenges and Opportunities

    E-Print Network [OSTI]

    Weeks, Eric R.

    , Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Department of Polymer Science; Department of Polymer Science, UniVersity of Akron, Akron, Ohio 44325; Department of Chemical Engineering opportunities, the National Science Foundation through the Polymers Program of the Division of Materials

  14. Directed Organization of Functional Materials at Inorganic-Macromolecular

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB PacketDiesel prices continueDileep

  15. Continuous mutual improvement of macromolecular structure models in the PDB

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing BacteriaConnect Collider Tests ofOExperimentsMeasurements (Technical Report)and of

  16. Continuous mutual improvement of macromolecular structure models in the PDB

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing BacteriaConnect Collider Tests ofOExperimentsMeasurements (Technical Report)and

  17. The Development of the GCPCC Protein Crystallography Beamline at CAMD

    E-Print Network [OSTI]

    Phillips, George N. Jr.

    ) monochromator and a focusing toroidal mirror. Built off of the CAMD 7 T superconducting, energy-shifting wiggler. The radiation source for this beamline is a 7 T superconducting, energy-shifting wiggler at the Center of the flux produced by the superconducting side poles relative to the central pole is 16% at 7 keV, 3 % at 12

  18. Workshop: New Advances in Crystallography with Synchrotrons and...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    with Synchrotrons and X-FELs Tuesday, October 25, 2011 - 8:00am 2011 SSRLLCLS Annual Users Conference This workshop, part of the 2011 SSRLLCLS Annual Users...

  19. Serial snapshot crystallography for materials science with SwissFEL

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dejoie, Catherine; Smeets, Stef; Baerlocher, Christian; Tamura, Nobumichi; Pattison, Philip; Abela, Rafael; McCusker, Lynne B.

    2015-04-21

    New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of datamore »can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10–50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.« less

  20. 37A Focus on Crystallography Crystals and mathematics

    E-Print Network [OSTI]

    Greuel, Gert-Martin

    , or as polished gems. Less known is that the largest part (about 98%) of the solid ground is crystalline. This means that crystals are a stable state of the condensed matter. The term "crystal" is derived from

  1. Goniometer-based femtosecond crystallography with X-ray free...

    Office of Scientific and Technical Information (OSTI)

    I. ; McPhillips, Scott E. ; Nelson, Silke ; Peters, John W. ; Sauter, Nicholas K. ; Smith, Clyde A. ; Song, Jinhu ; Stevenson, Hilary P. ; Tsai, Yingssu ; Uervirojnangkoorn,...

  2. Serial femtosecond crystallography of soluble proteins in lipidic...

    Office of Scientific and Technical Information (OSTI)

    are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector....

  3. Account / Revue Use of polynuclear metal clusters in protein crystallography

    E-Print Network [OSTI]

    (2005). © 2005 Académie des sciences. Published by Elsevier SAS. All rights reserved. Résumé L/ 1631-0748/$ - see front matter © 2005 Académie des sciences. Published by Elsevier SAS. All rights; accepted after revision 8 November 2004 Available online 14 July 2005 Abstract Application of polynuclear

  4. Eighth Shull Fellow to Focus on Biochemistry and Crystallography...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    program began in 2006. Named for the 1994 Nobel Prize winner in Physics who did his early neutron scattering research at Oak Ridge from 1946 to 1955, the Shull fellowship program...

  5. Time-Resolved Biochemical Crystallography: A Mechanistic Perspective Keith Moffat*

    E-Print Network [OSTI]

    Moffat, Keith

    of Biochemistry & Molecular Biology, The Institute for Biophysical Dynamics and The Center for Advanced Radiation enforces a phase change in the crystal that alters the cell dimensions, the space group, or both with different reaction intermediate and * To whom correspondence should be addressed. Phone: (773) 702- 2116

  6. Crystallography The new Anatrace Neopentyl Glycol (NG) class detergents

    E-Print Network [OSTI]

    Lebendiker, Mario

    -1008. Lauryl Maltose Neopentyl Glycol NG310 1 gm 5 gm 25 gm Octyl Glucose Neopentyl Glycol NG311 1 gm 5 gm 25 gm Decyl Maltose Neopentyl Glycol NG322 1 gm 5 gm 25 gm #12;Affymetrix, Inc. Anatrace® Products 434 W

  7. Goniometer-based femtosecond crystallography with X-ray free...

    Office of Scientific and Technical Information (OSTI)

    Sciences (SC-22) Country of Publication: United States Language: English Subject: solar (fuels), biofuels (including algae and biomass), bio-inspired, hydrogen and fuel cells...

  8. Nanostructure, Chemistry and Crystallography of Iron Nitride Magnetic

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankADVANCED MANUFACTURING OFFICESpecialAPPENDIX FOriginMaterials by Ultra-High-Resolution Electron

  9. Serial femtosecond crystallography of soluble proteins in lipidic cubic

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail. (Conference) |Janka,FerraraTechnologies (Conference)

  10. Serial femtosecond crystallography of soluble proteins in lipidic cubic

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail. (Conference) |Janka,FerraraTechnologies (Conference)phase (Journal Article) |

  11. Time-resolved serial crystallography captures high-resolution intermediates

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory of rare Kaon and Pion decaysArticle) |errors(Technicalof photoactive yellow

  12. Genentech Uses ALS Crystallography for Therapeutic Antibody Research

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HABFESOpportunities Nuclearlong version)shortGate Hours &Gearing

  13. Media invited to join students in crystallography experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJesse BergkampCentermillion Measurement of Muon

  14. arXiv:0709.2711v1[astro-ph]17Sep2007 Population synthesis at short wavelengths and

    E-Print Network [OSTI]

    Buzzoni, Alberto

    @inaoep.mx, mchavez@inaoep.mx, lino@inaoep.mx) 3 IAM - Instituto de Astronomia y Meteorologia, Universidad de

  15. M.X. {ynarnAHrl 510 }nbrJrgbrrbrna "Vf AYIATH OKYJTAPbI"

    E-Print Network [OSTI]

    to focus on liquid fuels, such as biodiesel and bioethanol to be used with or instead of the conventional

  16. The Dynamic Selection of Coordination Mechanisms Cora Beatriz Excelente-Toledo (cora@lania.mx)

    E-Print Network [OSTI]

    López-Sánchez, Maite

    mechanisms move from the realm of something that is imposed upon the system at design time, to something to respond to requests for coordination. The framework is empirically evaluated, in a grid world scenario) and market protocols (Malone, 1987), to one-shot (short-term) mechanisms like the Contract-Net Protocol

  17. Microbial Fuel Cell Technologies-MxCs: Can They Scale? | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankADVANCED MANUFACTURING OFFICESpecial ReportProposal toDepartment ofEnergy Michigan3

  18. ? ? ? ? ? ? ? ? ? 2 cos 8 cos 4 cos 2 cos lim ? ? ? ? , where ?

    E-Print Network [OSTI]

    puillaw

    2014-08-13

    lim lim tan tan tan tan sin sin lim. 1 1 sin sin cos cos x x x m mx n nx m mx n nx mnx mx nx mx nx mnx m mx n nx. m n mnx mnx. n m. m n mx nx. n m mnx mx mnx

  19. Late transition metal bimetallics for photocatalytic hydrogen production, M-X and C-H bond activation

    E-Print Network [OSTI]

    Esswein, Arthur J

    2007-01-01

    Broadly defined this thesis has focused on the design and study of molecular catalysts that engender multi-electron reactions and photoreactions on small molecule substrates relevant to solar energy conversion. Specifically ...

  20. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Hattne, Hattne

    Diffraction patterns from thermolysin microcrystals and one dark run, collected in December 2011. This data was used for metrology calibration and general cctbx.xfel development.

  1. Dynamics simulations for engineering macromolecular interactions Avi Robinson-Mosher,1,2,a)

    E-Print Network [OSTI]

    Zordan, Victor

    is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding-like spheres with rigid connections. To address whether our framework could generate useful predictions, we

  2. Macromolecular coatings on porous silicon : applications in drug delivery, biosensing, and composites

    E-Print Network [OSTI]

    Perelman, Loren Avery

    2008-01-01

    Sailor, M. J. , Engineering the chemistry and nanostructureSailor, M. J. , Engineering the chemistry and nanostructureSailor, M. J. , Engineering the chemistry and nanostructure

  3. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Hattne, Hattne

    2014-03-04

    Diffraction patterns from thermolysin microcrystals and one dark run, collected in December 2011. This data was used for metrology calibration and general cctbx.xfel development.

  4. Responsive polymers for dynamic modulation of bio-macromolecular transport properties

    E-Print Network [OSTI]

    Deshmukh, Smeet

    2008-01-01

    Responsive self-assembling polymers are used in wide range of applications in the food, pharmaceutical, agricultural, electronic and environmental industries, as well as in the biomedical field. The proper design of such ...

  5. Macromolecular coatings on porous silicon : applications in drug delivery, biosensing, and composites

    E-Print Network [OSTI]

    Perelman, Loren Avery

    2008-01-01

    a similarly rapid volume phase transition 9, 26 . 4.4.9to undergo rapid volume phase transition upon heating orrapid compared with the published rates attributed to the volume phase transition

  6. Journal of Macromolecular Science R , Part C: Polymer Reviews, 49:2563, 2009

    E-Print Network [OSTI]

    Mather, Patrick T.

    (nanofibers16,17 and carbon nanotubes15,18,19 ). Applications ranging from automotive components to food or otherwise modified with organic groups (commonly alkyl ammonium surfactants) similar or compatible

  7. Macromolecular coatings on porous silicon : applications in drug delivery, biosensing, and composites

    E-Print Network [OSTI]

    Perelman, Loren Avery

    2008-01-01

    of nanoporous silicon after coating with a polymer. J. Appl.biosensor was constructed by coating the surface of the23 2.3.4 Protein coating……………………………………………………23 2.3.5

  8. Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

    SciTech Connect (OSTI)

    Brown, Alan; Long, Fei; Nicholls, Robert A.; Toots, Jaan; Emsley, Paul; Murshudov, Garib, E-mail: garib@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (United Kingdom)

    2015-01-01

    A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions. The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.

  9. Definition of Systematic, Approximately Separable and Modular Internal Coordinates (SASMIC) for macromolecular simulation

    E-Print Network [OSTI]

    Pablo Echenique; J. L. Alonso

    2006-12-04

    A set of rules is defined to systematically number the groups and the atoms of organic molecules and, particularly, of polypeptides in a modular manner. Supported by this numeration, a set of internal coordinates is defined. These coordinates (termed Systematic, Approximately Separable and Modular Internal Coordinates, SASMIC) are straightforwardly written in Z-matrix form and may be directly implemented in typical Quantum Chemistry packages. A number of Perl scripts that automatically generate the Z-matrix files for polypeptides are provided as supplementary material. The main difference with other Z-matrix-like coordinates normally used in the literature is that normal dihedral angles (``principal dihedrals'' in this work) are only used to fix the orientation of whole groups and a somewhat non-standard type of dihedrals, termed ``phase dihedrals'', are used to describe the covalent structure inside the groups. This physical approach allows to approximately separate soft and hard movements of the molecule using only topological information and to directly implement constraints. As an application, we use the coordinates defined and ab initio quantum mechanical calculations to assess the commonly assumed approximation of the free energy, obtained from ``integrating out'' the side chain degree of freedom chi, by the Potential Energy Surface (PES) in the protected dipeptide HCO-L-Ala-NH2. We also present a sub-box of the Hessian matrix in two different sets of coordinates to illustrate the approximate separation of soft and hard movements when the coordinates defined in this work are used.

  10. Effects of plasma proteins on the sieving of macromolecular tracers in the kidney

    E-Print Network [OSTI]

    Lazzara, Matthew J

    2003-01-01

    The ultrafiltration of plasma in the mammalian glomerulus is the first step in the processing of blood by the kidney. Proper functioning of this process is critical to the kidney's ability to effectively eliminate waste ...

  11. WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures

    E-Print Network [OSTI]

    Brutlag, Doug

    1 WebFEATURE: An interactive web tool for identifying and visualizing functional sites University, Stanford CA 94305 USA Abstract WebFEATURE (http://feature.stanford.edu/webfeature/) is a web and nucleic acids. WebFEATURE is the public interface to the scanning algorithm of the FEATURE package

  12. ActaCryst.(1998).D54,1105-1108 Deposition of Macromolecular Structures

    E-Print Network [OSTI]

    Barton, Geoffrey J.

    1998-01-01

    more, and higher quality, information on each structure to be made available. The ultimate source to consider briefly how the information is used.This falls into two broad categories. Firstly, the use Outstation,European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton, Cambridge CB10 LSD

  13. A stoichiometric model of Escherichia coli 's macromolecular synthesis machinery and its integration with metabolism

    E-Print Network [OSTI]

    Thiele, Ines

    2009-01-01

    Protein Folding. . . . . . . . . . . . . . . . . . . . . . . . . . .of chaperonin-dependent protein folding in Escherichia coli.Chaperonin-mediated protein folding at the surface of groEL

  14. Macromolecular coatings on porous silicon : applications in drug delivery, biosensing, and composites

    E-Print Network [OSTI]

    Perelman, Loren Avery

    2008-01-01

    hybrid’ s OT returns to its original value, demonstrating the reversibility of the system through heating-system Figure 4.4 Optical thickness changes of a porous SiO 2 /poly(NIPAM) hybrid upon three consecutive heating/

  15. Video Article A Cell-to-cell Macromolecular Transport Assay in Planta Utilizing Biolistic

    E-Print Network [OSTI]

    Citovsky, Vitaly

    measurements do not include petiole) are selected for the experiments. 2) Preparation of the Gene Gun Cartridge of the experiment. For this assay, it is important to ascertain that the prepared cartridge does not transform two). The quality of the each cartridge can be checked by analyzing the expression of the protein 16-20 hours post

  16. Macromolecular Research, Vol. 23, No. 1, pp 118-123 (2015) The Polymer Society of Korea

    E-Print Network [OSTI]

    Rogers, John A.

    2015-01-01

    to tissue engineering and electronics. Keywords: electrohydrodynamic jet printing, nanofiber patterning on Electrohydrodynamic Jet Printing Chiho Song1 , John A. Rogers2 , Jong-Man Kim*,3,4 , and Heejoon Ahn*,1,4 1 Department of Organic and Nano Engineering, Hanyang University, 17 Haengdang-Dong, Seongdong-Gu, Seoul 133-791, Korea 2

  17. Macromolecular coatings on porous silicon : applications in drug delivery, biosensing, and composites

    E-Print Network [OSTI]

    Perelman, Loren Avery

    2008-01-01

    S. A. , Polymerized colloidal crystal hydrogel films asS. A. , Polymerized colloidal crystal hydrogel films ashydrogels with silica colloidal crystal templates 9, 14, or

  18. The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter

    E-Print Network [OSTI]

    California at Berkeley, University of

    , Wissenschaftszentrum Weihenstephan fuÈr ErnaÈhrung, Landnutzung und Umwelt, Technische UniversitaÈt MuÈnchen, D-85350

  19. Inflammasome activation causes dual recruitment of NLRC4 and NLRP3 to the same macromolecular complex

    E-Print Network [OSTI]

    Ming Man, Si; Hopkins, Lee J.; Nugent, Eileen; Cox, Susan; Glück, Ivo M.; Tourlomousis, Panagiotis; Wright, John A.; Cicuta, Pietro; Monie, Tom P.; Bryant, Clare E.

    2014-05-06

    and nucleotide-binding domain and leucine-rich repeat pyrin domain 3 are simultaneously present in the same inflammasome, where both NLRs are required to drive IL-1? processing within the Salmonella-infected cell and to regulate the bacterial burden in mice...

  20. Understanding Structural Stability of Pharmaceutically Relevant Macromolecular Complexes: A Biophysical and Biochemical Approach

    E-Print Network [OSTI]

    Esfandiary, Reza

    2009-08-10

    Macromolecules, due to their large size and complexity are prone to a variety of physical and chemical degradations. Development of stable formulations that retain the macromolecule's stability and activity over its ...

  1. Collaborative Computational Project for Electron cryo-Microscopy

    SciTech Connect (OSTI)

    Wood, Chris; Burnley, Tom [Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA (United Kingdom); Patwardhan, Ardan [European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom); Scheres, Sjors [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Topf, Maya [University of London, Malet Street, London WC1E 7HX (United Kingdom); Roseman, Alan [University of Manchester, Oxford Road, Manchester M13 9PT (United Kingdom); Winn, Martyn, E-mail: martyn.winn@stfc.ac.uk [Science and Technology Facilities Council, Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA (United Kingdom)

    2015-01-01

    The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. Progress in supporting the users and developers of cryoEM software is reported. The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has recently been established. The aims of the project are threefold: to build a coherent cryoEM community which will provide support for individual scientists and will act as a focal point for liaising with other communities, to support practising scientists in their use of cryoEM software and finally to support software developers in producing and disseminating robust and user-friendly programs. The project is closely modelled on CCP4 for macromolecular crystallography, and areas of common interest such as model fitting, underlying software libraries and tools for building program packages are being exploited. Nevertheless, cryoEM includes a number of techniques covering a large range of resolutions and a distinct project is required. In this article, progress so far is reported and future plans are discussed.

  2. Processing incommensurately modulated protein diffraction data with Eval15

    SciTech Connect (OSTI)

    Porta, Jason [Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Lovelace, Jeffrey J. [Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Schreurs, Antoine M. M.; Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Borgstahl, Gloria E. O., E-mail: gborgstahl@unmc.edu [Nebraska Medical Center, Omaha, NE 68198-7696 (United States); Nebraska Medical Center, Omaha, NE 68198-7696 (United States)

    2011-07-01

    Data processing of an incommensurately modulated profilin–actin crystal is described. Recent challenges in biological X-ray crystallography include the processing of modulated diffraction data. A modulated crystal has lost its three-dimensional translational symmetry but retains long-range order that can be restored by refining a periodic modulation function. The presence of a crystal modulation is indicated by an X-ray diffraction pattern with periodic main reflections flanked by off-lattice satellite reflections. While the periodic main reflections can easily be indexed using three reciprocal-lattice vectors a*, b*, c*, the satellite reflections have a non-integral relationship to the main lattice and require a q vector for indexing. While methods for the processing of diffraction intensities from modulated small-molecule crystals are well developed, they have not been applied in protein crystallography. A recipe is presented here for processing incommensurately modulated data from a macromolecular crystal using the Eval program suite. The diffraction data are from an incommensurately modulated crystal of profilin–actin with single-order satellites parallel to b*. The steps taken in this report can be used as a guide for protein crystallographers when encountering crystal modulations. To our knowledge, this is the first report of the processing of data from an incommensurately modulated macromolecular crystal.

  3. Damage by X-rays: A Case Study for Metallo-Protein Crystallography

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent Bonding Low-Cost2 DOE HQSiteo n n(Technical Report) |Damage by

  4. Integrated crystal mounting and alignment system for high-throughput biological crystallography

    DOE Patents [OSTI]

    Nordmeyer, Robert A.; Snell, Gyorgy P.; Cornell, Earl W.; Kolbe, William; Yegian, Derek; Earnest, Thomas N.; Jaklevic, Joseph M.; Cork, Carl W.; Santarsiero, Bernard D.; Stevens, Raymond C.

    2005-07-19

    A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following removal. The samples must additionally be stably aligned to within a few microns at a point in space. The ability to accurately perform these tasks remotely and automatically leads to a significant increase in sample throughput and reliability for high-volume protein characterization efforts. Since the protein samples are placed in a shipping-compatible layered stack of sample cassettes each holding many samples, a large number of samples can be shipped in a single cryogenic shipping container.

  5. Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ibrahim, Mohamed; Chatterjee, Ruchira; Hellmich, Julia; Tran, Rosalie; Bommer, Martin; Yachandra, Vittal K.; Yano, Junko; Kern, Jan; Zouni, Athina

    2015-07-01

    In photosynthesis, photosystem II (PSII) is the multi-subunit membrane protein complex that catalyzes photo-oxidation of water into dioxygen through the oxygen evolving complex (OEC). To understand the water oxidation reaction, it is important to get structural information about the transient and intermediate states of the OEC in the dimeric PSII core complex (dPSIIcc). In recent times, femtosecond X-ray pulses from the free electron laser (XFEL) are being used to obtain X-ray diffraction (XRD) data of dPSIIcc microcrystals at room temperature that are free of radiation damage. In our experiments at the XFEL, we used an electrospun liquid microjet setup thatmore »requires microcrystals less than 40 ?m in size. In this study, we explored various microseeding techniques to get a high yield of monodisperse uniform-sized microcrystals. Monodisperse microcrystals of dPSIIcc of uniform size were a key to improve the stability of the jet and the quality of XRD data obtained at the XFEL. This was evident by an improvement of the quality of the datasets obtained, from 6.5 Å, using crystals grown without the micro seeding approach, to 4.5 Å using crystals generated with the new method.« less

  6. Crystallography Reviews Vol. 15, No. 1, JanuaryMarch 2009, 5783

    E-Print Network [OSTI]

    Müller, Peter

    crystal structures Peter Mu¨ ller* Department of Chemistry, Massachusetts Institute of Technology improve the quality of their crystal structures. Keywords: structure refinement; crystal growth; data 2. Pre-refinement strategies 58 2.1. Crystal growth and crystal handling 59 2.2. Choosing a crystal

  7. Chaotic Crystallography: How the physics of information reveals structural order in materials

    E-Print Network [OSTI]

    Dowman P. Varn; James P. Crutchfield

    2014-11-10

    We review recent progress in applying information- and computation-theoretic measures to describe material structure that transcends previous methods based on exact geometric symmetries. We discuss the necessary theoretical background for this new toolset and show how the new techniques detect and describe novel material properties. We discuss how the approach relates to well known crystallographic practice and examine how it provides novel interpretations of familiar structures. Throughout, we concentrate on disordered materials that, while important, have received less attention both theoretically and experimentally than those with either periodic or aperiodic order.

  8. Real-Time Observation of Cuprates Structural Dynamics by Ultrafast Electron Crystallography

    E-Print Network [OSTI]

    Carbone, F.

    The phonon-mediated attractive interaction between carriers leads to the Cooper pair formation in conventional superconductors. Despite decades of research, the glue holding Cooper pairs in high-temperature superconducting ...

  9. Reprinted from Journal of Applied Crystallography, Vol. 1, Part 2, June 1968 PRINTED IN DENMARK

    E-Print Network [OSTI]

    Harrison, Stephen C.

    in aperture. One can use Bragg reflection from dense planes in a suitably chosen, bent crystal, or total

  10. DIRECT CORRELATION OF PROTEIN STRUCTURE AND FUNCTION USING HIGH-PRESSURE X-RAY CRYSTALLOGRAPHY

    E-Print Network [OSTI]

    Gruner, Sol M.

    protein Citrine as a model system under high-pressure perturbation. Citrine has been compressed by high Buz Michael Barstow, Ph. D. Cornell University 2009 A protein molecule is an intricate system whose is used to refer to my co-authors: Nozomi Ando, Chae Un Kim, and my advisor, Sol Gruner, to whom I owe

  11. In meso in situ serial X-ray crystallography of soluble and membrane...

    Office of Scientific and Technical Information (OSTI)

    Trinity College, Dublin (Ireland) Paul Scherrer Institute, CH-5232 Villigen (Switzerland) Universitt Konstanz, M647, D-78457 Konstanz (Germany) Publication Date:...

  12. Journal of Chemical Crystallography, Vol. 29, No. 7, 1999 Synthesis and structure of bis(dibenzoylmethane)

    E-Print Network [OSTI]

    Gao, Song

    of aromatic stacking. KEY WORDS: Copper complex; crystal structure; dibenzoylmethane complex. Introduction) dissolved in 10 mL meth- anol was added to a 10 mL methanol solution con- taining 2 mmol dbm. The mixture solution were ad- justed to pH 6 with methanol solution of sodium methoxide and stirred for 4 h at room

  13. Direct Observation of Optically Induced Transient Structures in Graphite Using Ultrafast Electron Crystallography

    E-Print Network [OSTI]

    initio density functional calculations, we trace the governing mechanism back to electronic structure changes in the electronic properties, direct de- termination of lattice structural dynamics from opticalDirect Observation of Optically Induced Transient Structures in Graphite Using Ultrafast Electron

  14. Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

    SciTech Connect (OSTI)

    Barends, Thomas R. M., E-mail: thomas.barends@mpimf-heidelberg.mpg.de [MPI for Medical Research, Heidelberg (Germany); Brosi, Richard W. W. [Freie Universitat Berlin, Berlin (Germany); Steinmetz, Andrea; Scherer, Anna; Hartmann, Elisabeth; Eschenbach, Jessica; Lorenz, Thorsten [MPI for Medical Research, Heidelberg (Germany); Seidel, Ralf [MPI for Molecular Physiology, Dortmund (Germany); Shoeman, Robert L.; Zimmermann, Sabine [MPI for Medical Research, Heidelberg (Germany); Bittl, Robert [Freie Universitat Berlin, Berlin (Germany); Schlichting, Ilme; Reinstein, Jochen [MPI for Medical Research, Heidelberg (Germany)

    2013-08-01

    The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.

  15. Generalized splines for Radon transform on compact Lie groups with applications to crystallography

    E-Print Network [OSTI]

    Swanhild Bernstein; Svend Ebert; Isaac Z. Pesenson

    2012-04-27

    The Radon transform Rf of functions f on SO(3) has recently been applied extensively in texture analysis, i.e. the analysis of preferred crystallographic orientation. In practice one has to determine the orientation probability density function f \\in L2(SO(3)) from Rf \\in L2(S2\\times S2) which is known only on a discrete set of points. Since one has only partial information about Rf the inversion of the Radon transform becomes an ill-posed inverse problem. Motivated by this problem we define a new notion of the Radon transform Rf of functions f on general compact Lie groups and introduce two approximate inversion algorithms which utilize our previously developed generalized variational splines on manifolds. Our new algorithms fit very well to the application of Radon transform on SO(3) to texture analysis.

  16. Three phase crystallography and solute distribution analysis during residual austenite decomposition in tempered nanocrystalline bainitic steels

    SciTech Connect (OSTI)

    Caballero, F.G. [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo, 8, Madrid E-28040 (Spain); Yen, Hung-Wei [Department of Materials Science and Engineering, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 10617, Taiwan (China); Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006 (Australia); Miller, M.K. [Oak Ridge National Laboratory (ORNL), Materials Science and Technology Division, Oak Ridge, TN 37831-6139 (United States); Cornide, J. [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo, 8, Madrid E-28040 (Spain); Chang, Hsiao-Tzu [Department of Materials Science and Engineering, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 10617, Taiwan (China); Garcia-Mateo, C. [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo, 8, Madrid E-28040 (Spain); Yang, Jer-Ren [Department of Materials Science and Engineering, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 10617, Taiwan (China)

    2014-02-15

    Interphase carbide precipitation due to austenite decomposition was investigated by high resolution transmission electron microscopy and atom probe tomography in tempered nanostructured bainitic steels. Results showed that cementite (?) forms by a paraequilibrium transformation mechanism at the bainitic ferrite–austenite interface with a simultaneous three phase crystallographic orientation relationship. - Highlights: • Interphase carbide precipitation due to austenite decomposition • Tempered nanostructured bainitic steels • High resolution transmission electron microscopy and atom probe tomography • Paraequilibrium ? with three phase crystallographic orientation relationship.

  17. The crystallography of fatigue crack initiation in Incoloy-908 and A-286 steel

    SciTech Connect (OSTI)

    Krenn, C.R. |

    1996-12-01

    Fatigue crack initiation in the austenitic Fe-Ni superalloys Incoloy-908 and A-286 is examined using local crystallographic orientation measurements. Results are consistent with sharp transgranular initiation and propagation occurring almost exclusively on {l_brace}111{r_brace} planes in Incoloy-908 but on a variety of low index planes in A-286. This difference is attributed to the influence of the semicoherent grain boundary {eta} phase in A-286. Initiation in each alloy occurred both intergranularly and transgranularly and was often associated with blocky surface oxide and carbide inclusions. Taylor factor and resolved shear stress and strain crack initiation hypotheses were tested, but despite an inconclusive suggestion of a minimum required {l_brace}111{r_brace} shear stress, none of the hypotheses were found to convincingly describe preferred initiation sites, even within the subsets of transgranular cracks apparently free from the influence of surface inclusions. Subsurface inclusions are thought to play a significant role in crack initiation. These materials have applications for use in structural conduit for high field superconducting magnets designed for fusion energy use.

  18. Integrated crystal mounting and alignment system for high-throughput biological crystallography

    DOE Patents [OSTI]

    Nordmeyer, Robert A. (San Leandro, CA); Snell, Gyorgy P. (Richmond, CA); Cornell, Earl W. (Antioch, CA); Kolbe, William F. (Moraga, CA); Yegian, Derek T. (Oakland, CA); Earnest, Thomas N. (Berkeley, CA); Jaklevich, Joseph M. (Lafayette, CA); Cork, Carl W. (Walnut Creek, CA); Santarsiero, Bernard D. (Chicago, IL); Stevens, Raymond C. (La Jolla, CA)

    2007-09-25

    A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following removal. The samples must additionally be stably aligned to within a few microns at a point in space. The ability to accurately perform these tasks remotely and automatically leads to a significant increase in sample throughput and reliability for high-volume protein characterization efforts. Since the protein samples are placed in a shipping-compatible layered stack of sample cassettes each holding many samples, a large number of samples can be shipped in a single cryogenic shipping container.

  19. Workshop: New Advances in Crystallography with Synchrotrons and X-FELs |

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservationBio-Inspired SolarAbout /Two0PhotosPresentations Workshop PresentationsWorkshop

  20. Serial time-resolved crystallography of photosystem II using a femtosecond

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory ofDidDevelopment Top Scientific Impact Since itsimpactChannelsX-ray

  1. In meso in situ serial X-ray crystallography of soluble and membrane

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing(Journal Article)lasers(Journal Article)CurvesAnodic Materials inSciTech

  2. Goniometer-based femtosecond crystallography with X-ray free electron

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing(Journal Article)

  3. Goniometer-based femtosecond crystallography with X-ray free electron

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing(Journal Article)lasers (Journal Article) | SciTech Connect González, Ana ; Aguila,

  4. Goniometer-based femtosecond crystallography with X-ray free electron

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing(Journal Article)lasers (Journal Article) | SciTech Connect González, Ana ;

  5. FG Systemdynamik und Reibungsphysik

    E-Print Network [OSTI]

    Berlin,Technische Universität

    2 mx K = , potentielle Energie der Fe- der ist 2 2 cx U = . Lagrangefunktion ist gleich 2 2 2 2 mx cx L K U= - = - . Die Ableitungen lau- ten: 2 2 2 2 2 2 L mx cx mx mx x x x = - = = , d L d mx mx dt x dt = = , 2 2 2 2 2 2 L mx cx cx cx x x x = - = - = - . Die

  6. Energiemethoden der Mechanik / Prof. Popov / Vorlesung 1. Generalisierte Koordinaten, Lagrangefunktion, Lagrangegleichungen II. Art

    E-Print Network [OSTI]

    Berlin,Technische Universität

    = , potentielle Energie der Fe- der ist 2 2 cx U = . Lagrangefunktion ist gleich 2 2 2 2 mx cx L K U= - = - . Die Ableitungen lau- ten: 2 2 2 2 2 2 L mx cx mx mx x x x = - = = , d L d mx mx dt x dt = = , 2 2 2 2 2 2 L mx cx cx cx x x x = - = - = - . Die Lagrangegleichung lautet 0 d L L

  7. The carburization of transition metal molybdates (MxMoO?, M= Cu, Ni or Co) and the generation of highly active metal/carbide catalysts for CO? hydrogenation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Rodriguez, Jose A.; Xu, Wenqian; Ramirez, Pedro J.; Stachiola, Dario; Brito, Joaquin L.

    2015-05-06

    A new approach has been tested for the preparation of metal/Mo?C catalysts using mixed-metal oxide molybdates as precursors. Synchrotron-based in situ time-resolved X-ray diffraction was used to study the reduction and carburization processes of Cu?(MoO?)?(OH)?, a-NiMoO? and CoMoO?•nH?O by thermal treatment under mixtures of hydrogen and methane. In all cases, the final product was ?-Mo?C and a metal phase (Cu, Ni, or Co), but the transition sequence varied with the different metals, and it could be related to the reduction potential of the Cu²?, Ni²? and Co²? cations inside each molybdate. The synthesized Cu/Mo?C, Ni/Mo?C and Co/Mo?C catalysts were highlymore »active for the hydrogenation of CO?. The metal/Mo?C systems exhibited large variations in the selectivity towards methanol, methane and CnH?n?? (n > 2) hydrocarbons depending on the nature of the supported metal and its ability to cleave C-O bonds. Cu/Mo?C displayed a high selectivity for CO and methanol production. Ni/Mo?C and Co/Mo?C were the most active catalysts for the activation and full decomposition of CO?, showing high selectivity for the production of methane (Ni case) and CnH?n?? (n > 2) hydrocarbons (Co case).« less

  8. Superficies y Vaco 12, 39-44, Junio 2001 Sociedad Mexicana de Ciencia de Superficies y de Vaco. *Corresponding author, e-mail: mlopez@fis.cinvestav.mx

    E-Print Network [OSTI]

    Meléndez Lira, Miguel Angel

    impurezas, desorden en las aleaciones, rugosidad en las interfaces, etc. Estos aspectos dependen fuertemente dependen del tipo de proceso de interrupción realizado en la capa colchón de GaAs. Se calculó la rugosidad

  9. The carburization of transition metal molybdates (MxMoO?, M= Cu, Ni or Co) and the generation of highly active metal/carbide catalysts for CO? hydrogenation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Rodriguez, Jose A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Xu, Wenqian [Brookhaven National Lab. (BNL), Upton, NY (United States); Ramirez, Pedro J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Univ. Central De Venezuela, Caracas (Venesuela); Stachiola, Dario [Brookhaven National Lab. (BNL), Upton, NY (United States); Brito, Joaquin L. [Inst. Venezolano de Investigaciones Cientificas, Caracas (Venezuela)

    2015-05-06

    A new approach has been tested for the preparation of metal/Mo?C catalysts using mixed-metal oxide molybdates as precursors. Synchrotron-based in situ time-resolved X-ray diffraction was used to study the reduction and carburization processes of Cu?(MoO?)?(OH)?, a-NiMoO? and CoMoO?•nH?O by thermal treatment under mixtures of hydrogen and methane. In all cases, the final product was ?-Mo?C and a metal phase (Cu, Ni, or Co), but the transition sequence varied with the different metals, and it could be related to the reduction potential of the Cu²?, Ni²? and Co²? cations inside each molybdate. The synthesized Cu/Mo?C, Ni/Mo?C and Co/Mo?C catalysts were highly active for the hydrogenation of CO?. The metal/Mo?C systems exhibited large variations in the selectivity towards methanol, methane and CnH?n?? (n > 2) hydrocarbons depending on the nature of the supported metal and its ability to cleave C-O bonds. Cu/Mo?C displayed a high selectivity for CO and methanol production. Ni/Mo?C and Co/Mo?C were the most active catalysts for the activation and full decomposition of CO?, showing high selectivity for the production of methane (Ni case) and CnH?n?? (n > 2) hydrocarbons (Co case).

  10. Lat. Am. J. Phys. Educ. Vol. 2 No. 3, Sept. 2008 205 http://www.journal.lapen.org.mx Teaching Nonlinear Dynamics and Chaos for

    E-Print Network [OSTI]

    Rey Juan Carlos, Universidad

    Ambientales e Informática. El uso extensivo de herramientas computacionales, internet y prácticas de. An extensive use of computational tools, the internet and laboratory experiments are key ingredients

  11. Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement

    SciTech Connect (OSTI)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2003-07-01

    A procedure for iterative model-building, statistical density modification and refinement at moderate resolution (up to about 2.8 Å) is described. An iterative process for improving the completeness and quality of atomic models automatically built at moderate resolution (up to about 2.8 Å) is described. The process consists of cycles of model building interspersed with cycles of refinement and combining phase information from the model with experimental phase information (if any) using statistical density modification. The process can lead to substantial improvements in both the accuracy and completeness of the model compared with a single cycle of model building. For eight test cases solved by MAD or SAD at resolutions ranging from 2.0 to 2.8 Å, the fraction of models built and assigned to sequence was 46–91% (mean of 65%) after the first cycle of building and refinement, and 78-95% (mean of 87%) after 20 cycles. In an additional test case, an incorrect model of gene 5 protein (PDB code 2gn5; r.m.s.d. of main-chain atoms from the more recent refined structure 1vqb at 1.56 Å) was rebuilt using only structure-factor amplitude information at varying resolutions from 2.0 to 3.0 Å. Rebuilding was effective at resolutions up to about 2.5 Å. The resulting models had 60-80% of the residues built and an r.m.s.d. of main-chain atoms from the refined structure of 0.20 to 0.62 Å. The algorithm is useful for building preliminary models of macromolecules suitable for an experienced crystallographer to extend, correct and fully refine.

  12. The effects of captan and dieldrin on the growth and macromolecular synthesis of the cellular slime mold Dictyostelium discoideum 

    E-Print Network [OSTI]

    Bushway, Rodney John

    1973-01-01

    cyclodiene, is a chlorinated hydrocarbon insecticide. Like many of the chlorinated hydrocarbon pesticides, it persists in the environment (1, 2). The amount of dieldrin and related com- pounds produced yearly in the United States is 107-115 million pounds... in the cellular slime mold. 55 LITERATURE CITED 1. C. M. Wang and F. Matsumura, Dieldrin, effect on the ion transport activities in liver tissues, Bu7. 1. Environ. Contamin. Tomieol. 4, 144 (1969). 2. V. H. Freed, Global distribution of pesticides, in "The...

  13. Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods

    SciTech Connect (OSTI)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Berendzen, Joel [Biophysics Group, Mail Stop D454, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    1999-02-01

    The presence of distinct regions of high and low density variation in electron-density maps is found to be a good indicator of the correctness of a heavy-atom solution in the MIR and MAD methods. An automated examination of the native Fourier is tested as a means of evaluation of a heavy-atom solution in MAD and MIR methods for macromolecular crystallography. It is found that the presence of distinct regions of high and low density variation in electron-density maps is a good indicator of the correctness of a heavy-atom solution in the MIR and MAD methods. The method can be used to evaluate heavy-atom solutions during MAD and MIR structure solutions and to determine the handedness of the structure if anomalous data have been measured.

  14. Station for X-ray structural analysis of materials and single crystals (including nanocrystals) on a synchrotron radiation beam from the wiggler at the Siberia-2 storage ring

    SciTech Connect (OSTI)

    Kheiker, D. M. Kovalchuk, M. V.; Korchuganov, V. N.; Shilin, Yu. N.; Shishkov, V. A.; Sulyanov, S. N.; Dorovatovskii, P. V.; Rubinsky, S. V.; Rusakov, A. A.

    2007-11-15

    The design of the station for structural analysis of polycrystalline materials and single crystals (including nanoobjects and macromolecular crystals) on a synchrotron radiation beam from the superconducting wiggler of the Siberia-2 storage ring is described. The wiggler is constructed at the Budker Institute of Nuclear Physics of the Siberian Division of the Russian Academy of Sciences. The X-ray optical scheme of the station involves a (1, -1) double-crystal monochromator with a fixed position of the monochromatic beam and a sagittal bending of the second crystal, segmented mirrors bent by piezoelectric motors, and a (2{theta}, {omega}, {phi}) three-circle goniometer with a fixed tilt angle. Almost all devices of the station are designed and fabricated at the Shubnikov Institute of Crystallography of the Russian Academy of Sciences. The Bruker APEX11 two-dimensional CCD detector will serve as a detector in the station.

  15. Towards phasing using high X-ray intensity

    SciTech Connect (OSTI)

    Galli, Lorenzo; Son, Sang -Kil; Barends, Thomas R. M.; White, Thomas A.; Barty, Anton; Botha, Sabine; Boutet, Sébastien; Caleman, Carl; Doak, R. Bruce; Nanao, Max H.; Nass, Karol; Shoeman, Robert L.; Timneanu, Nicusor; Santra, Robin; Schlichting, Ilme; Chapman, Henry N.

    2015-09-30

    X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential `bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. In conclusion, a pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.

  16. The uTPC Method: Improving the Position Resolution of Neutron Detectors Based on MPGDs

    E-Print Network [OSTI]

    Pfeiffer, Dorothea; Birch, Jens; Hall-Wilton, Richard; Höglund, Carina; Hultman, Lars; Iakovidis, George; Oliveri, Eraldo; Oksanen, Esko; Ropelewski, Leszek; Thuiner, Patrik

    2015-01-01

    Due to the Helium-3 crisis, alternatives to the standard neutron detection techniques are becoming urgent. In addition, the instruments of the European Spallation Source (ESS) require advances in the state of the art of neutron detection. The instruments need detectors with excellent neutron detection efficiency, high-rate capabilities and unprecedented spatial resolution. The Macromolecular Crystallography instrument (NMX) requires a position resolution in the order of 200 um over a wide angular range of incoming neutrons. Solid converters in combination with Micro Pattern Gaseous Detectors (MPGDs) are proposed to meet the new requirements. Charged particles rising from the neutron capture have usually ranges larger than several millimetres in gas. This is apparently in contrast with the requirements for the position resolution. In this paper, we present an analysis technique, new in the field of neutron detection, based on the Time Projection Chamber (TPC) concept. Using a standard Single-GEM with the catho...

  17. 2010 Diffraction Methods in Structural Biology

    SciTech Connect (OSTI)

    Dr. Ana Gonzalez

    2011-03-10

    Advances in basic methodologies have played a major role in the dramatic progress in macromolecular crystallography over the past decade, both in terms of overall productivity and in the increasing complexity of the systems being successfully tackled. The 2010 Gordon Research Conference on Diffraction Methods in Structural Biology will, as in the past, focus on the most recent developments in methodology, covering all aspects of the process from crystallization to model building and refinement, complemented by examples of structural highlights and complementary methods. Extensive discussion will be encouraged and it is hoped that all attendees will participate by giving oral or poster presentations, the latter using the excellent poster display area available at Bates College. The relatively small size and informal atmosphere of the meeting provides an excellent opportunity for all participants, especially younger scientists, to meet and exchange ideas with leading methods developers.

  18. Towards phasing using high X-ray intensity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Galli, Lorenzo; Son, Sang -Kil; Barends, Thomas R. M.; White, Thomas A.; Barty, Anton; Botha, Sabine; Boutet, Sébastien; Caleman, Carl; Doak, R. Bruce; Nanao, Max H.; et al

    2015-09-30

    X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential `bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. In conclusion, a pattern sorting schememore »is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.« less

  19. Structural analysis of flexible proteins in solution by Small Angle X-ray Scattering combined with crystallography

    E-Print Network [OSTI]

    Tsutakawa, Susan E.; Hura, Greg L.; Frankel, Ken A.; Cooper, Priscilla K.; Tainer, John A.

    2006-01-01

    suite of programs, including CREDO, based on their ab initioas input to the program CREDO, which built density on theadditional density built by CREDO. The regulatory domain was

  20. The Application of X-ray Crystallography towards the Design of Novel Inhibitors of MurA and CDK2

    E-Print Network [OSTI]

    Han, Huijong

    2008-10-23

    , respectively. MurA belongs to the enolpyruvyl transferase family of enzymes. MurA catalyzes the first committed step in the biosynthesis of cell wall peptidoglycan, and is the target of fosfomycin, a naturally occurring broad-spectrum antibiotic. Ever...

  1. Au133(SPh-tBu)52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis

    SciTech Connect (OSTI)

    Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy; Kumara, Chanaka; Jupally, Vijay Reddy; Fortunelli, Alessandro; Sementa, Luca; Barcaro, Giovanni; Zuo, Xiaobing; Noll, Bruce C.

    2015-04-15

    Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the “nanostructure problem”. Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au133(SPh-tBu)52, was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than in the slightly larger Au144(SCH2CH2Ph)60. Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.

  2. Structure and Dynamics of NBD1 from CFTR Characterized Using Crystallography and Hydrogen/Deuterium Exchange Mass Spectrometry

    SciTech Connect (OSTI)

    Lewis, H.A.; Wang, C.; Zhao, X.; Hamuro, Y.; Conners, K.; Kearins, M.C.; Lu, F.; Sauder, J.M.; Molnar, K.S.; Coales, S.J.; Maloney, P.C.; Guggino, W.B.; Wetmore, D.R.; Weber, P.C.; Hunt, J.F. (SGX); (ExSAR); (Cystic); (JHU-MED); (Columbia)

    2012-04-30

    The {Delta}F508 mutation in nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) is the predominant cause of cystic fibrosis. Previous biophysical studies on human F508 and {Delta}F508 domains showed only local structural changes restricted to residues 509-511 and only minor differences in folding rate and stability. These results were remarkable because {Delta}F508 was widely assumed to perturb domain folding based on the fact that it prevents trafficking of CFTR out of the endoplasmic reticulum. However, the previously reported crystal structures did not come from matched F508 and {Delta}F508 constructs, and the {Delta}F508 structure contained additional mutations that were required to obtain sufficient protein solubility. In this article, we present additional biophysical studies of NBD1 designed to address these ambiguities. Mass spectral measurements of backbone amide {sup 1}H/{sup 2}H exchange rates in matched F508 and {Delta}F508 constructs reveal that {Delta}F508 increases backbone dynamics at residues 509-511 and the adjacent protein segments but not elsewhere in NBD1. These measurements also confirm a high level of flexibility in the protein segments exhibiting variable conformations in the crystal structures. We additionally present crystal structures of a broader set of human NBD1 constructs, including one harboring the native F508 residue and others harboring the {Delta}F508 mutation in the presence of fewer and different solubilizing mutations. The only consistent conformational difference is observed at residues 509-511. The side chain of residue V510 in this loop is mostly buried in all non-{Delta}F508 structures but completely solvent exposed in all {Delta}F508 structures. These results reinforce the importance of the perturbation {Delta}F508 causes in the surface topography of NBD1 in a region likely to mediate contact with the transmembrane domains of CFTR. However, they also suggest that increased exposure of the 509-511 loop and increased dynamics in its vicinity could promote aggregation in vitro and aberrant intermolecular interactions that impede trafficking in vivo.

  3. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

    2015-07-28

    Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier'smore »equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

  4. An evaluation of adhesive sample holders for advanced crystallographic experiments

    SciTech Connect (OSTI)

    Mazzorana, Marco; Sanchez-Weatherby, Juan Sandy, James; Lobley, Carina M. C.; Sorensen, Thomas

    2014-09-01

    Commercially available adhesives have been evaluated for crystal mounting when undertaking complex macromolecular crystallography experiments. Here, their use as tools for advanced sample mounting and cryoprotection is assessed and their suitability for room-temperature data-collection and humidity-controlled studies is investigated. The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposing it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed.

  5. Solutions to Dr. Z.'s Math 421(1), (Fall 2014, RU) REAL Quiz #4 1. Show that the given functions are orthogonal on the given interval.

    E-Print Network [OSTI]

    Zeilberger, Doron

    nx}, n = 1, 2, . . . is orthogonal over the interval [0, ]. Also find the norm of each function. Sol. We need to take two different, typical members of this family, so let's call them cos nx and cos mx, where n = m. We have to show that (cos mx, cos nx) = 0. (cos mx, cos nx) = 0 cos mx cos nx dx . We now

  6. xsxsxsxsxsxsxsxsxsxsxsxsxsxsxsxsxsx Michigan State University ExtensionBulletin E-657Major RevisionNov. 1993

    E-Print Network [OSTI]

    xsxsxsxsxsxsxsxsxsxsxsxsxsxsxsxsxsx x Mx Ix Cx Hx Ix Gx Ax Nx x Vx Ex Nx Ix Sx Ox Nx Michigan StateBUTCHERxPREPARE/COOK/PRESERVE #12;xsxsxsxsxsxsxsxsxsxsxsxsxsxsxsxsxsx x Mx Ix Cx Hx Ix Gx Ax N x Vx Ex Nx Ix Sx Ox Nxx Mx Ix Cx Hx bulletin "You and Your Wild Game." #12;x Mx Ix Cx Hx Ix Gx Ax N x Vx Ex Nx Ix Sx Ox Nxx Mx Ix Cx Hx Ix Gx

  7. D:\\352\\2014\\References.wpd EPSC 352: INTRODUCTION TO MINERALOGY

    E-Print Network [OSTI]

    , 1963). Elementary Crystallography. New York: John Wiley. Cox, K.G.; Price, N.B.; Harte, B. 1967. International Tables for X-Ray Crystallography. Vol. 1. International Union of Crystallography (Birmingham

  8. The study of biomass yield and macromolecular content of microalgae change as a function of physiological state and nutrient supply conditions

    E-Print Network [OSTI]

    Chen, Guo

    2013-12-31

    previous study reported that Scenedesmusobliquus and C. kessleri cultures, isolated from a treatment pond in a coal-fired thermoelectric power plant in Brazil, showed a capacity of bio-fixation of CO2(de Morais et al., 2007). Enhanced addition of CO2fine... ...................................................................... 25 Figure 4-5. Schematic of the freeze-dried sample preparation and analysis processes: (A) less than 5 ml algae obtained from centrifuging algal suspension; (B) liquid nitrogen which was used to flash freeze centrifuged algae pellets; (C) freeze...

  9. Studies of structure and dynamics of biological macro-molecular assemblies by low angle neutron diffraction and inelastic X-ray scattering

    E-Print Network [OSTI]

    Liu, Yun, 1973-

    2005-01-01

    This thesis is organized into two parts which focus on the studies of the dynamic structure factor and static inter-particle structure factor respectively. In the first part, we have measured and analyzed the dynamic ...

  10. Major Successes of Theory-and-Experiment-Combined Studies in Surface Chemistry and Heterogeneous Catalysis.

    E-Print Network [OSTI]

    Somorjai, Gabor A.

    2011-01-01

    sensitive techniques such as LEED, XPS, AES, ISS and SIMS,crystallography[2, 3] (LEED) to high resolution electronincluding the development of LEED surface crystallography,

  11. Interactions of a potent cyclic peptide inhibitor with the light chain of botulinum neurotoxin A: insights from x-ray crystallography

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kumaran, D.; Adler, M.; Levit, M.; Krebs, M.; Sweeney, R.; Swaminathan, S.

    2015-10-17

    The seven antigenically distinct serotypes (A to G) of botulinum neurotoxin (BoNT) are responsible for the deadly disease botulism. BoNT serotype A (BoNT/A) exerts its lethal action by cleaving the SNARE protein SNAP-25, leading to inhibition of neurotransmitter release, flaccid paralysis and autonomic dysfunction. BoNTs are dichain proteins: the heavy chain is responsible for neurospecific binding, internalization and translocation, and the light chain is responsible for substrate cleavage. Because of their extreme toxicity and prior history of weaponization, the BoNTs are considered to be potential bioterrorism agents. No post-symptomatic therapeutic interventions are available for BoNT intoxication other than critical care;more »therefore it is imperative to develop specific antidotes against this neurotoxin. To this end, a cyclic peptide inhibitor (CPI-1) was synthesized and found to inhibit BoNT/A light chain (Balc) with high affinity. When tested in a cell-free Förster resonance excitation transfer (FRET) assay, CPI-1 was found to have a Ki of 13.9 nM using full-length Balc448 and 42.1 nM using a truncated crystallizable form of light chain (Balc424). Co-crystallization of CPI-1 with Balc424 revealed that in the Balc-CPI-1 complex, the inhibitor adopts a helical conformation, occupies a high percentage of the active site cavity and interacts in an amphipathic manner with critical active site residues. The data suggest that CPI-1 prevents SNAP-25 from accessing the Balc active site by blocking both the substrate binding path at the surface and the Zn2+ binding region involved in catalysis. This is in contrast to linear peptide inhibitors described to date which block only the latter« less

  12. TRANSMISSION ELECTRON MICROSCOPY OF THE TEXTURED SILVER BACK REFLECTOR OF A THIN FILM SILICON SOLAR CELL: FROM CRYSTALLOGRAPHY TO OPTICAL ABSORPTION

    E-Print Network [OSTI]

    Dunin-Borkowski, Rafal E.

    in amorphous, microcrystalline and micromorph thin-film Si solar cells is an important and active field-reflector of thin-film Si solar cells. 1 INTRODUCTION The study of light trapping in thin-film Si solar cells for an optimized back reflector structure in a microcrystalline thin film Si solar cell, when compared with the use

  13. A Spring-Loaded State of NusG in Its Functional Cycle Is Suggested by X-ray Crystallography and Supported by Site-Directed Mutants

    E-Print Network [OSTI]

    [Steiner, T., Kaiser, J. T., Marinkovic, S., Huber, R., and Wahl, M. C. (2002) EMBO J. 21, 4641-4653]. We

  14. Improving experimental phases for strong reflections prior to density modification

    SciTech Connect (OSTI)

    Uervirojnangkoorn, Monarin [University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck (Germany); University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck (Germany); Hilgenfeld, Rolf, E-mail: hilgenfeld@biochem.uni-luebeck.de [University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck (Germany); Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, People’s Republic of (China); Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Read, Randy J. [University of Cambridge, Cambridge CB2 0XY (United Kingdom); University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck (Germany)

    2013-10-01

    A genetic algorithm has been developed to optimize the phases of the strongest reflections in SIR/SAD data. This is shown to facilitate density modification and model building in several test cases. Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005 ?), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. A computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.

  15. Learning Unbiased Features Yujia Li, Kevin Swersky, Richard Zemel

    E-Print Network [OSTI]

    Toronto, University of

    that are invariant to certain task irrelevant biases in the data. Multi-Distribution MMD 1 N NX n=1 (Xn) 1 M MX m=1 (Ym) 2 = 1 N2 NX n=1 NX n0=1 (Xn)> (Xn0 ) + 1 M2 MX m=1 MX m0=1 (Ym)> (Ym0 ) 2 NM NX n=1 MX m=1 (Xn)> (Ym) = 1 N2 NX n=1 NX n0=1 k(Xn, Xn0 ) + 1 M2 MX m=1 MX m0=1 k(Ym, Ym0 ) 2 MN NX n=1 NX m=1 k(Xn, Ym

  16. Applications of Geometry Processing CudaHull: Fast parallel 3D convex hull on the GPU

    E-Print Network [OSTI]

    El-Sana, Jihad

    detection, crystallography, metallurgy, carto- graphy, image processing, sphere packing, and point location

  17. Automated MAD and MIR structure solution

    SciTech Connect (OSTI)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Berendzen, Joel [Biophysics Group, Mail Stop D454, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    1999-04-01

    A fully automated procedure for solving MIR and MAD structures has been developed using a scoring scheme to convert the structure-solution process into an optimization problem. Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

  18. Covering complete proteomes with X-ray structures: A current snapshot

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-10-23

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtainedmore »through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.« less

  19. Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data

    SciTech Connect (OSTI)

    Dworkowski, Florian S. N.; Hough, Michael A.; Pompidor, Guillaume

    2015-01-01

    The particular challenge of the analysis of optical absorption and Raman spectroscopic data measured from protein crystals and how the SLS-APE software toolbox supports scientists in dealing with such data is described. Combining macromolecular crystallography with in crystallo micro-spectrophotometry yields valuable complementary information on the sample, including the redox states of metal cofactors, the identification of bound ligands and the onset and strength of undesired photochemistry, also known as radiation damage. However, the analysis and processing of the resulting data differs significantly from the approaches used for solution spectrophotometric data. The varying size and shape of the sample, together with the suboptimal sample environment, the lack of proper reference signals and the general influence of the X-ray beam on the sample have to be considered and carefully corrected for. In the present article, how to characterize and treat these sample-dependent artefacts in a reproducible manner is discussed and the SLS-APEin situ, in crystallo optical spectroscopy data-analysis toolbox is demonstrated.

  20. Covering complete proteomes with X-ray structures: A current snapshot

    SciTech Connect (OSTI)

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-10-23

    Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

  1. OR x

    E-Print Network [OSTI]

    1910-20-31

    A. Undamped Free Vibrations : mx ... C. Forced Vibrations : (F(t) = F0 cos?t or F(t) = F0 sin ?t, for example). (i) mx ... (Draw a picture to help with the analysis.).

  2. Universit Bordeaux 1 Les Sciences et les Technologies au service de l'Homme et de l'environnement

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    polyurethanes through ADMET polymerization in bulk and green solvent, 2013, Macromolecular Rapid Communications

  3. Narutoshi Nakata and Erin Krug Department of Civil Engineering

    E-Print Network [OSTI]

    Table Test Hybrid Test xg Effective Force Test x f = -mxg mx+cx+ R x( )= -mxg Eq. of Motion: Eq. of Motion: Eq. of Motion: mx+cx+ R x( )= -mxg mx+cx+ R x( )= -mxg #12;Comparison of Experimental Methods Shake Table Test Hybrid Test xg Effective Force Test x f = -mxg mx+cx+ R x( )= -mxg Eq. of Motion: Eq

  4. Land use/land cover change dynamics and drivers in a low-grade marginal coffee growing region of Veracruz, Mexico

    E-Print Network [OSTI]

    Ellis, Edward A.; Baerenklau, Kenneth A.; Marcos-Martínez, Raymundo; Chávez, Edgar

    2010-01-01

    Mexico (2007) Indice Nacional de Precios al Con- sumidor Agropecuarios. http://www.banxico.gob.mx/Sie Internet/

  5. DEPARTAMENTO DE ECOLOGA HUMANA

    E-Print Network [OSTI]

    @mda.cinvestav.mx María Teresa Castillo Burguete. Investigadora Adjunta. Maestra en Desa- rrollo Rural (1989) UAM-Xochimilco

  6. DIRECTORIO DE EXTENSIONES TELEFONICAS NUMERO CONMUTADOR: 942-94-00

    E-Print Network [OSTI]

    LOPEZ, Javier, C.P. INVENTARIO 2580 jdiaz@mda.cinvestav.mx A GONZALEZ COELLO, Bertha COMPRAS 9404 (999@mda.cinvestav.mx A CEBALLOS PEON, Gabriel, C.P. PROYECTOS 2366 gabriel@mda.cinvestav.mx A SOSA Y BRACAMONTE, Socorro 2202 soco

  7. 30 de enero 2012 ESTADO SLIDO

    E-Print Network [OSTI]

    Noguez, Cecilia

    hrs, Jueves de 16 a 18 hrs. Página web con información y tareas http://www.fisica.unam.mx/cecilia/teaching del edificio principal Email: cecilia@fisica.unam.mx Aydante: M.C. Francisco Hidalgo Moreno Instituto de Física UNAM Oficina 61 del edificio principal Email: hidalgo@fisica.unam.mx Lunes y Martes 13 a 15

  8. Performance optimization of mobile WiMAX netwoks for VoIP streams

    E-Print Network [OSTI]

    Gomez-Castellanos, Javier

    -I, 09340 - Mexico City milo@xanum.uam.mx Abstract-- Supporting as many VoIP (Voice over Internet Protocol. Department of Telecommunications UNAM, Mexico City {lortiz, victor, javierg}@fi-b.unam.mx R. Santos School of Telematics UCOL, Colima, Mexico aquinor@ucol.mx M. Lopez-Guerrero Department of Electrical Engineering UAM

  9. Physics 742 Graduate Quantum Mechanics 2 Midterm Exam, Spring 2015

    E-Print Network [OSTI]

    Anderson, Paul R.

    , cos 0, sin 0 even sin sin cos cos , 2 2 odd, sin cos 0 even sin a a a a nm a a n nnx nx dx dx a a n nx mx nx mx a dx dx a a a a an n m n mnx mx dx a a n m , , , 0 , , ,0 sin cos 4 cos cos cos 4 a n m p m n p p n m a n m p m n p p n m nx mx px a dx a a a nx mx

  10. Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

    SciTech Connect (OSTI)

    Opalka, N.; Brown, J; Lane, W; Twist, K; Landick, R; Asturias, F; Darst, S

    2010-01-01

    The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program. Transcription, or the synthesis of RNA from DNA, is one of the most important processes in the cell. The central enzyme of transcription is the DNA-dependent RNA polymerase (RNAP), a large, macromolecular assembly consisting of at least five subunits. Historically, much of our fundamental information on the process of transcription has come from genetic and biochemical studies of RNAP from the model bacterium Escherichia coli. More recently, major breakthroughs in our understanding of the mechanism of action of RNAP have come from high resolution crystal structures of various bacterial, archaebacterial, and eukaryotic enzymes. However, all of our high-resolution bacterial RNAP structures are of enzymes from the thermophiles Thermus aquaticus or T. thermophilus, organisms with poorly characterized transcription systems. It has thus far proven impossible to obtain a high-resolution structure of E. coli RNAP, which has made it difficult to relate the large collection of genetic and biochemical data on RNAP function directly to the available structural information. Here, we used a combination of approaches - high-resolution X-ray crystallography of E. coli RNAP fragments, ab initio structure prediction, homology modeling, and single-particle cryo-electron microscopy - to generate complete atomic models of E. coli RNAP. Our detailed and comprehensive structural models provide the heretofore missing structural framework for understanding the function of the highly characterized E. coli RNAP.

  11. Communications to the Editor Bull. Korean Chem. Soc. 2001, Vol. 22, No. 3 261 Novel Macromolecular Self-organization of Poly(ethylene glycol)-block-poly(L-histidine)

    E-Print Network [OSTI]

    Park, Jong-Sang

    -group protected bio- degradable poly(amino acid) chain have potential utility as drug delivery systems.6(L-histidine), which is a bio- degradable polypeptide10 and thought to possess an am- photeric nature due by repeated liquid phase peptide synthesis using fluoren-9-ylmethoxycarbonyl (Fmoc) chem- istry.13 m

  12. Membrane Protein Crystallization in Lipidic Mesophases. Hosting...

    Office of Scientific and Technical Information (OSTI)

    CATIONS; CRYSTALLIZATION; CRYSTALLOGRAPHY; CRYSTALS; HOST; LIPIDS; MEMBRANE PROTEINS; MEMBRANES; NUCLEAR MAGNETIC RESONANCE; PEPTIDES; RANGE; SHAPE; SIZE Word Cloud More...

  13. 391st Brookhaven Lecture

    ScienceCinema (OSTI)

    Bob Sweet

    2010-09-01

    A description of how crystallography methods work and how several results obtained using the NSLS have impacted biological science.

  14. Crystallography and Physical Properties of BaCo2As2, Ba0.94K0.06Co2As2, and Ba0.78K0.22Co2As2

    SciTech Connect (OSTI)

    Anand, V K; Quirinale, Dante G; Lee, Yongbin; Harmon, Bruce N; Furukawa, Yuji; Ogloblichev, V V; Huq, A; Abernathy, D L; Stephens, P W; McQueeney, Robert J; Kreyssig, Aandreas; Goldman, Alan I; Johnston, David C

    2014-08-01

    The crystallographic and physical properties of polycrystalline and single crystal samples of BaCo2As2 and K-doped Ba{1-x}K{x}Co2As2 (x = 0.06, 0.22) are investigated by x-ray and neutron powder diffraction, magnetic susceptibility chi, magnetization, heat capacity Cp, {75}As NMR and electrical resistivity rho measurements versus temperature T. The crystals were grown using both Sn flux and CoAs self-flux, where the Sn-grown crystals contain 1.6-2.0 mol% Sn. All samples crystallize in the tetragonal ThCr2Si2-type structure (space group I4/mmm). For BaCo2As2, powder neutron diffraction data show that the c-axis lattice parameter exhibits anomalous negative thermal expansion from 10 to 300 K, whereas the a-axis lattice parameter and the unit cell volume show normal positive thermal expansion over this T range. No transitions in BaCo2As2 were found in this T range from any of the measurements. Below 40-50 K, we find rho ~ T^2 indicating a Fermi liquid ground state. A large density of states at the Fermi energy D(EF) ~ 18 states/(eV f.u.) for both spin directions is found from low-T Cp(T) measurements, whereas the band structure calculations give D(EF) = 8.23 states/(eV f.u.). The {75}As NMR shift data versus T have the same T dependence as the chi(T) data, demonstrating that the derived chi(T) data are intrinsic. The observed {75}As nuclear spin dynamics are consistent with the presence of ferromagnetic and/or stripe-type antiferromagnetic spin fluctuations. The crystals of Ba{0.78}K{0.22}Co2As2 were grown in Sn flux and show properties very similar to those of undoped BaCo2As2. On the other hand, the crystals from two batches of Ba{0.94}K{0.06}Co2As2 grown in CoAs self-flux show evidence of weak ferromagnetism at T < 10 K with small ordered moments at 1.8 K of 0.007 and 0.03 muB per formula unit, respectively.

  15. Covering complete proteomes with X-ray structures: a current snapshot

    SciTech Connect (OSTI)

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-11-01

    The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins. Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

  16. Protein Characterisation by Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy

    SciTech Connect (OSTI)

    Wallace, B.

    2009-01-01

    Circular dichroism (CD) spectroscopy is a well-established technique for the study of proteins. Synchrotron radiation circular dichroism (SRCD) spectroscopy extends the utility of conventional CD spectroscopy (i.e. using laboratory-based instruments) because the high light flux from a synchrotron enables collection of data to lower wavelengths, detection of spectra with higher signal-to-noise levels and measurements in the presence of strongly absorbing non-chiral components such as salts, buffers, lipids and detergents. This review describes developments in instrumentation, methodologies and bioinformatics that have enabled new applications of the SRCD technique for the study of proteins. It includes examples of the use of SRCD spectroscopy for providing static and dynamic structural information on molecules, including determinations of secondary structures of intact proteins and domains, assessment of protein stability, detection of conformational changes associated with ligand and drug binding, monitoring of environmental effects, examination of the processes of protein folding and membrane insertion, comparisons of mutant and modified proteins, identification of intermolecular interactions and complex formation, determination of the dispositions of proteins in membranes, identification of natively disordered proteins and their binding partners and examination of the carbohydrate components of glycoproteins. It also discusses how SRCD can be used in conjunction with macromolecular crystallography and other biophysical techniques to provide a more complete picture of protein structures and functions, including how proteins interact with other macromolecules and ligands. This review also includes a discussion of potential new applications in structural and functional genomics using SRCD spectroscopy and future instrumentation and bioinformatics developments that will enable such studies. Finally, the appendix describes a number of computational/bioinformatics resources for secondary structure analyses that take advantage of the improved data quality available from SRCD. In summary, this review discusses how SRCD can be used for a wide range of structural and functional studies of proteins.

  17. Structure of acostatin, a dimeric disintegrin from Southern copperhead (Agkistrodon contortrix contortrix), at 1.7 Å resolution

    SciTech Connect (OSTI)

    Moiseeva, Natalia [National Synchrotron Light Source, Brookhaven National Laboratory, Building 725D, Upton, NY 11973 (United States); Bau, Robert, E-mail: bau@usc.edu [Chemistry Department, University of Southern California, Los Angeles, CA 90089 (United States); Swenson, Stephen D.; Markland, Francis S. Jr [Department of Biochemistry and Molecular Biology and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033 (United States); Choe, Jun-Yong [Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute/California Institute of Technology, Pasadena, CA 91125 (United States); Liu, Zhi-Jie [Departments of Biochemistry and Molecular Biology and Chemistry, University of Georgia, Athens, GA 30602 (United States); Allaire, Marc, E-mail: bau@usc.edu [National Synchrotron Light Source, Brookhaven National Laboratory, Building 725D, Upton, NY 11973 (United States)

    2008-04-01

    Two acostatin heterodimers interact together to form an ???? tetramer. Disintegrins are a family of small (4–14 kDa) proteins that bind to another class of proteins, integrins. Therefore, as integrin inhibitors, they can be exploited as anticancer and antiplatelet agents. Acostatin, an ?? heterodimeric disintegrin, has been isolated from the venom of Southern copperhead (Agkistrodon contortrix contortrix). The three-dimensional structure of acostatin has been determined by macromolecular crystallography using the molecular-replacement method. The asymmetric unit of the acostatin crystals consists of two heterodimers. The structure has been refined to an R{sub work} and R{sub free} of 18.6% and 21.5%, respectively, using all data in the 20–1.7 Å resolution range. The structure of all subunits is similar and is well ordered into N-terminal and C-terminal clusters with four intramolecular disulfide bonds. The overall fold consists of short ?-sheets, each of which is formed by a pair of antiparallel ?-strands connected by ?-turns and flexible loops of different lengths. Conformational flexibility is found in the RGD loops and in the C-terminal segment. The interaction of two N-terminal clusters via two intermolecular disulfide bridges anchors the ?? chains of the acostatin dimers. The C-terminal clusters of the heterodimer project in opposite directions and form a larger angle between them in comparison with other dimeric disintegrins. Extensive interactions are observed between two heterodimers, revealing an ???? acostatin tetramer. Further experiments are required to identify whether the ???? acostatin complex plays a functional role in vivo.

  18. Structure of Acostatin, a Dimeric Disintegrin From Southern Copperhead (Agkistrodon Contortrix Contortrix), at 1.7 Angstrom Resolution

    SciTech Connect (OSTI)

    Moiseeva, N.; Bau, R.; Swenson, S.D.; Marklund, F.S.; Jr.; Choe, J.-Y.; Liu, Z.-J.; Allaire, M.

    2009-05-26

    Disintegrins are a family of small (4-14 kDa) proteins that bind to another class of proteins, integrins. Therefore, as integrin inhibitors, they can be exploited as anticancer and antiplatelet agents. Acostatin, an {alpha}{beta} heterodimeric disintegrin, has been isolated from the venom of Southern copperhead (Agkistrodon contortrix contortrix). The three-dimensional structure of acostatin has been determined by macromolecular crystallography using the molecular-replacement method. The asymmetric unit of the acostatin crystals consists of two heterodimers. The structure has been refined to an R{sub work} and R{sub free} of 18.6% and 21.5%, respectively, using all data in the 20-1.7 {angstrom} resolution range. The structure of all subunits is similar and is well ordered into N-terminal and C-terminal clusters with four intramolecular disulfide bonds. The overall fold consists of short {beta}-sheets, each of which is formed by a pair of antiparallel {beta}-strands connected by {beta}-turns and flexible loops of different lengths. Conformational flexibility is found in the RGD loops and in the C-terminal segment. The interaction of two N-terminal clusters via two intermolecular disulfide bridges anchors the {alpha}{beta}chains of the acostatin dimers. The C-terminal clusters of the heterodimer project in opposite directions and form a larger angle between them in comparison with other dimeric disintegrins. Extensive interactions are observed between two heterodimers, revealing an {alpha}{beta}{beta}{alpha} acostatin tetramer. Further experiments are required to identify whether the {alpha}{beta}{beta}{alpha} acostatin complex plays a functional role in vivo.

  19. CrowdPhase: crowdsourcing the phase problem

    SciTech Connect (OSTI)

    Jorda, Julien; Sawaya, Michael R. [Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095 (United States); Yeates, Todd O., E-mail: yeates@mbi.ucla.edu [Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095 (United States); Molecular Biology Institute, 611 Charles Young Drive East, Los Angeles, CA 90095 (United States); University of California, 611 Charles Young Drive East, Los Angeles, CA 90095 (United States)

    2014-06-01

    The idea of attacking the phase problem by crowdsourcing is introduced. Using an interactive, multi-player, web-based system, participants work simultaneously to select phase sets that correspond to better electron-density maps in order to solve low-resolution phasing problems. The human mind innately excels at some complex tasks that are difficult to solve using computers alone. For complex problems amenable to parallelization, strategies can be developed to exploit human intelligence in a collective form: such approaches are sometimes referred to as ‘crowdsourcing’. Here, a first attempt at a crowdsourced approach for low-resolution ab initio phasing in macromolecular crystallography is proposed. A collaborative online game named CrowdPhase was designed, which relies on a human-powered genetic algorithm, where players control the selection mechanism during the evolutionary process. The algorithm starts from a population of ‘individuals’, each with a random genetic makeup, in this case a map prepared from a random set of phases, and tries to cause the population to evolve towards individuals with better phases based on Darwinian survival of the fittest. Players apply their pattern-recognition capabilities to evaluate the electron-density maps generated from these sets of phases and to select the fittest individuals. A user-friendly interface, a training stage and a competitive scoring system foster a network of well trained players who can guide the genetic algorithm towards better solutions from generation to generation via gameplay. CrowdPhase was applied to two synthetic low-resolution phasing puzzles and it was shown that players could successfully obtain phase sets in the 30° phase error range and corresponding molecular envelopes showing agreement with the low-resolution models. The successful preliminary studies suggest that with further development the crowdsourcing approach could fill a gap in current crystallographic methods by making it possible to extract meaningful information in cases where limited resolution might otherwise prevent initial phasing.

  20. STUDY PROGRAM Advanced Modules

    E-Print Network [OSTI]

    Ullmann, G. Matthias

    Biomacromolecules Biochemistry Microbiology Polymer Engineering and Technology Theory and Simulation Elite Study Macromolecular Science supports the most talented students in chemistry, bio- chemistry, polymer and colloid chemistry, polymer engineering, physics, biophysics and biology. Macromolecular Science is an accom- panying

  1. Materials Characterization | Advanced Materials | ORNL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Electron Microscopy X-ray Scattering Neutron Scattering Mechanical Properties Thermal Optical Spectroscopy Nuclear Magnetic Resonance Macromolecular Characterization Nuclear...

  2. Beamline 5.3.2.2

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    size at sample (FWHM) 25 nm (theoretical), 31 nm actual Scientific applications Photovoltaics, thin films, macromolecular chemistry, geology, cosmological chemistry,...

  3. Full Solutions to MATH 421(1), Fall 2014, Dr. Z.'s FINAL EXAM, Mon., Dec. 22, 2014, 8:00-11:00pm, SEC 212

    E-Print Network [OSTI]

    Zeilberger, Doron

    cos + 8 r5 sin 5 #12;2. (15 points altogether) (a) (8 pts.) Show that the set of functions {cos(nx. Ans. to (b): || cos(nx)|| = 2 2 Sol. to a: We must use the trig-identity: cos A cos B = 1 2 (cos(A + B) + cos(A - B)) . If m = n: (cos mx, cos nx) = 1 0 cos mx cos nx = 1 2 1 0 (cos(mx + nx) + cos

  4. Atividade DE DE ExP Est proj mon ic ext PET eJr PartEvtapEvtorgEvtcurProfrepAcadofDidporgInstvoluntCultArt Cert Carga Mx. Validvel 60 30 60 60 60 60 60 60 60 60 30 10 12 60 10 12 12 12 12 60

    E-Print Network [OSTI]

    Paraná, Universidade Federal do

    Oliveira Costa 4 4 22 Artur Victor Marino 12 12 23 Barbara N Rodrigues 2 2 24 Bruna de Miranda da Silva 60 Isabelle Cavalcanti Baroni 60 2 24 86 136 Jeovane Honório Alves 60 60 30 4 12 6 12 184 137 Jéssika de Paulo Leduc Braciak 0 146 João Pedro Fabricio de Meira Albach 4 12 12 28 148 Jonasta S 0 149 Jose A F

  5. A N U A R I O C I N V E S T A V 441 ELECTRNICADELESTADOSLIDO

    E-Print Network [OSTI]

    Ciencias de la Computación, orientada hacia el diseño de sistemas y procesos electromecánicos inteligentes investigación: Instrumentación Biomédica y Manufactura Moderna fruiz@cinvestav.mx GERARDO SILVA NAVARRO

  6. Hydrogen, Hydrocarbons, and Bioproduct Precursors from Wastewaters...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of Colorado Boulder Anaerobic MBR: Challenges and Opportunities, Art Umble, MWH Americas Microbial Fuel Cell Technologies-MxCs: Can They Scale? Bruce Logan, Penn State University...

  7. COMPUTATION OF COVARIANCE MATRICES FOR CONSTRAINED PARAMETER ESTIMATION PROBLEMS

    E-Print Network [OSTI]

    Stanford University

    f1(x) 2 2 s.t. f2(x) = 0, (1.1) where f1(x) is a vector of weighted residuals for a model of the form i = M(xtrue, ti) + i, i = 1, . . . , m1. (1.2) Thus, f1(x) = (1 - M(x, t1))/ ... (m1 - M(x, tm1 ))/ , f1(x) 2 2 := m1 i=1 (i - M(x, ti))2 2 . (1.3) The model M(x, t) R that describes the parameter

  8. Interpreted Applications within BOINC Infrastructure

    E-Print Network [OSTI]

    Fernandez, Thomas

    @cicese.mx 3 Ceta-Ciemat miguel.cardenas@ciemat.es 4 UNED lurdes@lsi.uned.es 5 University of Granada pedro

  9. Facolt di Architettura e Societ anno accademico 2012/2013 Attenzione! Controllare i corsi di laurea di riferimento

    E-Print Network [OSTI]

    Bahia (architettura specialistica) www.portal.ufba.br Dorigati 3 Universidade Federal de Santa (architettura specialistica) www.itesm.mx Molon 4 RUSSIA Moscow Institute of Architecture (architettura

  10. Institut fur Analysis und Scientific Computing TU Wien E. Weinmuller SS 2013

    E-Print Network [OSTI]

    Weinmüller, Ewa B.

    {en}nN definiert durch en(x) = 1 sin(nx). a) ¨Uberpr¨ufen Sie ob {en}nN tats¨achlich ein¨ur n 1 gilt en, en = 1 - sin(nx) sin(nx)dx = 1 2 - (1 - cos(2nx))dx = 1 2 2 = 1. F¨ur n = m haben wir en, em = 1 - sin(nx) sin(mx)dx = 1 2 - (cos(nx - mx) - cos(nx + mx))dx = 1 2 ( sin(nx-mx) n

  11. Project 1: Fourier coefficients Due: /////////////Wednesday,////////////September//8 Tuesday, September 14

    E-Print Network [OSTI]

    Achter, Jeff

    a function, we can try to approximate it as a sum of functions like sin(mx) and cos(nx). If f (x) and g the text (page 585): sin(mx) sin(nx) = 1 2 (cos((m - n)x) - cos((m + n)x)) (1) sin(mx) cos(nx) = 1 2 (sin((m - n)x) + sin((m + n)x)) (2) cos(mx) cos(nx) = 1 2 (cos((m - n)x) + cos((m + n)x)) (3) (a) Using

  12. Prof. Dr. H. Konig Ubungen zu "Analysis II" SS 2009 (a) Seien n, m N . Man zeige

    E-Print Network [OSTI]

    König, Hermann

    zeige: 1 2 0 sin(nx) sin(mx) dx = 1 2 0 cos(nx) cos(mx) dx = nm 1 2 0 sin(nx) cos(mx) dx = 0 , nm definiert durch f(x) := a0 2 + n=1 (an cos(nx) + bn sin(nx)) , x [0, 2]. Zeige f¨ur n N0 , m N an = 1 2 0 f(x) cos(nx) dx, bm = 1 2 0 f(x) sin(mx) dx. Aufgabe 27 Sei > 0 , x = (xi)n i=1 Kn und U := y

  13. Application to Export Electric Energy OE Docket No. EA-405 Del...

    Broader source: Energy.gov (indexed) [DOE]

    Del Norte Energy (MX).pdf More Documents & Publications Application to Export Electric Energy OE Docket No. EA-406 Sempra Generation, LLC: Federal Register Notice, Volume 80, No....

  14. MANUAL DE PROCEDIMIENTOS DEL DEPARTAMENTO DE BIOTECNOLOGIA Y BIOINGENIERIA. DISPOSICIONES GENERALES

    E-Print Network [OSTI]

    1 MANUAL DE PROCEDIMIENTOS DEL DEPARTAMENTO DE BIOTECNOLOGIA Y BIOINGENIERIA. DISPOSICIONES del Departamento (http://biotecnologia.cinvestav.mx) CAPITULO I 2.- Para los propósitos de este Manual

  15. A N U A R I O C I N V E S T A V780 DEPARTAMENTO DE ECOLOGA HUMANA

    E-Print Network [OSTI]

    el diseño y operación de sistemas de ahorro y crédito para los pobres. cuanalo@mda.cinvestav.mx BETTY

  16. Application to Export Electric Energy OE Docket No. EA-390 Global...

    Broader source: Energy.gov (indexed) [DOE]

    Global Pure Energy to export electric energy to Mexico. Federal Register Notice. EA-390 Global Pure Energy (MX).pdf More Documents & Publications Application to Export Electric...

  17. Acoustic inverse scattering via Helmholtz operator factorization and ...

    E-Print Network [OSTI]

    Shen Wang

    2010-09-01

    Aug 2, 2010 ... ces are usually fast, such as linear complexity matrix multiplications and system solutions. ..... Helmholtz equation problems, the condition number of this M(x) ..... [

  18. Propuesta de Seminario Agentes racionales y Aprendizaje

    E-Print Network [OSTI]

    Guerra Hernández, Alejandro

    Sebasti´an Camacho No 5, Xalapa, Ver., M´exico 91000 aguerra@uv.mx www.uv.mx/aguerra 9 de febrero de 2011 Logic in Multi-Agent Systems: 4th International Workshop, CLIMA IV, Fort Lauderdale, FL, USA, January 6

  19. Feature Selection on the Web People Search David Pinto, Mireya Tovar, Beatriz Beltran, Darnes Vilari~no, Hector Furlog

    E-Print Network [OSTI]

    Pinto, David Eduardo

    Puebla, Mexico, 72570 {dpinto, mtovar, bbeltran, darnes}@cs.buap.mx http://nlp.cs.buap.mx Abstract. Searching people on the Web is one of the most common ac- tivities carried out by Internet users. However that the user is searching people on Internet and, therefore, it brings together all the results (people

  20. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    & superfluidity(75) (1) crystallography (1) diffraction (1) electron correlation (1) harmonic generation (1) instrumentation related to nuclear science and technology (1) light...

  1. Two-Stage Robotic Crystal Mounting of Protein Crystals for X-Ray Data Collection

    E-Print Network [OSTI]

    Georgiev, Atanas

    Beamline Mounting Freezing Fig. 1. A simplified crystallography pipeline. The top row shows a basic outline it into a cryoprotecting liquid, cryogenically fre

  2. Taking snapshots of different redox states of the water oxidation...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    laser has achieved an important milestone in understanding the photosynthetic water oxidation catalytic process. Using femtosecond X-ray crystallography combined with laser...

  3. Giant Protease TPP II's Structure, Mechanism Uncovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Lab, the University of California, Berkeley, and the Max Planck Institute of Biochemistry combined single-particle cryo-electron microscopy and x-ray crystallography at ALS...

  4. SSRLUO 2012 Executive Committee Members | Stanford Synchrotron...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    at SSRL since 1986, and has managed the administration of protein crystallography experiments since 2000. Lisa earned her Bachelor of Science degree from San Jose State...

  5. SSRLUO 2011 Executive Committee Members | Stanford Synchrotron...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    at SSRL since 1986, and has managed the administration of protein crystallography experiments since 2000. Lisa earned her Bachelor of Science degree from San Jose State...

  6. De novo protein crystal structure determination from X-ray free-electron laser data

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Barends, Thomas, R.M.

    Serial femtosecond crystallography (SFX) data of microcrystals of a lysozyme gadolinium derivative. The data was used to demonstrate de-novo phasing by single anomalous dispersion.

  7. De novo protein crystal structure determination from X-ray free-electron laser data

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Barends, Thomas, R.M.

    2013-11-25

    Serial femtosecond crystallography (SFX) data of microcrystals of a lysozyme gadolinium derivative. The data was used to demonstrate de-novo phasing by single anomalous dispersion.

  8. Structure of the Kinase Domain of CaMKII and Modeling the Holoenzyme

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A group from the University of California, Berkeley, the Yale University School of Medicine, and Berkeley Lab has combined protein crystallography and small-angle x-ray...

  9. The atomic structure of the cleaved Si(111)-(2x1) surface refined by dynamical LEED

    E-Print Network [OSTI]

    2004-01-01

    Surface Crystallography by LEED”, p.30, Spinger-Verlag, Bby automated tensor LEED (the number of optimized parametersSurface Refined by Dynamical LEED Geng Xu, Bingcheng Deng,*

  10. Studies of Chemisorption with the Scanning Tunneling Microscope

    E-Print Network [OSTI]

    Salmeron, E.M.

    2012-01-01

    Tong, Surfilce Crystallography by LEED. Springer Series inmostly with low energy electron diffraction (LEED) [2].LEED, as all diffraction techniques, is sensitive to the

  11. Major Successes of Theory-and-Experiment-Combined Studies in Surface Chemistry and Heterogeneous Catalysis

    E-Print Network [OSTI]

    Somorjai, Gabor A.; Li, Yimin

    2010-01-01

    sensitive techniques such as LEED, XPS, AES, ISS and SIMS,crystallography [2, 3] (LEED) to high resolution electronincluding the development of LEED surface crystal- lography,

  12. National synchrotron light source. Activity report, October 1, 1995--September 30, 1996

    SciTech Connect (OSTI)

    Rothman, E.Z.; Hastings, J.B.

    1997-05-01

    The hard work done by the synchrotron radiation community, in collaboration with all those using large-scale central facilities during 1995, paid off in FY 1996 through the DOE`s Presidential Scientific Facilities Initiative. In comparison with the other DOE synchrotron radiation facilities, the National Synchrotron Light Source benefited least in operating budgets because it was unable to increase running time beyond 100%-nevertheless, the number of station hours was maintained. The major thrust at Brookhaven came from a 15% increase in budget which allowed the recruitment of seven staff in the beamlines support group and permitted a step increment in the funding of the extremely long list of upgrades; both to the sources and to the beamlines. During the December 1995 shutdown, the VUV Ring quadrant around U10-U12 was totally reconstructed. New front ends, enabling apertures up to 90 mrad on U10 and U12, were installed. During the year new PRTs were in formation for the infrared beamlines, encouraged by the investment the lab was able to commit from the initiative funds and by awards from the Scientific Facilities Initiative. A new PRT, specifically for small and wide angle x-ray scattering from polymers, will start work on X27C in FY 1997 and existing PRTs on X26C and X9B working on macromolecular crystallography will be joined by new members. Plans to replace aging radio frequency cavities by an improved design, originally a painfully slow six or eight year project, were brought forward so that the first pair of cavities (half of the project for the X-Ray Ring) will now be installed in FY 1997. Current upgrades to 350 mA initially and to 438 mA later in the X-Ray Ring were set aside due to lack of funds for the necessary thermally robust beryllium windows. The Scientific Facilities Initiative allowed purchase of all 34 windows in FY 1996 so that the power upgrade will be achieved in FY 1997.

  13. Two-Dimensional Self-Assembly in Diblock Copolymers

    E-Print Network [OSTI]

    Hosoi, A.E.

    2005-06-20

    Diblock copolymers confined to a two-dimensional surface may produce uniform features of macromolecular dimensions (10 â?? 100 nm). We present a mathematical model for nanoscale pattern

  14. Research Institute of Micro/Nanometer Science & Technology Multiple Openings : Chemistry, Materials Science, Nanotechnology

    E-Print Network [OSTI]

    Alpay, S. Pamir

    Science, Nanotechnology Shanghai, China We have several job openings for experienced polymer chemists / nanotechnology. We will consider hiring chemists who are skillful in macromolecular synthesis ("click chemistry

  15. Software News and Updates SHARPEN--Systematic Hierarchical Algorithms for

    E-Print Network [OSTI]

    Snow, Christopher

    Software News and Updates SHARPEN--Systematic Hierarchical Algorithms for Rotamers and Proteins benefits over existing software. We discuss CHOMP, a new object-oriented library for macromolecular

  16. Reversible CO2 absorption by the 6H perovskite Ba4Sb2O9 Matthew T. Dunstan,1 Wen Liu,2 Adriano F. Pavan,3 Justin A. Kimpton,4

    E-Print Network [OSTI]

    Jackson, Sophie

    O CO2 concentrated 900- 930°C CaCO3 (F0, fresh sorbent) CaO (purge) Existing power plant Hin CaO (FCa- 930°C CaCO3 (F0, fresh sorbent) CaO (purge) Existing power plant Hin CaO (FCaO) MxO + CO2 MxCO3 MxCO3 Synchrotron, performed under flowing CO2 using a capillary gas-flow cell. We were able to show that we

  17. Institut fur Analysis und Scientific Computing TU Wien E. Weinmuller SS 2013

    E-Print Network [OSTI]

    Weinmüller, Ewa B.

    := - f(x)g(x)dx. Weiters sei ein Orthonormalsystem {en}nN{0} definiert durch en(x) = 1 cos(nx), n N, e0 - cos(nx) cos(nx)dx = 1 2 - (cos(2nx) + 1)dx = 1 2 2 = 1, e0, e0 = 1 2 - 1dx = 1 2 2 = 1. F¨ur n = m und n, m = 0 haben wir en, em = 1 - cos(nx) cos(mx)dx = 1 2 - (cos(nx + mx) + cos(nx - mx))dx = 1

  18. Fourier Series [Constanda, pp. 1127] Motivation. Suppose f is a smooth function (all derivatives exist). Set

    E-Print Network [OSTI]

    Wirosoetisno, Djoko

    , if there are coefficients {an} and {bn} such that f(x) can be written as f(x) = a0 + n=1 an cos nx L + bn sin nx L =: S: L -L cos mx L cos nx L dx = 0 if m = n L if m = n = 0 2L if m = n = 0 (4.2) L -L sin mx L sin nx L dx = 0 if m = n, or m = n = 0 L if m = n = 0 (4.3) L -L sin mx L cos nx L dx = 0 (4.4) 36 #12

  19. Prof. Dr. H. Konig SS 2013 Ubungen zur Analysis II

    E-Print Network [OSTI]

    König, Hermann

    ) Seien n, m N . Man zeige: 1 2 0 sin(nx) sin(mx) dx = 1 2 0 cos(nx) cos(mx) dx = nm 1 2 0 sin(nx) cos : [0, 2] R definiert durch f(x) := a0 2 + n=1 (an cos(nx) + bn sin(nx)) , x [0, 2]. Zeige f¨ur n N0 , m N an = 1 2 0 f(x) cos(nx) dx, bm = 1 2 0 f(x) sin(mx) dx. 25. Man berechne die

  20. Inleiding PDV, eerste deeltentamen, 26-10-2007, 12.00-14.00 Geen formulebladen, geen rekenmachines. 1 punt voor elk onderdeel,

    E-Print Network [OSTI]

    Hulshof, Joost

    worden dat voor alle m, n IN met m = n - cos nx cos mx dx = - cos nx sin mx dx = - sin nx sin mx dx = 0 1. (a) Neem aan dat f(x) = a0 2 + N n=1 (an cos nx + bn sin nx), (1) met N IN en a0, . . . , aN , b1, . . . , bN IR. Laat zien dat an = 1 - f(x) cos nx dx, bn = 1 - f(x) sin nx dx. (2) (b) De

  1. Adaptive Monogenic Filtering and Normalization of ESPI Fringe Patterns

    E-Print Network [OSTI]

    Rivera, Mariano

    , Mexico. E-mail: jlm@fractal.cimat.mx J.A. Quiroga Depto. de Optica. Universidad Complutense de Madrid ·x+), where A, 0 and are constants, corrupted with a white (wide-band) noise process, a narrow band

  2. Optical NEP in Hot-Electron Nanobolometers

    E-Print Network [OSTI]

    Karasik, Boris S

    2010-01-01

    For the first time, we have measured the optical noise equivalent power (NEP) in titanium (Ti) superconducting hot-electron nanobolometers (nano-HEBs). The bolometers were 2{\\mu}mx1{\\mu}mx20nm and 1{\\mu}mx1{\\mu}mx20nm planar antenna-coupled devices. The measurements were done at {\\lambda} = 460 {\\mu}m using a cryogenic black body radiation source delivering optical power from a fraction of a femtowatt to a few 100s of femtowatts. A record low NEP = 3x10^{-19} W/Hz^{1/2} at 50 mK has been achieved. This sensitivity meets the requirements for SAFARI instrument on the SPICA telescope. The ways for further improvement of the nano-HEB detector sensitivity are discussed.

  3. SECCIN DE COMPUTACIN Personal acadmico y temas de investigacin

    E-Print Network [OSTI]

    , arquitectura de computadoras, redes de computadoras, sistemas distribuidos y lenguaje de programación de de algoritmos y arquitecturas de computadoras con dispositivos programables. Algoritmos paralelos computadoras. fraga@cs.cinvestav.mx Jorge Buenabad Chávez. Investigador Adjunto. Doctor en Ciencias (Com

  4. Fishing for Narrow Dibaryons in pd->pX Reaction

    E-Print Network [OSTI]

    L. V. Fil'kov; V. L. Kashevarov; E. S. Konobeevski; M. V. Mordovskoy; S. I. Potashev; V. A. Simonov; V. M. Skorkin; S. V. Zuev

    2000-09-15

    An analysis of experimental data, obtained at the Linear Accelerator of INR, is carried out with the aim of searching for supernarrow dibaryons in the reactions pd->p+X and pd->p+pX_1. Dibaryons with masses 1904\\pm 2, 1926\\pm 2, and 1942\\pm 2 MeV have been observed in M_{X} missing mass spectra. In M_{X_1} missing mass spectra, the peaks have been found at M_{X_1}=966\\pm 2, 986\\pm 2, and 1003\\pm 2 MeV. These values of M_{X_1} coincide with the ones obtained by a simulation of a decay of the dibaryons into \\gamma+pn. The analysis of the data obtained leads to the conclusion that the observed dibaryons are supernarrow dibaryons, the decay of which into two nucleons is forbidden by the Pauli exclusion principle. A possible interpretation of exited nucleon states with small masses is suggested.

  5. Electrochemistry, Electrocatalysis & Photoelectrocatalysis Photoelectrocatalysis

    E-Print Network [OSTI]

    Dutta, Indranath

    Electrochemistry, Electrocatalysis & Photoelectrocatalysis Photoelectrocatalysis 1. M Sun, X Ma, X." ELECTROCHEMISTRY COMMUNICATIONS. 16 (1), 26-29. 4. Song, P; Zhang, XY; Sun, MX; Cui, XL; Lin, YH. 2012. "Graphene

  6. A multi-objective approach to the design of low thrust space trajectories using optimal control

    E-Print Network [OSTI]

    -IPN, Computer Science Department, Mexico City, Mexico, schuetze@cs.cinvestav.mx 1 #12;1 Introduction Over was a solar-wind sample return mission between 2001 and 2004. The Hiten mission marked the first use of a weak

  7. Spectra and dynamics of calcium monochloride

    E-Print Network [OSTI]

    Clevenger, Jason O

    2002-01-01

    The alkaline earth monohalides (MX) represent an ideal molecule for studying molecular Rydberg states, as they are well described as by an ion-core containing two closed shell atomic ions (M2+,X-) and an unpaired electron. ...

  8. Approved by Principal Investigator: ____________________________ Date:___________ Approved by Laser Safety Officer: _____________________________ Date:___________

    E-Print Network [OSTI]

    Cohen, Ronald C.

    Hall Room B70 Coherent Genesis MX Optically Pumped Semiconductor (OPS) Laser (514 ± 3 nm) August 4 on proper safety protocol and must wear appropriate laser protective eyewear located on the premises. III

  9. SECCIN DE ELECTRNICA DEL ESTADO SLIDO

    E-Print Network [OSTI]

    ópticas y eléctricas de materia- les semiconductores. Diodos emisores de luz, transistores, MES artificiales. jmoreno@mail.cinvestav.mx Ma. de la Luz Olvera. Investigadora Titular. Doctora en Ciencias (1998

  10. Malliavin Calculus for Fractional Delay Equations

    E-Print Network [OSTI]

    2012-08-02

    Jun 7, 2010 ... Mexico e-mail: jleon@ctrl.cinvestav.mx. S. Tindel. Institut Élie Cartan Nancy, B.P. 239, 54506 Vandoeuvre-lès-Nancy Cedex, France e-mail: ...

  11. 550077 9966110011 66 7777332244 551166--22000077 FFAAXX

    E-Print Network [OSTI]

    Huang, Haimei

    @mx.nthu.edu.tw 2007 () I082 10/02() 3 Six Sigma I083 10/04() Six Sigma 10/09() I084 10/11() I085 10

  12. PHYSICAL REVIEW B 91, 115413 (2015) Simulated scanning tunneling microscopy images of few-layer phosphorus capped by graphene

    E-Print Network [OSTI]

    Tománek, David

    2015-01-01

    that of transition metal dichalcogenides (MX2s) [16]. Few-layer phosphorene bears promise for intriguing be revealed by STM imaging [46], and the main objective of this computational study is to establish whether di

  13. Cascaded Finite-State Parsing Steven Abney

    E-Print Network [OSTI]

    Abney, Steven P.

    | cdqlx) cd | (cdql | cdqlx)? cd+ cd; doll cdqlx? dol cdx; ci-st nnp+ cma place cma?; mx cdx h) ; name (nnp | nnps | i)+; #12;Noun Chunk PROPER = place | person | name | ci-st | doll; COMMON = nn

  14. A New Species of Ceratozamia (Cycadales, Zamiaceae) from Veracruz, Mexico

    E-Print Network [OSTI]

    González Astorga, Jorge Arturo - INECOL

    . *Author for correspondence: andrew.vovides@inecol.edu.mx Miguel A. Pe´rez-Farrera Escuela de Biologi´a, Universidad de Ciencias y Artes de Chiapas, Libramiento Nte. s/n, Tuxtla Gutierrez 29039, Chiapas, Mexico

  15. Mesoporous Block Copolymer Battery Separators

    E-Print Network [OSTI]

    Wong, David Tunmin

    2012-01-01

    electrode, and graphite (CGP-G8) was used as the activeMX-6). The graphite CGP-G8 used for the anode was purchasedinto coin cells. The CGP-G8 anode was prepared in the same

  16. Please cite this article in press as: Vargas-Mendoza, C. F., et al. Genetic diversity, outcrossing rate, and demographic history along a climatic gradi-ent in the ruderal plant Ruellia nudiflora (Acanthaceae). Revista Mexicana de Biodiversidad (2015), htt

    E-Print Network [OSTI]

    Herrera, Carlos M.

    2015-01-01

    (Acanthaceae). Revista Mexicana de Biodiversidad (2015), http://dx.doi.org/10.1016/j.rmb.2015.04.034 ARTICLE Biodiversidad www.ib.unam.mx/revista/ Revista Mexicana de Biodiversidad xxx (2015) xxx­xxx Evolution Genetic

  17. Application to Export Electric Energy OE Docket No. EA-402 Energia...

    Office of Environmental Management (EM)

    LLC Application to Export Electric Energy OE Docket No. EA-402 Energia Sierra Juarez U.S., LLC Application from ESJ to export electric energy to Mexico. EA-402 ESJ (MX).pdf More...

  18. Application to Export Electric Energy OE Docket No. EA-338-A...

    Broader source: Energy.gov (indexed) [DOE]

    Notice. EA-338-A Shell Energy-MX.pdf More Documents & Publications Application to Export Electric Energy OE Doc No. EA-339-A Shell Energy North America (US), L.P.: Federal...

  19. Factor structure analysis of the Comprehensive Effects of Alcohol - Spanish questionnaire among adolescents in Mexico 

    E-Print Network [OSTI]

    Flato, Claudia Graciela

    2007-09-17

    .F., Mexico. Available in http://www.consulta.com.mx/interiores/99_pdfs/15_otros_pdf/ENA.pdf Fabregat, A. A., (1996). Assessment some aspects of sexual behavior: Instruments for clinical measurement/evaluacion de algunos aspectos del comportamiento...

  20. EA-387 Energia Renovable S.C., LLC | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Energia Renovable S.C., LLC EA-387 Energia Renovable S.C., LLC Order authorizing Energia Renovable to export electric energy to Mexico. EA-387 Energia Renovable (MX).pdf More...

  1. EA-149 PacifiCorp | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    149 PacifiCorp EA-149 PacifiCorp Order authorizing PacifiCorp to export electric energy to Mexico. EA-149 PacifiCorp (MX).pdf More Documents & Publications EA-247-D Constellation...

  2. Electronic Structure, Phonon Dynamical Properties, and CO2 Capture...

    Office of Scientific and Technical Information (OSTI)

    Electronic Structure, Phonon Dynamical Properties, and CO2 Capture Capability of Na2-xMxZrO3 ( MLi ,K): Density-Functional Calculations and Experimental Validations Citation...

  3. Electronic Structure, Phonon Dynamical Properties, and CO2 Capture...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Electronic Structure, Phonon Dynamical Properties, and CO2 Capture Capability of Na2-xMxZrO3 ( MLi ,K): Density-Functional Calculations and Experimental...

  4. Solutions to Dr. Z.'s MATH 421 (2) Exam 2, Tue., Nov. 22, 2011, 12:00noon-1:20pm, 1. (15 pts.) Find the general expression, in polar coordinates, for the steady-state temperature

    E-Print Network [OSTI]

    Zeilberger, Doron

    that {sin nx}, n = 1, 2, . . . is orthogonal over the interval [0, ]. (b) Find the norm of each function. Ans. to (b): || sin nx|| = 2 Sol. of a.: (sin nx, sin mx) = 0 (sin nx)(sin mx) dx . From the cheatsheet (or from your head): (sin A)(sin B) = 1 2 (cos(A - B) - cos(A - B)) . So (sin nx)(sin mv) = 1 2

  5. Collection Policy: BIOCHEMISTRY, MOLECULAR AND CELL BIOLOGY Subject Scope | Priority Tables | Other policies . . .

    E-Print Network [OSTI]

    Angenent, Lars T.

    Collection Policy: BIOCHEMISTRY, MOLECULAR AND CELL BIOLOGY Subject Scope | Priority Tables | Other The Section teaches courses on the following subjects: general biochemistry, bimolecular structure crystallography, ethical issues and professional responsibilities, and laboratory courses in biochemistry

  6. Engineering Encodable Lanthanide-Binding Tags (LBTs) into Loop Regions of Proteins

    E-Print Network [OSTI]

    Barthelmes, Katja

    Lanthanide-binding tags (LBTs) are valuable tools for investigation of protein structure, function, and dynamics by NMR spectroscopy, X-ray crystallography, and luminescence studies. We have inserted LBTs into three different ...

  7. Recent developments in instrumentation and bioinformatics show that the technique of synchrotron radiation circular

    E-Print Network [OSTI]

    Janes, Bob

    567 Recent developments in instrumentation and bioinformatics show that the technique conventional lab-based circular dichroism instruments. Addresses *School of Crystallography, Birkbeck College for protein studies are available at the Synchrotron Radiation Source (SRS; UK) (http

  8. Calculation of Proteins' Total Side-Chain Torsional Entropy and Its Influence on ProteinLigand Interactions

    E-Print Network [OSTI]

    Geissler, Phillip

    are extremely dense, with packing fractions comparable to those of organic crystals.1 This observation motivated maps from crystallography expe- riments.11 The data accumulating from such studies paint a consistent

  9. RWD domain: a recurring module in kinetochore architecture shown by a Ctf19Mcm21 complex

    E-Print Network [OSTI]

    Harrison, Stephen C.

    ancestral modules. Keywords: COMA; mitosis; X-ray crystallography; yeast EMBO reports (2012) 13, 21621 becomes essential for chromosome biorientation in cells with reduced function of Ipl1, the Aurora

  10. Cell Recognition and Entry by Rhino-and Enteroviruses Michael G. Rossmann,*,1

    E-Print Network [OSTI]

    Baker, Timothy S.

    significantly in detail from the membrane- fusion strategy adopted by enveloped viruses. II. PICORNAVIRUSES-resolution structures have been determined for a variety of HRV and PV serotypes by means of X-ray crystallography

  11. On the ac magnetic susceptibility of spin-chains: solitons in one-dimensional systems

    E-Print Network [OSTI]

    Fominov, Yakov

    University, Krakow, Poland E. Pikina Institute for Problems of Oil and Gas RAS, Moscow, Russia W. Haase Shubnikov' Institute of Crystallography RAS, Moscow, Russia Z. Tomkowicz Institute of Physics, Jagiellonian

  12. Organometallic chemistry of metal surfaces

    SciTech Connect (OSTI)

    Muetterties, E.L.

    1981-06-01

    The organometallic chemistry of metal surfaces is defined as a function of surface crystallography and of surface composition for a set of cyclic hydrocarbons that include benzene, toluene, cyclohexadienes, cyclohexene, cyclohexane, cyclooctatetraene, cyclooctadienes, cyclooctadiene, cycloheptatriene and cyclobutane. 12 figures.

  13. Structural Studies of Bacteriophage Lysins and their Implication in Human Diseases 

    E-Print Network [OSTI]

    Sun, Qingan

    2011-08-08

    Structural biology lays the molecular foundation for the modern field of life sciences. In this thesis, X-ray crystallography is the primary resource for atomic detail structural information and is the major technology employed in our research...

  14. On the Characteristic Function of the Generalized Normal Distribution

    E-Print Network [OSTI]

    Sidorov, Nikita

    science and photo- graphic technology, information systems, acoustics, software engineering, optics imaging, transportation science and technology, manufacturing engineering, instruments and instrumentation, physics, analytical chemistry, cybernetics, crystallography, energy and fuels, environmental engineering

  15. letters to nature 974 NATURE |VOL 406 |31 AUGUST 2000 |www.nature.com

    E-Print Network [OSTI]

    Napp, Nils

    by nickel and palladium thiolates. Inorg. Chem. 34, 6287±6290 (1995). 28. Moffat, K. Time-resolved crystallography. Acta Crystallogr. A 54, 833±841 (1998). 29. Kong, J. et al. Nanotube molecular wires as chemical

  16. SOFTWARE STANDARDS IN CHEMISTRY. PROCEEDINGS OF THE CONFERENCE HELD AT UNIVERSITY OF UTAH, JULY 25-27, 1979. NRCC PROCEEDINGS NO. 7

    E-Print Network [OSTI]

    Harris, Frank E.

    2011-01-01

    Portable Software With Emphasis on Crystallography M0of WG4 Quantum Chemistry Software Base Report of WG5 QuantumMach. Trans. on Math. Software, 5, 308-323 (1979). (Also

  17. Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

    E-Print Network [OSTI]

    Fusco, Diana

    X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going ...

  18. NORMAL EMISSION PHOTOELECTRON DIFFRACTION: A NEW TECHNIQUE FOR DETERMINING SURFACE STRUCTURE

    E-Print Network [OSTI]

    Kevan, S.D.

    2010-01-01

    Surface Crystallography by LEED, Springer Verlag, 1979. 22.while PhD will never replace LEED, it may provide useful,Small mean-free-paths in the LEED energy range result in

  19. Low energy electron diffraction (LEED) and sum frequency generation (SFG) vibrational spectroscopy studies of solid-vacuum, solid-air and solid-liquid interfaces

    E-Print Network [OSTI]

    Hoffer, Saskia

    2002-01-01

    Surface Crystallography by LEED: Theory, Computation andFilms Chapter 2 Introduction to LEED…………………………………………..4 2.1Introduction 2.2 LEED Theory 2.2.1 Diffraction Condition

  20. Development of lanthanide-binding tags (LBTs) as powerful and versatile peptides for use in studies of proteins and protein interactions

    E-Print Network [OSTI]

    Martin, Langdon James

    2008-01-01

    To determine the function of proteins of interest, chemical biologists employ their full panoply of techniques, including X-ray crystallography and NMR spectroscopy for structural information, and luminescence spectroscopy ...

  1. The calibration of the WISE W1 and W2 Tully-Fisher relation

    SciTech Connect (OSTI)

    Neill, J. D. [California Institute of Technology, 1200 East California Boulevard, MC 278-17, Pasadena, CA 91125 (United States); Seibert, Mark; Scowcroft, Victoria [The Observatories of the Carnegie Institute of Washington, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Tully, R. Brent [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States); Courtois, Hélène; Sorce, Jenny G. [Institut de Physique Nucleaire, Université Claude Bernard Lyon I, F-69100 Lyon (France); Jarrett, T. H. [University of Cape Town, Private Bag X3, Rondebosch 7701, Republic of South Africa (South Africa); Masci, Frank J. [Image Processing and Analysis Center (IPAC), California Institute of Technology, 1200 East California Boulevard, MC 100-22, Pasadena, CA 91125 (United States)

    2014-09-10

    In order to explore local large-scale structures and velocity fields, accurate galaxy distance measures are needed. We now extend the well-tested recipe for calibrating the correlation between galaxy rotation rates and luminosities—capable of providing such distance measures—to the all-sky, space-based imaging data from the Wide-field Infrared Survey Explorer (WISE) W1 (3.4 ?m) and W2 (4.6 ?m) filters. We find a correlation of line width to absolute magnitude (known as the Tully-Fisher relation, TFR) of M{sub W1}{sup b,i,k,a}=?20.35?9.56(log?W{sub mx}{sup i}?2.5) (0.54 mag rms) and M{sub W2}{sup b,i,k,a}=?19.76?9.74(log?W{sub mx}{sup i}?2.5) (0.56 mag rms) from 310 galaxies in 13 clusters. We update the I-band TFR using a sample 9% larger than in Tully and Courtois. We derive M{sub I}{sup b,i,k}=?21.34?8.95(log?W{sub mx}{sup i}?2.5) (0.46 mag rms). The WISE TFRs show evidence of curvature. Quadratic fits give M{sub W1}{sup b,i,k,a}=?20.48?8.36(log?W{sub mx}{sup i}?2.5)+3.60(log?W{sub mx}{sup i}?2.5){sup 2} (0.52 mag rms) and M{sub W2}{sup b,i,k,a}=?19.91?8.40(log?W{sub mx}{sup i}?2.5)+4.32(log?W{sub mx}{sup i}?2.5){sup 2} (0.55 mag rms). We apply an I-band –WISE color correction to lower the scatter and derive M{sub C{sub W{sub 1}}}=?20.22?9.12(log?W{sub mx}{sup i}?2.5) and M{sub C{sub W{sub 2}}}=?19.63?9.11(log?W{sub mx}{sup i}?2.5) (both 0.46 mag rms). Using our three independent TFRs (W1 curved, W2 curved, and I band), we calibrate the UNION2 Type Ia supernova sample distance scale and derive H {sub 0} = 74.4 ± 1.4(stat) ± 2.4(sys) km s{sup –1} Mpc{sup –1} with 4% total error.

  2. Structures of two isomeric phenylethanolamine analogs containing the benzobicyclo[3.2.1]octane skeleton

    E-Print Network [OSTI]

    Grunewald, Gary L.; Ye, Qizhuang; Takusagawa, Fusao

    1987-01-01

    for X-ray Crystallography (1974). Vol. IV. Birmingham: Kynoch Press. (Present distributor D. Reidel, Dordrecht.) JOHNSON, C. K. (1976). ORTEPll. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA. MAIN, P., HULL, S. E., LESSINGER, L... for X-ray Crystallography (1974). Vol. IV. Birmingham: Kynoch Press. (Present distributor D. Reidel, Dordrecht.) JOHNSON, C. K. (1976). ORTEPll. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA. MAIN, P., HULL, S. E., LESSINGER, L...

  3. LCLS-II New Instruments Workshops Report

    SciTech Connect (OSTI)

    Baradaran, Samira; Bergmann, Uwe; Durr, Herrmann; Gaffney, Kelley; Goldstein, Julia; Guehr, Markus; Hastings, Jerome; Heimann, Philip; Lee, Richard; Seibert, Marvin; Stohr, Joachim; ,

    2012-08-08

    The LCLS-II New Instruments workshops chaired by Phil Heimann and Jerry Hastings were held on March 19-22, 2012 at the SLAC National Accelerator Laboratory. The goal of the workshops was to identify the most exciting science and corresponding parameters which will help define the LCLS-II instrumentation. This report gives a synopsis of the proposed investigations and an account of the workshop. Scientists from around the world have provided short descriptions of the scientific opportunities they envision at LCLS-II. The workshops focused on four broadly defined science areas: biology, materials sciences, chemistry and atomic, molecular and optical physics (AMO). Below we summarize the identified science opportunities in the four areas. The frontiers of structural biology lie in solving the structures of large macromolecular biological systems. Most large protein assemblies are inherently difficult to crystallize due to their numerous degrees of freedom. Serial femtosecond protein nanocrystallography, using the 'diffraction-before-destruction' approach to outrun radiation damage has been very successfully pioneered at LCLS and diffraction patterns were obtained from some of the smallest protein crystals ever. The combination of femtosecond x-ray pulses of high intensity and nanosized protein crystals avoids the radiation damage encountered by conventional x-ray crystallography with focused beams and opens the door for atomic structure determinations of the previously largely inaccessible class of membrane proteins that are notoriously difficult to crystallize. The obtained structures will allow the identification of key protein functions and help in understanding the origin and control of diseases. Three dimensional coherent x-ray imaging at somewhat lower resolution may be used for larger objects such as viruses. The chemistry research areas of primary focus are the predictive understanding of catalytic mechanisms, with particular emphasis on photo- and heterogeneous catalysis. Of particular interest is the efficient conversion of light to electrical or chemical energy, which requires understanding the non-adiabatic dynamics of electronic excited states. Ultrafast x-ray scattering presents an excellent opportunity to investigate structural dynamics of molecular systems with atomic resolution, and x-ray scattering and spectroscopy present an excellent opportunity to investigating the dynamics of the electronic charge distribution. Harnessing solar energy to generate fuels, either indirectly with photovoltaics and electrochemical catalysis or directly with photocatalysts, presents a critical technological challenge that will require the use of forefront scientific tools such as ultrafast x-rays. At the center of this technical challenge is the rational design of efficient and cost effective catalysts. Important materials science opportunities relate to information technology applications, in particular the transport and storage of information on increasingly smaller length- and faster time-scales. Of interest are the understanding of the intrinsic size limits associated with the storage of information bits and the speed limits of information or bit processing. Key questions revolve about how electronic charges and spins of materials can be manipulated by electric and magnetic fields. This requires the exploration of speed limits subject to the fundamental conservation laws of energy and linear and angular momentum and the different coupling of polar electric and axial magnetic fields to charge and spin. Of interest are novel composite materials, including molecular systems combining multi electric and magnetic functionality. Ultrafast x-rays offer the required probing speed, can probe either the charge or spin properties through polarization control and through scattering and spectroscopy cover the entire energy-time-momentum-distance phase space. In the field of atomic and molecular science, LCLS II promises to elucidate the fundamental interactions among electrons and between electrons and nuclei, and to explore the fron

  4. NSLS 2007 Activity Report (National Synchrotron Light Source Activity Report 2007)

    SciTech Connect (OSTI)

    Miller ,L.; Nasta, K.

    2008-05-01

    The National Synchrotron Light Source is one of the world's most productive and cost-effective user facilities. With 2,219 individual users, about 100 more than last year, and a record-high 985 publications, 2007 was no exception. In addition to producing an impressive array of science highlights, which are included in this Activity Report, many NSLS users were honored this year for their scientific accomplishments. Throughout the year, there were major strides in the development of the scientific programs by strengthening strategic partnerships with major research resources and with the Center for Functional Nanomaterials (CFN). Of particular note, the Consortium for Materials Properties Research in Earth Sciences (COMPRES) received renewed funding for the next five years through the National Science Foundation. COMPRES operates four high-pressure NSLS beamlines--X17B2, X17B3, X17C, and U2A--and serves the earth science community as well as the rapidly expanding segment of researchers using high-pressure techniques in materials, chemical, and energy-related sciences. A joint appointment was made between the NSLS and Stony Brook University to further enhance interactions with COMPRES. There was major progress on two key beamline projects outlined in the Five-Year Strategic Plan: the X25 beamline upgrade and the construction of the X9 small angle scattering (SAXS) beamline. The X25 overhaul, which began with the installation of the in-vacuum mini-gap undulator (MGU) in January 2006, is now complete. X25 is once again the brightest beamline for macromolecular crystallography at the NSLS, and in tandem with the X29 undulator beamline, it will keep the NSLS at the cutting edge in this important area of research. Upgrade work associated with the new MGU and the front end for the X9 SAXS beamline--jointly developed by the NSLS and the CFN--also was completed. Beamline X9 will host the SAXS program that currently exists at beamline X21 and will provide new microbeam SAXS capabilities and much-needed beam time for the life sciences, soft condensed matter physics, and nanoscience communities. Looking toward the future, a significant step has been made in expanding the user base and diversifying the work force by holding the first Historically Black Colleges and Universities (HBCU) Professors' Workshop. The workshop, which brought 11 professors to the NSLS to learn how to become successful synchrotron users, concluded with the formation of an HBCU User Consortium. Finally, significant contributions were made in optics and detector development to enhance the utilization of the NSLS and address the challenges of NSLS-II. In particular, x-ray detectors developed by the NSLS Detector Section have been adopted by an increasing number of research programs both at the NSLS and at light sources around the world, speeding up measurement times by orders of magnitude and making completely new experiments feasible. Significant advances in focusing and high-energy resolution optics have also been made this year.

  5. Next-Generation Photon Sources for Grand Challenges in Science and Energy

    SciTech Connect (OSTI)

    2009-05-01

    The next generation of sustainable energy technologies will revolve around transformational new materials and chemical processes that convert energy efficiently among photons, electrons, and chemical bonds. New materials that tap sunlight, store electricity, or make fuel from splitting water or recycling carbon dioxide will need to be much smarter and more functional than today's commodity-based energy materials. To control and catalyze chemical reactions or to convert a solar photon to an electron requires coordination of multiple steps, each carried out by customized materials and interfaces with designed nanoscale structures. Such advanced materials are not found in nature the way we find fossil fuels; they must be designed and fabricated to exacting standards, using principles revealed by basic science. Success in this endeavor requires probing, and ultimately controlling, the interactions among photons, electrons, and chemical bonds on their natural length and time scales. Control science - the application of knowledge at the frontier of science to control phenomena and create new functionality - realized through the next generation of ultraviolet and X-ray photon sources, has the potential to be transformational for the life sciences and information technology, as well as for sustainable energy. Current synchrotron-based light sources have revolutionized macromolecular crystallography. The insights thus obtained are largely in the domain of static structure. The opportunity is for next generation light sources to extend these insights to the control of dynamic phenomena through ultrafast pump-probe experiments, time-resolved coherent imaging, and high-resolution spectroscopic imaging. Similarly, control of spin and charge degrees of freedom in complex functional materials has the potential not only to reveal the fundamental mechanisms of high-temperature superconductivity, but also to lay the foundation for future generations of information science. This report identifies two aspects of energy science in which next-generation ultraviolet and X-ray light sources will have the deepest and broadest impact: (1) The temporal evolution of electrons, spins, atoms, and chemical reactions, down to the femtosecond time scale. (2) Spectroscopic and structural imaging of nano objects (or nanoscale regions of inhomogeneous materials) with nanometer spatial resolution and ultimate spectral resolution. The dual advances of temporal and spatial resolution promised by fourth-generation light sources ideally match the challenges of control science. Femtosecond time resolution has opened completely new territory where atomic motion can be followed in real time and electronic excitations and decay processes can be followed over time. Coherent imaging with short-wavelength radiation will make it possible to access the nanometer length scale, where intrinsic quantum behavior becomes dominant. Performing spectroscopy on individual nanometer-scale objects rather than on conglomerates will eliminate the blurring of the energy levels induced by particle size and shape distributions and reveal the energetics of single functional units. Energy resolution limited only by the uncertainty relation is enabled by these advances. Current storage-ring-based light sources and their incremental enhancements cannot meet the need for femtosecond time resolution, nanometer spatial resolution, intrinsic energy resolution, full coherence over energy ranges up to hard X-rays, and peak brilliance required to enable the new science outlined in this report. In fact, the new, unexplored territory is so expansive that no single currently imagined light source technology can fulfill the whole potential. Both technological and economic challenges require resolution as we move forward. For example, femtosecond time resolution and high peak brilliance are required for following chemical reactions in real time, but lower peak brilliance and high repetition rate are needed to avoid radiation damage in high-resolution spatial imaging and to avoid space-charge broadenin

  6. Switching Between Discrete and Continuous Models To Predict Genetic Activity

    E-Print Network [OSTI]

    Weld, Daniel S.

    Molecular biologists use a variety of models when they predict the behavior of genetic systems. A discrete model of the behavior of individual macromolecular elements forms the foundation for their theory of each system. ...

  7. Development of polymer and lipid materials for enhanced delivery of nucleic acids and proteins

    E-Print Network [OSTI]

    Eltoukhy, Ahmed Atef

    2013-01-01

    The development of synthetic vectors enabling efficient intracellular delivery of macromolecular therapeutics such as nucleic acids and proteins could potentially catalyze the clinical translation of many gene and protein-based ...

  8. Role of natural organic matter in governing the bioavailability of toxic metals to american oysters 

    E-Print Network [OSTI]

    Haye, Jennifer Marcelle

    2006-08-16

    Colloidal macromolecular organic matter (COM), which makes up a large portion of the bulk dissolved organic matter (DOM) in marine environments, has the capability to modify the bioavailability of potentially toxic metals ...

  9. SSRLUO 2002 Executive Committee Members | Stanford Synchrotron...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Pingitore University of Texas at El Paso Environmental & Geosciences El Paso, TX 79968-0555 Phone: 915-747-5754 Fax: 915-747-5073 E-mail: nick@geo.utep.edu MACROMOLECULAR...

  10. Annu. Rev. Biophys. Biomol. Struct. 2001. 30:21143 Copyright c 2001 by Annual Reviews. All rights reserved

    E-Print Network [OSTI]

    Wang, Wei

    -mail: odonini@kintekpharm.com Key Words molecular dynamics, molecular recognition, electronic structural calculations s Abstract Computer modeling has been developed and widely applied in studying molecules) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE

  11. Structural reorganization in films of cellulose derivatives in the presence of colloidal particles

    E-Print Network [OSTI]

    Dutta, Pulak

    Structural reorganization in films of cellulose derivatives in the presence of colloidal particles of two ethers of cellulose, hydroxypropylcellulose (HPC) and hydroxyethylcellulose (HEC), with dispersed-ray reflectivity; Cellulose derivatives; Silica particles 1. Introduction In recent years, macromolecular

  12. Vaccine delivery with microneedle skin patches in nonhuman primates

    E-Print Network [OSTI]

    Li, Adrienne V

    Transcutaneous drug delivery from planar skin patches is effective for small-molecule drugs and skin-permeable vaccine adjuvants. However, to achieve efficient delivery of vaccines and other macromolecular therapeutics ...

  13. Structure-based model for light-harvesting properties of nucleic acid nanostructures

    E-Print Network [OSTI]

    Pan, Keyao

    Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary ...

  14. Structural studies of large architectural nucleoporins and coat proteins

    E-Print Network [OSTI]

    Whittle, James Richardson Ross

    2010-01-01

    The Nuclear Pore Complex (NPC) is a ~50 MDa protein complex that forms the sole conduit for macromolecular transport across the nuclear envelope. It assembles from ~30 proteins, termed nucleoporins or nups, symmetrically ...

  15. Probing metal nanoparticles and assemblies with analytical ultracentrifugation

    E-Print Network [OSTI]

    Carney, Randy (Randy Patrick)

    2010-01-01

    Analytical Ultracentrifugation (AUC) is a powerful tool to obtain statistically relevant size and shape measurements for macromolecular systems. Metal nanoparticles coated by a ligand shell of thiolated molecules provide ...

  16. Micro-and macromechanics of single crystal and polygrannular lamellar block copolymers

    E-Print Network [OSTI]

    Tzianetopoulou, Theodora, 1974-

    2007-01-01

    Block copolymers (BCPs) are a relatively new class of thermoplastic elastomers. Their macromolecular chain consists of covalently bonded repeating blocks of thermoplastic and elastomeric molecular chains. When given the ...

  17. Mechanical Engineering Department "The Lindbergh Lectures"

    E-Print Network [OSTI]

    Wisconsin at Madison, University of

    . and Nancy P. Seitz Professor of Advanced Materials and Energy in the Department of Macromolecular Science-Italy, Medellin-Columbia, Campina Grande-Brazil, Zalakaros-Hungary, Salvador-Brazil, Pretoria-South Africa, Quebec

  18. Functional genomics reveals serine synthesis is essential in PHGDH-amplified breast cancer

    E-Print Network [OSTI]

    Possemato, Richard

    Cancer cells adapt their metabolic processes to drive macromolecular biosynthesis for rapid cell growth and proliferation[superscript 1, 2]. RNA interference (RNAi)-based loss-of-function screening has proven powerful for ...

  19. The A-like matrices for a hypercube

    E-Print Network [OSTI]

    Miklavic, Stefko

    2010-01-01

    Let $D$ denote a positive integer and let $Q_D$ denote the graph of the $D$-dimensional hypercube. Let $X$ denote the vertex set of $Q_D$ and let $A \\in \\MX$ denote the adjacency matrix of $Q_D$. A matrix $B \\in \\MX$ is called $A$-{\\em like} whenever both (i) $BA = AB$; (ii) for all $x,y \\in X$ that are not equal or adjacent, the $(x,y)$-entry of $B$ is zero. Let $\\Al$ denote the subspace of $\\MX$ consisting of the $A$-like elements. We decompose $\\Al$ into the direct sum of its symmetric part and antisymmetric part. We give a basis for each part. The dimensions of the symmetric part and antisymmetric part are $D+1$ and ${D \\choose 2}$, respectively.

  20. Automatic computation of Taylor's series which are powers of Taylor's series 

    E-Print Network [OSTI]

    Cappellucci, Theodore Joseph

    1963-01-01

    AS THE COEFFICIENTS OF THE FIN 2AL POWER SERIES+i'IH e15X ~ 50HTHESE ARE ARRANGED IN INCREASING PO 3WERS OF FLAMDoii) JX~I MX~I NX~I 1%~26 JJX44 50 OUTPUTS 903 ' JX 903 FORMAT( IHO ~ 23X ~ 25HTHE COEFFICIENTS FOR PtL(o 13&6H) ARE&i/') OUTPUTt904o...) Mxa1 NXa1 Ixa26 JJXa4 50 OUTPUT&903+JX 903 FORMAT(1HO ~ 23Xs25HTHE COEFFICIENTS FOR PIL( e 13 ~ 6H) AREoii) OUTPUT ~ 904 ~ (PIL (KX & iKXaMXaNX ) 904 FORMAT( IH ~ 7X) 3E20a8) M JaMX MXa NX+ I NXAMX MJ+MX JXaJX+I FJXaJX HJXaJJX JJXa...

  1. The Effect of File Sharing on Record Sales: An Empirical Analysis

    E-Print Network [OSTI]

    Oberholzer-Gee, Felix; Strumpf, Koleman

    2007-01-01

    in understanding the KaZaA, OpenNap, and WinMX search protocols and database indices. Sarah Woolverton and Christina Hsiung Chen provided superb research assistance. The financial support of the George F. Baker Foundation (Oberholzer-Gee) and the Kenan Faculty Fund...

  2. Equisolvability of Series vs. Controller's Topology in Synchronous Language Equations

    E-Print Network [OSTI]

    Brayton, Robert K.

    Equisolvability of Series vs. Controller's Topology in Synchronous Language Equations Nina operators for abstract languages: synchronous composition, #15;, and parallel composition, #5;, and we studied the solutions of the equations defined over finite state machines (FSMs) of the type MA #15; MX

  3. Cool transition region loops observed by the Interface Region Imaging Spectrograph

    E-Print Network [OSTI]

    by magnetic reconnection occurring at the blue-shifted footpoints where magnetic cancellation with a rate is reflected in the line profiles of explosive events, and a magnetic cancellation rate of 3 × 1015 Mx s-1 ob to 25 km s-1 were determined. These physical properties suggest that these loops are impulsively heated

  4. FROM REPRESENTATION THEORY TO HOMOTOPY GROUPS ...

    E-Print Network [OSTI]

    Then v-11ss2m(X; p) = (coker(OEm ))# and v-11ss2m-1(X; p) = (ker(OEm ))#; where .... 24 D. DAVIS Now let P = 24k, and write w4 as a unit times 54 times the

  5. RHODORA. Vol. lOS, No. 924, pp. 379-38~. 2003 NEW CYCAD (ZAMIACEAE) REPORTSFROM CHIAP.~s.

    E-Print Network [OSTI]

    Vovides, Andrew Peter - INECOL

    Mexico e-mail: vovidesa@ecologia.edu.mx MIGUEL ANGEL PEREZ-FARRERA Universidad de Ciencias y Artes del Estado de Chiapas, Calz. Samuel Leon Brindis 151. A.P. 57, Tuxtla Gutierrez, Chiapas 29000. Mexico CARLOS rainforestin'Chiapas.Uponcomparingthis populationwith therecently describ~dC. :::oquorumPerez

  6. Robust phase demodulation of interferograms with open or closed fringes

    E-Print Network [OSTI]

    Rivera, Mariano

    Investigacion en Matematicas A.C., Apdo. Postal 402, Guanajuato, Gto. Mexico 36000 mrivera@cimat.mx We present if the processed fringe pattern has a wide band, it is not normalized and it is corrupted by noise. In this paper

  7. Out of Step Phase Shifting Mariano Rivera1, Rocky Bizuet1, Amalia Martinez2

    E-Print Network [OSTI]

    Rivera, Mariano

    Centro de Investigacion en Matematicas A.C. Apdo. Postal 402, Guanajuato, Gto., 36000, Mexico 2Centro de Investigaciones en Optica A.C. Apdo. Postal 1-948, Leon, Gto., 37150, Mexico mrivera@cimat.mx http is presented as a phase refinement strategy that uses as initial guess a coarsely computed phase corrupted

  8. Module 8: Calculating & Using Mixture Ratios ISHI 2010 Mixture Workshop October 11, 2010

    E-Print Network [OSTI]

    ratios · PROTOCOLS ­ Approaches and benefits to calculating mixture ratios ­ Variation across loci Proportion(s) (what is determined from the data by relative peak heights) Other terms sometimes used Mixture proportion (Mx), proportion (p) or mass ratio Mixture ratios can help deduce contributor profiles SWGDAM

  9. SECCIN DE COMPUTACIN Personal acadmico y temas de investigacin

    E-Print Network [OSTI]

    , arquitectura de computadoras, redes de computadoras, sistemas distribuidos y lenguaje de programación de computadoras. fraga@cs.cinvestav.mx Jorge Buenabad Chávez. Investigador Adjunto. Doctor en Ciencias (Com digitales aplicados en ruteadores para sistemas de computadoras paralelas. Control de procesos industriales

  10. SECCIN DE COMPUTACIN Personal acadmico y temas de investigacin

    E-Print Network [OSTI]

    Eléctrica, 1998) Cinvestav. Temas de investigación: Diseño de algoritmos y arquitecturas de computadoras con investigación: Sistemas operativos, arquitectura de computadoras, redes de computadoras, sistemas distribuidos y de computadoras paralelas. Control de procesos industriales. dlap@cs.cinvestav.mx Xiaoou Li Zhang

  11. Helminth Parasites of Freshwater Fishes of the Ayuquila River, Sierra de Manantlan Biosphere Reserve, West Central Mexico

    E-Print Network [OSTI]

    Mercado-Silva, Norman

    Reserve, West Central Mexico GUILLERMO SALGADO-MALDONADO,1,5 NORMAN MERCADO-SILVA,2 GUILLERMINA CABAN~ AS Instituto de Biologi´a, Universidad Nacional Auto´noma de Me´xico, Apartado Postal 70-153, CP 04510, Me´xico D. F., Mexico (e-mail: gsalgado@mail.ibiologia.unam.mx), 2 Center for Limnology, University

  12. Helminth Parasites of Freshwater Fishes of the Pnuco River Basin, East Central Mexico

    E-Print Network [OSTI]

    Mercado-Silva, Norman

    Helminth Parasites of Freshwater Fishes of the Pµnuco River Basin, East Central Mexico GUILLERMO Biologi´a, Universidad Nacional Auto´noma de Me´xico, Apartado Postal 70-153, CP 04510, Me´xico D. F., Mexico (e-mail: gsalgado@mail.ibiologia.unam.mx), 2 Laboratorio de Ictiologi´a y Limnologi´a, Escuela

  13. Evidence of the dominance of higher-mode surface waves in the lake-bed zone of the Valley of Mexico

    E-Print Network [OSTI]

    Shapiro, Nikolai

    Evidence of the dominance of higher-mode surface waves in the lake-bed zone of the Valley of Mexico, Coyoacan 04510, Me´xico DF, Mexico. E-mail: krishna@ollin.igeofcu.unam.mx 2 Instituto de Ingeneri´a, UNAM, CU, Coyoacan 04510, Me´xico DF, Mexico Accepted 2001 May 4. Received 2001 April 2; in original form

  14. AHEC MEXICO / LATIN AMERICA MARKET REPORT August -September, 2004

    E-Print Network [OSTI]

    AHEC MEXICO / LATIN AMERICA MARKET REPORT August - September, 2004 AMERICAN HARDWOOD EXPORT COUNCIL US Agricultural Trade Office Jaime Balmes No.8, Piso 2 Col. Los Morales Polanco 11510 Mexico, D.F., Mexico TEL: +(52) 55 5282-0909 FAX: +(52) 55 5282-0919 e-mail: ahecmx@infosel.net.mx 1 #12;AHEC Mexico

  15. Int. J. Mol. Sci. 2011, 12, 1908-1920; doi:10.3390/ijms12031908 International Journal of

    E-Print Network [OSTI]

    North Texas, University of

    , with the objective to diminish the use of synthetic petroleum-based raw materials. Natural polymers have diverse, Queretaro, Mexico; E-Mail: analaura@fata.unam.mx 4 Laboratory of Advanced Polymers & Optimized Materials (LAPOM), Department of Materials Science & Engineering and Center for Advanced Research and Technology

  16. Hardware/Software Codesign for Embbeded Implementation of Neural Networks

    E-Print Network [OSTI]

    Girau, Bernard

    , Mexico ctorres@inaoep.mx 2 CORTEX team, LORIA-INRIA Lorraine Campus Scientifique, B. P. 239, Vandoeuvre circuits such as Field Programmable Gate Arrays (FPGA) increases at a very fast rate. Their fine-Specific Programmable Cir- cuits) approach that requires a strong hardware expertise. In this paper a high-level design

  17. A numerical modeling study of the upwelling source waters along the Oregon

    E-Print Network [OSTI]

    Kurapov, Alexander

    Rivas and R.M. Samelson College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis. E-mail: drivasc@ipn.mx #12;2 Abstract. Regional ocean circulation along the Oregon coast is studied arrives from points offshore and west of the zone. For both year 2005 and the climatological simulations

  18. RESEARCH ARTICLE Adaptive Resistance in Bacteria Requires

    E-Print Network [OSTI]

    Cluzel, Philippe

    RESEARCH ARTICLE Adaptive Resistance in Bacteria Requires Epigenetic Inheritance, Genetic Noise Resistance in Bacteria Requires Epigenetic Inheritance, Genetic Noise, and Cost of Efflux Pumps. PLoS ONE 10, Cambridge, Massachusetts, United States of America * max@fis.unam.mx Abstract Adaptive resistance emerges

  19. 8080TST.ASM

    E-Print Network [OSTI]

    ... 39 DAD D ; 19 DAD H ; 29 DAD B ; 9 DCR A ; 3d DCR B ; 5 DCR C ; d DCR D ... 26 x1 MVI L,x ; 2e x1 MVI M,x ; 36 x1 NOP ; 0 ORA L ; b5 ORA M ; b6 ORA A ...

  20. MIRO: MIDDLEWARE FOR CONTROLLING BIOLOGICALLY INSPIRED MOBILE ROBOTS

    E-Print Network [OSTI]

    Weitzenfeld, Alfredo

    . These animals react both to fixed and mobile objects. Within the fixed group we find, for example, a water@itam.mx Abstract The study of animal behavior has inspired many robotic designs. In general, there are two ways. The goal within this architecture is to reduce robot complexity, size, cost and energy consumption

  1. Giant Outbursts of Luminous Blue Variables and the Formation of the Homunculus Nebula Around j Carinae

    E-Print Network [OSTI]

    Low, Mordecai-Mark Mac

    70­264, 04510 Mexico D.F., Mexico; ggs@astroscu.unam.mx and Mordecai­Mark Mac Low 3;4 Max and very dense wind, strongly confined to the equatorial plane, is followed by a fast and almost spherical wind. We compute two­dimensional hydrodynamic models of the evolution of the nebula formed from

  2. e-Polymers 2007, no. 083 http://www.e-polymers.org

    E-Print Network [OSTI]

    North Texas, University of

    -Atlacomulco, San Cayetano 50200, Mexico. Fax +52-722- 2175109; email: gonzomartinez02@yahoo.com.mx. 2 Laboratory), Km 36.5 Carr. México-Toluca, Ocoyoacac 52045, Estado de México, Mexico; email: meep environments (wind, moisture, etc.), lower weight and lower costs. Along these lines, polymer concrete (PC

  3. e-Polymers 2010, no. 042 http://www.e-polymers.org

    E-Print Network [OSTI]

    North Texas, University of

    Toluca-Atlacomulco, San Cayetano 50200, Mexico; fax +52-722- 2175109; email: gonzomartinez02@yahoo Morelos, Cuernavaca, Morelos 62210, Mexico; ecmenchaca@yahoo.com.mx (Received: 14 May, 2009; published: 06 and abrasive strength; c) service in adverse environments (wind, moisture, etc.); d) lower weight and costs; e

  4. Analysis of chosen plaintext attacks on the WAKE Stream Cipher Marina Pudovkina

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    data; stream ciphers operate with a time­ varying transformation on individual plaintext digits into block and stream ciphers. Block ciphers operate with a fixed transformation on large blocks of plaintext­1 , a i­1 , b i­1 , c i­1 , d i­1 ). The transformation M(x, y, T) is an invertible transformation

  5. Probabilistic Adaptive Load Balancing for Parallel Daniel M. Yellin #1

    E-Print Network [OSTI]

    Paton, Norman

    , Jerusalem, Israel 96951 1 dmy@us.ibm.com Departmento de Computaci´on, CINVESTAV-IPN Av. Inst. Pol. Nal. 2508 D.F, M´exico 07360 2 jbuenabad@cs.cinvestav.mx + School of Computer Science, University partitioned or pipelined parallelism. Partitioned parallelism has the potential to provide scaleable query

  6. 71Revista Mexicana de Mastozoologa 10:71-74. 2006. ASPECTOS BSICOS SOBRE LA ECOLOGA DE

    E-Print Network [OSTI]

    Nacional Autónoma de México, Universidad

    @prodigy.net.mx Abstract: Southern river otter densities of 0.03 to 0.62/km of river were estimated for three rivers for the 19 perennial rivers of the state was 495. Scat analysis showed that crustaceans, fish, insects, Santiago Astata y San Miguel del Puerto, con corrientes permanentes con #12;vol. 10Revista Mexicana de

  7. Tunneling evidence of half-metallicity in epitaxial films of ferromagnetic perovskite manganites and ferrimagnetic magnetite

    E-Print Network [OSTI]

    Yeh, Nai-Chang

    Tunneling evidence of half-metallicity in epitaxial films of ferromagnetic perovskite manganites with the perovskite manganites are discussed. © 1998 American Institute of Physics. S0021-8979 98 45811-0 Half magnetoresistance CMR in the perovskite manganites, Ln1 xMxMnO3 Ln: trivalent rare earth ions, M divalent alkaline

  8. Affinit omologiche generali e speciali. di Maurizio Santangelo (approfondimento tratto dal testo: Maraschini-

    E-Print Network [OSTI]

    Spagnolo, Filippo

    , denominata asse dell'a.o.g., (di equazione : y=mx+h) 2) una direzione privilegiata di coefficiente angolare k appartengo- no all'asse, giacciono su una medesima retta del fascio di rette parallele di coefficiente angolare k. 3) Un rapporto r=P'Q/PQ con P e P' una coppia di punti, distinti dall'asse, che si

  9. Effects of artificial lighting on the detection of plant stress with spectral

    E-Print Network [OSTI]

    Schuerger, Andrew C.

    bioregenerative technologies have been proposed for long-term human missions to both the Moon and Mars at 25 xC, 70% relative humidity, and 300 mmol mx2 sx1 of photosynthetically active radiation (PAR; from in these experiments were optimized for plant productivity and not the collection of remote sensing data. Thus, we

  10. Learner's Workbook 20072010 CareFusion Corporation or one of its subsidiaries. All rights reserved.

    E-Print Network [OSTI]

    Oliver, Douglas L.

    This course will provide you with the knowledge to operate the Alaris® System infusion and monitoring modules. The Guardrails® Suite MX acts as a second check to alert you when an infusion is programmed to be delivered outside these limits, thus helping to prevent an IV administration error before an infusion begins. If you

  11. Characterizing Weblog Corpora Fernando Perez-Tellez1

    E-Print Network [OSTI]

    Rosso, Paolo

    1 Social Media Research Group, Institute of Technology Tallaght, Dublin, Ireland fernandoperez@itnet.ie, John.Cardiff@ittdublin.ie 2 Benemerita Universidad Autónoma de Puebla, Mexico dpinto@cs.buap.mx 3 this will have no impact on the clustering blog process. The stylometry measure indicates a general language

  12. The Soundex Phonetic Algorithm Revisited for SMS Text Representation

    E-Print Network [OSTI]

    Pinto, David Eduardo

    has had a major social and technological impact such as the growing use of Short Message Services (SMS Benemérita Universidad Autónoma de Puebla, Mexico {dpinto,darnes}@cs.buap.mx, {yuridiana, Mexico hgimenezs@gmail.com Abstract. The growing use of information technologies such as mobile devices

  13. Volume 120 (2015) http://dx.doi.org/10.6028/jres.120.009 Journal of Research of the National Institute of Standards and Technology

    E-Print Network [OSTI]

    2015-01-01

    on A ) consists of layers or columns of mostly computing nodes, or neurons, arranged from left to right (see Fig of computing neurons (except for the last neuron which is a bias neuron). From left to right in the network@cinvestav.mx SAGRAD (Simulated Annealing GRADient), a Fortran 77 program for computing neural networks

  14. Visual Information Systems Pr. Robert Laurini Chapter VI: Visual Portals to Multimedia Information Systems 1

    E-Print Network [OSTI]

    Laurini, Robert

    Visual Information Systems Pr. Robert Laurini Chapter VI: Visual Portals to Multimedia Information Systems 1 Chapter VI Visual Portals to Multimedia Information Systems http://puebla.turista.com.mx/ What is a portal? · Portal = an entry mechanism for an information system · A good portal = a portail allowing

  15. University of Connecticut Lecture Notes for ME5507 Fall 2014

    E-Print Network [OSTI]

    Chandy, John A.

    with orthogonal basis {sin nx, cos nx, 1} n=1. To check, we first notice that the functions are all periodic, . . . (1) ^ - sin nxdx = 0, n = 1, 2, . . . This confirms the orthogonality between 1 and sin nx or cos nx. Furthermore, using (1) we immediately know cos nx, cos mx = ^ - cos nx cos mxdx = ^ - cos (n + m) x + cos (n

  16. CURRICULUM VITAE Carlos Artemio Coello Coello

    E-Print Network [OSTI]

    ://delta.cs.cinvestav.mx/~ccoello Educaci´on PROFESIONAL : Facultad de Ingenier´ia Civil Universidad Aut´onoma de Chiapas 1985-1990 Tesis Asesor de tesis: Dr. Alan D. Christiansen DOCTORADO : PhD in Computer Science Tulane University New Orleans, Louisiana. Estados Unidos Tesis: "An Empirical Study of Evolutionary Techniques

  17. Imagen de esfera parcialmente sumergidaImagen de esfera pa rcialmente sumergida

    E-Print Network [OSTI]

    Vela-Arevalo, Luz V.

    Teorema Pi y la modelaci´on P´ag. 29 Luis Quintanar Medina La trayectoria del cometa Oterma P´ag. 35 Luz Morales Comit´e Editorial: Dr. Jorge Eduardo Mac´ias D´iaz, jmacias@correo.uaa.mx Dra. Luz Vianey Vela Ar

  18. Imagen de esfera parcialmente sumergidaImagen de esfera pa rcialmente sumergida

    E-Print Network [OSTI]

    Vela-Arevalo, Luz V.

    y la modelaci´on P´ag. 29 Luis Quintanar Medina La trayectoria del cometa Oterma P´ag. 35 Luz Vianey´e Editorial: Dr. Jorge Eduardo Mac´ias D´iaz, jmacias@correo.uaa.mx Dra. Luz Vianey Vela Ar´evalo, lvela

  19. Requisitos para el Alta en el Catlogo de Cuenta de Beneficiarios En el Sistema Integral de la Administracin Financiera Federal (SIAFF), As como el Alta para pago

    E-Print Network [OSTI]

    para su revisión en formato .pdf al correo electrónico contabilidad@qro.cinvestav.mx, en asunto favor importante que una vez que cuente con su acuse de recibo lo envíe al correo de contabilidad

  20. ORIGINAL PAPER Vulnerable island carnivores: the endangered endemic

    E-Print Network [OSTI]

    Gompper, Matthew E.

    ) and dwarf coati (Nasua nelsoni) on Cozumel Island, Mexico, we worked island-wide to identify the presence´a-Vasco Instituto de Ecologi´a, A. C., 91070 Xalapa, Veracruz, Mexico e-mail: denise.vasco@posgrado.inecol.edu.mx D´n, 77660 Cozumel, Quintana Roo, Mexico A. D. Cuaro´n Multicriteria SC, Unidad Independencia IMSS, Torre

  1. Peromyscus mexicanus (Rodentia: Cricetidae) ANA LILIA TRUJANO-ALVAREZ AND SERGIO TICUL ALVAREZ-CASTAN~ EDA

    E-Print Network [OSTI]

    Hayssen, Virginia

    , Me´xico; sticul@cibnor.mx (STA-C) Abstract: Peromyscus mexicanus (Saussure, 1860) is a medium the tropical lowlands of Mexico to Panama and it exhibits geographic and seasonal variation in coat color. Its deermouse, Mexico, peromyscine, rodent E 26 May 2010 American Society of Mammalogists Synonymy completed 1

  2. Isolation in habitat refugia promotes rapid diversification in a montane tropical

    E-Print Network [OSTI]

    Zamudio, Kelly R.

    ´a, Instituto de Biologi´a, Universidad Nacional Auto´noma de Me´xico, Distrito Federal 04510, Me´xico, 2 Me´xico, Distrito Federal 04510, Me´xico. E-mail: gparra@ibiologia.unam.mx Present address: CIBIO and mechanisms of divergence in the Trans-Volcanic Belt of Mexico. Location The Trans-Volcanic Belt (TVB

  3. Peromyscus levipes (Rodentia: Cricetidae) SERGIO TICUL A LVAREZ-CASTAN~ EDA AND NOE GONZA LEZ-RUIZ

    E-Print Network [OSTI]

    Hayssen, Virginia

    , Baja California Sur 23000, Me´xico; sticul@cibnor.mx (STA-C) Universidad Auto´noma Metropolitana, Unidad Iztapalapa, Departmento de Biologi´a, Apartado Postal 55-535, Me´xico 09340, Distrito Federal, Me´xico-183, Me´xico, Distrito Federal, 111340, Me´xico (NG-R) Abstract: Peromyscus levipes Merriam, 1898

  4. THE ASTROPHYSICAL JOURNAL, 534:482489, 2000 May 1 2000. The American Astronomical Society. All rights reserved. Printed in U.S.A.(

    E-Print Network [OSTI]

    Aulanier, Guillaume

    Meudon, FranceDe partement Plane taire, AND T. SAKURAI National Astronomical Observatory, Mitaka, Tokyo. This event is related to the emergence of a new magnetic Ñux of about 3 ] 1020 Mx. The impulsive enhancement: magnetic Ðelds È Sun: X-rays, gamma rays 1. INTRODUCTION It is widely accepted that solar Ñares frequently

  5. FINE-SCALE STRUCTURES OF FLUX ROPES TRACKED BY ERUPTING MATERIAL

    SciTech Connect (OSTI)

    Li Ting; Zhang Jun E-mail: zjun@nao.cas.cn

    2013-06-20

    We present Solar Dynamics Observatory observations of two flux ropes tracked out by material from a surge and a failed filament eruption on 2012 July 29 and August 4, respectively. For the first event, the interaction between the erupting surge and a loop-shaped filament in the east seems to 'peel off' the filament and add bright mass into the flux rope body. The second event is associated with a C-class flare that occurs several minutes before the filament activation. The two flux ropes are, respectively, composed of 85 {+-} 12 and 102 {+-} 15 fine-scale structures, with an average width of about 1.''6. Our observations show that two extreme ends of the flux rope are rooted in opposite polarity fields and each end is composed of multiple footpoints (FPs) of fine-scale structures. The FPs of the fine-scale structures are located at network magnetic fields, with magnetic fluxes from 5.6 Multiplication-Sign 10{sup 18} Mx to 8.6 Multiplication-Sign 10{sup 19} Mx. Moreover, almost half of the FPs show converging motion of smaller magnetic structures over 10 hr before the appearance of the flux rope. By calculating the magnetic fields of the FPs, we deduce that the two flux ropes occupy at least 4.3 Multiplication-Sign 10{sup 20} Mx and 7.6 Multiplication-Sign 10{sup 20} Mx magnetic fluxes, respectively.

  6. Adjectives and Infinitives in Composition

    E-Print Network [OSTI]

    Fleisher, Nicholas

    2008-01-01

    CP(@)(x) vi. JbeK M,g (Ja pos attr @ long book to assignK M,x) vii. JpresK M,g (Jbe a pos attr @ long book to assignK M,CP(@)(x) viii. Jpres be a pos attr @ long book to assignK M,

  7. SECCIN DE ELECTRNICA DEL ESTADO SLIDO

    E-Print Network [OSTI]

    Titular. Doctor en Ciencias (1990) Universidad de Osaka, Japón. Temas de investigación: Celdas solares de-FET, celdas solares. jmimila@mail.cinvestav.mx Arturo Morales Acevedo. Investigador Titular. Doctor en Ciencias (1987) Cinvestav. Temas de investigación: Celdas solares. Física de dispositivos. Semiconductor

  8. SECCIN DE ELECTRNICA DEL ESTADO SLIDO

    E-Print Network [OSTI]

    (1990) Universidad de Osaka, Japón. Temas de investigación: Celdas solares de películas delgadas a base-FET, celdas solares. jmimila@mail.cinvestav.mx Arturo Morales Acevedo. Investigador Titular. Doctor en Ciencias (1987) Cinvestav. Temas de investigación: Celdas solares. Física de dispositivos. Semiconductores

  9. Optimal Static Pricing of Reverse-Link DS-CDMA Multiclass Traffic

    E-Print Network [OSTI]

    Tuffin, Bruno

    -Iztapalapa 09340 Iztapalapa, Mexico vicman@xanum.uam.mx Bruno Tuffin IRISA/INRIA Rennes Campus Universitaire de Networks, Opti- mization. I. INTRODUCTION With the widespread use of the Internet, telecommu- nications are nowadays of common use in our daily life. Moreover, the Internet is expected to converge into a single

  10. On the Difficulty of Clustering Company Tweets Fernando Perez-Tellez

    E-Print Network [OSTI]

    Rosso, Paolo

    Science Benemérita Universidad Autonóma de Puebla Puebla, Mexico dpinto@cs.buap.mx John Cardiff Institute analysis 1. INTRODUCTION In recent years, the Internet has emerged as an impor- tant tool of communication and socialization. As a part of this evolution of Internet, new Web 2.0 applications such as wikis, weblogs

  11. 3D MAPPING FOR MOBILE ROBOTS USING INTERACTIVE VIRTUAL WORLDS AND INTERNET TELEOPERATION

    E-Print Network [OSTI]

    Minguez, Javier

    3D MAPPING FOR MOBILE ROBOTS USING INTERACTIVE VIRTUAL WORLDS AND INTERNET TELEOPERATION J. M N° 2508, San Pedro Zacatenco, Mexico D.F., MEXICO jibarra@ctrl.cinvestav.mx ** Robotics and Real, is actualized on line with 3D models of the objects present in the real workplace. Internet interaction between

  12. Multipurpose Mobility Services for the Future Internet Francisco A. Gonzalez-Horta, 1

    E-Print Network [OSTI]

    Mejia-Alvarez, Pedro

    1 Multipurpose Mobility Services for the Future Internet Francisco A. Gonzalez-Horta, 1 Pedro Mejia-Alvarez, 2 Eldamira Buenfil-Alpuche 3 1, 2 CINVESTAV-IPN, Computer Science Department, Mexico City 3 UNILA, Research Department, Cuernavaca, Mor., Mexico 1 fglez@computacion.cs.cinvestav.mx, 2 pmalvarez

  13. gr-qc/9902051 SU{GP{1998/12{1

    E-Print Network [OSTI]

    Sorkin, Rafael Dolnick

    -543, D.F. 04510, Mexico and Department of Physics, Syracuse University, Syracuse, NY 13244-1130, U.S.A. internet address: sorkin@physics.syr.edu Daniel Sudarsky Departamento de Gravitaci#19;on y Teor#19;#16;a de-543 M#19;exico 04510 D.F, M#19;exico internet address: sudarsky@xochitl.nuclecu.unam.mx Abstract We

  14. A Generic Infrastructure for Object Streaming And Mobile Agents on ProActive

    E-Print Network [OSTI]

    Pinto, David Eduardo

    & Blvd.Valsequillo CU PUEBLA, PUE., MEXICO {dpinto, beristain, mtmargarita}@cs.buap.mx, http infrastructures; in this case, the aglet represents the next step forward in the evolution of executable Internet with its state information. Aglets are Java objects than can move from one Internet host to another

  15. Revista Mexicana de Fsica ISSN: 0035-001X

    E-Print Network [OSTI]

    Fernandez, Thomas

    Revista Mexicana de Física ISSN: 0035-001X rmf@ciencias.unam.mx Sociedad Mexicana de Física A Through Genetic Programming Revista Mexicana de Física, vol. 57, núm. 2, abril, 2011, pp. 110-116 Sociedad REVISTA MEXICANA DE F´ISICA 57 (2) 110­116 ABRIL 2011 Evolutionary Associative Memories Through Genetic

  16. Tsovaltzi, D., Weinberger, A., Scheuer, O., Dragon, T. & McLaren, B.M., (2012). Argument diagrams in Facebook: Facilitating the formation of scientifically sound opinions. In: A. Ra-

    E-Print Network [OSTI]

    McLaren, Bruce Martin

    2012-01-01

    in Facebook: Facilitating the formation of scientifically sound opinions. In: A. Ra- venscroft, S. Lindstaedt in Facebook: Facilitating the Formation of Scientifically Sound Opinions Dimitra Tsovaltzi, Armin Weinberger Dimitra.tsovalzi@mx.uni-saarland.de Students use Facebook to organize their classroom experiences [1

  17. Synthesis, Characterization, and Activation of Zirconium and Hafnium Dialkyl Complexes that Contain a

    E-Print Network [OSTI]

    Müller, Peter

    Synthesis, Characterization, and Activation of Zirconium and Hafnium Dialkyl Complexes that Contain of zirconium and hafnium complexes, [MepyN]MX2 (M ) Zr, X ) NMe2, Cl, OSO2CF3, CH2CHMe2, CH2Ph; M ) Hf, X ) NMe

  18. ESnet Update Steve Cotter, Dept Head

    E-Print Network [OSTI]

    Model Operations End-site education, best practices and consulting services Performance management' integrated services that deliver `end-to-end' high-performance data transfer, HPC/cloud computing-CHI, EQX-SJ, LASV, LVK, NREL, NSO, SNLA, SRS · PPPL M120: to be replaced with MX480 TBD #12;Lawrence

  19. Alternative formulations of the theory of evidence

    E-Print Network [OSTI]

    Cuzzolin, Fabio

    (x)=1/3 A={x,y} x y z · b(x,y)={x,y} m() = m(x)=1/3 (sure support) · pl(x,y)={x,y} m() = m(x)+m(x,y,z)=1/3+2/3=1

  20. The Instability of the NbTe2 Surface Structure D. Cukjati (a), A. Prodan1

    E-Print Network [OSTI]

    Hla, Saw-Wai

    reports published on low energy electron diffraction (LEED) stu- dies of the MX2 compounds. It was shown that after Na intercalation into VSe2 the corresponding LEED patterns become only fainter­250 (2002) #12;detected in the corresponding LEED patterns [8]. LEED also shows very well charge density

  1. UNIDAD SALTILLO La Unidad Saltillo se cre con el fin de fortalecer la capacidad tecnolgica del pas

    E-Print Network [OSTI]

    investigación: Fenómenos de flujo de fluídos y transferencia de calor en el procesamiento de metales. facosta British Columbia, Vancouver, Canadá. Temas de investigación: Fenómenos de flujo de fluidos y transferencia de calor en el procesamiento de metales. hcastill@saltillo.cinvestav.mx Manuel de Jesús Castro Román

  2. untitled

    E-Print Network [OSTI]

    baby's weight is given by W (0:1 .2t+7.4 where WU) is the weight in pounds and ris the number of months. This model is of the form f(x)=mx+b. 5) What does b ...

  3. Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery

    SciTech Connect (OSTI)

    Medina, Jesus R.; Blackledge, Charles W.; Heerding, Dirk A.; Campobasso, Nino; Ward, Paris; Briand, Jacques; Wright, Lois; Axten, Jeffrey M.

    2012-05-29

    Fragment screening of phosphoinositide-dependent kinase-1 (PDK1) in a biochemical kinase assay afforded hits that were characterized and prioritized based on ligand efficiency and binding interactions with PDK1 as determined by NMR. Subsequent crystallography and follow-up screening led to the discovery of aminoindazole 19, a potent leadlike PDK1 inhibitor with high ligand efficiency. Well-defined structure-activity relationships and protein crystallography provide a basis for further elaboration and optimization of 19 as a PDK1 inhibitor.

  4. Fifth Annual Meeting of the Advanced Light Source User`s Association

    SciTech Connect (OSTI)

    Not Available

    1993-10-01

    This report discusses the following topics: ALS Project Status; Accelerator Commissioning; Experimental Systems: Supersmooth Optics and Ultra-Precise Undulators; Planning for Users and User Services; ALS Scientific Program; High Resolution Core-Level Photoemission; Photoelectron Diffraction and Holography; Soft X-Ray Emission Spectroscopy of Solids at the NSLS and the ALS; Gas-Phase Spectrometry; Spectromicroscopy; X-Ray Dichroism Experiments Using Circular Polarization; Magnetic Circular X-Ray Dichroism and MCXD Microscopy; Applications of Soft X-Ray Optics to Sub-Micron Silicon Device Technology; Bend Magnet Microprobe; Protein Crystallography: Recent Developments and Plans for the ALS; and Applications of High-Brightness Synchrotron Radiation to Protein Crystallography.

  5. S-H bond activation in H{sub 2}S and thiols by [RhMn(CO){sub 4}(Ph{sub 2}PCH{sub 2}PPh{sub 2}){sub 2}]. Compounds containing terminal or bridging sulfhydryl and thiolato groups

    SciTech Connect (OSTI)

    Li-Sheng Wang; McDonald, R.; Cowie, M. [Univ. of Alberta, Edmonton (Canada)

    1994-08-17

    A rhodium-magnesium carbonyl-phosphines reacted with thiols to yield the products of S-H addition. Further reactions result in bridging sulfide can be alkylated or protonated at the sulfur. The compound, [RhMn(CO){sub 4}({mu}-S)(dppm){sub 2}], was structurally characterized by X-ray crystallography.

  6. Curriculum Vitae Vincent Soustelle

    E-Print Network [OSTI]

    Demouchy, Sylvie

    . Tommasi. 2006-2007: Master 2nd year (master research degree) in Geodynamic, first in one's year with magna and 2nd year with magna cum laude, at University of Montpellier2, France. Education experiences 2007-2010: In charge of practical classes for 1st and 2nd year students on: - Mineralogy and crystallography, 2nd year

  7. JOURNAL OF MATERIALS SCIENCE 35 (2000) 4635 4647 Crystal plasticity analysis of stressassisted

    E-Print Network [OSTI]

    Grujicic, Mica

    2000-01-01

    JOURNAL OF MATERIALS SCIENCE 35 (2000) 4635­ 4647 Crystal plasticity analysis of stress@ces.clemson.edu A new model based on crystal­plasticity, crystallography, thermodynamics, kinetics and statistics Martensitictransformationisgenerallycharacterizedas a diffusionless, displacive change in materials crystal structure in which both the morphology

  8. January 26, 2012 1 Curriculum Vitae

    E-Print Network [OSTI]

    Glyde, Henry R.

    Department, Faculty of Science, Chulalongkorn University, Bangkok, Thailand since 25 January 1978. 1979 of the XVI Congress/General Assembly on the "Application of Synchrotron Radiation in Crystallography on High Temperature Superconductivity in Thailand" from 1988 till 1991. The project was sponsored by STDB

  9. Ligand migration pathway and protein dynamics in myoglobin: A time-resolved crystallographic

    E-Print Network [OSTI]

    Schmidt, Marius

    Ligand migration pathway and protein dynamics in myoglobin: A time-resolved crystallographic study-resolved x-ray crystallography at room temperature, structural relaxations and ligand migration were examined completely relaxed into its domed deoxy structure, and there is no photodissociated CO visible at the primary

  10. Variant selection in samples of austenitic stainless steel cold

    E-Print Network [OSTI]

    Cambridge, University of

    austenitic stainless steels such as AISI- 304L and 301L partially transform to martensite when deformed. #12Variant selection in samples of austenitic stainless steel cold rolled and deformed by tension of martensite crystallography (PMTC ) and Patel-Cohen´s theory for variant selection to predict crystallographic

  11. 504 Min et al. Human NDP kinase A Acta Cryst. (2000). D56, 504505 crystallization papers

    E-Print Network [OSTI]

    Suh, Se Won

    2000-01-01

    -ray crystallographic analysis of human nucleoside diphosphate kinase A Kyeongsik Min,a ² Sun Young Kim,b ² Hyun Kyu. Correspondence e-mail: sewonsuh@snu.ac.kr # 2000 International Union of Crystallography Printed in Denmark ± all, 1973). The reaction has a ping-pong mechanism via a high-energy phosphohistidine intermediate

  12. 456th Brookhaven Lecture

    ScienceCinema (OSTI)

    Allen Orville

    2010-09-01

    Orville presents ?Getting More From Less: Correlated Single-Crystal Spectroscopy and X-ray Crystallography at the NSLS? in which he discusses how researchers can use many different tools and techniques to study atomic structure and electronic structure to provide insights into chemistry.

  13. Jianlin Cheng, PhD Assistant Professor

    E-Print Network [OSTI]

    Cheng, Jianlin Jack

    magnetic field (800 MHz, 18.8 T) NMR spectrometer being loaded with a sample. Wikipedia, the free&feature=fvw #12;Alpha-Helix Jurnak, 2003 #12;Beta-Sheet Anti-Parallel Parallel #12;Non-Repetitive Secondary;Protein Structure Determination · X-ray crystallography · Nuclear Magnetic Resonance (NMR) Spectroscopy

  14. A force field for virtual atom molecular mechanics of proteins

    E-Print Network [OSTI]

    Hendrickson, Wayne A.

    , Columbia University, New York, NY 10032 Contributed by Wayne A. Hendrickson, July 13, 2009 (sent for review for which crystallography can specify atomic details of alternative end states, but the course distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features

  15. Appears in the Working Notes of the ICML Workshop on Machine Learning in Bioinformatics, August 2003 Using Pictorial Structures to Identify Proteins

    E-Print Network [OSTI]

    Shavlik, Jude W.

    2003 Using Pictorial Structures to Identify Proteins in X-ray Crystallographic Electron Density Maps in determining a protein's structure via x-ray crystallography is interpretation of the electron density map of a protein. However, due to the intractably large space of conformations the protein can adopt, building

  16. SUPPLEMENTARY DATA DNAshape: a method for the high-throughput prediction

    E-Print Network [OSTI]

    Rohs, Remo

    central base pairs (underlined in Supplementary Table S2), and (C-D) comparisons with crystal structures 3 in Figure 2 include data from X-ray crystallography (1bna, 2bna, 355d, 428d, 455d, 1dou, 1fq2, and 1jgr

  17. X-ray Structure of Novamyl, the Five-Domain "Maltogenic" R-Amylase from Bacillus stearothermophilus: Maltose and Acarbose Complexes at 1.7

    E-Print Network [OSTI]

    X-ray Structure of Novamyl, the Five-Domain "Maltogenic" R-Amylase from Bacillus stearothermophilus "maltogenic" R-amylase, Novamyl, has been determined by X-ray crystallography at a resolution of 1.7 Å. Unlike conventional R-amylases from glycoside hydrolase family 13, Novamyl exhibits the five-domain structure more

  18. short communications 190 doi:10.1107/S0907444904027118 Acta Cryst. (2005). D61, 190193

    E-Print Network [OSTI]

    2005-01-01

    Crystallographica Section D Biological Crystallography ISSN 0907-4449 Structure of a Bacillus halmapalus family 13 a-amylase of starch by -amylases is one of the key biotechnological reactions of recent times. In the search for industrial biocatalysts, the family GH13 -amylase BHA from Bacillus halmapalus has been cloned and expressed

  19. Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque

    E-Print Network [OSTI]

    Dekker, Nynke

    in this paper. HelixMC advances crystallography-derived base-pair level models (BPLMs) to simulate kilobase. These calculations recovered the experimental bending persistence length of dsRNA within the error of the simulations modulus relative to dsDNA. Further blind predictions of helix torsional properties, however, exposed

  20. Hydrogen bond dynamics in the active site of photoactive yellow protein

    E-Print Network [OSTI]

    Herschlag, Dan

    Hydrogen bond dynamics in the active site of photoactive yellow protein Paul A. Sigala, Mark A for review February 5, 2009) Hydrogen bonds play major roles in biological structure and function. Nonetheless, hydrogen-bonded protons are not typically observed by X-ray crystallography, and most structural

  1. electronic reprint Acta Crystallographica Section E

    E-Print Network [OSTI]

    Downs, Robert T.

    : W. Clegg and D. G. Watson Goethite, «-FeO(OH), from single-crystal data Hexiong Yang, Ren Lu, Robert Crystallographica Section E Structure Reports Online ISSN 1600-5368 Goethite, a-FeO(OH), from single-crystal data Union of Crystallography All rights reserved This is the first reported structure refinement of goethite

  2. Unique opportunities for NMR methods in structural genomics Gaetano T. Montelione Cheryl Arrowsmith

    E-Print Network [OSTI]

    Powers, Robert

    Unique opportunities for NMR methods in structural genomics Gaetano T. Montelione Æ Cheryl of structural genomics Á Functional genomics Á NMR Á Crystallography Á NMR methods Á Protein Structure contribu- tions of structural genomics (SG) for biomedical research, we envision many future opportunities

  3. Structure Report Structure of the scorpion toxin BmBKTtx1 solved from

    E-Print Network [OSTI]

    Tian, Weidong

    Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA b Institute of Human (anomalous signal) collected to the resolution 1.72 A using the conventional X-radiation generator (k for X-ray diffraction experiments was its high solubility in various precipitant solutions (in excess

  4. Nickel(II) and copper(II) complexes with pyridine-containing macrocycles bearing an aminopropyl pendant arm: synthesis,

    E-Print Network [OSTI]

    Nazarenko, Alexander

    pendant arm: synthesis, characterization, and modifications of the pendant amino group Aida M. Herrera of three five-coordinate nickel(II) complexes with pendant arm-containing macrocycles has been achieved and two copper(II) complexes were determined by X-ray crystallography. Protonation of the pendant arm (p

  5. Laboratoire de Biochimie Thorique Institut de Biologie Physico-Chimique

    E-Print Network [OSTI]

    Pasquali, Samuela

    is the first of its kind to explore protein folding. Peppytide is a 3D-printed coarse-grained model models. While tremendous advances have been made in computational biology, the cutting-edge 3D printing-centric transition from X-ray crystallography type data to CAD-based models to 3D-prints. This CAD

  6. title author journal vol page year type order primary data Directionally controlled superconductivity in

    E-Print Network [OSTI]

    title author journal vol page year type order primary data Directionally controlled Review B 81 94512 2010 journal 1 Asterix Dynamical theory calculations of spin-echo resolved grazing. Maranville, C. Majkrzak, W. Lee, W. Schaich and R. Pynn Journal of Applied Crystallography 43 455 2010

  7. Crystallographic Characteristics of Grain Boundaries in Dense Yttria-Stabilized Zirconia

    E-Print Network [OSTI]

    Rohrer, Gregory S.

    polycrystalline yttria-stabilized zirconia, to understand interfacial crystallography in solid oxide fuel cells correlated to the boundary energy distribution. Introduction Solid oxide fuel cells (SOFCs) are attractive The performance of a SOFC is coupled strongly to microstructural features, which have now been nearly optimized

  8. Research Opportunities 2015-16 Professor Malcolm Halcrow Professor Malcolm Halcrow

    E-Print Network [OSTI]

    Rzepa, Henry S.

    organic and inorganic synthesis, crystallography, solid and solution-phase magnetic measurements and other://www.chem.leeds.ac.uk/People/Halcrow.html Spin-Crossover Compounds ­ Switchable Materials from Simple Metal Complexes This project involves the synthesis and structural chemistry of switchable metal complexes. Spin-crossover compounds undergo a change

  9. Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

    E-Print Network [OSTI]

    Walter, Nils G.

    Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H+ Forms. Biochemical and structural data have implicated guanine 8 (G8) and adenine 38 (A38) as catalytic participants of the protonation states of G8 and A38, and the inactivating A-1(2-methoxy) substitution employed in crystallography

  10. THE AMERICAN MINERALOGIST, VOL. 53, NOVEMBER-DECEMBER, 1968 CRYSTAL CHEMISTRY OF THE BASIC MANGANESE

    E-Print Network [OSTI]

    Smyth, Joseph R.

    in Table 1, and the Fobs-Fcalc data are given in Table 2.1 TABLE 1.EVEITE. ATOMIC COORDINATES AND ISOTROPIC in eveite are in five-fold coordination which, excepting its dimorph sarkinite, is hitherto undocumented+ , and O1- were 1841 #12;obtained from International Tables for X-ray Crystallography, Vol. 3 (1962

  11. Structure and Reaction Mechanism of Basil Eugenol Gordon V. Louie1

    E-Print Network [OSTI]

    Pichersky, Eran

    and pollinator attraction, contain a propenyl side chain. Eugenol synthase (EGS) catalyzes the reductive-phenylpropene eugenol. We report here the structure determination of EGS from basil (Ocimum basilicum) by protein x-ray crystallography. EGS is structurally related to the short- chain dehydrogenase/reductases (SDRs

  12. Optimization of a pyrazole hit from FBDD into a novel series of indazoles as ketohexokinase inhibitors

    SciTech Connect (OSTI)

    Zhang, Xuqing; Song, Fengbing; Kuo, Gee-Hong; Xiang, Amy; Gibbs, Alan C.; Abad, Marta C.; Sun, Weimei; Kuo, Lawrence C.; Sui, Zhihua (J) [J; (J-PRD)

    2013-11-20

    A series of indazoles have been discovered as KHK inhibitors from a pyrazole hit identified through fragment-based drug discovery (FBDD). The optimization process guided by both X-ray crystallography and solution activity resulted in lead-like compounds with good pharmaceutical properties.

  13. electronic reprint Acta Crystallographica Section D

    E-Print Network [OSTI]

    Sussman, Joel L.

    International Union of Crystallography Printed in Denmark ± all rights reserved Automation of the steps of Energy, Brookhaven Science Association and the European Molecular Biology Laboratory (EMBL). The workshop the pilot level to a more massive production mode (see, for example, the National Institute of General

  14. Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential

    E-Print Network [OSTI]

    Chan, Hue Sun

    the important contributions that computational methods can make in providing insights into protein folding. Understanding protein folding at the atomic level is a critical but elusive goal in structural biology. A protein's folded state can often be studied by x-ray crystallography or NMR spectroscopy, and recent

  15. Applying Near-Optimal Alignments to Protein Structure Prediction

    E-Print Network [OSTI]

    -ray crystallography and nuclear magnetic resonance (NMR), but this can be difficult as well as costly. Using homology BLAST search. IMPALA is a software package designed by NCBI that can search a target sequence against criteria and therefore may be more accurate (Gracy a

  16. Polarized deuteron charge-exchange reaction $dp->{pp}_sN?$ in the Delta-isobar region

    E-Print Network [OSTI]

    Yu. N. Uzikov; J. Haidenbauer; C. Wilkin

    2015-02-16

    Mechanisms of the charge exchange reaction $dp\\to \\{pp\\}_{\\!s} N\\pi$, where $\\{pp\\}_{\\!s}$ is a two-proton system at low excitation energy, are studied at beam energies 1 -- 2 GeV and for invariant masses $M_X$ of the final $N\\pi $ system that correspond to the formation of the $\\Delta(1232)$ isobar. The direct mechanism, where the initial proton is excited into the $\\Delta(1232)$, dominates and explains the existing data on the unpolarized differential cross section and spherical tensor analyzing power $T_{22}$ for $M_X> 1.2$ GeV/$c^2$. However, this model fails to describe $T_{20}.

  17. de recherche ISSN0249-6399ISRNINRIA/RR--7513--FR+ENG

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    , structural biology, nuclear pore complex. Union of balls, curved Voronoi diagrams, curved -shapes, stability RECHERCHE EN INFORMATIQUE ET EN AUTOMATIQUE Assessing the Reconstruction of Macro-molecular Assemblies: the Example of the Nuclear Pore Complex Frédéric Cazals -- Tom Dreyfus N° 7513 -- version 2 version initiale

  18. NURBS based B-rep Models for Macromolecules and their Properties

    E-Print Network [OSTI]

    Texas at Austin, University of

    -rep data structure that aims to be useful both for visualization and modeling purposes. This requires and graphics libraries for NURBS rendering are available (e.g. openGL, Open- Inventor [IS]). Moreover is not sufficient. In order to have an exact representation of a macromolecular structure we also need to represent

  19. TIFR Centre for Interdisciplinary Sciences, Narsingi, Hyderabad 500075

    E-Print Network [OSTI]

    Shyamasundar, R.K.

    -resolution crystallographic studies on organic small and biological macromolecular systems Dr. Parthapratim Munshi Neutron Scattering Science Directorate, Biology and Soft Mater Division Oak Ridge National Laboratory, Oak Ridge, TN with complementary neutron diffraction technique, when both performed at high-resolution. While neutron diffraction

  20. Numerical Optimization Algorithms and Software for Systems Biology

    SciTech Connect (OSTI)

    Saunders, Michael

    2013-02-02

    The basic aims of this work are: to develop reliable algorithms for solving optimization problems involving large stoi- chiometric matrices; to investigate cyclic dependency between metabolic and macromolecular biosynthetic networks; and to quantify the significance of thermodynamic constraints on prokaryotic metabolism.

  1. brief communications 1102 | VOL.10 NO.11 | NOVEMBER2013 | nature methods

    E-Print Network [OSTI]

    Cai, Long

    -resolution crystallographic refinement with Phenix and rosetta Frank DiMaio1,6, Nathaniel Echols2,6, Jeffrey J Headd2, Thomas C Terwilliger3, Paul D Adams2,4 & David Baker1,5 refinement of macromolecular structures against low

  2. Artificial Trinuclear Metallopeptidase Synthesized by Cross-Linkage of a Molecular Bowl with a Polystyrene Derivative

    E-Print Network [OSTI]

    Paik Suh, Myunghyun

    -linkage of catalytic elements with a macromolecular spacer, and self-assembly from catalytic elements.10-14 ManyArtificial Trinuclear Metallopeptidase Synthesized by Cross-Linkage of a Molecular Bowl* Contribution from the School of Chemistry and Molecular Engineering and Center for Molecular Catalysis, Seoul

  3. 1. Awarding Institution/Body Imperial College London 2. Teaching Institution Imperial College London

    E-Print Network [OSTI]

    in the following areas. ` Knowledge and understanding A. Knowledge and understanding of: 1. Key topics in Genomics and Bioinformatics, including genome mapping, sequence analysis, transcriptomics, host/pathogen genomics, use of DNA/protein databases, functional and comparative genomics, phylogenetic analysis. 2. Key topics in Macromolecular

  4. Water Order Profiles on Phospholipid/Cholesterol Membrane Bilayer Surfaces

    E-Print Network [OSTI]

    O'Shea, Paul

    Water Order Profiles on Phospholipid/Cholesterol Membrane Bilayer Surfaces DAVID ROBINSON,1 2011 in Wiley Online Library (wileyonlinelibrary.com). Abstract: Water is pivotal in the stabilization of macromolecular biological structures, although the dynamic en- semble structure of water near to molecular

  5. NATURE METHODS ADVERTISING FEATURE

    E-Print Network [OSTI]

    Cai, Long

    uses low-dose radiation to produce images of individual proteins or macromolecular complexes process.An advantage of this process is that low- dose radiation used during the image capture stage and embedded on a sample grid. Second, a tilt series of micrographs is taken at low-dose radiation using

  6. Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives

    E-Print Network [OSTI]

    Rau, Don C.

    Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives V. A, osmotic stress, preferential interaction, and crowding, to describe the indirect effect of solutes of osmotic stress (1) has been used to measure the changes in macromolecular hydration for several reactions

  7. GEOC Martial Taillefert Wednesday, April 10, 2013 187 Mechanisms of ferrihydriteorganic matter complex formation via adsorption and coprecipitation

    E-Print Network [OSTI]

    Sparks, Donald L.

    compared the chemical fractionation of the organic matter and the mechanisms of ferrihydriteOM complex edges was employed to study the spatial distribution, macromolecular structure, and chemical composition Center Room: R05 *ACS does not own copyrights to the individual abstracts. For permission, please

  8. DOI: 10.1002/asia.200800427 Chemical Modification of Proteins at Cysteine: Opportunities in Chemistry

    E-Print Network [OSTI]

    Davis, Ben G.

    ;Abstract: Chemical modification of proteins is a rapidly expanding area in chemical biology. SelectiveDOI: 10.1002/asia.200800427 Chemical Modification of Proteins at Cysteine: Opportunities and macromolecular func- tion. In other cases such chemical alterations have changed the protein function entirely

  9. Macromolecules 1995,28,6795-6798 6795 Dependence of Structure of PolyelectrolyteMicelle Complexes

    E-Print Network [OSTI]

    Dubin, Paul D.

    Macromolecules 1995,28,6795-6798 6795 Dependence of Structure of PolyelectrolyteMicelle Complexes, Germany Zdenek Tuzar Institute of Macromolecular Chemistry, Prague, Czech Republic Received March 28, 1995; Revised Manuscript Received July 24, 1995@ ABSTRACT: Static light scattering and dynamic light scattering

  10. TiO2 Polymer Nanocomposites In conjunction with Dr. Ashok Kumar in the Mechanical Engineering Department at

    E-Print Network [OSTI]

    Harmon, Julie P.

    TiO2 Polymer Nanocomposites In conjunction with Dr. Ashok Kumar in the Mechanical Engineering and Engineering, C 23, 737 (2003). 17. "Polymer-TiO2 Nanocomposites: A route Towards Visually Transparent Broadband UV filters and High Refractive Index Materials", Macromolecular Materials Engineering, 288, 44

  11. Biological Science courses BE 513 Molecuar and Celluar Biology

    E-Print Network [OSTI]

    Fang-Yen, Christopher

    Biological Science courses BE 513 Molecuar and Celluar Biology BE 555 Nanoscale Systems Biology. BIOM 501 Mechanisms of Disease and Therapeutic BIOM 600 Cell Biology BMB 508 Molecular Biophysics I BMB 509 Macromolecular Biophysics II BMB 567 Bioinorganic Chemistry BMB 590 Biological Physics BMB 614

  12. VOLUME 86, NUMBER 2 P H Y S I C A L R E V I E W L E T T E R S 8 JANUARY 2001 Stretch-Induced Hairpin-Coil Transitions in Designed Polynucleotide Chains

    E-Print Network [OSTI]

    Zhang, Yang

    the statistical weights of elementary nucleotide arrangements is by single-macromolecular mechanical measurements-Induced Hairpin-Coil Transitions in Designed Polynucleotide Chains Haijun Zhou,* Yang Zhang, and Zhong-Can Ou on specifically designed polynucleotides. DOI: 10.1103/PhysRevLett.86.356 PACS numbers: 87.15.By, 05.50.+q, 64

  13. Biochemical transformation of coals

    DOE Patents [OSTI]

    Lin, Mow S. (Rocky Point, NY); Premuzic, Eugene T. (East Moriches, NY)

    1999-03-23

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed.

  14. Biochemical transformation of solid carbonaceous material

    DOE Patents [OSTI]

    Lin, Mow S. (Rocky Point, NY); Premuzic, Eugene T. (East Moriches, NY)

    2001-09-25

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed.

  15. The many faces of the helix-turn-helix domain: Transcription regulation and beyond q

    E-Print Network [OSTI]

    Babu, M. Madan

    for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 5N50 *, Vivek Anantharaman, Santhanam Balaji, M. Mohan Babu, Lakshminarayan M. Iyer National Center­protein interactions in diverse signaling contexts. Beyond their basic role in mediating macromolecular interactions

  16. Mechanism of the Acid-Catalyzed Si-O Bond Cleavage in Siloxanes and Siloxanols. A Theoretical Study

    E-Print Network [OSTI]

    Apeloig, Yitzhak

    Marek Cypryk*, and Yitzhak Apeloig Center of Molecular and Macromolecular Studies of Polish Academy. Introduction Acid-catalyzed condensation of silanol groups is the most important reaction leading considerable interest of theoreticians.5 Kinetic studies showed that in acidic media silanol condensation

  17. Orientation Refinement of Virus Structures with Unknown Symmetry Yongchang Ji, Dan C. Marinescu

    E-Print Network [OSTI]

    Baker, Timothy S.

    Orientation Refinement of Virus Structures with Unknown Symmetry Yongchang Ji, Dan C. Marinescu, in particular the structure determina- tion of viruses and other large macromolecular complexes leads to data determina- tion of viruses, the orientation refinement. 1. Introduction and Motivation Viruses are large

  18. The third, use of quantum mechanics to evaluate the molecular energy and forces, holds promise for future refinements when applied wholesale,

    E-Print Network [OSTI]

    Sali, Andrej

    The third, use of quantum mechanics to evaluate the molecular energy and forces, holds promise for future refinements when applied wholesale, but is already capable of producing valuable insight when applied to struc- tural detail. Calculation of macromolecular energy and forces with quan- tum mechanics

  19. Science Arts & Mtiers (SAM) is an open access repository that collects the work of Arts et Mtiers ParisTech

    E-Print Network [OSTI]

    Boyer, Edmond

    . However, the main limitations of PLA as a packaging material are a high gas permeability (CO2, O2/PHBV Films with Improved Mechanical and Gas Barrier Properties - Macromolecular Materials and Engineering.201200285 #12;PLA/PHBV Films with Improved Mechanical and Gas Barrier Properties Majdi Boufarguine, Alain

  20. Biochemical transformation of coals

    DOE Patents [OSTI]

    Lin, M.S.; Premuzic, E.T.

    1999-03-23

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed. 7 figs.

  1. Simple fold composition and modular architecture of the nuclear pore complex

    E-Print Network [OSTI]

    Sali, Andrej

    and California Institute for Quantitative Biomedical Research, University of California, Mission Bay QB3, 1700 4 York, NY 10021-6399 Edited by Peter Walter, University of California School of Medicine, San Francisco in the nuclear envelope that mediates macromolecular transport be- tween the cytosol and the nucleus. With

  2. Yanjie Zhang James Madison University

    E-Print Network [OSTI]

    Zhang, Yanjie

    University, China Graduated with highest honors Awards Changbai Science and Technology Award for Outstanding;2 Colloid and Polymer Science, Macromolecular Rapid Communications, Polymer, PLOS ONE, and Surface Research Area: On-Chip Investigations of Polymer and Protein Folding and Aggregation Postdoctoral Research

  3. Jamie M. Messman Research and Development Staff

    E-Print Network [OSTI]

    Pennycook, Steve

    , Hattiesburg, MS. Polymer Science and Engineering Ph.D. 2004 Professional Experience 2007-present Research/2003-9/2003 Early Identification (EID) Intern , Polymer and Specialty Chemical Technologies, Performance Polymers; Journal of Polymer Science, Langmuir, Macromolecules, Macromolecular Rapid Communications, and Australian

  4. Carnegie Mellon University CARNEGIE INSTITUTE OF TECHNOLOGY

    E-Print Network [OSTI]

    Stephen Hittinger B.S.E., Polymer Science and Engineering, Case Western Reserve University Mi Carnegie Mellon University CARNEGIE INSTITUTE OF TECHNOLOGY THESIS SUBMITTED IN PARTIAL.S., Macromolecular Science, Case Western Reserve University Carnegie Mellon University Pittsburgh, PA August, 2012

  5. Wortmannin Reduces Insulin Signaling and Death in Seizure-Prone Pcmt12/2

    E-Print Network [OSTI]

    Clarke, Steven

    . elllisonfoundation.org). The funders had no role in study design, data collection and analysis, decision to publish's ability to protect its macromolecular machinery over time, and if this is not sufficient, to repair or replace that machinery [1,2,3]. Protein damage due to the spontaneous deamidation and isomerization

  6. Measurement and Verification for Commissioning Projects: Challenges and Opportunities 

    E-Print Network [OSTI]

    Heinemeier, K.

    2005-01-01

    ) (KCM) model Direct Stiffness Cross-Coupled Stiffness xx xy xx xybx yx yyyx yyby f k k c cx x y c c yf k k ? ? ? ? ? ? ? ?? ?? ? ? ? ? ?? ? ? ?? ? ? ? ? ?? ? ? ?? ?? ? ? ?? ? ? ?? ?? ?? ?? ? ? = + ?? xx xy xx xy xx xybx yx yy yx yyyx yyby f k k... c c m mx x x y c c m my yf k k ? ? ? ? ? ? ? ?? ? ? ?? ?? ? ? ? ? ? ? ?? ? ? ? ? ?? ? ? ? ? ? ? ?? ? ? ? ? ?? ?? ? ? ? ? ?? ? ? ? ? ?? ? ? ?? ?? ?? ? ? = + +? ??? ?? Introduction: Tilting Pad Journal Bearings (TPJB) ? Composed of multiple pads...

  7. EMERGING DIMMINGS OF ACTIVE REGIONS OBSERVED BY THE SOLAR DYNAMICS OBSERVATORY

    SciTech Connect (OSTI)

    Zhang Jun; Yang Shuhong [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China); Liu Yang; Sun Xudong, E-mail: zjun@nao.cas.cn, E-mail: shuhongyang@nao.cas.cn, E-mail: yliu@sun.stanford.edu, E-mail: xudong@sun.stanford.edu [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305-4085 (United States)

    2012-12-01

    Using the observations from the Atmospheric Imaging Assembly and the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we statistically investigate the emerging dimmings (EDs) of 24 isolated active regions (IARs) from 2010 June to 2011 May. All the IARs show EDs in lower-temperature lines (e.g., 171 A) at their early emerging stages. Meanwhile, in higher temperature lines (e.g., 211 A), the ED regions brighten continuously. There are two types of EDs: fan-shaped and halo-shaped. There are 19 fan-shaped EDs and 5 halo-shaped ones. The EDs appear to be delayed by several to more than ten hours relative to the first emergence of the IARs. The shortest delay is 3.6 hr and the longest is 19.0 hr. The EDs last from 3.3 hr to 14.2 hr, with a mean duration of 8.3 hr. Before the appearance of the EDs, the emergence rate of the magnetic flux of the IARs is between 1.2 Multiplication-Sign 10{sup 19} Mx hr{sup -1} to 1.4 Multiplication-Sign 10{sup 20} Mx hr{sup -1}. The larger the emergence rate is, the shorter the delay time is. While the dimmings appear, the magnetic flux of the IARs ranges from 8.8 Multiplication-Sign 10{sup 19} Mx to 1.3 Multiplication-Sign 10{sup 21} Mx. These observations imply that the reconfiguration of the coronal magnetic fields due to reconnection between the newly emerging flux and the surrounding existing fields results in a new thermal distribution which leads to a dimming for the cooler channel (171 A) and brightening in the warmer channels.

  8. Analise Matematica IV 6 de Maio de 2000

    E-Print Network [OSTI]

    Matos, João Palhoto

    ¸c~oes) e Engenharia de Gest~ao Industrial Apresente todos os c´alculos e justifica¸c~oes relevantes 1. (a)2 dz e utilize um desses c´alculos para obter o valor de + - cos y (y2 + 1)2 dy. (d) Decida se existe em 0 percorrida "uma vez no sentido directo". 2. Considere uma equa¸c~ao diferencial da forma M(x, y

  9. Analise Matematica IV 6 de Maio de 2000

    E-Print Network [OSTI]

    Matos, João Palhoto

    Telecomunicaâ?ºcâ?oes) e Engenharia de Gestâ?ao Industrial Apresente todos os câ??alculos e justifica - # . Para # > 1 calcule # C + # e z (z 2 - 1) 2 dz e # C - # e z (z 2 - 1) 2 dz e utilize um desses câ??alculos ``uma vez no sentido directo''. 2. Considere uma equaâ?ºcâ?ao diferencial da forma M(x, y) +N(x, y)y # = 0

  10. Analise Matematica IV 6 de Maio de 2000

    E-Print Network [OSTI]

    Matos, João Palhoto

    â?ºcâ?oes Apresente todos os câ??alculos e justificaâ?ºcâ?oes relevantes 1. Considere a equaâ?ºcâ?ao diferencial (4,0) y # = 2â?ºcâ?ao diferencial da forma M(x, y) +N(x, y)y # = 0. (a) Determine em que circunstâ??ancias uma tal equaâ?ºcâ?ao diferencial possui um factor inte­ (2,0) grante sâ??o dependente do produto xy. (b) Aproveite o resultado

  11. Hydrodynamic calculation of the frequency dependent friction on the bond of a diatomic molecule

    E-Print Network [OSTI]

    Berne, Bruce J.

    is the translational friction coefficient. Stokes calcu- lated the drag force on a sphere moving with constant veloc direction is mx¨ x x 0 t d t x F t , 1 where F(t) is the random force, (t) is the dynamic friction, k- tional displacement moves. The random force has the follow- ing properties: F t 0, 2 F 0 F t kBT t . 3

  12. Some continuous and discrete distributions Table of contents

    E-Print Network [OSTI]

    Voloch, Felipe

    ? How long until this lightbulb burns out? How long until the next campaign contribution comes in? A key feature is that it is memoryless: a one-year- old lightbulb has the same change of burning out tomorrow as a brand new lightbulb. fX(x) = e-x , x > 0 FX(x) = 1 - e-x , x > 0 3 #12;E(X) = 1 V ar(X) = 1 MX(t) = 1

  13. Ambient-pressure organic superconductor

    DOE Patents [OSTI]

    Williams, Jack M. (Downers Grove, IL); Wang, Hsien-Hau (Willowbrook, IL); Beno, Mark A. (Woodridge, IL)

    1986-01-01

    A new class of organic superconductors having the formula (ET).sub.2 MX.sub.2 wherein ET represents bis(ethylenedithio)-tetrathiafulvalene, M is a metal such as Au, Ag, In, Tl, Rb, Pd and the like and X is a halide. The superconductor (ET).sub.2 AuI.sub.2 exhibits a transition temperature of 5 K which is high for organic superconductors.

  14. Ambient-temperature superconductor symetrical metal-dihalide bis-(ethylenedithio)-tetrathiafulvalene compounds

    DOE Patents [OSTI]

    Williams, Jack M. (Downers Grove, IL); Wang, Hsien-Hau (Willowbrook, IL); Beno, Mark A. (Woodridge, IL)

    1987-01-01

    A new class of organic superconductors having the formula (ET).sub.2 MX.sub.2 wherein ET represents bis(ethylenedithio)-tetrathiafulvalene, M is a metal such as Au, Ag, In, Tl, Rb, Pd and the like and X is a halide. The superconductor (ET).sub.2 AuI.sub.2 exhibits a transition temperature of 5 K. which is high for organic superconductors.

  15. Comparison of Hartmann analysis methods Carmen Canovas and Erez N. Ribak

    E-Print Network [OSTI]

    Ribak, Erez

    Comparison of Hartmann analysis methods Carmen Canovas and Erez N. Ribak Analysis of Hartmann is the Hartmann­Shack device, where the wavefront is sampled by a lenslet array, providing an array of focal spots in the Hartmann­Shack detector, in a flat wavefront case, as a regular grid,3­6 I0 x, y m,n am,n cos 2 mx P cos 2

  16. Electronic Journal of Differential Equations, Vol. 2009(2009), No. 98, pp. 110. ISSN: 1072-6691. URL: http://ejde.math.txstate.edu or http://ejde.math.unt.edu

    E-Print Network [OSTI]

    Anderson, Douglas R.

    2009-01-01

    such that the left end is clamped and the right end is free with vanishing bending moment and shearing force. Let E be the modulus of elasticity, I(x) the area moment of inertia about the neutral axis and m(x) the mass per unit- tinuous problems we refer to the recent papers [1, 9, 16, 17, 18], and for functional boundary value

  17. Post Canonical System: Examples First The definition follows some examples.

    E-Print Network [OSTI]

    Stansifer, Ryan

    : N Nx Nx | Ny +y = y x +y = z x | +y = z | A Post system for Hoftstadter's MU puzzle: MI xI xIU Mx is equivalent to all the others. #12;Post System: Tally Notation Two productions: N Nx Nx | This Post system, and z, and the signs {N,|,+,=}. N Nx Nx | Ny +y = y x +y = z x | +y = z | The last two rules reflect

  18. Why Cogeneration Development Projects Fail 

    E-Print Network [OSTI]

    Greenwood, R. W.

    1987-01-01

    ENERATION DEVElDHmNT PROJECTS FAIL RALPH w. GRBBtMX>D Regional Manager Bbasco Services Incorporated Houston, Texas ABSTRACT Cogeneration projects that are organized by developers fail to reach fruition for reasons other than the basic economical... here to discuss those additional problems unique to small projects. A developnent project is defined as one where a third party, the developer, provides preliminary econanic options, licensing, business structure, financing, detailed engineering...

  19. Current Knowledge of Leishmania Vectors in Mexico: How Geographic Distributions of Species Relate to Transmission Areas

    E-Print Network [OSTI]

    Gonzá lez, Camila; Rebollar-Té llez, Eduardo A.; Ibá ñ ez-Bernal, Sergio; Becker-Fauser, Ingeborg; Martí nez-Meyer, Enrique; Peterson, A. Townsend; Sá nchez-Cordero, Ví ctor

    2011-01-01

    Entomología Médica, Departamento de Zoología de Invertebrados, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Nuevo León, Mexico; Instituto de Ecología, AC Red Ambiente y Sustentabilidad, Xalapa, Veracruz, Mexico; Laboratorio de...-Bernal, Instituto de Ecología, AC Red Ambiente y Sustentabilidad, Carretera Antigua a Coatepec No. 351, El Haya, Xalapa, 91070, Veracruz, México, E-mail: sergio.ibanez@inecol.edu .mx . Ingeborg Becker-Fauser, Laboratorio de Inmunoparasitología, Facultad de...

  20. Measurement of diffraction dissociation cross sections in pp collisions at sqrt(s) = 7 TeV

    E-Print Network [OSTI]

    CMS Collaboration

    2015-07-14

    Measurements of diffractive dissociation cross sections in pp collisions at sqrt(s) = 7 TeV are presented in kinematic regions defined by the masses M[X] and M[Y] of the two final-state hadronic systems separated by the largest rapidity gap in the event. Differential cross sections are measured as a function of xi[X]= M[X]^2/s in the region -5.5 measured as a function of the width of the central pseudorapidity gap Delta eta for Delta eta > 3, log[10]M[X] > 1.1, and log[10]M[Y] > 1.1, a region dominated by DD. The cross sections integrated over these regions are found to be, respectively, 2.99 +/- 0.02 (stat) +0.32 -0.29 (syst) mb, 1.18 +/- 0.02 (stat) +/- 0.13 (syst) mb, and 0.58 +/- 0.01 (stat) +0.13 -0.11 (syst) mb, and are used to extract total SD and DD cross sections. In addition, the inclusive differential cross section, d sigma /d Delta eta[F], for events with a pseudorapidity gap adjacent to the edge of the detector, is measured over Delta eta[F] = 8.4 units of pseudorapidity. The results are compared to those of other experiments and to theoretical predictions, and found compatible with slowly-rising diffractive cross sections as a function of center-of-mass energy.