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Sample records for molecular biology csmb

  1. Structural Molecular Biology, SSRL

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Molecular Biology Group hosted a 3-day comprehensive workshop on the use of non-crystalline small-angle x-ray scattering and diffraction techniques in structural biology research. ...

  2. Structural Molecular Biology, SSRL

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Our Mission Our Mission The SSRL Structural Molecular Biology program operates as a integrated resource and has three primary areas (or cores) of technological research and ...

  3. Structural Molecular Biology, SSRL

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Toggle navigation SMB Home Mission Facilities Macromolecular Crystallography Small Angle X-Ray Scattering X-Ray Spectroscopy & Imaging User Resources User Resources User Portal Schedules Deadlines Highlights Training Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating Biological Structures at the Atomic and Molecular Levels Your browser does not support the video tag. SMB Mission SSRL's SMB program operates as an integrated resource and has three cores of

  4. Molecular biology of signal transduction in plants

    SciTech Connect

    Not Available

    1991-01-01

    This volume contains abstracts of oral presentations and poster sessions of the 1991 Cold Springs Harbor Meeting entitled Molecular Biology of Signal Transduction in Plants.

  5. Genetics and molecular biology of breast cancer

    SciTech Connect

    King, M.C.; Lippman, M.

    1992-12-31

    This volume contains the abstracts of oral presentations and poster sessions presented at the Cold Springs Harbor Meeting on Cancer Cells, this meeting entitled Genetics and Molecular Biology of Breast Cancer.

  6. Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate...

    Office of Scientific and Technical Information (OSTI)

    Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate-Reducing Bacteria Citation Details In-Document Search Title: Genetics and Molecular Biology of Hydrogen Metabolism ...

  7. Molecular Mechanism of Biological Proton Transport

    SciTech Connect

    Pomes, R.

    1998-09-01

    Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, the authors have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or water wires, which are emerging as ubiquitous H{sup +}-transport devices in biological systems.

  8. Frontiers of NMR in Molecular Biology

    SciTech Connect

    1999-08-25

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  9. Ringleader: Jay Nix, Beamline Director for the Molecular Biology...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Jay Nix, Beamline Director for the Molecular Biology Consortium Print Jay Nix started started the user program at Beamline 4.2.2 back in 2004, shortly after the Molecular Biology ...

  10. Ringleader: Jay Nix, Beamline Director for the Molecular Biology...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    the Molecular Biology Consortium Print Jay Nix started started the user program at Beamline 4.2.2 back in 2004, shortly after the Molecular Biology Consortium built the beamline. ...

  11. 2011 Archaea: Ecology, Metabolism, & Molecular Biology

    SciTech Connect

    Keneth Stedman

    2011-08-05

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  12. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    SciTech Connect

    Dr. Julie Maupin- Furlow

    2009-07-26

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses; and industrial applications. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  13. 2010 Plant Molecular Biology Gordon Research Conference

    SciTech Connect

    Michael Sussman

    2010-07-23

    The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2010 conference will continue in that tradition. Emerging concerns about food security have inspired a program with three main themes: (1) genomics, natural variation and breeding to understand adaptation and crop improvement, (2) hormonal cross talk, and (3) plant/microbe interactions. There are also sessions on epigenetics and proteomics/metabolomics. Thus this conference will bring together a range of disciplines, will foster the exchange of ideas and enable participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner. In particular, this conference plays a key role in enabling students and postdocs (the next generation of research leaders) to mingle with pioneers in multiple areas of plant science.

  14. Third international congress of plant molecular biology: Molecular biology of plant growth and development

    SciTech Connect

    Hallick, R.B.

    1995-02-01

    The Congress was held October 6-11, 1991 in Tucson with approximately 3000 scientists attending and over 300 oral presentations and 1800 posters. Plant molecular biology is one of the most rapidly developing areas of the biological sciences. Recent advances in the ability to isolate genes, to study their expression, and to create transgenic plants have had a major impact on our understanding of the many fundamental plant processes. In addition, new approaches have been created to improve plants for agricultural purposes. This is a book of presentation and posters from the conference.

  15. Molecular biology of signal transduction in plants. Abstracts

    SciTech Connect

    Not Available

    1991-12-31

    This volume contains abstracts of oral presentations and poster sessions of the 1991 Cold Springs Harbor Meeting entitled Molecular Biology of Signal Transduction in Plants.

  16. Overview of selected molecular biological databases

    SciTech Connect

    Rayl, K.D.; Gaasterland, T.

    1994-11-01

    This paper presents an overview of the purpose, content, and design of a subset of the currently available biological databases, with an emphasis on protein databases. Databases included in this summary are 3D-ALI, Berlin RNA databank, Blocks, DSSP, EMBL Nucleotide Database, EMP, ENZYME, FSSP, GDB, GenBank, HSSP, LiMB, PDB, PIR, PKCDD, ProSite, and SWISS-PROT. The goal is to provide a starting point for researchers who wish to take advantage of the myriad available databases. Rather than providing a complete explanation of each database, we present its content and form by explaining the details of typical entries. Pointers to more complete ``user guides`` are included, along with general information on where to search for a new database.

  17. Computational approaches to discovering semantics in molecular biology

    SciTech Connect

    Lipton, R.J. ); Marr, T.G. . Theoretical Div.); Welsh, J.D. . Dept. of Biology)

    1989-07-01

    One of the central questions of molecular biology is the discovery of the semantics of DNA. This discovery relies in a critical way on a variety of expensive computations. In order to solve these computations, both parallel computers and special-purpose hardware play a major role.

  18. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    SciTech Connect

    Eisenberg, David S.

    2008-07-15

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  19. International Conference on the Cell and Molecular Biology of Chlamydomonas

    SciTech Connect

    Dr. Stephen Miller

    2010-06-10

    The 2010 Conference on the Cell and Molecular Biology of Chlamydomonas was held June 6-10 near Boston, MA, and attracted a record 273 participants, 146 from US labs, 10 from Canada, and the remainder from 18 other countries. The single-celled algal protist Chlamydomonas is a key research organism for many investigators, including those who study photosynthesis, cell motility, adaptation to environmental stresses, the evolution of multicellularity, and the production of biofuels. Chlamydomonas researchers gather every two years at a research conference to exchange methods, develop collaborative efforts, disseminate recent findings, and plan large-scale studies to improve the usefulness of this unique research organism. This conference provides the only opportunity for Chlamydomonas scientists who work on different research problems to meet face to face, and greatly speeds progress in their respective fields. An important function of these Chlamydomonas conferences is to promote and showcase the work of younger scientists, and to attract new investigators into the Chlamydomonas community. DOE award SC0004085 was used to offset the travel and registration costs for 18 young investigators, 9 of whom were women, including one African American. Most of these scientists would not have been able to attend the conference without DOE support. A total of 208 research presentations were made at the meeting, 80 talks (63 presented by students, postdocs, and pre-tenured faculty) and 128 posters. Cell motility and biofuels/metabolism were the best-represented research areas, with a total of 77 presentations. This fact underscores the growing importance of Chlamydomonas as a research and production tool in the rapidly expanding world of biofuels research. A total of 28 talks and posters were presented on the topics of photosynthesis and stress responses, which were among the next best-represented research areas. As at several recent Chlamydomonas meetings, important advances were

  20. Molecular biology of Homo sapiens: Abstracts of papers presented at the 51st Cold Spring Harbor symposium on quantitative biology

    SciTech Connect

    Watson, J.D.; Siniscalco, M.

    1986-01-01

    This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Genetic Diagnosis, Human Evolution, Drugs Made Off Human Genes, Receptors, and Gene Therapy. (DT)

  1. 2012 PLANT MOLECULAR BIOLOGY GORDON RESEARCH CONFERENCE, JULY 15-20, 2012

    SciTech Connect

    Sussman, Michael

    2013-07-20

    The 2012 Gordon Conference on Plant Molecular Biology will present cutting-edge research on molecular aspects of plant growth and development, with particular emphasis on recent discoveries in molecular mechanisms involved with plant signaling systems. The Conference will feature a wide range of topics in plant molecular biology including hormone receptors and early events in hormone signaling, plant perception of and response to plant pathogen and symbionts, as well as technological and biological aspects of epigenomics particularly as it relates to signaling systems that regulate plant growth and development. Genomic approaches to plant signaling will be emphasized, including genomic profiling technologies for quantifying various biological subsystems, such as the epigenome, transcriptome, phosphorylome, and metabolome. The meeting will include an important session devoted to answering the question, "What are the biological and technological limits of plant breeding/genetics, and how can they be solved"?

  2. 2012 CELLULAR & MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 17 - 22, 2012

    SciTech Connect

    Judith Berman

    2012-06-22

    The Gordon Research Conference on CELLULAR & MOLECULAR FUNGAL BIOLOGY was held at Holderness School, Holderness New Hampshire, June 17 - 22, 2012. The 2012 Gordon Conference on Cellular and Molecular Fungal Biology (CMFB) will present the latest, cutting-edge research on the exciting and growing field of molecular and cellular aspects of fungal biology. Topics will range from yeast to filamentous fungi, from model systems to economically important organisms, and from saprophytes and commensals to pathogens of plants and animals. The CMFB conference will feature a wide range of topics including systems biology, cell biology and morphogenesis, organismal interactions, genome organisation and regulation, pathogenesis, energy metabolism, biomass production and population genomics. The Conference was well-attended with 136 participants. Gordon Research Conferences does not permit publication of meeting proceedings.

  3. Workshop in computational molecular biology, April 15, 1991--April 14, 1994

    SciTech Connect

    Tavare, S.

    1995-04-12

    Funds from this award were used to the Workshop in Computational Molecular Biology, `91 Symposium entitled Interface: Computing Science and Statistics, Seattle, Washington, April 21, 1991; the Workshop in Statistical Issues in Molecular Biology held at Stanford, California, August 8, 1993; and the Session on Population Genetics a part of the 56th Annual Meeting, Institute of Mathematical Statistics, San Francisco, California, August 9, 1993.

  4. Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate-Reducing

    Office of Scientific and Technical Information (OSTI)

    Bacteria (Technical Report) | SciTech Connect Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate-Reducing Bacteria Citation Details In-Document Search Title: Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate-Reducing Bacteria The degradation of our environment and the depletion of fossil fuels make the exploration of alternative fuels evermore imperative. Among the alternatives is biohydrogen which has high energy content by weight and produces only water when

  5. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    SciTech Connect

    Not Available

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  6. Modeling human risk: Cell & molecular biology in context

    SciTech Connect

    1997-06-01

    It is anticipated that early in the next century manned missions into outer space will occur, with a mission to Mars scheduled between 2015 and 2020. However, before such missions can be undertaken, a realistic estimation of the potential risks to the flight crews is required. One of the uncertainties remaining in this risk estimation is that posed by the effects of exposure to the radiation environment of outer space. Although the composition of this environment is fairly well understood, the biological effects arising from exposure to it are not. The reasons for this are three-fold: (1) A small but highly significant component of the radiation spectrum in outer space consists of highly charged, high energy (HZE) particles which are not routinely experienced on earth, and for which there are insufficient data on biological effects; (2) Most studies on the biological effects of radiation to date have been high-dose, high dose-rate, whereas in space, with the exception of solar particle events, radiation exposures will be low-dose, low dose-rate; (3) Although it has been established that the virtual absence of gravity in space has a profound effect on human physiology, it is not clear whether these effects will act synergistically with those of radiation exposure. A select panel will evaluate the utilizing experiments and models to accurately predict the risks associated with exposure to HZE particles. Topics of research include cellular and tissue response, health effects associated with radiation damage, model animal systems, and critical markers of Radiation response.

  7. Inhibition Of Molecular And Biological Processes Using Modified Oligonucleotides

    DOEpatents

    Kozyavkin, Sergei A.; Malykh, Andrei G.; Polouchine, Nikolai N.; Slesarev, Alexei I.

    2003-04-15

    A method of inhibiting at least one molecular process in a sample, comprising administering to the sample an oligonucleotide or polynucleotide containing at least one monomeric unit having formula (I): wherein A is an organic moiety, n is at least 1, and each X is independently selected from the group consisting of --NRCOCONu, --NHCOCR.sub.2 CR.sub.2 CONu, --NHCOCR.dbd.CRCONu, and --NHCOSSCONu, wherein each R independently represents H or a substituted or unsubstituted alkyl group, and Nu represents a nucleophile, or a salt of the compound.

  8. Facilities for exploring molecular biology databases on the Web: A comparative study

    SciTech Connect

    Markowitz, V.M.; Chen, I.M.A.; Kosky, A.S.; Szeto, E.

    1996-12-31

    We discuss criteria for evaluating and comparing the main facilities provided by molecular biology databases (MBDs) for exploring (that is, retrieving and interpreting data) on the Web. We use these criteria for examining the facilities supported by typical MBDs such as Genbank, AtDB, GSDB, GDB, and MGD (as of September 5, 1996). 19 refs.

  9. Molecular biology in marine science: Scientific questions, technological approaches, and practical implications

    SciTech Connect

    1994-12-31

    This report describes molecular techniques that could be invaluable in addressing process-oriented problems in the ocean sciences that have perplexed oceanographers for decades, such as understanding the basis for biogeochemical processes, recruitment processes, upper-ocean dynamics, biological impacts of global warming, and ecological impacts of human activities. The coupling of highly sophisticated methods, such as satellite remote sensing, which permits synoptic monitoring of chemical, physical, and biological parameters over large areas, with the power of modern molecular tools for ``ground truthing`` at small scales could allow scientists to address questions about marine organisms and the ocean in which they live that could not be answered previously. Clearly, the marine sciences are on the threshold of an exciting new frontier of scientific discovery and economic opportunity.

  10. Molecular Biology for the Environment: an EC-US hands-on Course in Environmental Biotechnology

    SciTech Connect

    Victor de Lorenzo; Juan Luis Ramos; Jerome Kukor; Gerben J. Zylstra

    2004-02-15

    One of the central goals of this activity is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that should result in future collaborations. The course is designed to give scientists hands-on experience in modern, up-to-date biotechnological methods at the interface between molecular biology and environmental biotechnology for the analysis of microorganisms and their activities with regard to the remediation of pollutants in the environment.

  11. Plant Molecular Biology 2008 Gordon Research Conference - July 13-18, 2008

    SciTech Connect

    Richard M. Amasino

    2009-08-28

    The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2008 conference will continue in that tradition. There will be sessions on metabolism; new methods to study genomes, proteomes and metabolomes; plant-microbe interactions; plant hormones; epigenetics. A new topic for the conference this year will be bioenergy. Thus this conference will bring together a range of disciplines to foster the exchange ideas and to permit the participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner.

  12. 2010 CELL AND MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 13-18, 2010

    SciTech Connect

    Michelle Momany

    2010-06-18

    The Cellular and Molecular Fungal Biology Conference provides a forum for presentation of the latest advances in fungal research with an emphasis on filamentous fungi. This open-registration scientific meeting brings together the leading scientists from academia, government and industry to discuss current research results and future directions at Holderness School, an outstanding venue for scientific interaction. A key objective of the conference is to foster interaction among scientists working on model fungi such as Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa and Aspergillus nidulans and scientists working on a variety of filamentous fungi whose laboratory tractability is often inversely proportional to their medical, industrial or ecological importance. Sessions will be devoted to Systems Biology, Fungi and Cellulosic Biomass, Small RNAs, Population Genomics, Symbioses, Pathogenesis, Membrane Trafficking and Polarity, and Cytoskeleton and Motors. A session will also be devoted to hot topics picked from abstracts. The CMFB conference provides a unique opportunity to examine the breadth of fungal biology in a small meeting format that encourages in-depth discussion among the attendees.

  13. Biology

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biology @WIPP Life Begins at 250,000,000 Years WIPP's underground isn't just suited for ... radiation, one biology experiment actually conducts tests related to this phenomenon. ...

  14. Theoretical Biology and Biophysics

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Theoretical Biology and Biophysics Modeling biological systems and analysis and informatics of molecular and cellular biological data Mathematical BiologyImmunology Fundamental ...

  15. WHOLE CELL TOMOGRAPHY/MOLECULAR BIOLOGY/STRUCTURAL BIOLOGY: Affordable x-ray microscopy with nanoscale resolution

    SciTech Connect

    Evans, James E.; Blackborow, Paul; Horne, Stephen J.; Gelb, Jeff

    2013-03-01

    Biological research spans 10 orders of magnitude from angstroms to meters. While electron microscopy can reveal structural details at most of these spatial length scales, transmission electron tomography only reliably reconstructs three-dimensional (3-D) volumes of cellular material with a spatial resolution between 1-5 nm from samples less than 500 nm thick1. Most biological cells are 2-30 times thicker than this threshold, which means that a cell must be cut into consecutive slices with each slice reconstructed individually in order to approximate the contextual information of the entire cell. Fortunately, due to a larger penetration depth2, X-ray computed tomography bypasses the need to physically section a cell and enables imaging of intact cells and tissues on the micrometer or larger scale with tens to hundreds of nanometer spatial resolution. While the technique of soft x-ray microscopy has been extensively developed in synchrotron facilities, advancements in laboratory x-ray source designs now increase its accessibility by supporting commercial systems suitable for a standard laboratory. In this paper, we highlight a new commercial compact cryogenic soft x-ray microscope designed for a standard laboratory setting and explore its capabilities for mesoscopic investigations of intact prokaryotic and eukaryotic cells.

  16. Molecular Dynameomics

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Dynameomics Molecular Dynameomics DaggettHiResWhitebg.png Key Challenges: Perform molecular dynamics simulations to characterize both native (i.e. biologically active) and...

  17. FINAL REPORT: DOE CONTRACT NUMBER FG0205ER64026 Biological Neutron Scattering: A Collaboration with the Oak Ridge Center for Structural Molecular Biology

    SciTech Connect

    Jill Trewhella

    2011-01-12

    The overarching goal of this project was to promote applications of small-angle scattering in structural molecular biology by providing model examples of cutting edge applications that demonstrate the unique capabilities and potential of the DOE national user facilities at Oak Ridge, especially the newly commissioned BioSANS. The approach taken was three-fold: (1) to engage in high impact collaborative research projects that would benefit from small-angle neutron scattering to both demonstrate the power of the technique while expanding the potential user community; (2) to provide access to scattering facilities established at the University of Utah to as broad a set of researchers as possible to increase the expertise in small-angle scattering generally; and (3) to develop new methods and tools for small-angle scattering. To these ends, three major research collaborations were pursued that resulted in a significant body of published work where neutron scattering and contrast variation played a major role. These major collaborations involved studies of protein complexes involved in (1) bacterial transcription regulation and adaptive response (a DOE/BER priority area); (2) regulation of cardiac muscle; and (3) neuronal disorders. In addition, to broaden the impact of the project, smaller collaborative efforts were supported that used either small-angle X-ray or neutron scattering. Finally, the DOE supported facilities at the University of Utah were made available to researchers on a service basis and a number of independent groups took advantage of this opportunity. In all of this work, there was an emphasis on the training of students and post docs in scattering techniques, and a set of publications (a book chapter, a review, and an encyclopedia article) were produced to guide the non-specialist potential user of scattering techniques in successful applications of the techniques. We also developed a suite of user friendly web-based computational tools currently

  18. Structural Molecular Biology, SSRL

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Science Highlights Science Highlights Structure of Chinese Herbal-based Medicine Captured by ATP on a Human tRNA Synthetase For approximately 2,000 years, the Chinese have been ...

  19. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Behzad Rad Rad Senior Scientific Engineering Associate, Biological Nanostructures BRad@lbl.gov 510.486.5795 Biography Education Postdoctoral Fellow Molecular Foundry Lawrence Berkeley National Labs Ph.D. in Biophysics University of California at Davis Dissertation Title: "The Unwinding Mechanism of the E. coli RecQ helicase" Dissertation Advisor: Dr. Stephen C. Kowalczykowski Bachelor's in Molecular and Cellular Biology University of California at Berkeley Expertise Behzad's interests

  20. (Biological dosimetry)

    SciTech Connect

    Sega, G.A.

    1990-11-06

    The traveler participated in an International Symposium on Trends in Biological Dosimetry and presented an invited paper entitled, Adducts in sperm protamine and DNA vs mutation frequency.'' The purpose of the Symposium was to examine the applicability of new methods to study quantitatively the effects of xenobiotic agents (radiation and chemicals) on molecular, cellular and organ systems, with special emphasis on human biological dosimetry. The general areas covered at the meeting included studies on parent compounds and metabolites; protein adducts; DNA adducts; gene mutations; cytogenetic end-points and reproductive methods.

  1. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Rita Garcia Brand Principal Research Associate, Biological Nanostructures Facility RLGarcia@lbl.gov 510.486.4125 Biography Education B.A. Molecular Biology, Scripps College, Claremont, CA, 2005 Previous Professional Positions Principal Research Associate, Lawrence Berkeley National Lab, Berkeley, CA, May 2009 - present Office Manager, Microsoft, San Francisco, CA, August 2008 - December 2008 Office Manager, Powerset, Inc., San Francisco, CA, January 2007 - July 2008 Post-Baccalaureate Intramural

  2. Report on the research conducted under the funding of the Sloan foundation postdoctoral fellowship in Computational Molecular Biology [Systematic study of protein-protein complexes] Final report

    SciTech Connect

    Sheinerman, Felix

    2001-06-01

    A central question in molecular biology is what structural features are common at protein-protein interfaces and what energetic factors define the affinity and specificity of protein-protein association. Analysis of structural and mutational data on protein-protein interfaces revealed that protein-protein interfaces of different functional classes contain many more energetically important charged and polar residues than was previously thought. Since, in the context of protein folding studies, polar interactions are believed to destabilize the folded proteins, this observation raised the question as to the forces that determine the stability of protein complexes. To investigate this issue in detail, the authors developed a number of partitioning schemes that allowed them to investigate the role of selected residues, ion pairs, and networks of polar interactions in protein-protein association. The methods developed were applied to the analysis of four different protein-protein interfaces: the ribonuclease barnase and its inhibitor barstar, the human growth hormone and its receptor, subtype N9 influenze virus neuraminidase and NC41 antibody, and the Ras Binding Domain of kinase cRaf and a Ras homologue Rap1A. The calculations revealed a surprising variability in how polar interactions affect the stability of different complexes. The finding that positions of charged and polar residues on protein-protein interfaces are optimized with respect to electrostatic interactions suggests that this property can be employed for the discrimination between native conformations and trial complexes generated by a docking algorithm. Analysis indicated the presence of SH2 domains in Janus family of non-receptor protein tyrosine kinases.

  3. Molecular and biological characterization of the 5 human-bovine rotavirus (WC3)-based reassortant strains of the pentavalent rotavirus vaccine, RotaTeq (registered)

    SciTech Connect

    Matthijnssens, Jelle; Joelsson, Daniel B.; Warakomski, Donald J.; Zhou, Tingyi; Mathis, Pamela K.; Maanen, Marc-Henri van; Ranheim, Todd S.; Ciarlet, Max

    2010-08-01

    RotaTeq (registered) is a pentavalent rotavirus vaccine that contains five human-bovine reassortant strains (designated G1, G2, G3, G4, and P1) on the backbone of the naturally attenuated tissue culture-adapted parental bovine rotavirus (BRV) strain WC3. The viral genomes of each of the reassortant strains were completely sequenced and compared pairwise and phylogenetically among each other and to human rotavirus (HRV) and BRV reference strains. Reassortants G1, G2, G3, and G4 contained the VP7 gene from their corresponding HRV parent strains, while reassortants G1 and G2 also contained the VP3 gene (genotype M1) from the HRV parent strain. The P1 reassortant contained the VP4 gene from the HRV parent strain and all the other gene segments from the BRV WC3 strain. The human VP7s had a high level of overall amino acid identity (G1: 95-99%, G2: 94-99% G3: 96-100%, G4: 93-99%) when compared to those of representative rotavirus strains of their corresponding G serotypes. The VP4 of the P1 reassortant had a high identity (92-97%) with those of serotype P1A[8] HRV reference strains, while the BRV VP7 showed identities ranging from 91% to 94% to those of serotype G6 HRV strains. Sequence analyses of the BRV or HRV genes confirmed that the fundamental structure of the proteins in the vaccine was similar to those of the HRV and BRV references strains. Sequences analyses showed that RotaTeq (registered) exhibited a high degree of genetic stability as no mutations were identified in the material of each reassortant, which undergoes two rounds of replication cycles in cell culture during the manufacturing process, when compared to the final material used to fill the dosing tubes. The infectivity of each of the reassortant strains of RotaTeq (registered) , like HRV strains, did not require the presence of sialic acid residues on the cell surface. The molecular and biologic characterization of RotaTeq (registered) adds to the significant body of clinical data supporting the

  4. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Caroline M. Ajo-Franklin Ajo-Franklin Staff Scientist, Biological Nanostructures cajo-franklin@lbl.gov 510.486.4299 personal website Biography Dr. Ajo-Franklin has been a Staff Scientist at the Molecular Foundry since 2007. Before that, she received her Ph.D. in Chemistry from Stanford University with Prof. Steve Boxer and was a post-doctoral fellow with Prof. Pam Silver in the Department of Systems Biology at Harvard Medical School. Dr. Ajo-Franklin is fascinated by the incredible, diverse

  5. DockingShop: A Tool for Interactive Molecular Docking (Conference...

    Office of Scientific and Technical Information (OSTI)

    Country of Publication: United States Language: English Subject: 59 BASIC BIOLOGICAL ... FEEDBACK; FORECASTING; MOLECULAR STRUCTURE; NAVIGATION; OPTIMIZATION; PROTEINS; ...

  6. Biological Safety

    Office of Energy Efficiency and Renewable Energy (EERE)

    The DOE's Biological Safety Program provides a forum for the exchange of best practices, lessons learned, and guidance in the area of biological safety. This content is supported by the Biosurety Executive Team. The Biosurety Executive Team is a DOE-chartered group. The DOE Office of Worker Safety and Health Policy provides administrative support for this group. The group identifies biological safety-related issues of concern to the DOE and pursues solutions to issues identified.

  7. Biological Applications

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biological Applications Biological Applications Bioscience technologies for biosecurity, infectious disease, and other threats. Bioscience Capabilities-for Collaboration View our capability sheets: get details of what we do. Atomic Magnetometer Micro Imaging MOL PCR Raman LIBS Waveguide Biosensor How we deploy innovation bioscience-foundational-science Cell biology hasn't been the same since Los Alamos pioneered flow cytometry in mid-1960s when a Lab scientist invented a cell separator that

  8. Algal Biology Toolbox Workshop Summary Report

    Office of Energy Efficiency and Renewable Energy (EERE)

    The Algal Biology Toolbox Workshop Summary Report summarizes an event hosted by the U.S. Department of Energy’s Bioenergy Technologies Office’s Advanced Algal Systems Program in May 2016. The purpose of the Algal Biology Toolbox Workshop was to collect input from experts in the field of algal biology regarding (1) the current state of algal biological tools, including our understanding of algal biology and biochemistry, available molecular toolboxes, omics databases, and other resources; (2) challenges to developing and applying a full suite of biological tools to improve algae performance and system robustness; and (3) strategies to advance progress toward commercial algal biofuels.

  9. Responses of Cell Renewal Systems to Long-term Low-Level Radiation Exposure: A Feasibility Study Applying Advanced Molecular Biology Techniques on Available Histological and Cytological Material of Exposed Animals and Men

    SciTech Connect

    Fliedner Theodor M.; Feinendegen Ludwig E.; Meineke Viktor; Fritz Thomas E.

    2005-02-28

    First results of this feasibility study showed that evaluation of the stored material of the chronically irradiated dogs with modern molecular biological techniques proved to be successful and extremely promising. Therefore an in deep analysis of at least part of the huge amount of remaining material is of outmost interest. The methods applied in this feasibility study were pathological evaluation with different staining methods, protein analysis by means of immunohistochemistry, strand break analysis with the TdT-assay, DNA- and RNA-analysis as well as genomic examination by gene array. Overall more than 50% of the investigated material could be used. In particular the results of an increased stimulation of the immune system within the dogs of the 3mSv group as both compared to the control and higher dose groups gives implications for the in depth study of the cellular events occurring in context with low dose radiation. Based on the findings of this study a further evaluation and statistically analysis of more material can help to identify promising biomarkers for low dose radiation. A systematic evaluation of a correlation of dose rates and strand breaks within the dog tissue might moreover help to explain mechanisms of tolerance to IR. One central problem is that most sequences for dog specific primers are not known yet. The discovery of the dog genome is still under progress. In this study the isolation of RNA within the dog tissue was successful. But up to now there are no gene arrays or gene chips commercially available, tested and adapted for canine tissue. The uncritical use of untested genomic test systems for canine tissue seems to be ineffective at the moment, time consuming and ineffective. Next steps in the investigation of genomic changes after IR within the stored dog tissue should be limited to quantitative RT-PCR of tested primer sequences for the dog. A collaboration with institutions working in the field of the discovery of the dog genome could

  10. National Laboratory] Basic Biological Sciences(59) Biological...

    Office of Scientific and Technical Information (OSTI)

    Achievements of structural genomics Terwilliger, Thomas C. Los Alamos National Laboratory Basic Biological Sciences(59) Biological Science Biological Science Abstract Not...

  11. Biological preconcentrator

    DOEpatents

    Manginell, Ronald P.; Bunker, Bruce C.; Huber, Dale L.

    2008-09-09

    A biological preconcentrator comprises a stimulus-responsive active film on a stimulus-producing microfabricated platform. The active film can comprise a thermally switchable polymer film that can be used to selectively absorb and desorb proteins from a protein mixture. The biological microfabricated platform can comprise a thin membrane suspended on a substrate with an integral resistive heater and/or thermoelectric cooler for thermal switching of the active polymer film disposed on the membrane. The active polymer film can comprise hydrogel-like polymers, such as poly(ethylene oxide) or poly(n-isopropylacrylamide), that are tethered to the membrane. The biological preconcentrator can be fabricated with semiconductor materials and technologies.

  12. (Biological dosimetry)

    SciTech Connect

    Preston, R.J.

    1990-12-17

    The traveler attended the 1st International Conference on Biological Dosimetry in Madrid, Spain. This conference was organized to provide information to a general audience of biologists, physicists, radiotherapists, industrial hygiene personnel and individuals from related fields on the current ability of cytogenetic analysis to provide estimates of radiation dose in cases of occupational or environmental exposure. There is a growing interest in Spain in biological dosimetry because of the increased use of radiation sources for medical and occupational uses, and with this the anticipated and actual increase in numbers of overexposure. The traveler delivered the introductory lecture on Biological Dosimetry: Mechanistic Concepts'' that was intended to provide a framework by which the more applied lectures could be interpreted in a mechanistic way. A second component of the trip was to provide advice with regard to several recent cases of overexposure that had been or were being assessed by the Radiopathology and Radiotherapy Department of the Hospital General Gregorio Maranon'' in Madrid. The traveler had provided information on several of these, and had analyzed cells from some exposed or purportedly exposed individuals. The members of the biological dosimetry group were referred to individuals at REACTS at Oak Ridge Associated Universities for advice on follow-up treatment.

  13. The Molecular Foundry (TMF) | U.S. DOE Office of Science (SC...

    Office of Science (SC)

    Foundry is fully equipped with state-of-the-art, sometimes one-of-a-kind instruments providing laborites for materials science, physics, chemistry, biology, and molecular biology. ...

  14. Ninth International Workshop on Plant Membrane Biology

    SciTech Connect

    Not Available

    1993-12-31

    This report is a compilation of abstracts from papers which were discussed at a workshop on plant membrane biology. Topics include: plasma membrane ATP-ases; plant-environment interactions, membrane receptors; signal transduction; ion channel physiology; biophysics and molecular biology; vaculor H+ pumps; sugar carriers; membrane transport; and cellular structure and function.

  15. Molecular Science

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Molecular Science NETL's Molecular Science competency provides technology-enabling computational and experimental insight into the atomic-level processes occurring in condensed matter and gas phase systems or at the heterogeneous surface-gas interfaces used for energy applications. Research includes molecular optimization as well as both classical and high-throughput material design, specifically: Molecular Optimization Development and application of new computational approaches in the general

  16. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Mike Brady ed_barnard Joint Molecular Foundry/ALS Project Scientist mabrady@lbl.gov 510.486.6548

  17. Systems biology approach to bioremediation

    SciTech Connect

    Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

    2012-06-01

    Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

  18. Genomics and Systems Biology

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Genomics and Systems Biology Los Alamos scientists perform research in functional genomics ... and experimental biology as the foundation of a dynamic systems biology capability. ...

  19. Genomes, Phylogeny, and Evolutionary Systems Biology

    SciTech Connect

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  20. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    EVENTS ARCHIVE The Molecular Foundry regularly offers seminars and events that feature compelling research and information for those who investigate at the nanoscale. Seminars occur on Tuesdays at 11:00 am, in Building 67, Room 3111 unless otherwise noted. < seminars and events Molecular Foundry Annual User Meeting The Molecular Foundry is hosting its annual onsite nanoscience conference on August 11-12, 2016. Past, present and prospective users, as well as anyone curious about the

  1. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Flatter and Faster: Transition Metal Dichalcogendies at the Molecular Foundry (Part II) Brain Imaging and Optical Manipulation Active Nanointerfaces for Electrochemistry SAXS-WAXS...

  2. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    ... Discovery Could Dramatically Boost Efficiency of Perovskite Solar Cells Nanoscale images by researchers at the Molecular Foundry yield surprise that could push efficiency to 31 ...

  3. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Dmitry Soustin dmitry User Program Administrator dsoustin@lbl.gov 510.486.7687 Biography Dmitry Soustin is the Molecular Foundry's User Program Administrator. In this role, Dmitry...

  4. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Theory of Nanostructured Materials jbneaton@lbl.gov 510.486.4527 personal website Biography Jeffrey B. Neaton is Director of the Molecular Foundry, a Department of Energy...

  5. Modern concepts in molecular modeling

    SciTech Connect

    Bajorath, J.; Klein, T.E.

    1996-12-31

    This session focused on the application of computer models and the development and application of various energy functions to study the structure, energetics and dynamics of proteins and their interactions with ligands. These studies provide an exciting view of current developments in computer-aided molecular modeling and theoretical analysis of biological molecules.

  6. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Agenda March 24, 2016 Lawrence Berkeley National Laboratory AGENDA Registration 8:30 am - 9:00 am The Molecular Foundry's History and Impact 9:00 am - 10:30 am Jeff Neaton, Molecular Foundry Welcome Paul Alivisatos, Berkeley Lab/UC Berkeley The Creation of the Molecular Foundry Michael Witherell, Berkeley Lab Berkeley Lab Impact Brian Schowengerdt, Magic Leap Industry Impact Representative Mike Honda (D-CA) National Impact Break 10:30 am - 11:00 am Session 1: Functional Nanointerfaces 11:00 am -

  7. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Ralph J. Greenspan, Director, Center for Brain Activity Mapping; Professor of BiologyNeurobiology Section and of Cognitive Science, UC San Diego; Co-Director, Cal-BRAIN. Roger ...

  8. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biological Nanostructures This facility studies the synthesis, analysis and mimicry of biological nanostructures. Expertise and capabilities are available to develop new materials based on the folding and assembly of sequence-defined, bioinspired polymers (including peptides,,nucleic acids, and peptoids). New biocompatible imaging probes based on organic dyes and functionalized inorganic nanocrystals are being developed and are available to facilitate state-of-the-art bioimaging studies.

  9. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    ... silicon solar cells by applying a new mix of materials to a standard design. MORE Molecular Foundry and ALS Users, aBeam Technologies, Make Metrology History The research ...

  10. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Seminars occur on Tuesdays at 11:00 am, in Building 67, Room 3111 unless otherwise noted. To be added to the Molecular Foundry's seminar mailing list, please email Jason Sweet. ...

  11. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Meg Holm Meg Senior Administrator mcholm@lbl.gov 510.486.5135 Biography Meg is the Molecular Foundry's Senior Administrator. In this role, she supervises the Foundry budget...

  12. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Alison Hatt allison User Program Director ajhatt@lbl.gov 510.486.7154 Biography Alison Hatt is the Director of the User Program at the Molecular Foundry and a former Foundry...

  13. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Gil Torres Gil Torres gjtorres@lbl.gov 510.486.4395 Biography Gil is the Building Manager for MSD in buildings 62, 66, 2, 30, JCAP and the Molecular Foundry. Gil supports Foundry...

  14. Work with Biological Materials

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    cells, viruses), plant or soil samples (USDA quarantines), recombinant DNA, or blood-borne pathogen. Biological Use Authorization The great majority of biological work at...

  15. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Media and Resources MEDIA Molecular Foundry Youtube Channel Berkeley Lab Youtube Channel Berkeley Lab Photo Archive Webcam The Molecular Foundry and its users benefit from its location at Berkeley Lab within the Bay Area's vibrant scientific ecosystem. The expansive views serve to fuel the imagination and build connections among the Foundry's diverse research community. Baycam Click here for a full screen view from our webcam. RESOURCES Style Guide PDF 308 KB Logos Signature Preferred 41 KB ZIP

  16. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Publications Advanced Materials Special Issue » The Molecular Foundry publication database lists peer-reviewed work that has resulted from internal and user research. New publications can be added to the database here. All published work resulting from the use of this facility must acknowledge the Molecular Foundry, regardless of whether Foundry staff are included as authors. Proper acknowledgement text can be found here. Citation Year Facility User Loading data from server

  17. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Foundry Molecular Foundry HOME REGISTRATION AGENDA SYMPOSIA POSTERS EXHIBITOR INFO TRAVEL & LODGING Molecular Foundry User Meeting: August 11-12, 2016 This conference focuses on frontier research topics in nanoscale science, providing a forum for discussion and development of new results and ideas. Whether you are a returning user, a prospective user, or someone who is curious about the Foundry, you are encouraged to attend the User Meeting. Participants are invited to submit abstracts for

  18. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    See the Foundry's full equipment list Organic and Macromolecular Synthesis Capabilities & Tools Instrument Scheduler Major Instruments and Capabilities AB SCIEX TF4800 MALDI TOF-TOF Mass Spectrometer This instrument is the tandem time-of-flight mass spectrometer systems, providing the excellent level of molecular mass coverage in the range of molecular masses 500 and 150,000 Da, high throughput, and confidence in both qualitative and quantitative analyses. The analyzer combines all of the

  19. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Molecular Foundry Advanced Materials Special Issue Advanced Materials Cover Art The multidisciplinary science that is central to the Molecular Foundry's mission is well represented throughout the October 14, 2015 special issue of Advanced Materials. In three Review articles, we highlight recent areas of particular innovation and promise at the Foundry: the development of advanced electron tomography for both hard and soft materials with near-atomic resolution, the creation of designer biomimetic

  20. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Branden Brough Branden Deputy Director (acting) Director of Strategy and External Relations bbrough@lbl.gov 510.486.4206 Biography Branden Brough is the Molecular Foundry's Acting Deputy Director. In this role, Dr. Brough is responsible for the development and implementation of strategies, goals and objectives that ensure the efficient and effective support of the Molecular Foundry's mission, and assists the Director in all aspects of the management of Foundry scientific operations. Dr. Brough

  1. Micro/nanofabricated environments for synthetic biology

    SciTech Connect

    Collier, Pat [ORNL; Simpson, Michael L [ORNL

    2011-01-01

    A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial micro- and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of micro- and nanofabricated topological constraints.

  2. Molecular fountain.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  3. [Studies of biologic activation associated with molecular receptor increase and tumor response in ChL6/L6 protocol patients; Studies in phantoms; Quantitative SPECT; Preclinical studies; and Clinical studies]. DOE annual report, 1994--95

    SciTech Connect

    DeNardo, S.J.

    1995-12-31

    The authors describe results which have not yet been published from their associated studies listed in the title. For the first, they discuss Lym-1 single chain genetically engineered molecules, analysis of molecular genetic coded messages to enhance tumor response, and human dosimetry and therapeutic human use radiopharmaceuticals. Studies in phantoms includes a discussion of planar image quantitation, counts coincidence correction, organ studies, tumor studies, and {sup 90}Y quantitation with Bremsstrahlung imaging. The study on SPECT discusses attenuation correction and scatter correction. Preclinical studies investigated uptake of {sup 90}Y-BrE-3 in mice using autoradiography. Clinical studies discuss image quantitation verses counts from biopsy samples, S factors for radiation dose calculation, {sup 67}Cu imaging studies for lymphoma cancer, and {sup 111}In MoAb imaging studies for breast cancer to predict {sup 90}Y MoAb therapy.

  4. Biological conversion system

    DOEpatents

    Scott, C.D.

    A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

  5. Physics Meets Biology (LBNL Summer Lecture Series)

    ScienceCinema

    Chu, Steve [Director, LBNL

    2016-07-12

    Summer Lecture Series 2006: If scientists could take advantage of the awesomely complex and beautiful functioning of biologys natural molecular machines, their potential for application in many disciplines would be incalculable. Nobel Laureate and Director of the Lawrence Berkeley National Laboratory Steve Chu explores Possible solutions to global warming and its consequences.

  6. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    See the Foundry's full equipment list Research Themes Discovering the Future, Atom by Atom The six-story, 94,000 square-foot Molecular Foundry building at LBNL overlooks the UC Berkeley campus and, from a distance, the San Francisco Bay. Directly adjacent to the Foundry is the NCEM complex that was established in 1983 to maintain a forefront research center for electron microscopy with state-of-the-art instrumentation and expertise. Merged with the Molecular Foundry in 2014 to take advantage of

  7. Environmental Molecular Sciences Laboratory (EMSL) | U.S. DOE Office of

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Science (SC) Environmental Molecular Sciences Laboratory (EMSL) Biological and Environmental Research (BER) BER Home About Research Facilities User Facilities Atmospheric Radiation Measurement Climate Research Facility (ARM) Environmental Molecular Sciences Laboratory (EMSL) Joint Genome Institute (JGI) Science Highlights Benefits of BER Funding Opportunities Biological & Environmental Research Advisory Committee (BERAC) Community Resources Contact Information Biological and

  8. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    See the Foundry's full equipment list Biological Nanostructures Capabilities & Tools Instrument Scheduler Major Capabilities: Instruments and Labs AAPPTec Apex 396 Peptide Synthesizer The Aapptec is a robotic multiple peptide synthesizer, capable of synthesizing up to 40 peptides and or peptoids in parallel via solid-phase synthesis. Jobin Yvon Fluoromax Fluorometer The fluorometer is a quality spectrophotometer used to characterize the fluorescent properties of

  9. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Bruce Cohen Cohen Staff Scientist, Biological Nanostructures becohen@lbl.gov 510.486.6640 personal website Biography Dr. Cohen was a postdoctoral fellow with Lily Y. Jan at the Howard Hughes Medical Institute and Department of Physiology at the University of California San Francisco. He received his Ph.D. from the Department of Chemistry at the University of California Berkeley and his A.B. from Princeton University's Department of Chemistry, where he graduated cum laude. Research Interests

  10. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Ron Zuckermann Ron Zuckermann Facility Director, Biological Nanostructures User Program Senior Advisor rnzuckermann@lbl.gov 510.486.7091 personal website Biography Education Ph.D. Chemistry, UC Berkeley, 1989. Advisor: Prof. Peter Schultz B.S. Chemistry, Harvey Mudd College, 1984 Past professional positions 2003 - 2005 Research Fellow, Chiron Corp. 1996 - 2003 Director of Bioorganic Chemistry, Chiron Corp. 1993 - 1996 Associate Director, Bioorganic Chemistry, Chiron Corp. 1991 - 1993 Sr.

  11. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    and Dinner On March 24, 2016, the Molecular Foundry celebrated the 10th anniversary of the dedication of its iconic building with a full day scientific symposium and dinner event. This celebration recognized the Foundry's major scientific and operational milestones and looked forward to the promising future of nanoscience. Leaders from Congress, DOE, academia, industry, and Berkeley Lab joined prominent Foundry users and staff, both past and present, to participate in this celebration.

  12. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    One of the World's Premier Nanoscience Research Institutions Supported by the Department of Energy Office of Basic Energy Sciences (BES) through their Nanoscale Science Research Center (NSRC) program, the Molecular Foundry is a national User Facility for nanoscale science serving hundreds of academic, industrial and government scientists around the world each year. Users come to the Foundry to perform multidisciplinary research beyond the scope of an individual's own laboratory. By taking

  13. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Theory of Nanostructured Materials The Theory of Nanostructured Materials Facility at the Molecular Foundry is focused on expanding our understanding of materials at the nanoscale. Our research connects the structural and dynamical properties of materials to their functions, such as electrical conductivity and storage, light-harvesting for electricity and fuel, or gas separation and sequestration. We develop and employ a broad range of tools, including advanced electronic-structure theory,

  14. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    POLICIES AND DEFINITIONS PROPOSAL GUIDE USER GUIDE USER PROGRAM SUBMIT A PROPOSAL » Reviewer Login » Proposal Deadline March 31, 2017 Instrument Scheduler Nanofabrication Instrument Scheduler User Program The Molecular Foundry user program gives researchers access to expertise and equipment for cutting-edge nanoscience in a collaborative, multidisciplinary environment. The program is open to scientists from academia, industry, and research institutes worldwide. These users join a vibrant

  15. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    SEMINARS ARCHIVE The Molecular Foundry regularly offers seminars and events that feature compelling research and information for those who investigate at the nanoscale. Seminars occur on Tuesdays at 11:00 am, in Building 67, Room 3111 unless otherwise noted. < seminars and events Monday, November 14, 2016 at 11am Thiophene Rust in Single-Molecule Electronics and Singlet Fission Luis Campos, Columbia University [MORE] Tuesday, November 1, 2016 at 11am Nanoscale Investigations of Solar Cell

  16. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    See the Foundry's full equipment list Nanofabrication Capabilities & Tools Instrument Scheduler Major Capabilities: Instruments and Labs Zeiss Crossbeam 1540 EsB The Molecular Foundry Zeiss Cross-beam is one of the most versatile lithographic and inspection tools allowing fabrication of complex prototypes for nanoelectronics, nano-optical antenna, modifying scanning probe tips, rapid electrical contacting and many other applications. The 1500XB Cross Beam combines the Gemini field emission

  17. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    David Prendergast David Prendergast Director, Theory of Nanostructured Materials dgprendergast@lbl.gov 510.486.4948 personal website Biography Education 2002 Ph.D., Physics, University College Cork, Ireland 1999 B.Sc., Physics and Mathematics, University College Cork, Ireland Research Interests My research focuses on employing and developing first-principles electronic structure theory and molecular dynamics simulations on high-performance computing infrastructure to reveal energy relevant

  18. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Emory Chan Brand Staff Scientist, Inorganic Nanostructures EMChan@lbl.gov 510.486.7874 personal website Biography Education Postdoctoral fellow, Molecular Foundry with Dr. Delia Milliron Ph. D., Chemistry, UC Berkeley with Prof. Paul Alivisatos and Prof. Richard Mathies, B. S., Chemistry, Stanford University with Prof. Hongjie Dai Expertise Dr. Chan's expertise lies in the combinatorial and high-throughput synthesis of colloidal inorganic nanoparticles. As part of the Foundry's Combinatorial

  19. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Nate Hohman Nate Hohman Staff Scientist, Inorganic Nanostructures JNHohman@lbl.gov 510.486.6155 Biography Education Staff Scientist in Inorganic Nanomaterials, The Molecular Foundry, 2015- Postdoc in Material Science, Stanford University, 2012-2014 Ph.D in Chemistry, The Pennsylvania State University, 2011 B.S. in Chemistry, Butler University, 2004 Research Interests Blending organic and inorganic components into a hybrid system unlocks a wider range of structural variety than would be

  20. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Sarah Gutierrez Meg Senior Resource Analyst SMGutierrez@lbl.gov 510.486.6419 Biography Sarah Gutierrez is the Molecular Foundry's Senior Resource Analyst. In this role, she is responsible for providing financial consultation and guidance, complex program/project budget management, advanced budget planning and analysis, and broad-based forecasting and long range contingency planning for Strategic Partnership Projects and DOE non-Core projects. Sarah started her finance and grants administration

  1. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Tracy Mattox TMMattox Principal Scientific Engineering Associate, Inorganic Nanostructures TMMattox@lbl.gov 510.495.2649 Biography Education M.S. in Chemistry, Miami University, 2006 B.S. in Chemistry, University of Portland, 2003 Tracy Mattox has been a member of the Inorganic Facility at the Molecular Foundry as a Scientific Engineering Associate since 2007. Expertise Tracy's main focus is assisting users with their research projects (helping design reactions and analyze results). She is well

  2. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    User Guide Download the complete Users' Guide (PDF) Submit a Proposal Learn about the Molecular Foundry and its user program Explore Foundry capabilities and plan your proposal Prepare responses to proposal questions Create and submit your proposal through the online proposal portal After your proposal is approved* Complete secondary safety screening Become a badged LBNL "affiliate" Contact your assigned Foundry scientist When you arrive* Go to your appointment with the Affiliate

  3. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Molecular Foundry User Policies and Definitions Download the complete User Policies and Definitions (PDF) Guiding principles Safety Costs 50/50 staff time model User proposal types Proposal questions and evaluation criteria Proposal Review Board (PRB) and review process User agreements with Berkeley Lab Access to other user facilities at LBNL Final project report Publications and acknowledgement User feedback and end-of-project survey Users' Executive Committee (UEC) Scientific Advisory Board

  4. Molecular Foundry

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biological Nanostructures Staff Ron Zuckerman Ron Zuckermann Facility Director rnzuckermann@lbl.gov 510.486.7091 Caroline Ajo-Franklin Caroline Ajo-Franklin Staff Scientist cajo-franklin@lbl.gov 510.486.4299 Bruce Cohen Bruce Cohen Staff Scientist becohen@lbl.gov 510.486.6640 Connolly Michael Connolly Principal Scientific Engineering Associate mdconnolly@lbl.gov 510.486.6388 Rad Behzad Rad Senior Scientific Engineering Associate brad@lbl.gov 510.486.5795 Rita Rita Garcia Principal Research

  5. Biology and Medicine Division: Annual report 1986

    SciTech Connect

    Not Available

    1987-04-01

    The Biology and Medicine Division continues to make important contributions in scientific areas in which it has a long-established leadership role. For 50 years the Division has pioneered in the application of radioisotopes and charged particles to biology and medicine. There is a growing emphasis on cellular and molecular applications in the work of all the Division's research groups. The powerful tools of genetic engineering, the use of recombinant products, the analytical application of DNA probes, and the use of restriction fragment length polymorphic DNA are described and proposed for increasing use in the future.

  6. Modular Construction - on a Molecular Scale | U.S. DOE Office...

    Office of Science (SC)

    ... Research, together with the National Institutes of Health, supported the Structural Molecular Biology beamline (BL12-2) at SSRL, a DOE Office of Science User Facility. ...

  7. Biological tracer method

    DOEpatents

    Strong-Gunderson, J.M.; Palumbo, A.V.

    1998-09-15

    The present invention is a biological tracer method for characterizing the movement of a material through a medium, comprising the steps of: introducing a biological tracer comprising a microorganism having ice nucleating activity into a medium; collecting at least one sample of the medium from a point removed from the introduction point; and analyzing the sample for the presence of the biological tracer. The present invention is also a method for using a biological tracer as a label for material identification by introducing a biological tracer having ice nucleating activity into a material, collecting a sample of a portion of the labelled material and analyzing the sample for the presence of the biological tracer. 2 figs.

  8. Biological tracer method

    DOEpatents

    Strong-Gunderson, Janet M. (Ten Mile, TN); Palumbo, Anthony V. (Oak Ridge, TN)

    1998-01-01

    The present invention is a biological tracer method for characterizing the movement of a material through a medium, comprising the steps of: introducing a biological tracer comprising a microorganism having ice nucleating activity into a medium; collecting at least one sample of the medium from a point removed from the introduction point; and analyzing the sample for the presence of the biological tracer. The present invention is also a method for using a biological tracer as a label for material identification by introducing a biological tracer having ice nucleating activity into a material, collecting a sample of a portion of the labelled material and analyzing the sample for the presence of the biological tracer.

  9. Genomics and Systems Biology

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Genomics and Systems Biology Genomics and Systems Biology Los Alamos scientists perform research in functional genomics and structural genomics, and applications for such work cover diverse fields such as energy, agriculture, and environmental cleanup. Contact Us Babetta Marrone Biofuels Program Manager Email Cheryl Kuske DOE BER Biological System Science Division Program Manager Email Kirsten McCabe Emerging Threats Program Manager Email Rebecca McDonald Bioscience Communications Email "We

  10. Biological detector and method

    DOEpatents

    Sillerud, Laurel; Alam, Todd M.; McDowell, Andrew F.

    2015-11-24

    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  11. Biological detector and method

    DOEpatents

    Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

    2013-02-26

    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  12. Biological detector and method

    DOEpatents

    Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

    2014-04-15

    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  13. Genomics and Systems Biology

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    This approach promises to enhance all aspects of biological research such as: * Increasing the specificity of pathogen detection * Designing more effective drugs through ...

  14. The Intersection of Physics and Biology

    ScienceCinema

    Liphardt, Jan [University of California, Berkeley, California, United States

    2016-07-12

    In April 1953, Watson and Crick largely defined the program of 20th century biology: obtaining the blueprint of life encoded in the DNA. Fifty years later, in 2003, the sequencing of the human genome was completed. Like any major scientific breakthrough, the sequencing of the human genome raised many more questions than it answered. I'll brief you on some of the big open problems in cell and developmental biology, and I'll explain why approaches, tools, and ideas from the physical sciences are currently reshaping biological research. Super-resolution light microscopies are revealing the intricate spatial organization of cells, single-molecule methods show how molecular machines function, and new probes are clarifying the role of mechanical forces in cell and tissue function. At the same time, Physics stands to gain beautiful new problems in soft condensed matter, quantum mechanics, and non-equilibrium thermodynamics.

  15. Integrated Biological Control

    SciTech Connect

    JOHNSON, A.R.

    2002-09-01

    Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects; and microorganisms such as molds that adversely affect the quality of the workplace environment). Biological control activities may be either preventive (apriori) or in response to existing contamination spread (aposteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and apriori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, aposteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response.

  16. Integrated Biological Control

    SciTech Connect

    JOHNSON, A.R.

    2003-10-09

    Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects, and microorganisms such as molds that adversely affect the quality of the workplace environment). Biological control activities may be either preventive (a priori) or in response to existing contamination spread (a posteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and a priori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, a posteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response.

  17. Biological sample collector

    DOEpatents

    Murphy, Gloria A.

    2010-09-07

    A biological sample collector is adapted to a collect several biological samples in a plurality of filter wells. A biological sample collector may comprise a manifold plate for mounting a filter plate thereon, the filter plate having a plurality of filter wells therein; a hollow slider for engaging and positioning a tube that slides therethrough; and a slide case within which the hollow slider travels to allow the tube to be aligned with a selected filter well of the plurality of filter wells, wherein when the tube is aligned with the selected filter well, the tube is pushed through the hollow slider and into the selected filter well to sealingly engage the selected filter well and to allow the tube to deposit a biological sample onto a filter in the bottom of the selected filter well. The biological sample collector may be portable.

  18. Biological and Chemical Security

    SciTech Connect

    Fitch, P J

    2002-12-19

    The LLNL Chemical & Biological National Security Program (CBNP) provides science, technology and integrated systems for chemical and biological security. Our approach is to develop and field advanced strategies that dramatically improve the nation's capabilities to prevent, prepare for, detect, and respond to terrorist use of chemical or biological weapons. Recent events show the importance of civilian defense against terrorism. The 1995 nerve gas attack in Tokyo's subway served to catalyze and focus the early LLNL program on civilian counter terrorism. In the same year, LLNL began CBNP using Laboratory-Directed R&D investments and a focus on biodetection. The Nunn-Lugar-Domenici Defense Against Weapons of Mass Destruction Act, passed in 1996, initiated a number of U.S. nonproliferation and counter-terrorism programs including the DOE (now NNSA) Chemical and Biological Nonproliferation Program (also known as CBNP). In 2002, the Department of Homeland Security was formed. The NNSA CBNP and many of the LLNL CBNP activities are being transferred as the new Department becomes operational. LLNL has a long history in national security including nonproliferation of weapons of mass destruction. In biology, LLNL had a key role in starting and implementing the Human Genome Project and, more recently, the Microbial Genome Program. LLNL has over 1,000 scientists and engineers with relevant expertise in biology, chemistry, decontamination, instrumentation, microtechnologies, atmospheric modeling, and field experimentation. Over 150 LLNL scientists and engineers work full time on chemical and biological national security projects.

  19. Institute for Molecular Medicine Research Program

    SciTech Connect

    Phelps, Michael E

    2012-12-14

    The objectives of the project are the development of new Positron Emission Tomography (PET) imaging instrumentation, chemistry technology platforms and new molecular imaging probes to examine the transformations from normal cellular and biological processes to those of disease in pre-clinical animal models. These technology platforms and imaging probes provide the means to: 1. Study the biology of disease using pre-clinical mouse models and cells. 2. Develop molecular imaging probes for imaging assays of proteins in pre-clinical models. 3. Develop imaging assays in pre-clinical models to provide to other scientists the means to guide and improve the processes for discovering new drugs. 4. Develop imaging assays in pre-clinical models for others to use in judging the impact of drugs on the biology of disease.

  20. Geometric and electrostatic modeling using molecular rigidity functions

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | DOE PAGES Geometric and electrostatic modeling using molecular rigidity functions This content will become publicly available on March 1, 2018 Title: Geometric and electrostatic modeling using molecular rigidity functions Geometric and electrostatic modeling is an essential component in computational biophysics and molecular biology. Commonly used geometric representations admit geometric singularities such as cusps, tips and self-intersecting facets that lead to

  1. Computational Biology: A Recipe for Ligand-Binding Proteins

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Computational Biology: A Recipe for Ligand-Binding Proteins Authors: Ghirlanda, G. Title: Computational Biology: A Recipe for Ligand-Binding Proteins Source: Nature Year: 2013 Volume: 501 Pages: 177-178 ABSTRACT: Cellular cross-talk, enzymatic catalysis and regulation of gene expression all depend on molecular recognition. A method that allows the design of proteins with desired recognition sites could thus be revolutionary Date of online publication: Thu, 2013-09-12 Link online:

  2. Biological Hydrogen Production Workshop

    Energy.gov [DOE]

    The U.S. Department of Energy's (DOE's) National Renewable Energy Laboratory (NREL) held a Biological Hydrogen Production Workshop on September 24–25, 2013, in Golden, Colorado. The workshop...

  3. Universal Biology, the Genetic

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Universal Biology, the Genetic Code and the First Billion Years of Life on Earth Nigel Goldenfeld University of Illinois May 25, 2016 4:00 p.m. - Wilson Hall, One West This ...

  4. Work with Biological Materials

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Work with Biological Materials Print Planning A complete Experiment Safety Sheet (ESS) is required before work can be done at the ALS. This ESS is either a part of the proposal...

  5. Genomics and Systems Biology

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Genomics and Systems Biology Los Alamos National Laboratory leads the world in computational finishing of microbial genomes Read caption + In 2013, Los Alamos scientist Richard Sayre and his team genetically modified the organisms to harvest light more efficiently for maximum production. Overview of Research and Highlights Researchers at Los Alamos National Laboratory are using their renowned expertise in genomics, computation, and experimental biology as the foundation of a dynamic systems

  6. Biological and Environmental Research

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biological and Environmental Research Biological and Environmental Research Understanding how genomic information is translated to functional capabilities, and the roles of Earth's biogeochemical systems so we can predict climate decades or centuries into the future. Get Expertise James Bossert (505) 667-3644 Email Cathy Wilson (505) 667-0202 Email Srinivas Iyer (505) 667-2690 Email Conducting research into sustainable biofuel production, improved carbon storage, and climate driven by a

  7. Biological Effects of Ionizing Radiation

    DOE R&D Accomplishments

    Ingram, M.; Mason, W. B.; Whipple, G. H.; Howland, J. W.

    1952-04-07

    This report presents a review of present knowledge and concepts of the biological effects of ionizing radiations. Among the topics discussed are the physical and chemical effects of ionizing radiation on biological systems, morphological and physiological changes observed in biological systems subjected to ionizing radiations, physiological changes in the intact animal, latent changes following exposure of biological systems to ionizing radiations, factors influencing the biological response to ionizing radiation, relative effects of various ionizing radiations, and biological dosimetry.

  8. Michael Levitt and Computational Biology

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biology Resources with Additional Information * Publications Michael Levitt Courtesy of Linda A. Cicero Stanford News Service Michael Levitt, PhD, professor of structural biology ...

  9. Biological Applications of Synchrotron Radiation:

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    A BioSync Report. Issued by the Structural Biology Synchrotron users Organization, ... of those beams has had a major impact on many areas of science, including biology. ...

  10. Green Biologics | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    Biologics Jump to: navigation, search Name: Green Biologics Place: Oxfordshire, United Kingdom Sector: Biomass, Renewable Energy Product: Oxfordshire-based industrial biotech...

  11. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    SciTech Connect

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

  12. Biological effectiveness of neutrons: Research needs

    SciTech Connect

    Casarett, G.W.; Braby, L.A.; Broerse, J.J.; Elkind, M.M.; Goodhead, D.T.; Oleinick, N.L.

    1994-02-01

    The goal of this report was to provide a conceptual plan for a research program that would provide a basis for determining more precisely the biological effectiveness of neutron radiation with emphasis on endpoints relevant to the protection of human health. This report presents the findings of the experts for seven particular categories of scientific information on neutron biological effectiveness. Chapter 2 examines the radiobiological mechanisms underlying the assumptions used to estimate human risk from neutrons and other radiations. Chapter 3 discusses the qualitative and quantitative models used to organize and evaluate experimental observations and to provide extrapolations where direct observations cannot be made. Chapter 4 discusses the physical principles governing the interaction of radiation with biological systems and the importance of accurate dosimetry in evaluating radiation risk and reducing the uncertainty in the biological data. Chapter 5 deals with the chemical and molecular changes underlying cellular responses and the LET dependence of these changes. Chapter 6, in turn, discusses those cellular and genetic changes which lead to mutation or neoplastic transformation. Chapters 7 and 8 examine deterministic and stochastic effects, respectively, and the data required for the prediction of such effects at different organizational levels and for the extrapolation from experimental results in animals to risks for man. Gaps and uncertainties in this data are examined relative to data required for establishing radiation protection standards for neutrons and procedures for the effective and safe use of neutron and other high-LET radiation therapy.

  13. Biological response modifiers

    SciTech Connect

    Weller, R.E.

    1991-10-01

    Much of what used to be called immunotherapy is now included in the term biological response modifiers. Biological response modifiers (BRMs) are defined as those agents or approaches that modify the relationship between the tumor and host by modifying the host's biological response to tumor cells with resultant therapeutic effects.'' Most of the early work with BRMs centered around observations of spontaneous tumor regression and the association of tumor regression with concurrent bacterial infections. The BRM can modify the host response in the following ways: Increase the host's antitumor responses through augmentation and/or restoration of effector mechanisms or mediators of the host's defense or decrease the deleterious component by the host's reaction; Increase the host's defenses by the administration of natural biologics (or the synthetic derivatives thereof) as effectors or mediators of an antitumor response; Augment the host's response to modified tumor cells or vaccines, which might stimulate a greater response by the host or increase tumor-cell sensitivity to an existing response; Decrease the transformation and/or increase differentiation (maturation) of tumor cells; or Increase the ability of the host to tolerate damage by cytotoxic modalities of cancer treatment.

  14. Biological particle identification apparatus

    DOEpatents

    Salzman, Gary C.; Gregg, Charles T.; Grace, W. Kevin; Hiebert, Richard D.

    1989-01-01

    An apparatus and method for making multiparameter light scattering measurements from suspensions of biological particles is described. Fourteen of the sixteen Mueller matrix elements describing the particles under investigation can be substantially individually determined as a function of scattering angle and probing radiations wavelength, eight elements simultaneously for each of two apparatus configurations using an apparatus which incluees, in its simplest form, two polarization modulators each operating at a chosen frequency, one polarizer, a source of monochromatic electromagnetic radiation, a detector sensitive to the wavelength of radiation employed, eight phase-sensitive detectors, and appropriate electronics. A database of known biological particle suspensions can be assembled, and unknown samples can be quickly identified once measurements are performed on it according to the teachings of the subject invention, and a comparison is made with the database.

  15. BIOLOGICAL IRRADIATION FACILITY

    DOEpatents

    McCorkle, W.H.; Cern, H.S.

    1962-04-24

    A facility for irradiating biological specimens with neutrons is described. It includes a reactor wherein the core is off center in a reflector. A high-exposure room is located outside the reactor on the side nearest the core while a low-exposure room is located on the opposite side. Means for converting thermal neutrons to fast neutrons are movably disposed between the reactor core and the high and low-exposure rooms. (AEC)

  16. Report of The Structural Biology Subcommittee of The Biological and

    Office of Science (SC)

    Environmental Research Advisory Committee | U.S. DOE Office of Science (SC) Report of The Structural Biology Subcommittee of The Biological and Environmental Research Advisory Committee Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings Members Charges/Reports Current BERAC Charges Archive of BERAC Reports Charter .pdf file (135KB) BER Committees of Visitors Federal Advisory Committees BER Home Charges/Reports Report of The Structural Biology Subcommittee of

  17. Abengoa Mojave Final Biological Opinion

    Energy.gov [DOE]

    Biological Opinion on Mojave Solar, LLC's Mojave Solar Project, San Bernardino County, California (8-8-11-F-3)

  18. Computational methods for molecular docking

    SciTech Connect

    Klebe, G.; Lengauer, T.

    1995-12-31

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

  19. Method and apparatus for the gas phase decontamination of chemical and biological agents

    DOEpatents

    O'Neill, Hugh J.; Brubaker, Kenneth L.

    2003-10-07

    An apparatus and method for decontaminating chemical and biological agents using the reactive properties of both the single atomic oxygen and the hydroxyl radical for the decontamination of chemical and biological agents. The apparatus is self contained and portable and allows for the application of gas reactants directly at the required decontamination point. The system provides for the use of ultraviolet light of a specific spectral range to photolytically break down ozone into molecular oxygen and hydroxyl radicals where some of the molecular oxygen is in the first excited state. The excited molecular oxygen will combine with water vapor to produce two hydroxyl radicals.

  20. Elements in biological AMS

    SciTech Connect

    Vogel, J.S.; McAninch, J.; Freeman, S.

    1996-08-01

    AMS (Accelerator Mass Spectrometry) provides high detection sensitivity for isotopes whose half-lives are between 10 years and 100 million years. {sup 14}C is the most developed of such isotopes and is used in tracing natural and anthropogenic organic compounds in the Earth`s biosphere. Thirty-three elements in the main periodic table and 17 lanthanides or actinides have long lived isotopes, providing potential tracers for research in elemental biochemistry. Overlap of biologically interesting heavy elements and possible AMS tracers is discussed.

  1. Neutron instrumentation for biology

    SciTech Connect

    Mason, S.A.

    1994-12-31

    In the October 1994 round of proposals at the ILL, the external biology review sub- committee was asked to allocate neutron beam time to a wide range of experiments, on almost half the total number of scheduled neutron instruments: on 3 diffractometers, on 3 small angle scattering instruments, and on some 6 inelastic scattering spectrometers. In the 3.5 years since the temporary reactor shutdown, the ILL`s management structure has been optimized, budgets and staff have been trimmed, the ILL reactor has been re-built, and many of the instruments up-graded, many powerful (mainly Unix) workstations have been introduced, and the neighboring European Synchrotron Radiation Facility has established itself as the leading synchrotron radiation source and has started its official user program. The ILL reactor remains the world`s most intense dedicated neutron source. In this challenging context, it is of interest to review briefly the park of ILL instruments used to study the structure and energetics of small and large biological systems. A brief summary will be made of each class of experiments actually proposed in the latest ILL proposal round.

  2. Biological hydrogen photoproduction

    SciTech Connect

    Nemoto, Y.

    1995-09-01

    Following are the major accomplishments of the 6th year`s study of biological hydrogen photoproduction which were supported by DOE/NREL. (1) We have been characterizing a biological hydrogen production system using synchronously growing aerobically nitrogen-fixing unicellular cyanobacterium, Synechococcus sp. Miami BG 043511. So far it was necessary to irradiate the cells to produce hydrogen. Under darkness they did not produce hydrogen. However, we found that, if the cells are incubated with oxygen, they produce hydrogen under the dark. Under 80% argon + 20% oxygen condition, the hydrogen production activity under the dark was about one third of that under the light + argon condition. (2) Also it was necessary so far to incubate the cells under argon atmosphere to produce hydrogen in this system. Argon treatment is very expensive and should be avoided in an actual hydrogen production system. We found that, if the cells are incubated at a high cell density and in a container with minimum headspace, it is not necessary to use argon for the hydrogen production. (3) Calcium ion was found to play an important role in the mechanisms of protection of nitrogenase from external oxygen. This will be a clue to understand the reason why the hydrogen production is so resistant to oxygen in this strain. (4) In this strain, sulfide can be used as electron donor for the hydrogen production. This result shows that waste water can be used for the hydrogen production system using this strain.

  3. Biological Performance Assessment

    Energy Science and Technology Software Center

    2013-07-09

    The BioPA provides turbine designers with a set of tools that can be used to assess biological risks of turbines during the design phase, before expensive construction begins. The toolset can also be used to assess existing installations under a variety of operating conditions, supplementing data obtained through expensive field testing. The BioPA uses computational fluid dynamics (CFD) simulations of a turbine design to quantify the exposure of passing fish to a set of knownmore » injury mechanisms. By appropriate sampling of the fluid domain, the BioPA assigns exposure probabilities to each mechanism. The exposure probabilities are combined with dose-response data from laboratory stress studies of fish to produce a set of biological BioPA Scores. These metrics provide an objective measure that can be used to compare competing turbines or to refine a new design. The BioPA process can be performed during the turbine design phase and is considerably less expensive than prototype-scale field testing.« less

  4. 6th Annual Systems Biology Symposium: Systems Biology and the Environment

    SciTech Connect

    Galitski, Timothy, P.

    2007-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology is an annual two-day event gathering the most influential researchers transforming biology into an integrative discipline investigating complex systems. In recognition of the fundamental similarity between the scientific problems addressed in environmental science and systems biology studies at the molecular, cellular, and organismal levels, the 2007 Symposium featured global leaders in “Systems Biology and the Environment.” The objective of the 2007 “Systems Biology and the Environment” International Symposium was to stimulate interdisciplinary thinking and research that spans systems biology and environmental science. This Symposium was well aligned with the DOE’s Genomics:GTL program efforts to achieve scientific objectives for each of the three DOE missions: • Develop biofuels as a major secure energy source for this century, • Develop biological solutions for intractable environmental problems, and • Understand biosystems’ climate impacts and assess sequestration strategies Our scientific program highlighted world-class research exemplifying these priorities. The Symposium featured 45 minute lectures from 12 researchers including: Penny/Sallie Chisholm of MIT gave the keynote address “Tiny Cells, Global Impact: What Prochlorococcus Can Teach Us About Systems Biology”, plus Jim Fredrickson of PNNL, Nitin Baliga of ISB, Steve Briggs of UCSD, David Cox of Perlegen Sciences, Antoine Danchin of Institut Pasteur, John Delaney of the U of Washington, John Groopman of Johns Hopkins, Ben Kerr of the U of Washington, Steve Koonin of BP, Elliott Meyerowitz of Caltech, and Ed Rubin of LBNL. The 2007 Symposium promoted DOE’s three mission areas among scientists from multiple disciplines representing academia, non-profit research institutions, and the private sector. As in all previous

  5. Biology Division progress report, October 1, 1993--September 30, 1995

    SciTech Connect

    1995-10-01

    This Progress Report summarizes the research endeavors of the Biology Division of the Oak Ridge National Laboratory during the period October 1, 1993, through September 30, 1995. The report is structured to provide descriptions of current activities and accomplishments in each of the Division`s major organizational units. Lists of information to convey the entire scope of the Division`s activities are compiled at the end of the report. Attention is focused on the following research activities: molecular, cellular, and cancer biology; mammalian genetics and development; genome mapping program; and educational activities.

  6. 2013 Biological Hydrogen Production Workshop Summary Report ...

    Energy Saver

    Biological Hydrogen Production Workshop Summary Report 2013 Biological Hydrogen Production Workshop Summary Report November 2013 summary report for the 2013 Biological Hydrogen ...

  7. Biological Lignin Depolymerization Presentation for BETO 2015...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    depolymerization with new synthetic biology techniques and new process concepts in biological funneling High-Level Objective: * Employ biology for depolymerization and aromatic ...

  8. Accelerated Molecular Dynamics Methods

    Energy.gov [DOE]

    This presentation on Accelerated Molecular Dynamics Methods was given at the DOE Theory Focus Session on Hydrogen Storage Materials on May 18, 2006.

  9. Plant Vascular Biology 2010

    SciTech Connect

    Ding, Biao

    2014-11-17

    This grant supported the Second International Conference on Plant Vascular Biology (PVB 2010) held July 24-28, 2010 on the campus of Ohio State University, Columbus, Ohio. Biao Ding (Ohio State University; OSU) and David Hannapel (Iowa State University; ISU) served as co-chairs of this conference. Biao Ding served as the local organizer. PVB is defined broadly here to include studies on the biogenesis, structure and function of transport systems in plants, under conditions of normal plant growth and development as well as of plant interactions with pathogens. The transport systems cover broadly the xylem, phloem, plasmodesmata and vascular cell membranes. The PVB concept has emerged in recent years to emphasize the integrative nature of the transport systems and approaches to investigate them.

  10. William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) | U.S.

    Office of Science (SC)

    DOE Office of Science (SC) William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) Biological and Environmental Research (BER) BER Home About Research Biological Systems Science Division (BSSD) Climate and Environmental Sciences Division (CESD) ARM Climate Research Facility Atmospheric System Research (ASR) Program Climate Model Development and Validation (CMDV) Data Management Earth System Modeling (ESM) Program William R. Wiley Environmental Molecular Sciences Laboratory (EMSL)

  11. Biochemical Process Improvements & Synthetic Biology Validation...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Process Improvements & Synthetic Biology Validation Projects This presentation ... Develop efficient, inexpensive synthetic biology methods and tools to convert biomass into ...

  12. Biological Safety | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Biological Select Agents Inspection Report: IG-0681, Concerns Regarding a Non-Viable (Dead) "Anthrax Sport" Research Project at the Oak Ridge National Laboratory Inspection ...

  13. Biological & Environmental Research Abstracts Database

    Office of Scientific and Technical Information (OSTI)

    Welcome to the Biological and Environmental Research Abstracts Database The U.S. ... This database contains abstracts of research projects supported by the program. Work was ...

  14. Environmental Molecular Sciences Laboratory 2004 Annual Report

    SciTech Connect

    White, Julia C.

    2005-04-17

    This 2004 Annual Report describes the research and accomplishments of staff and users of the W.R. Wiley Environmental Molecular Sciences Laboratory (EMSL), located in Richland, Washington. EMSL is a multidisciplinary, national scientific user facility and research organization, operated by Pacific Northwest National Laboratory (PNNL) for the U.S. Department of Energy's Office of Biological and Environmental Research. The resources and opportunities within the facility are an outgrowth of the U.S. Department of Energy's (DOE) commitment to fundamental research for understanding and resolving environmental and other critical scientific issues.

  15. THE DARK MOLECULAR GAS

    SciTech Connect

    Wolfire, Mark G.; Hollenbach, David; McKee, Christopher F. E-mail: dhollenbach@seti.or

    2010-06-20

    The mass of molecular gas in an interstellar cloud is often measured using line emission from low rotational levels of CO, which are sensitive to the CO mass, and then scaling to the assumed molecular hydrogen H{sub 2} mass. However, a significant H{sub 2} mass may lie outside the CO region, in the outer regions of the molecular cloud where the gas-phase carbon resides in C or C{sup +}. Here, H{sub 2} self-shields or is shielded by dust from UV photodissociation, whereas CO is photodissociated. This H{sub 2} gas is 'dark' in molecular transitions because of the absence of CO and other trace molecules, and because H{sub 2} emits so weakly at temperatures 10 K molecular component. This component has been indirectly observed through other tracers of mass such as gamma rays produced in cosmic-ray collisions with the gas and far-infrared/submillimeter wavelength dust continuum radiation. In this paper, we theoretically model this dark mass and find that the fraction of the molecular mass in this dark component is remarkably constant ({approx}0.3 for average visual extinction through the cloud A-bar{sub V{approx_equal}}8) and insensitive to the incident ultraviolet radiation field strength, the internal density distribution, and the mass of the molecular cloud as long as A-bar{sub V}, or equivalently, the product of the average hydrogen nucleus column and the metallicity through the cloud, is constant. We also find that the dark mass fraction increases with decreasing A-bar{sub V}, since relatively more molecular H{sub 2} material lies outside the CO region in this case.

  16. Optical Modulation of Molecular Conductance

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Transient absorption spectra of these molecular layers are consistent with formation of a long-lived charge separated state, a finding with implications for the design of molecular ...

  17. Biological Science | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Biological Science Biological Science The protozoan Plasmodium falciparum gliding through a cell in the gut of a mosquito, its primary host. Although five different species of Plasmodium can cause malaria, Plasmodium falciparum causes the most severe disease. | Photo courtesy of Wikipedia Commons. <a href="http://energy.gov/articles/malaria-researchers-find-weakness-global-killer">Read more</a> The protozoan Plasmodium falciparum gliding through a cell in the gut of a

  18. Molecular Science Research Center annual report

    SciTech Connect

    Knotek, M.L.

    1991-01-01

    The Chemical Structure and Dynamics group is studying chemical kinetics and reactions dynamics of terrestrial and atmospheric processes as well as the chemistry of complex waste forms and waste storage media. Staff are using new laser systems and surface-mapping techniques in combination with molecular clusters that mimic adsorbate/surface interactions. The Macromolecular Structure and Dynamics group is determining biomolecular structure/function relationships for processes the control the biological transformation of contaminants and the health effects of toxic substances. The Materials and Interfaces program is generating information needed to design and synthesize advanced materials for the analysis and separation of mixed chemical waste, the long-term storage of concentrated hazardous materials, and the development of chemical sensors for environmental monitoring of various organic and inorganic species. The Theory, Modeling, and Simulation group is developing detailed molecular-level descriptions of the chemical, physical, and biological processes in natural and contaminated systems. Researchers are using the full spectrum of computational techniques. The Computer and Information Sciences group is developing new approaches to handle vast amounts of data and to perform calculations for complex natural systems. The EMSL will contain a high-performance computing facility, ancillary computing laboratories, and high-speed data acquisition systems for all major research instruments.

  19. Substructured multibody molecular dynamics.

    SciTech Connect

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  20. Experimental Data from the Proteomics Research Center for Integrative Biology

    DOE Data Explorer

    Smith, Richard D.

    The possible roles and importance of proteomics are rapidly growing across essentially all areas of biological research. The precise and comprehensive measurement of levels of expressed proteins and their modified forms can provide new insights into the molecular nature of cell-signaling pathways and networks, the cell cycle, cellular differentiation, and other processes relevant to understanding human health and the progression of various disease states. The ability to characterize protein complexes complements this capability, allowing hypotheses to be tested and the biological system operation to be defined. The Proteomics Research Center for Integrative Biology is a national user facility established and funded by the National Institute of General Medical Sciences component of the National Institutes of Health. This Center has been established to serve the biomedical research community by developing and integrating new proteomic technologies for collaborative and service studies, disseminating the new technologies, and training scientists in their use. The Center is housed in DOEs William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory.

  1. Experimental Data from the Proteomics Research Center for Integrative Biology

    DOE Data Explorer

    Smith, Richard D.

    The possible roles and importance of proteomics are rapidly growing across essentially all areas of biological research. The precise and comprehensive measurement of levels of expressed proteins and their modified forms can provide new insights into the molecular nature of cell-signaling pathways and networks, the cell cycle, cellular differentiation, and other processes relevant to understanding human health and the progression of various disease states. The ability to characterize protein complexes complements this capability, allowing hypotheses to be tested and the biological system operation to be defined. The Proteomics Research Center for Integrative Biology is a national user facility established and funded by the National Institute of General Medical Sciences component of the National Institutes of Health. This Center has been established to serve the biomedical research community by developing and integrating new proteomic technologies for collaborative and service studies, disseminating the new technologies, and training scientists in their use. The Center is housed in DOE’s William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory.

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

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Systems Biology in Prokaryote - Eukaryote Symbiosis Monday, June 25, 2012 - 12:00pm SLAC, ... there are over 130 beamlines at synchrotrons worldwide devoted to structural biology. ...

  3. Artificial photosynthesis combines biology with technology for...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    biology with technology for sustainable energy transformation Authors: Moore, T.A., Moore, A.L., and Gust, D. Title: Artificial photosynthesis combines biology with ...

  4. Autofermentative Biological Hydrogen Production by Cyanobacteria...

    Energy.gov [DOE] (indexed site)

    More Documents & Publications 2013 Biological Hydrogen Production Workshop Summary Report Renewable Hydrogen Production from Biological Systems Anthropogenic CO2 as a Feedstock for ...

  5. Repurposing the translation apparatus for synthetic biology ...

    Office of Scientific and Technical Information (OSTI)

    biology Citation Details In-Document Search This content will become publicly available on July 14, 2017 Title: Repurposing the translation apparatus for synthetic biology ...

  6. Innovative Breakthrough Demonstrated for Biological Ethanol Production...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Innovative Breakthrough Demonstrated for Biological Ethanol Production Innovative Breakthrough Demonstrated for Biological Ethanol Production June 30, 2015 - 11:43am Addthis ...

  7. Molecular Foundry Bay Cam

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Baycam The Molecular Foundry is a Department of Energy-funded nanoscience research facility at Berkeley Lab that provides users from around the world with access to cutting-edge expertise and instrumentation in a collaborative, multidisciplinary environment. twitter instagram facebook

  8. Molecular ion photofragment spectroscopy

    SciTech Connect

    Bustamente, S.W.

    1983-11-01

    A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O/sub 2//sup +/(/sup 4/..pi../sub u/) metastable state which is found to consist of two main components: the /sup 4/..pi../sub 5/2/ and /sup 4/..pi../sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the /sup 4/..pi../sub 3/2/ and /sup 4/..pi../sub 1/2/ spin components having a short lifetime (approx. 6 ms).

  9. Statistical Inference for Big Data Problems in Molecular Biophysics

    SciTech Connect

    Ramanathan, Arvind; Savol, Andrej; Burger, Virginia; Quinn, Shannon; Agarwal, Pratul K; Chennubhotla, Chakra

    2012-01-01

    We highlight the role of statistical inference techniques in providing biological insights from analyzing long time-scale molecular simulation data. Technologi- cal and algorithmic improvements in computation have brought molecular simu- lations to the forefront of techniques applied to investigating the basis of living systems. While these longer simulations, increasingly complex reaching petabyte scales presently, promise a detailed view into microscopic behavior, teasing out the important information has now become a true challenge on its own. Mining this data for important patterns is critical to automating therapeutic intervention discovery, improving protein design, and fundamentally understanding the mech- anistic basis of cellular homeostasis.

  10. ANAEROBIC BIOLOGICAL TREATMENT OF PRODUCED WATER

    SciTech Connect

    John R. Gallagher

    2001-07-31

    During the production of oil and gas, large amounts of water are brought to the surface and must be disposed of in an environmentally sensitive manner. This is an especially difficult problem in offshore production facilities where space is a major constraint. The chief regulatory criterion for produced water is oil and grease. Most facilities have little trouble meeting this criterion using conventional oil-water separation technologies. However, some operations have significant amounts of naphthenic acids in the water that behave as oil and grease but are not well removed by conventional technologies. Aerobic biological treatment of naphthenic acids in simulated-produced water has been demonstrated by others; however, the system was easily overloaded by the large amounts of low-molecular-weight organic acids often found in produced waters. The objective of this research was to determine the ability of an anaerobic biological system to treat these organic acids in a simulated produced water and to examine the potential for biodegradation of the naphthenic acids in the anaerobic environment. A small fixed-film anaerobic biological reactor was constructed and adapted to treat a simulated produced water. The bioreactor was tubular, with a low-density porous glass packing material. The inocula to the reactor was sediment from a produced-water holding pond from a municipal anaerobic digester and two salt-loving methanogenic bacteria. During start-up, the feed to the reactor contained glucose as well as typical produced-water components. When glucose was used, rapid gas production was observed. However, when glucose was eliminated and the major organic component was acetate, little gas was generated. Methane production from acetate may have been inhibited by the high salt concentrations, by sulfide, or because of the lack, despite seeding, of microbes capable of converting acetate to methane. Toluene, a minor component of the produced water (0.1 g/L) was removed in the

  11. Biological responses to engineered nanomaterials: Needs for the next decade

    DOE PAGES [OSTI]

    Murphy, Catherine J.; Vartanian, Ariane M.; Geiger, Franz M.; Hamers, Robert J.; Pedersen, Joel A.; Cui, Qiang; Haynes, Christy L.; Carlson, Erin E.; Hernandez, Rigoberto; Klaper, Rebecca D.; et al

    2015-06-09

    In this study, the interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial-biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterialmore » effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.« less

  12. Biological responses to engineered nanomaterials: Needs for the next decade

    SciTech Connect

    Murphy, Catherine J.; Vartanian, Ariane M.; Geiger, Franz M.; Hamers, Robert J.; Pedersen, Joel A.; Cui, Qiang; Haynes, Christy L.; Carlson, Erin E.; Hernandez, Rigoberto; Klaper, Rebecca D.; Orr, Galya; Rosenzweig, Ze'ev

    2015-06-09

    In this study, the interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial-biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.

  13. The interactions of peripheral membrane proteins with biological membranes

    DOE PAGES [OSTI]

    Johs, Alexander; Whited, A. M.

    2015-01-01

    The interactions of peripheral proteins with membrane surfaces are critical to many biological processes, including signaling, recognition, membrane trafficking, cell division and cell structure. On a molecular level, peripheral membrane proteins can modulate lipid composition, membrane dynamics and protein-protein interactions. Biochemical and biophysical studies have shown that these interactions are in fact highly complex, dominated by several different types of interactions, and have an interdependent effect on both the protein and membrane. Here we examine three major mechanisms underlying the interactions between peripheral membrane proteins and membranes: electrostatic interactions, hydrophobic interactions, and fatty acid modification of proteins. While experimental approachesmore » continue to provide critical insights into specific interaction mechanisms, emerging bioinformatics resources and tools contribute to a systems-level picture of protein-lipid interactions. Through these recent advances, we begin to understand the pivotal role of protein-lipid interactions underlying complex biological functions at membrane interfaces.« less

  14. The interactions of peripheral membrane proteins with biological membranes

    SciTech Connect

    Johs, Alexander; Whited, A. M.

    2015-01-01

    The interactions of peripheral proteins with membrane surfaces are critical to many biological processes, including signaling, recognition, membrane trafficking, cell division and cell structure. On a molecular level, peripheral membrane proteins can modulate lipid composition, membrane dynamics and protein-protein interactions. Biochemical and biophysical studies have shown that these interactions are in fact highly complex, dominated by several different types of interactions, and have an interdependent effect on both the protein and membrane. Here we examine three major mechanisms underlying the interactions between peripheral membrane proteins and membranes: electrostatic interactions, hydrophobic interactions, and fatty acid modification of proteins. While experimental approaches continue to provide critical insights into specific interaction mechanisms, emerging bioinformatics resources and tools contribute to a systems-level picture of protein-lipid interactions. Through these recent advances, we begin to understand the pivotal role of protein-lipid interactions underlying complex biological functions at membrane interfaces.

  15. Towards a Semantic Lexicon for Biological Language Processing

    DOE PAGES [OSTI]

    Verspoor, Karin

    2005-01-01

    This paper explores the use of the resources in the National Library of Medicine's Unified Medical Language System (UMLS) for the construction of a lexicon useful for processing texts in the field of molecular biology. A lexicon is constructed from overlapping terms in the UMLS SPECIALIST lexicon and the UMLS Metathesaurus to obtain both morphosyntactic and semantic information for terms, and the coverage of a domain corpus is assessed. Over 77% of tokens in the domain corpus are found in the constructed lexicon, validating the lexicon's coverage of the most frequent terms in the domain and indicating that the constructedmore » lexicon is potentially an important resource for biological text processing.« less

  16. Method and apparatus to image biological interactions in plants

    DOEpatents

    Weisenberger, Andrew; Bonito, Gregory M.; Reid, Chantal D.; Smith, Mark Frederick

    2015-12-22

    A method to dynamically image the actual translocation of molecular compounds of interest in a plant root, root system, and rhizosphere without disturbing the root or the soil. The technique makes use of radioactive isotopes as tracers to label molecules of interest and to image their distribution in the plant and/or soil. The method allows for the study and imaging of various biological and biochemical interactions in the rhizosphere of a plant, including, but not limited to, mycorrhizal associations in such regions.

  17. Molecular-beam scattering

    SciTech Connect

    Vernon, M.F.

    1983-07-01

    The molecular-beam technique has been used in three different experimental arrangements to study a wide range of inter-atomic and molecular forces. Chapter 1 reports results of a low-energy (0.2 kcal/mole) elastic-scattering study of the He-Ar pair potential. The purpose of the study was to accurately characterize the shape of the potential in the well region, by scattering slow He atoms produced by expanding a mixture of He in N/sub 2/ from a cooled nozzle. Chapter 2 contains measurements of the vibrational predissociation spectra and product translational energy for clusters of water, benzene, and ammonia. The experiments show that most of the product energy remains in the internal molecular motions. Chapter 3 presents measurements of the reaction Na + HCl ..-->.. NaCl + H at collision energies of 5.38 and 19.4 kcal/mole. This is the first study to resolve both scattering angle and velocity for the reaction of a short lived (16 nsec) electronic excited state. Descriptions are given of computer programs written to analyze molecular-beam expansions to extract information characterizing their velocity distributions, and to calculate accurate laboratory elastic-scattering differential cross sections accounting for the finite apparatus resolution. Experimental results which attempted to determine the efficiency of optically pumping the Li(2/sup 2/P/sub 3/2/) and Na(3/sup 2/P/sub 3/2/) excited states are given. A simple three-level model for predicting the steady-state fraction of atoms in the excited state is included.

  18. Molecular Gearing Systems

    Office of Scientific and Technical Information (OSTI)

    ENABLING SCIENCE Molecular gearing systems These molecules that mimic mechanical devices have interesting-and perhaps useful-chemical properties. Andrei A. Gakli Richard A. Sachleben Jeffrey C. Bryan T he race to create smaller devices is fueling much of the research in electronics. The competition has intensified with the advent of microelectromechani- cal systems (MEMS), in which miniaturization is already reaching the dimensional limits imposed by physics of current lithographic techniques

  19. Two protein studies discover molecular secrets to recycling carbon and

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    healing cells | Argonne National Laboratory You may also like Cancer's big data problem October 19, 2016 Two protein studies discover molecular secrets to recycling carbon and healing cells September 9, 2016 Two Argonne-led projects among $39.8 million in first-round Exascale Computing Project awards September 7, 2016 X-rays reveal the photonic crystals in butterfly wings that create color June 10, 2016 New Microbiome Center to combine UChicago, Marine Biological Laboratory and Argonne

  20. Molecular Dynamics Studies of Biomass Degradation in Biofuel Production |

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Argonne Leadership Computing Facility Dynamics Studies of Biomass Degradation in Biofuel Production PI Name: Klaus Schulten PI Email: kschulte@illinois.edu Institution: University of Illinois at Urbana--Champaign Allocation Program: ALCC Allocation Hours at ALCF: 50 Million Year: 2016 Research Domain: Biological Sciences Biofuels are a well--known carbon neutral alternative to fossil fuels. Cellulose is an important molecular building block of many plants but is resistant to easy conversion

  1. MOLECULAR VACUUM PUMP

    DOEpatents

    Eckberg, E.E.

    1960-09-27

    A multiple molecular vacuum pump capable of producing a vacuum of the order of 10/sup -9/ mm Hg is described. The pump comprises a casing of an aggregate of paired and matched cylindrical plates, a recessed portion on one face of each plate concentrically positioned formed by a radially extending wall and matching the similarly recessed portion of its twin plate of that pair of plates and for all paired and matched plates; a plurality of grooves formed in the radially extending walls of each and all recesses progressing in a spiral manner from their respective starting points out at the periphery of the recess inwardly to the central area; a plurality of rotors rotatably mounted to closely occupy the spaces as presented by the paired and matched recesses between all paired plates; a hollowed drive-shaft perforated at points adjacent to the termini of all spiral grooves; inlet ports at the starting points of all grooves and through all plates at common points to each respectively; and a common outlet passage presented by the hollow portion of the perforated hollowed drive-shaft of the molecular pump. (AEC)

  2. Engineering Molecular Transformations for Sustainable Energy...

    Office of Scientific and Technical Information (OSTI)

    Engineering Molecular Transformations for Sustainable Energy Conversion Citation Details In-Document Search Title: Engineering Molecular Transformations for Sustainable Energy ...

  3. Algal Biology Toolbox Workshop Summary Report

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Biology Toolbox Workshop Summary Report San Diego, California May 2016 Summary report from the May 24-25, 2016, Algal Biology Toolbox Workshop in San Diego, California Workshop and ...

  4. A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

    SciTech Connect

    Aderem, Alan; Adkins, Joshua N.; Ansong, Charles; Galagan, James; Kaiser, Shari; Korth, Marcus J.; Law, G. L.; McDermott, Jason E.; Proll, Sean; Rosenberger, Carrie; Schoolnik, Gary; Katze, Michael G.

    2011-02-01

    The 20th century was marked by extraordinary advances in our understanding of microbes and infectious disease, but pandemics remain, food and water borne illnesses are frequent, multi-drug resistant microbes are on the rise, and the needed drugs and vaccines have not been developed. The scientific approaches of the pastincluding the intense focus on individual genes and proteins typical of molecular biologyhave not been sufficient to address these challenges. The first decade of the 21st century has seen remarkable innovations in technology and computational methods. These new tools provide nearly comprehensive views of complex biological systems and can provide a correspondingly deeper understanding of pathogen-host interactions. To take full advantage of these innovations, the National Institute of Allergy and Infectious Diseases recently initiated the Systems Biology Program for Infectious Disease Research. As participants of the Systems Biology Program we think that the time is at hand to redefine the pathogen-host research paradigm.

  5. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun [University of South Florida, Tampa (USF)] [University of South Florida, Tampa (USF); Cheng, Xiaolin [ORNL] [ORNL; Monticelli, Luca [Institut National de la Sant et de la Recherche Mdicale (INSERM) and INTS, France] [Institut National de la Sant et de la Recherche Mdicale (INSERM) and INTS, France; Heberle, Frederick A [ORNL] [ORNL; Kucerka, Norbert [Atomic Energy of Canada Limited (AECL), Canadian Neutron Beam Centre (CNBC) and Comenius University,] [Atomic Energy of Canada Limited (AECL), Canadian Neutron Beam Centre (CNBC) and Comenius University,; Tieleman, D. Peter [University of Calgary, ALberta, Canada] [University of Calgary, ALberta, Canada; Katsaras, John [ORNL] [ORNL

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  6. Assessment of Molecular Modeling & Simulation

    SciTech Connect

    2002-01-03

    This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.

  7. Semiconductor Nanocrystals for Biological Imaging

    SciTech Connect

    Fu, Aihua; Gu, Weiwei; Larabell, Carolyn; Alivisatos, A. Paul

    2005-06-28

    Conventional organic fluorophores suffer from poor photo stability, narrow absorption spectra and broad emission feature. Semiconductor nanocrystals, on the other hand, are highly photo-stable with broad absorption spectra and narrow size-tunable emission spectra. Recent advances in the synthesis of these materials have resulted in bright, sensitive, extremely photo-stable and biocompatible semiconductor fluorophores. Commercial availability facilitates their application in a variety of unprecedented biological experiments, including multiplexed cellular imaging, long-term in vitro and in vivo labeling, deep tissue structure mapping and single particle investigation of dynamic cellular processes. Semiconductor nanocrystals are one of the first examples of nanotechnology enabling a new class of biomedical applications.

  8. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect

    Nesbitt, David J.

    2011-07-11

    Yuan T. Lee & Professor George Schatz. Professor Lees research has been based on the development & use of advanced chemical kinetics & molecular beams to investigate & manipulate the behavior of fundamental chemical reactions. Lees work has been recognized by many awards, including the Nobel Prize for Chemistry in 1986, as well as Sloan Fellow, Dreyfus Scholar, Fellowship in the American Academy of Arts & Sciences, Fellowship in the American Physical Society, Guggenheim Fellow, Member National Academy of Sciences, Member Academia Sinica, E.O. Lawrence Award, Miller Professor, Berkeley, Fairchild Distinguished Scholar, Harrison Howe Award, Peter Debye Award, & the National Medal of Science. Lee also has served as the President of the Academia Sinica in Taiwan (ROC). Professor Schatzs research group is interested in using theory & computation to describe physical phenomena in a broad range of applications relevant to chemistry, physics, biology & engineering. Among the types of applications that we interested are: optical properties of nanoparticles & nanoparticle assemblies; using theory to model polymer properties; DNA structure, thermodynamics & dynamics; modeling self assembly & nanopatterning; & gas phase reaction dynamics. Among his many awards & distinctions have been appointment as an Alfred P. Sloan Research Fellow, Camille & Henry Dreyfus Teacher-Scholar, the Fresenius Award, Fellow of the American Physical Society, the Max Planck Research Award, Fellowship in the American Association for the Advancement of Science, & election to the International Academy of Quantum Molecular Sciences & the American Academy of Arts & Sciences. Dr Schatz is also lauded for his highly successful work as Editor for the Journal of Physical Chemistry. We requested $10,000 from DOE in support of this meeting. The money was distributed widely among the student & post doctoral fellows & some used to attract the very best scientists in the field. The organizers were committed to

  9. Lubricant characterization by molecular simulation

    SciTech Connect

    Moore, J.D.; Cui, S.T.; Cummings, P.T.; Cochran, H.D.

    1997-12-01

    The authors have reported the calculation of the kinematic viscosity index of squalane from nonequilibrium molecular dynamics simulations. This represents the first accurate quantitative prediction of this measure of lubricant performance by molecular simulation. Using the same general alkane potential model, this computational approach offers the possibility of predicting the performance of potential lubricants prior to synthesis. Consequently, molecular simulation is poised to become an important tool for future lubricant development.

  10. Mysteries of 'molecular machines' revealed

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Mysteries of 'molecular machines' revealed Mysteries of 'molecular machines' revealed Scientists are making it easier for pharmaceutical companies and researchers to see the detailed inner workings of molecular machines. December 22, 2014 A picture of a membrane protein called cysZ determined with Phenix software using data that could not previously be analyzed. A picture of a membrane protein called cysZ determined with Phenix software using data that could not previously be analyzed. Contact

  11. Interface-assisted molecular spintronics

    SciTech Connect

    Raman, Karthik V.

    2014-09-15

    Molecular spintronics, a field that utilizes the spin state of organic molecules to develop magneto-electronic devices, has shown an enormous scientific activity for more than a decade. But, in the last couple of years, new insights in understanding the fundamental phenomena of molecular interaction on magnetic surfaces, forming a hybrid interface, are presenting a new pathway for developing the subfield of interface-assisted molecular spintronics. The recent exploration of such hybrid interfaces involving carbon based aromatic molecules shows a significant excitement and promise over the previously studied single molecular magnets. In the above new scenario, hybridization of the molecular orbitals with the spin-polarized bands of the surface creates new interface states with unique electronic and magnetic character. This study opens up a molecular-genome initiative in designing new handles to functionalize the spin dependent electronic properties of the hybrid interface to construct spin-functional tailor-made devices. Through this article, we review this subject by presenting a fundamental understanding of the interface spin-chemistry and spin-physics by taking support of advanced computational and spectroscopy tools to investigate molecular spin responses with demonstration of new interface phenomena. Spin-polarized scanning tunneling spectroscopy is favorably considered to be an important tool to investigate these hybrid interfaces with intra-molecular spatial resolution. Finally, by addressing some of the recent findings, we propose novel device schemes towards building interface tailored molecular spintronic devices for applications in sensor, memory, and quantum computing.

  12. Electron Trapping by Molecular Vibration

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    here, Rathbone et al. observe a nominally "forbidden" electronic transition that is activated by molecular vibrational modes that break the molecule's symmetry. Their...

  13. Electron Trapping by Molecular Vibration

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally...

  14. Molecular Foundry User Meeting - JCAP

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Molecular Foundry User Meeting Molecular Foundry User Meeting Thu, Aug 11, 2016 5:00pm 17:00 Fri, Aug 12, 2016 6:00pm 18:00 Lawrence Berkeley National Laboratory Berkeley, CA USA The Molecular Foundry is hosting its annual Users' Meeting - a nanoscience conference at Lawrence Berkeley National Lab - on August 11-12, 2016. The Molecular Foundry is a Department of Energy user facility for academic, national laboratory and industrial researchers. Whether you are a returning user, a prospective

  15. Rapid classification of biological components

    DOEpatents

    Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

    2013-10-15

    A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

  16. Rapid classification of biological components

    DOEpatents

    Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

    2010-03-23

    A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

  17. Rapid classification of biological components

    DOEpatents

    Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

    2006-01-24

    A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine, methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to the surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to the subject's identity.

  18. Rapid classification of biological components

    SciTech Connect

    Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

    2010-03-23

    A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, Cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens of the surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

  19. Impact of Radiation Biology on Fundamental Insights in Biology

    DOE R&D Accomplishments

    Setlow, Richard B.

    1982-07-27

    Research supported by OHER [Office of Health and Environmental Research] and its predecessors has as one of its major goals an understanding of the effects of radiation at low doses and dose rates on biological systems, so as to predict their effects on humans. It is not possible to measure such effects directly. They must be predicted from basic knowledge on how radiation affects cellular components such as DNA and membranes and how cells react to such changes. What is the probability of radiation producing human mutations and what are the probabilities of radiation producing cancer? The end results of such studies are radiation exposure standards for workers and for the general population. An extension of these goals is setting standards for exposure to chemicals involved in various energy technologies. This latter problem is much more difficult because chemical dosimetry is a primitive state compared to radiation dosimetry.

  20. Impact of Radiation Biology on Fundamental in Biology

    SciTech Connect

    Setlow, Richard B.

    1983-01-20

    Research supported by OHER and its predecessors has as one of its major goals an understanding of the effects of radiation at low doses and dose rates on biological systems, so as to predict their effects on humans. It is not possible to measure such effects directly. They must be predicted from basic knowledge on how radiation affects cellular components such as DNA and membranes and how cells react to such changes. What is the probability of radiation producing human mutations and what are the probabilities of radiation producing cancer? The end results of such studies are radiation exposure standards for workers and for the general population. An extension of these goals is setting standards for exposure to chemicals involved in various energy technologies. This latter problem is much more difficult because chemical dosimetry is is a primitive state compared to radiation dosimetry.

  1. Method of measurement in biological systems

    DOEpatents

    Turteltaub, K.W.; Vogel, J.S.; Felton, J.S.; Gledhill, B.L.: Davis, J.C.; Stanker, L.H.

    1993-05-11

    A method is disclosed of quantifying molecules in biological substances, comprising: selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere; preparing a long-lived radioisotope labeled reactive chemical specie; administering the chemical specie to the biological host in doses sufficiently low to avoid significant overt damage to the biological system; allowing a period of time to elapse sufficient for dissemination and interaction of the chemical specie with the host throughout the biological system of the host; isolating a reacted fraction of the biological substance from the host in a manner sufficient to avoid contamination of the substance from extraneous sources; converting the fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation; and measuring the radioisotope concentration in the material by means of direct isotopic counting.

  2. Biological and Environmental Research (BER) Homepage | U.S. DOE...

    Office of Science (SC)

    EXPLORING the frontiers of genome-enabled biology. Understanding Complex Biological and ... and inquiry in atmospheric chemistry and physics, ecology, biology, and biogeochemistry. ...

  3. Breaking the Biological Barriers to Cellulosic Ethanol, June...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Breaking the Biological Barriers to Cellulosic ...

  4. Cerenkov emission induced by external beam radiation stimulates molecular fluorescence

    SciTech Connect

    Axelsson, Johan; Davis, Scott C.; Gladstone, David J.; Pogue, Brian W.

    2011-07-15

    Purpose: Cerenkov emission is induced when a charged particle moves faster than the speed of light in a given medium. Both x-ray photons and electrons produce optical Cerenkov photons in everyday radiation therapy of tissue; yet, this phenomenon has never been fully documented. This study quantifies the emissions and also demonstrates that the Cerenkov emission can excite a fluorophore, protoporphyrin IX (PpIX), embedded in biological phantoms. Methods: In this study, Cerenkov emission induced by radiation from a clinical linear accelerator is investigated. Biological mimicking phantoms were irradiated with x-ray photons, with energies of 6 or 18 MV, or electrons at energies 6, 9, 12, 15, or 18 MeV. The Cerenkov emission and the induced molecular fluorescence were detected by a camera or a spectrometer equipped with a fiber optic cable. Results: It is shown that both x-ray photons and electrons, at MeV energies, produce optical Cerenkov photons in tissue mimicking media. Furthermore, we demonstrate that the Cerenkov emission can excite a fluorophore, protoporphyrin IX (PpIX), embedded in biological phantoms. Conclusions: The results here indicate that molecular fluorescence monitoring during external beam radiotherapy is possible.

  5. OTEC environmental biological oceanographic program

    SciTech Connect

    Hartwig, E.O.

    1981-07-01

    One of the major goals of the OTEC biological field measurement program is to assess the effect of OTEC operations on the environment. Prior understanding of the natural variability of the tropical oceanic plankton community is the most important method for determining changes due to operation of an OTEC plant. The spatial and temporal patterns of the plankton community in terms of absolute number, biomass and species composition have been investigated at potential OTEC sites. Considerable data exist which document the changes with depth of all three measurements. Diel fluctuations in number and species composition have been studied at one site. While horizontal and seasonal patterns of variability likely exist at all sites, they are subtle and remain somewhat unclear. Attempts are now being made to determine the overall trophic structure of the plankton community at these sites using these data, gut content analysis, and information already in the literature.

  6. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    SciTech Connect

    De Yoreo, J J; Bartelt, M C; Orme, C A; Villacampa, A; Weeks, B L; Miller, A E

    2002-01-31

    Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

  7. HIV Molecular Immunology 2014

    SciTech Connect

    Yusim, Karina; Korber, Bette Tina Marie; Barouch, Dan; Koup, Richard; de Boer, Rob; Moore, John P.; Brander, Christian; Haynes, Barton F.; Walker, Bruce D.

    2015-02-03

    HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2014 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as crossreactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins are provided.

  8. International symposium on cellular and molecular biology of phosphate and phosphorylated compounds in microorganisms: Proceedings

    SciTech Connect

    1993-12-31

    This report contains the abstracts of papers presented at the conference. Attention is focused on the following topics: regulation of phosphate metabolism in bacteria; structure-function of alkaline phosphatase; regulation of phosphate metabolism in yeast; transport of phosphate and phosphorylated compounds; and phosphate regulation in pathogenesis and secondary metabolism.

  9. Molecular biological enhancement of coal biodesulfurization. Technical report, March 1, 1994--May 31, 1994

    SciTech Connect

    Kilbane, J.J. II

    1994-09-01

    IGT has developed a microbial culture of Rhodococcus rhodochrous, designated as IGTS8, that is capable of specifically cleaving carbon-sulfur bonds in a range of organosulfur model compounds and is capable of removing organic sulfur from coal and petroleum without significantly sacrificing the calorific value of the fuel. Although IGTS8 possesses the ability to specifically remove organic sulfur from coal, a major research need is to develop improved strains of microorganisms that possess higher levels of desulfurization activity and therefore will permit more favorable biodesulfurization process conditions: faster rates, more complete removal, and smaller reactor size. Strain improvement is the single most important aspect to the development of a practical coal biodesulfurization process and accordingly is the focus of research in this project. During this quarter the DNA sequences and transcriptional initiation sites of several promoters derived from the chromosome of Rhodococcus rhodochrous IGTS8 were determined. Several strong promoters have been used to replace the promoter of the desulfurization genes with the intent of obtaining cultures with enhanced levels of desulfurization activity. The evaluation of the ability of improved cultures to desulfurize coal will be evaluated during the final quarter of this project.

  10. Electrostatic thin film chemical and biological sensor

    DOEpatents

    Prelas, Mark A.; Ghosh, Tushar K.; Tompson, Jr., Robert V.; Viswanath, Dabir; Loyalka, Sudarshan K.

    2010-01-19

    A chemical and biological agent sensor includes an electrostatic thin film supported by a substrate. The film includes an electrostatic charged surface to attract predetermined biological and chemical agents of interest. A charge collector associated with said electrostatic thin film collects charge associated with surface defects in the electrostatic film induced by the predetermined biological and chemical agents of interest. A preferred sensing system includes a charge based deep level transient spectroscopy system to read out charges from the film and match responses to data sets regarding the agents of interest. A method for sensing biological and chemical agents includes providing a thin sensing film having a predetermined electrostatic charge. The film is exposed to an environment suspected of containing the biological and chemical agents. Quantum surface effects on the film are measured. Biological and/or chemical agents can be detected, identified and quantified based on the measured quantum surface effects.

  11. Developing Biological Specifications for Fish Friendly Turbines |

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Department of Energy Developing Biological Specifications for Fish Friendly Turbines Developing Biological Specifications for Fish Friendly Turbines This factsheet explains studies conducted in a highly reproducible manner to examine the biological effects to fish exposed to a shear environment in the laboratory. bio_specific_fish_friendly_turbines.pdf (59.94 KB) More Documents & Publications Environmental Effects of Hydrokinetic Turbines on Fish: Desktop and Laboratory Flume Studies

  12. Method for photo-altering a biological system to improve biological effect

    DOEpatents

    Hill, Richard A.; Doiron, Daniel R.; Crean, David H.

    2000-08-01

    Photodynamic therapy is a new adjunctive therapy for filtration surgery that does not use chemotherapy agents or radiation, but uses pharmacologically-active sensitizing compounds to produce a titratable, localized, transient, post operative avascular conjunctiva. A photosensitizing agent in a biological system is selectively activated by delivering the photosensitive agent to the biological system and laser activating only a spatially selected portion of the delivered photosensitive agent. The activated portion of the photosensitive agent reacts with the biological system to obtain a predetermined biological effect. As a result, an improved spatial disposition and effectuation of the biological effect by the photosensitive agent in the biological system is achieved.

  13. A brief history of the Biology Complex

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Complex Most of the "Biology" buildings were constructed in early 1945 and were built as expansion capability for the uranium preparation operations being conducted across the...

  14. Autofermentative Biological Hydrogen Production by Cyanobacteria

    Office of Energy Efficiency and Renewable Energy (EERE)

    Presentation by Charles Dismukes, Rutgers University, at the Biological Hydrogen Production Workshop held September 24-25, 2013, at the National Renewable Energy Laboratory in Golden, Colorado.

  15. Developing Biological Specifications for Fish Friendly Turbines

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Biological Specifications for Fish Friendly Turbines The U.S. Department of Energy's ... which environmen- tal attributes, such as entrainment survival for fish, are emphasized. ...

  16. Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

    SciTech Connect

    Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.

    2010-03-14

    Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

  17. Apparatus for molecular weight separation

    DOEpatents

    Smith, Richard D.; Liu, Chuanliang

    2001-01-01

    The present invention relates generally to an apparatus and method for separating high molecular weight molecules from low molecular weight molecules. More specifically, the invention relates to the use of microdialysis for removal of the salt (low molecular weight molecules) from a nucleotide sample (high molecular weight molecules) for ESI-MS analysis. The dialysis or separation performance of the present invention is improved by (1) increasing dialysis temperature thereby increasing desalting efficiency and improving spectrum quality; (2) adding piperidine and imidazole to the dialysis buffer solution and reducing charge states and further increasing detection sensitivity for DNA; (3) using low concentrations (0-2.5 mM NH4OAc) of dialysis buffer and shifting the DNA negative ions to higher charge states, producing a nearly 10-fold increase in detection sensitivity and a slightly decreased desalting efficiency, (4) conducting a two-stage separation or (5) any combination of (1), (2), (3) and (4).

  18. Institute for Molecular Engineering | Argonne National Laboratory

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Learn more about the Institute for Molecular Engineering. When completed in early 2015, the William Eckhardt Research Center at the University of Chicago will be the home of the Institute of Molecular Engineering. Institute for Molecular Engineering The new Institute for Molecular Engineering explores innovative technologies that address fundamental societal problems through advances in nanoscale manipulation and design at a molecular scale. Addressing Societal Problems with Molecular Science

  19. From systems biology to photosynthesis and whole-plant modeling: a conceptual model for integrating multi-scale networks

    SciTech Connect

    Weston, David; Hanson, Paul J; Norby, Richard J; Tuskan, Gerald A; Wullschleger, Stan D

    2012-01-01

    Network analysis is now a common statistical tool for molecular biologists. Network algorithms are readily used to model gene, protein and metabolic correlations providing insight into pathways driving biological phenomenon. One output from such an analysis is a candidate gene list that can be responsible, in part, for the biological process of interest. The question remains, however, as to whether molecular network analysis can be used to inform process models at higher levels of biological organization. In our previous work, transcriptional networks derived from three plant species were constructed, interrogated for orthology and then correlated to photosynthetic inhibition at elevated temperature. One unique aspect of that study was the link from co-expression networks to net photosynthesis. In this addendum, we propose a conceptual model where traditional network analysis can be linked to whole-plant models thereby informing predictions on key processes such as photosynthesis, nutrient uptake and assimilation, and C partitioning.

  20. Protein Structure Suggests Role as Molecular Adapter

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Structure Suggests Role as Molecular Adapter Print To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the...

  1. Connecting the Molecular and the Continuum Scales

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    range of phenomena, from climate change to contaminant remediation. Accomplishments: Used molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients of...

  2. Protein Structure Suggests Role as Molecular Adapter

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Protein Structure Suggests Role as Molecular Adapter Print To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the...

  3. SPITZER INFRARED SPECTROGRAPH DETECTION OF MOLECULAR HYDROGEN...

    Office of Scientific and Technical Information (OSTI)

    MOLECULAR HYDROGEN ROTATIONAL EMISSION TOWARDS TRANSLUCENT CLOUDS Citation Details In-Document Search Title: SPITZER INFRARED SPECTROGRAPH DETECTION OF MOLECULAR HYDROGEN ...

  4. Division of Biological and Medical Research research summary 1984-1985

    SciTech Connect

    Barr, S.H.

    1985-08-01

    The Division of Biological and Medical Research at Argonne National Laboratory conducts multidisciplinary research aimed at defining the biological and medical hazards to man from energy technologies and new energy options. These technically oriented studies have a strong base in fundamental research in a variety of scientific disciplines, including molecular and cellular biology, biophysics, genetics, radiobiology, pharmacology, biochemistry, chemistry, environmental toxicology, and epidemiology. This research summary is organized into six parts. The first five parts reflect the Divisional structure and contain the scientific program chapters, which summarize the activities of the individual groups during the calendar year 1984 and the first half of 1985. To provide better continuity and perspective, previous work is sometimes briefly described. Although the summaries are short, efforts have been made to indicate the range of research activities for each group.

  5. Final report for Conference Support Grant "From Computational Biophysics to Systems Biology - CBSB12"

    SciTech Connect

    Hansmann, Ulrich H.E.

    2012-07-02

    This report summarizes the outcome of the international workshop “From Computational Biophysics to Systems Biology (CBSB12)” which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previous years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.

  6. Sealable femtoliter chamber arrays for cell-free biology

    DOE PAGES [OSTI]

    Retterer, Scott T.; Fowlkes, Jason Davidson; Collier, Charles Patrick; Simpson, Michael L.; Norred, Sarah Elizabeth; Caveney, Patrick M.; Boreyko, Jonathan B.

    2015-03-11

    Cell-free systems provide a flexible platform for probing specific networks of biological reactions isolated from the complex resource sharing (e.g. global gene expression, cell division) encountered within living cells. However, such systems, used in conventional macro-scale bulk reactors, often fail to exhibit the dynamic behaviors and efficiencies characteristic of their living micro-scale counterparts. Understanding the impact of internal cell structure and scale on reaction dynamics is crucial to understanding complex gene networks. Here we report a microfabricated device that confines cell-free reactions in cellular scale volumes while allowing flexible characterization of the enclosed molecular system. This multilayered poly(dimethylsiloxane) (PDMS) devicemore » contains femtoliter-scale reaction chambers on an elastomeric membrane which can be actuated (open and closed). When actuated, the chambers confine Cell-Free Protein Synthesis (CFPS) reactions expressing a fluorescent protein, allowing for the visualization of the reaction kinetics over time using time-lapse fluorescent microscopy. Lastly, we demonstrate how this device may be used to measure the noise structure of CFPS reactions in a manner that is directly analogous to those used to characterize cellular systems, thereby enabling the use of noise biology techniques to characterize CFPS gene circuits and their interactions with the cell-free environment.« less

  7. A national facility for biological cryo-electron microscopy

    SciTech Connect

    Saibil, Helen R.; Grnewald, 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.

  8. Matrix Effects in Biological Mass Spectrometry Imaging: Identification and Compensation

    SciTech Connect

    Lanekoff, Ingela T.; Stevens, Susan; Stenzel-Poore, Mary; Laskin, Julia

    2014-07-21

    Matrix effects in mass spectrometry imaging (MSI) may affect the observed molecular distribution in chemical and biological systems. In this study, we introduce an experimental approach that efficiently compensates for matrix effects in nanospray desorption electrospray ionization (nano-DESI) MSI without introducing any complexity into the experimental protocol. We demonstrate compensation for matrix effects in nano-DESI MSI of phosphatidylcholine (PC) in normal and ischemic mouse brain tissue by doping the nano-DESI solvent with PC standards. Specifically, we use mouse brain tissue of a middle cerebral artery occlusion (MCAO) stroke model with an ischemic region localized to one hemisphere of the brain. Due to similar suppression in ionization of endogenous PC molecules extracted from the tissue and PC standards added to the solvent, matrix effects are eliminated by normalizing the intensity of the sodium and potassium adducts of endogenous PC to the intensity of the corresponding adduct of the PC standard. This approach efficiently compensates for signal variations resulting from differences in the local concentrations of sodium and potassium in tissue sections and from the complexity of the extracted analyte mixture derived from local variations in molecular composition.

  9. Method of measurement in biological systems

    DOEpatents

    Turteltaub, K.W.; Vogel, J.S.; Felton, J.S.; Gledhill, B.L.; Davis, J.C.

    1994-12-27

    Disclosed is a method of quantifying molecules in biological substances comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering the chemical specie to the biological host in doses sufficiently low to avoid significant overt damage to the biological system, d. allowing a period of time to elapse sufficient for dissemination and interaction of the chemical specie with the host throughout the biological system of the host, e. isolating a reacted fraction of the biological substance from the host in a manner sufficient to avoid contamination of the substance from extraneous sources, f. converting the fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in the material by means of direct isotopic counting. 5 figures.

  10. Method of measurement in biological systems

    DOEpatents

    Turteltaub, Kenneth W.; Vogel, John S.; Felton, James S.; Gledhill, Barton L.; Davis, Jay C.; Stanker, Larry H.

    1993-05-11

    Disclosed is a method of quantifying molecules in biological substances, comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering said chemical specie to said biological host in doses sufficiently low to avoid significant overt damage to the biological system thereof, d. allowing a period of time to elapse sufficient for dissemination and interaction of said chemical specie with said host throughout said biological system of said host, e. isolating a reacted fraction of the biological substance from said host in a manner sufficient to avoid contamination of said substance from extraneous sources, f. converting said fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in said material by means of direct isotopic counting.

  11. Method of measurement in biological systems

    DOEpatents

    Turteltaub, Kenneth W.; Vogel, John S.; Felton, James S.; Gledhill, Barton L.; Davis, Jay C.

    1994-01-01

    Disclosed is a method of quantifying molecules in biological substances comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering said chemical specie to said biological host in doses sufficiently low to avoid significant overt damage to the biological system thereof, d. allowing a period of time to elapse sufficient for dissemination and interaction of said chemical specie with said host throughout said biological system of said host, e. isolating a reacted fraction of the biological substance from said host in a manner sufficient to avoid contamination of said substance from extraneous sources, f. converting said fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in said material by means of direct isotopic counting.

  12. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    SciTech Connect

    Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology.

  13. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    DOE PAGES [OSTI]

    Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

  14. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    SciTech Connect

    Aradi, Blint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian BornOppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology.

  15. Molecular separation method and apparatus

    DOEpatents

    Villa-Aleman, Eliel

    1996-01-01

    A method and apparatus for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve.

  16. Molecular separation method and apparatus

    DOEpatents

    Villa-Aleman, E.

    1996-04-09

    A method and apparatus are disclosed for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular sieve. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve. 2 figs.

  17. SU-E-I-39: Molecular Image Guided Cancer Stem Cells Therapy

    SciTech Connect

    Abdollahi, H

    2014-06-01

    Purpose: Cancer stem cells resistance to radiation is a problematic issue that has caused a big fail in cancer treatment. Methods: As a primary work, molecular imaging can indicate the main mechanisms of radiation resistance of cancer stem cells. By developing and commissioning new probes and nanomolecules and biomarkers, radiation scientist will able to identify the essential pathways of radiation resistance of cancer stem cells. As the second solution, molecular imaging is a best way to find biological target volume and delineate cancer stem cell tissues. In the other hand, by molecular imaging techniques one can image the treatment response in tumor and also in normal tissue. In this issue, the response of cancer stem cells to radiation during therapy course can be imaged, also the main mechanisms of radiation resistance and finding the best radiation modifiers (sensitizers) can be achieved by molecular imaging modalities. In adaptive radiotherapy the molecular imaging plays a vital role to have higher tumor control probability by delivering high radiation doses to cancer stem cells in any time of treatment. The outcome of a feasible treatment is dependent to high cancer stem cells response to radiation and removing all of which, so a good imaging modality can show this issue and preventing of tumor recurrence and metastasis. Results: Our results are dependent to use of molecular imaging as a new modality in the clinic. We propose molecular imaging as a new radiobiological technique to solve radiation therapy problems due to cancer stem cells. Conclusion: Molecular imaging guided cancer stem cell diagnosis and therapy is a new approach in the field of cancer treatment. This new radiobiological imaging technique should be developed in all clinics as a feasible tool that is more biological than physical imaging.

  18. Charge exchange molecular ion source

    DOEpatents

    Vella, Michael C.

    2003-06-03

    Ions, particularly molecular ions with multiple dopant nucleons per ion, are produced by charge exchange. An ion source contains a minimum of two regions separated by a physical barrier and utilizes charge exchange to enhance production of a desired ion species. The essential elements are a plasma chamber for production of ions of a first species, a physical separator, and a charge transfer chamber where ions of the first species from the plasma chamber undergo charge exchange or transfer with the reactant atom or molecules to produce ions of a second species. Molecular ions may be produced which are useful for ion implantation.

  19. All-Optical Molecular Orientation

    SciTech Connect

    Oda, Keita; Hita, Masafumi; Minemoto, Shinichirou; Sakai, Hirofumi [Department of Physics, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)

    2010-05-28

    We report clear evidence of all-optical orientation of carbonyl sulfide molecules with an intense nonresonant two-color laser field in the adiabatic regime. The technique relies on the combined effects of anisotropic hyperpolarizability interaction and anisotropic polarizability interaction and does not rely on the permanent dipole interaction with an electrostatic field. It is demonstrated that the molecular orientation can be controlled simply by changing the relative phase between the two wavelength fields. The present technique brings researchers a new steering tool of gaseous molecules and will be quite useful in various fields such as electronic stereodynamics in molecules and ultrafast molecular imaging.

  20. Frontiers of Plant Cell Biology: Signals and Pathways, System-Based Approaches 22nd Symposium in Plant Biology (University of California-Riverside)

    SciTech Connect

    Minorsky, Peter V.

    2003-06-01

    The symposium ''Frontiers of Plant Cell Biology: Signals and Pathways, Systems-Based Approaches'' was held January 15-18, 2003 at the Riverside Convention Center in Riverside, California. The host organization for the symposium was the Center for Plant Cell Biology (CEPCEB) at the University of California, Riverside (UCR). The meeting, focusing on systems-based approaches to plant cell biology research, was the first of this kind in the field of plant biology. The speakers and nearly 100 posters placed emphasis on recent developments in plant cellular biology and molecular genetics, particularly those employing emerging genomic tools, thereby sharing the most current knowledge in the field and stimulating future advances. In attendance were many well-established scientists and young investigators who approach plant cell biology from different but complementary conceptual and technical perspectives. Indeed, many disciplines are converging in the field of cell biology, producing synergies that will enable plant scientists to determine the function of gene products in the context of living cells in whole organisms. New, cross-disciplinary collaborations, as well as the involvement of computer scientists and chemists in plant biology research, are likely additional outcomes of the symposium. The program included 39 invited session speakers and workshop/panel speakers. Sessions were convened on the following themes: Cell-Cell Communication; Protein Trafficking; Cell Surface, Extracellular Matrix and Cell Wall; Signal Transduction; Signal Transduction and Proteosome; and Systems-Based Approaches to Plant Cell Biology. Workshops on Chemical Genetics and Visual Microscopy were also presented. Abstracts from each of the speaker presentations, as well as the posters presented at the meeting were published in a program booklet given to the 239 faculty members, researchers, postdoctoral scientists and graduate students in attendance. The booklet thus serves as a reference for

  1. Algal Biology Program at Los Alamos

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Algal Biology Program at Los Alamos gets a star October 11, 2011 LOS ALAMOS, New Mexico, October 11, 2011-Richard Sayre, one of the nation's top specialists in algae and...

  2. Renewable Hydrogen Production from Biological Systems

    Office of Energy Efficiency and Renewable Energy (EERE)

    Presentation by Matthew Posewitz, Colorado School of Mines, at the Biological Hydrogen Production Workshop held September 24-25, 2013, at the National Renewable Energy Laboratory in Golden, Colorado.

  3. Biological denitrification of high concentration nitrate waste

    DOEpatents

    Francis, Chester W.; Brinkley, Frank S.

    1977-01-01

    Biological denitrification of nitrate solutions at concentrations of greater than one kilogram nitrate per cubic meter is accomplished anaerobically in an upflow column having as a packing material a support for denitrifying bacteria.

  4. Biological and Environmental Research Advisory Committee

    Office of Science (SC)

    February 26-27, 2015, Tysons, Virginia | U.S. DOE Office of Science (SC) February 26-27, 2015, Tysons, Virginia Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (135KB) BER Committees of Visitors Federal Advisory Committees BER Home Meetings Biological and Environmental Research Advisory Committee February 26-27, 2015, Tysons, Virginia Print Text Size: A A A FeedbackShare Page

  5. Biological and Environmental Research Advisory Committee

    Office of Science (SC)

    October 28-29, 2013 | U.S. DOE Office of Science (SC) October 28-29, 2013 Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (135KB) BER Committees of Visitors Federal Advisory Committees BER Home Meetings Biological and Environmental Research Advisory Committee October 28-29, 2013 Print Text Size: A A A FeedbackShare Page Agenda .pdf file (10KB) Presentations: Sharlene Weatherwax

  6. Renewable Hydrogen Production from Biological Systems

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Hydrogen Production from Biological Systems Matthew Posewitz Colorado School of Mines DOE Biological Hydrogen Production Workshop September 24 th , 2013 H 2 production PSII/PSI pathway PSI/nonphotochemical PQ Dark fermentation H 2 uptake oxyhydrogen reaction photoreduction Photosynthetic H 2 pathways Peters JW et al. Science 1998 Nicolet Y et al. Structure and Folding Des. 1999 Phototroph Hydrogenases * Cyanobacteria - Only [NiFe]-hydrogenases identified to date. - Typically dark H 2 production.

  7. SINGLE MOLECULE APPROACHES TO BIOLOGY, 2010 GORDON RESEARCH CONFERENCE, JUNE 27-JULY 2, 2010, ITALY

    SciTech Connect

    Professor William Moerner

    2010-07-09

    The 2010 Gordon Conference on Single-Molecule Approaches to Biology focuses on cutting-edge research in single-molecule science. Tremendous technical developments have made it possible to detect, identify, track, and manipulate single biomolecules in an ambient environment or even in a live cell. Single-molecule approaches have changed the way many biological problems are addressed, and new knowledge derived from these approaches continues to emerge. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of biomolecular machines: what they do, how they work individually, how they work together, and finally, how they work inside live cells. The burgeoning use of single-molecule methods to elucidate biological problems is a highly multidisciplinary pursuit, involving both force- and fluorescence-based methods, the most up-to-date advances in microscopy, innovative biological and chemical approaches, and nanotechnology tools. This conference seeks to bring together top experts in molecular and cell biology with innovators in the measurement and manipulation of single molecules, and will provide opportunities for junior scientists and graduate students to present their work in poster format and to exchange ideas with leaders in the field. A number of excellent poster presenters will be selected for short oral talks. Topics as diverse as single-molecule sequencing, DNA/RNA/protein interactions, folding machines, cellular biophysics, synthetic biology and bioengineering, force spectroscopy, new method developments, superresolution imaging in cells, and novel probes for single-molecule imaging will be on the program. Additionally, the collegial atmosphere of this Conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings in the beauty of the Il Ciocco site in

  8. The Development of New User Research Capabilities in Environmental Molecular Science: Workshop Report

    SciTech Connect

    Felmy, Andrew R.; Baer, Donald R.; Fredrickson, Jim K.; Gephart, Roy E.; Rosso, Kevin M.

    2006-10-31

    On August 1, and 2, 2006, 104 scientists representing 40 institutions including 24 Universities and 5 National Laboratories gathered at the W.R. Wiley Environmental Molecular Sciences Laboratory, a National scientific user facility, to outline important science challenges for the next decade and identify major capabilities needed to pursue advanced research in the environmental molecular sciences. EMSL’s four science themes served as the framework for the workshop. The four science themes are 1) Biological Interactions and Interfaces, 2) Geochemistry/Biogeochemistry and Surface Science, 3) Atmospheric Aerosol Chemistry, and 4) Science of Interfacial Phenomena.

  9. Phytochrome from Green Plants: Properties and biological Function

    SciTech Connect

    Quail, Peter H.

    2014-07-25

    Plants constantly monitor the light environment for informational light signals used to direct adaptational responses to the prevailing conditions. One major such response, the Shade-Avaoidance Response (SAR), triggered when plants sense the presence of competing neighbors, results in enhanced channeling of photosynthetically-fixed carbon into stem elongation at the expense of deposition in reproductive tissues. This response has been selected against in many modern food crops to ensure maximum edible yield (e.g. seeds). Converse enhancement of the SAR, with consequent increased carbon channeling into vegetative cellulose, could contribute to the generation of crops with improved yield of tissues suitable for cellulosic biofuel production. The signal for this response is light enriched in far-red wavelengths. This signal is produced by sunlight filtered through, or reflected from, neighboring vegetation, as a result of preferential depletion of red photons through chlorophyll absorption. The plant phytochrome (phy) photoreceptor system (predominantly phyB) senses this signal through its capacity to switch reversibly, in milliseconds, between two molecular states: the biologically inactive Pr (red-light-absorbing) and biologically active Pfr (far-red-light-absorbing) conformers. The photoequilibrium established between these two conformers in light-grown plants is determined by the ratio of red-to-far-red wavelengths in the incoming signal. The levels of Pfr then dictate the recipient plant’s growth response: high levels suppress elongation growth; low levels promote elongation growth. Studies on seedling deetiolation have advanced our understanding considerably in recent years, of the mechanism by which the photoactivated phy molecule transduces its signal into cellular growth responses. The data show that a subfamily of phy-interacting bHLH transcription factors (PIFs) promote skotomorphogenic seedling development in post-germinative darkness, but that the phy

  10. UK Biotechnology and Biological Sciences Research Council | Open...

    OpenEI (Open Energy Information) [EERE & EIA]

    Biotechnology and Biological Sciences Research Council Jump to: navigation, search Name: UK Biotechnology and Biological Sciences Research Council Place: London, United Kingdom...

  11. Techno-Economic Boundary Analysis of Biological Pathways to Hydrogen...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Techno-Economic Boundary Analysis of Biological Pathways to Hydrogen Production (2009) Techno-Economic Boundary Analysis of Biological Pathways to Hydrogen Production (2009) ...

  12. Kahuku Wind Power Biological Opinion | Department of Energy

    Energy Saver

    Kahuku Wind Power Biological Opinion Kahuku Wind Power Biological Opinion Kahuku Wind Power, LLC, Construction of the Kahuku Wind Power Facility in Kahuku, O'ahu, Hawaii Kahuku ...

  13. Algal Biology Toolbox Workshop Brings Lead Experts to Inform...

    Office of Environmental Management (EM)

    Algal Biology Toolbox Workshop Brings Lead Experts to Inform Algae-Based Biofuel Strategy Algal Biology Toolbox Workshop Brings Lead Experts to Inform Algae-Based Biofuel Strategy ...

  14. EERE Success Story-California: Breakthrough in Algae Biology...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Breakthrough in Algae Biology EERE Success Story-California: Breakthrough in Algae Biology January 31, 2014 - 12:00am Addthis Researchers at the Scripps Institution of Oceanography ...

  15. Solar Energy Education. Renewable energy activities for biology...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    biology Citation Details In-Document Search Title: Solar Energy Education. Renewable energy activities for biology You are accessing a document from the Department of Energy's ...

  16. Flow cytometry aids basic cell biology research and drug discovery

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Flow cytometry aids basic cell biology research and drug discovery Flow cytometry aids basic cell biology research and drug discovery Life Technologies Corporation and LANL have ...

  17. DOE Publishes Roadmap for New Biological Research for Energy...

    Office of Science (SC)

    plan for a new generation of biology research that builds on genome project ... The Genomics: GTL Roadmap: Systems Biology for Energy and Environment outlines a plan to ...

  18. Nanojunction Sensors for the Detection of chemical and Biological...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Nanojunction Sensors for the Detection of chemical and Biological Species DOE Grant ... gaps for various applications, including chemical and biological sensors, magnetoresistive ...

  19. Detter, John C. [Los Alamos National Laboratory] Basic Biological

    Office of Scientific and Technical Information (OSTI)

    State of the Art for Autonomous Detection Systems using Genomic Sequencing Detter, John C. Los Alamos National Laboratory Basic Biological Sciences(59) Biological Science...

  20. Hydro Review: Computational Tools to Assess Turbine Biological...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Hydro Review: Computational Tools to Assess Turbine Biological Performance Hydro Review: Computational Tools to Assess Turbine Biological Performance This review covers the BioPA ...

  1. Copy of Synthetic Biology of Novel Thermophilic Bacteria for...

    Office of Scientific and Technical Information (OSTI)

    Copy of Synthetic Biology of Novel Thermophilic Bacteria for Enhanced Production of ... Title: Copy of Synthetic Biology of Novel Thermophilic Bacteria for Enhanced Production of ...

  2. Comparative systems biology across an evolutionary gradient within...

    Office of Scientific and Technical Information (OSTI)

    Comparative systems biology across an evolutionary gradient within the Shewanella genus Citation Details In-Document Search Title: Comparative systems biology across an ...

  3. Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress...

    Office of Scientific and Technical Information (OSTI)

    Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses Citation Details In-Document Search Title: Systems biology analysis of Zymomonas mobilis ZM4 ethanol ...

  4. Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen Production Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen Production Report documenting the ...

  5. Synthetic Biology for Advanced Fuels (Opening Keynote Address...

    Office of Scientific and Technical Information (OSTI)

    Synthetic Biology for Advanced Fuels (Opening Keynote Address - 2010 JGI User Meeting) Citation Details In-Document Search Title: Synthetic Biology for Advanced Fuels (Opening ...

  6. California: Breakthrough in Algae Biology | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Breakthrough in Algae Biology California: Breakthrough in Algae Biology January 31, 2014 - 12:00am Addthis Researchers at the Scripps Institution of Oceanography at University of ...

  7. Sealable femtoliter chamber arrays for cell-free biology (Journal...

    Office of Scientific and Technical Information (OSTI)

    Sealable femtoliter chamber arrays for cell-free biology Prev Next Title: Sealable femtoliter chamber arrays for cell-free biology You are accessing a document from the ...

  8. Importance of systems biology in engineering microbes for biofuel...

    Office of Scientific and Technical Information (OSTI)

    Importance of systems biology in engineering microbes for biofuel production Citation Details In-Document Search Title: Importance of systems biology in engineering microbes for ...

  9. Atomic force microscopy of biological samples

    SciTech Connect

    Doktycz, Mitchel John

    2010-01-01

    The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate how this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH).

  10. Hierarchical analysis of molecular spectra

    SciTech Connect

    Davis, M.J.

    1996-03-01

    A novel representation of molecular spectra in terms of hierarchical trees has proven to be an important aid for the study of many significant problems in gas-phase chemical dynamics. Trees are generated from molecular spectra by monitoring the changes that occur in a spectrum as resolution is changed in a continuous manner. A tree defines a genealogy among all lines of a spectrum. This allows for a detailed understanding of the assignment of features of a spectrum that may be difficult to obtain any other way as well as an understanding of intramolecular energy transfer time scales, mechanisms, and pathways. The methodology has been applied to several problems: transition state spectroscopy, intramolecular energy transfer in highly excited molecules, high-resolution overtone spectroscopy, and the nature of the classical-quantum correspondence when there is classical chaos (``quantum chaos``).

  11. Molecular engineering with bridged polysilsesquioxanes

    SciTech Connect

    LOY,DOUGLAS A.; SHEA,KENNETH J.

    2000-05-09

    Bridged polysilsesquioxanes are a class of hybrid organic-inorganic materials that permit molecular engineering of bulk properties including porosity. Prepared by sol-gel polymerization of monomers with two or more trialkoxysilyl groups, the materials are highly cross-linked amorphous polymers that are readily obtained as gels. The bridging configuration of the hydrocarbon group insures that network polymers are readily formed and that the organic functionality is homogeneously distributed throughout the polymeric scaffolding at the molecular level. This permits the bulk properties, including surface area, pore size, and dielectric constant to be engineered through the selection of the bridging organic group. Numerous bridging groups have been incorporated. This presentation will focus on the effects that the length, flexibility, and substitution geometry of the hydrocarbon bridging groups have on the properties of the resulting bridged polysilsesquioxanes. Details of the preparation, characterization, and some structure property relationships of these bridged polysilsesquioxanes will be given.

  12. Radioprotectors and Tumors: Molecular Studies in Mice

    SciTech Connect

    Gayle Woloschak, David Grdina

    2010-03-10

    This proposal investigated effects of radiation using a set of archival tissues. Main interests of this proposal were to investigate effects of irradiation alone or in the presence or radioprotectors; to investigate these effects on different tissues; and to use/develop molecular biology techniques that would be suitable for work with archived tissues. This work resulted in several manuscripts published or in preparation. Approach for evaluation of gene copy numbers by quantitative real time PCR has been developed and we are striving to establish methods to utilize Q-RT-PCR data to evaluate genomic instability caused by irradiation(s) and accompanying treatments. References: 1. Paunesku D, Paunesku T, Wahl A, Kataoka Y, Murley J, Grdina DJ, Woloschak GE. Incidence of tissue toxicities in gamma ray and fission neutron-exposed mice treated with Amifostine. Int J Radiat Biol. 2008, 84(8):623-34. PMID: 18661379, http://informahealthcare.com/doi/full/10.1080/09553000802241762?cookieSet=1 2. Wang Q, Paunesku T and Woloschak GE. Tissue and data archives from irradiation experiments conducted at Argonne National Laboratory over a period of four decades, in press in Radiation and Environmental Biophysics. 3. Alcantara M, Paunesku D, Rademaker A, Paunesku T and Woloschak GE. A RETROSPECTIVE ANALYSIS OF TISSUE TOXICITIES IN B6CF1 MICE IRRADIATED WITH FISSION NEUTRONS OR COBALT 60 GAMMA RAYS: Gender modulates accumulation of tissue toxicities caused by low dose rate fractionated irradiation; in preparation; this document has been uploaded as STI product 4. Wang Q, Paunesku T Wanzer B and Woloschak GE. Mitochondrial gene copy number differences in different tissues of irradiated and control mice with lymphoid cancers; in preparation 5. Wang Q, Raha, S, Paunesku T and Woloschak GE. Evaluation of gene copy number differences in different tissues of irradiated and control mice; in preparation

  13. Molecular Science Computing: 2010 Greenbook

    SciTech Connect

    De Jong, Wibe A.; Cowley, David E.; Dunning, Thom H.; Vorpagel, Erich R.

    2010-04-02

    This 2010 Greenbook outlines the science drivers for performing integrated computational environmental molecular research at EMSL and defines the next-generation HPC capabilities that must be developed at the MSC to address this critical research. The EMSL MSC Science Panel used EMSL’s vision and science focus and white papers from current and potential future EMSL scientific user communities to define the scientific direction and resulting HPC resource requirements presented in this 2010 Greenbook.

  14. 14th international symposium on molecular beams

    SciTech Connect

    Not Available

    1992-09-01

    This report discusses research being conducted with molecular beams. The general topic areas are as follows: Clusters I; reaction dynamics; atomic and molecular spectroscopy; clusters II; new techniques; photodissociation & dynamics; and surfaces.

  15. 14th international symposium on molecular beams

    SciTech Connect

    Not Available

    1992-01-01

    This report discusses research being conducted with molecular beams. The general topic areas are as follows: Clusters I; reaction dynamics; atomic and molecular spectroscopy; clusters II; new techniques; photodissociation dynamics; and surfaces.

  16. Protein Structure Suggests Role as Molecular Adapter

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Suggests Role as Molecular Adapter Print Wednesday, 24 June 2009 00:00 To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known...

  17. Molecular evolution meets biophysics: the history of the RubisCO enzyme and

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    the Fenna-Matthews-Olson (FMO) complex | MIT-Harvard Center for Excitonics evolution meets biophysics: the history of the RubisCO enzyme and the Fenna-Matthews-Olson (FMO) complex February 9, 2016 at 3:00pm/36-428* Romain Studer, The European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI) studer_romain_web Ancestral sequence reconstruction allows the inference of a protein's past characteristics at a particular point during its evolution. The inferred ancestral

  18. LBNL's Molecular and Biosciences Division Employee Engagement |

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Department of Energy LBNL's Molecular and Biosciences Division Employee Engagement LBNL's Molecular and Biosciences Division Employee Engagement November 4, 2016 9:00AM to 5:00PM EDT LBNL's Molecular and Biosciences Division Employee Engagement - (For Awareness) LBNL's Molecular and Biosciences Division is going to introduce OneDOE at their workforce engagement event on Friday, November 4th. (POC Lida Gifford)

  19. The acquisition of dangerous biological materials :

    SciTech Connect

    Aceto, Donato Gonzalo; Astuto-Gribble, Lisa M.; Gaudioso, Jennifer M.

    2007-11-01

    Numerous terrorist organizations have openly expressed interest in producing and deploying biological weapons. However, a limiting factor for many terrorists has been the acquisition of dangerous biological agents, as evidenced by the very few successful instances of biological weapons use compared to the number of documented hoaxes. Biological agents vary greatly in their ability to cause loss of life and economic damage. Some agents, if released properly, can kill many people and cause an extensive number of secondary infections; other agents will sicken only a small number of people for a short period of time. Consequently, several biological agents can potentially be used to perpetrate a bioterrorism attack but few are likely capable of causing a high consequence event. It is crucial, from a US national security perspective, to more deeply understand the likelihood that terrorist organizations can acquire the range of these agents. Few studies have attempted to comprehensively compile the technical information directly relevant to the acquisition of dangerous bacteria, viruses and toxins. In this report, technical fact sheets were assembled for 46 potentially dangerous biological agents. Much of the information was taken from various research sources which could ultimately and significantly expedite and improve bioterrorism threat assessments. By systematically examining a number of specific agent characteristics included in these fact sheets, it may be possible to detect, target, and implement measures to thwart future terrorist acquisition attempts. In addition, the information in these fact sheets may be used as a tool to help laboratories gain a rudimentary understanding of how attractive a method laboratory theft is relative to other potential acquisition modes.

  20. Biological cell classification by multiangle light scattering

    DOEpatents

    Salzman, G.C.; Crowell, J.M.; Mullaney, P.F.

    1975-06-03

    The specification is directed to an apparatus and method for detecting light scattering from a biological cell. Light, preferably from a coherent source of radiation, intercepts an individual biological cell in a stream of cells passing through the beam. Light scattered from the cell is detected at a selected number of angles between 0 and 90/sup 0/ to the longitudinal axis of the beam with a circular array of light responsive elements which produce signals representative of the intensity of light incident thereon. Signals from the elements are processed to determine the light-scattering pattern of the cell and therefrom its identity.

  1. Biological and Environmental Research Advisory Committee

    Office of Science (SC)

    March 03-04, 2014 | U.S. DOE Office of Science (SC) March 03-04, 2014 Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (135KB) BER Committees of Visitors Federal Advisory Committees BER Home Meetings Biological and Environmental Research Advisory Committee March 03-04, 2014 Print Text Size: A A A FeedbackShare Page Agenda .pdf file (21KB) Presentations: Sharlene Weatherwax .pdf

  2. Biological and Environmental Research Advisory Committee

    Office of Science (SC)

    October 1-2, 2014, Rockville, MD | U.S. DOE Office of Science (SC) October 1-2, 2014, Rockville, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (135KB) BER Committees of Visitors Federal Advisory Committees BER Home Meetings Biological and Environmental Research Advisory Committee October 1-2, 2014, Rockville, MD Print Text Size: A A A FeedbackShare Page Agenda .pdf file

  3. Spectroscopic diagnostics for bacteria in biologic sample

    DOEpatents

    El-Sayed, Mostafa A.; El-Sayed, Ivan H.

    2002-01-01

    A method to analyze and diagnose specific bacteria in a biologic sample using spectroscopy is disclosed. The method includes obtaining the spectra of a biologic sample of a non-infected patient for use as a reference, subtracting the reference from the spectra of an infected sample, and comparing the fingerprint regions of the resulting differential spectrum with reference spectra of bacteria in saline. Using this diagnostic technique, specific bacteria can be identified sooner and without culturing, bacteria-specific antibiotics can be prescribed sooner, resulting in decreased likelihood of antibiotic resistance and an overall reduction of medical costs.

  4. Autofermentative Biological Hydrogen Production by Cyanobacteria

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    BioSolarH 2  Autofermentative biological hydrogen production by cyanobacteria G.C. Dismukes Rutgers University Waksman Institute and Department of Chemistry & Chemical Biology DOE Biohydrogen Production Workshop NREL October, 2013 -BioSolarH 2  Ghirardi et al., 2007 Tamagnini et al., 2007 Soluble NiFe hydrogenase (SH) Group 5 AH in Ralstonia eutropha H16 Schäfer et al., 2013 Formate dehydrogenase Hydrogenase Bagramyan et al., 2003 Ferredoxin Km (MV) = 16.1µM Kcat (MV) = 1242 s -1

  5. Mass Spectrometry Data from the Biological MS Data and Software Distribution Center

    DOE Data Explorer

    Anderson, Gordon

    The mass spectrometry capabilities at Pacific Northwest National Laboratory (PNNL) are primarily applied to biological research, with an emphasis on proteomics and metabolomics. Many of these cutting-edge mass spectrometry capabilities and bioinformatics methods are housed in the Department of Energy's Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility operated by PNNL. These capabilities have been developed and acquired through cooperation between the EMSL national scientific user program and PNNL programmatic research. At the website of the Biological MS Data and Software Distribution Center, the following resources are made available: PNNL-developed software tools and source code, PNNL-generated raw data and processed results, links to publications that used the data and results available on this site, and tutorials and user manuals. [taken from http://omics.pnl.gov/

  6. Transport and Self-Assembly in Molecular Nanosystems

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Transport and Self-Assembly in Molecular Nanosystems Key Challenges: Use classical molecular dynamics and coarse grain molecular dynamics to enable "bottom-up" material...

  7. Structural Biology | U.S. DOE Office of Science (SC)

    Office of Science (SC)

    Structural Biology Biological and Environmental Research (BER) BER Home About Research Biological Systems Science Division (BSSD) Genomic Science DOE Bioenergy Research Centers Bioimaging Technology DOE Joint Genome Institute Structural Biology Radiochemistry & Imaging Instrumentation Radiobiology: Low Dose Radiation Research DOE Human Subjects Protection Program Climate and Environmental Sciences Division (CESD) Research Abstracts Searchable Archive of BER Highlights External link

  8. EERE Success Story—California: Breakthrough in Algae Biology

    Office of Energy Efficiency and Renewable Energy (EERE)

    Breakthrough in algae biology will have a significant impact in the economics of algal biofuel production.

  9. Biological Conversion of Sugars To Hydrocarbons | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    To Hydrocarbons Biological Conversion of Sugars To Hydrocarbons PDF explaining the biological process of bioenergy Biological Conversion of Sugars To Hydrocarbons (190.69 KB) More Documents & Publications Catalytic Upgrading Sugars To Hydrocarbons Catalytic Upgrading of Sugars to Hydrocarbons Technology Pathway Biological Conversion of Sugars to Hydrocarbons Technology Pathway

  10. Modular microfluidic system for biological sample preparation

    DOEpatents

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

  11. Composites comprising biologically-synthesized nanomaterials

    DOEpatents

    Curran, Seamus; Dias, Sampath; Blau, Werner; Wang, Jun; Oremland, Ronald S; Baesman, Shaun

    2013-04-30

    The present disclosure describes composite materials containing a polymer material and a nanoscale material dispersed in the polymer material. The nanoscale materials may be biologically synthesized, such as tellurium nanorods synthesized by Bacillus selenitireducens. Composite materials of the present disclosure may have optical limiting properties and find use in optical limiting devices.

  12. Radiological/biological/aerosol removal system

    DOEpatents

    Haslam, Jeffery J

    2015-03-17

    An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

  13. Apparatus for automated testing of biological specimens

    DOEpatents

    Layne, Scott P.; Beugelsdijk, Tony J.

    1999-01-01

    An apparatus for performing automated testing of infections biological specimens is disclosed. The apparatus comprise a process controller for translating user commands into test instrument suite commands, and a test instrument suite comprising a means to treat the specimen to manifest an observable result, and a detector for measuring the observable result to generate specimen test results.

  14. Combinatorial synthesis and screening of non-biological polymers

    DOEpatents

    Schultz, Peter G.; Xiang, Xiao-Dong; Goldwasser, Isy; Briceno, Gabriel; Sun, Xiao-Dong; Wang, Kai-An

    2006-04-25

    Methods and apparatus for the preparation and use of a substrate having an array of diverse materials in predefined regions thereon. A substrate having an array of diverse materials thereon is generally prepared by delivering components of materials to predefined regions on a substrate, and simultaneously reacting the components to form at least two materials. Materials which can be prepared using the methods and apparatus of the present invention include, for example, covalent network solids, ionic solids and molecular solids. More particularly, materials which can be prepared using the methods and apparatus of the present invention include, for example, inorganic materials, intermetallic materials, metal alloys, ceramic materials, organic materials, organometallic materials, non-biological organic polymers, composite materials (e.g., inorganic composites, organic composites, or combinations thereof), etc. Once prepared, these materials can be screened for useful properties including, for example, electrical, thermal, mechanical, morphological, optical, magnetic, chemical, or other properties. Thus, the present invention provides methods for the parallel synthesis and analysis of novel materials having useful properties.

  15. Bias-dependent molecular-level structure of electrical double layer in ionic liquid on graphite

    SciTech Connect

    Black, Jennifer M; Walters, Deron; Labuda, Aleksander; Feng, Guang; Hillesheim, Patrick C; Dai, Sheng; Cummings, Peter T; Kalinin, Sergei V; Proksch, Roger; Balke, Nina

    2013-01-01

    Bias-dependent structure of electrochemical double layers at liquid-solid interfaces underpin a multitude of phenomena in virtually all areas of scientific enquiry ranging from energy storage and conversion systems, biology, to geophysics and geochemistry. Here we report the bias-evolution of the electric double layer structure of an ionic liquid on highly ordered pyrolytic graphite as a model system for carbon-based electrodes for electrochemical supercapacitors measured by atomic force microscopy. Matching the observed structures to molecular dynamics simulations allows us to resolve steric effects due to cation and anion layers. We observe reconfiguration under applied bias and the orientational transitions in the Stern layer. The synergy between molecular dynamics simulation and experiment provides a comprehensive picture of structural phenomena and long- and short range interactions. This insight will improve understanding of the mechanism of charge storage in electrochemical capacitors on a molecular level which can be used to enhance their electrochemical performance.

  16. Toward Molecular Catalysts by Computer

    SciTech Connect

    Raugei, Simone; DuBois, Daniel L.; Rousseau, Roger J.; Chen, Shentan; Ho, Ming-Hsun; Bullock, R. Morris; Dupuis, Michel

    2015-02-17

    Rational design of molecular catalysts requires a systematic approach to designing ligands with specific functionality and precisely tailored electronic and steric properties. It then becomes possible to devise computer protocols to predict accurately the required properties and ultimately to design catalysts by computer. In this account we first review how thermodynamic properties such as oxidation-reduction potentials (E0), acidities (pKa), and hydride donor abilities (ΔGH-) form the basis for a systematic design of molecular catalysts for reactions that are critical for a secure energy future (hydrogen evolution and oxidation, oxygen and nitrogen reduction, and carbon dioxide reduction). We highlight how density functional theory allows us to determine and predict these properties within “chemical” accuracy (~ 0.06 eV for redox potentials, ~ 1 pKa unit for pKa values, and ~ 1.5 kcal/mol for hydricities). These quantities determine free energy maps and profiles associated with catalytic cycles, i.e. the relative energies of intermediates, and help us distinguish between desirable and high-energy pathways and mechanisms. Good catalysts have flat profiles that avoid high activation barriers due to low and high energy intermediates. We illustrate how the criterion of a flat energy profile lends itself to the prediction of design points by computer for optimum catalysts. This research was carried out in the Center for Molecular Electro-catalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory (PNNL) is operated for the DOE by Battelle.

  17. 2012 SINGLE MOLECULE APPROACHES TO BIOLOGY GORDON RESEARCH CONFERENCE (JULY 15-20, 2012 - MOUNT SNOW RESORT, WEST DOVER VT)

    SciTech Connect

    Fernandez, Julio

    2012-04-20

    Single molecule techniques are rapidly occupying a central role in biological research at all levels. This transition was made possible by the availability and dissemination of robust techniques that use fluorescence and force probes to track the conformation of molecules one at a time, in vitro as well as in live cells. Single-molecule approaches have changed the way many biological problems are studied. These novel techniques provide previously unobtainable data on fundamental biochemical processes that are essential for all forms of life. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of the molecular systems that underpin the functioning of living cells. Hence, our conference seeks to disseminate the implementation and use of single molecule techniques in the pursuit of new biological knowledge. Topics covered include: Molecular Motors on the Move; Origin And Fate Of Proteins; Physical Principles Of Life; Molecules and Super-resolution Microscopy; Nanoswitches In Action; Active Motion Or Random Diffusion?; Building Blocks Of Living Cells; From Molecular Mechanics To Physiology; Tug-of-war: Force Spectroscopy Of Single Proteins.

  18. Biological warfare in the littorals. Final report

    SciTech Connect

    Larsen, R.W.

    1997-05-01

    Biological warfare (BW) has emerged as a significant threat to military operations and is particularly challenging at the operational level of warfare in a littoral environment. There are compelling reasons why an operational commander should be concerned about BW: global proliferation of biotechnology and biological weapons capabilities; suitability of BW for disrupting force projection across the littorals; and the vulnerability of American, allied and coalition forces to BW. The threat of facing an adversary capable and willing to use biological weapons will influence the commander`s application of the operational art across the six operational functions. Degradation of operational tempo, effects of psychological responses among the force, and stress on the organizational structure may challenge the command and control process. Operational intelligence will demand robust integration of technical analysis, intentions and warnings, meteorological information, and medical intelligence. The maneuver and movement processes will be taxed to function effectively when ports and airfields offer such lucrative BW targets. Biological weapons may dictate the location of operational fires assets as well as the make-up of the target lists. Operational logistics assumes great importance in the medical functions, decontamination processes, and troop replacement and unit reconstitution. Operational protection encompasses nearly every aspect of BW defense and will demand a balance between what is necessary and what is possible to protect. As daunting as the challenges appear, the operational-level commander has at his disposal many tools necessary to prepare for biological warfare in the littorals. Ultimately, the commander must convince his force, his allies, and his enemies that the command can fight effectively in a BW environment, on land and sea.

  19. Uranium molecular laser isotope separation

    SciTech Connect

    Jensen, R.J.; Sullivan, A.

    1982-01-01

    The Molecular Laser Isotope Separation program is moving into the engineering phase, and it is possible to determine in some detail the plant cost terms involved in the process economics. A brief description of the MLIS process physics is given as a motivation to the engineering and economics discussion. Much of the plant cost arises from lasers and the overall optical system. In the paper, the authors discuss lasers as operating units and systems, along with temporal multiplexing and Raman shifting. Estimates of plant laser costs are given.

  20. Molecular pathways of angiogenesis inhibition

    SciTech Connect

    Tabruyn, Sebastien P.; Griffioen, Arjan W. . E-mail: aw.griffioen@path.unimaas.nl

    2007-03-30

    A large body of evidence now demonstrates that angiostatic therapy represents a promising way to fight cancer. This research recently resulted in the approval of First angiostatic agent for clinical treatment of cancer. Progress has been achieved in decrypting the cellular signaling in endothelial cells induced by angiostatic agents. These agents predominantly interfere with the molecular pathways involved in migration, proliferation and endothelial cell survival. In the current review, these pathways are discussed. A thorough understanding of the mechanism of action of angiostatic agents is required to develop efficient anti-tumor therapies.

  1. A superradiance-based biological switch

    SciTech Connect

    Borgonovi, Fausto; Celardo, Giuseppe L.

    2014-10-15

    Using the concept of Superradiance Transition, we formulate the operational principles of a quantum device which can be used as a witness of wave-like behavior in molecular chains. We also test its reliability under the action of static diagonal noise, dephasing and phonon thermal bath at room temperature.

  2. Application of Monte Carlo Methods in Molecular Targeted Radionuclide Therapy

    SciTech Connect

    Hartmann Siantar, C; Descalle, M-A; DeNardo, G L; Nigg, D W

    2002-02-19

    Targeted radionuclide therapy promises to expand the role of radiation beyond the treatment of localized tumors. This novel form of therapy targets metastatic cancers by combining radioactive isotopes with tumor-seeking molecules such as monoclonal antibodies and custom-designed synthetic agents. Ultimately, like conventional radiotherapy, the effectiveness of targeted radionuclide therapy is limited by the maximum dose that can be given to a critical, normal tissue, such as bone marrow, kidneys, and lungs. Because radionuclide therapy relies on biological delivery of radiation, its optimization and characterization are necessarily different than for conventional radiation therapy. We have initiated the development of a new, Monte Carlo transport-based treatment planning system for molecular targeted radiation therapy as part of the MINERVA treatment planning system. This system calculates patient-specific radiation dose estimates using a set of computed tomography scans to describe the 3D patient anatomy, combined with 2D (planar image) and 3D (SPECT, or single photon emission computed tomography) to describe the time-dependent radiation source. The accuracy of such a dose calculation is limited primarily by the accuracy of the initial radiation source distribution, overlaid on the patient's anatomy. This presentation provides an overview of MINERVA functionality for molecular targeted radiation therapy, and describes early validation and implementation results of Monte Carlo simulations.

  3. Geometric and electrostatic modeling using molecular rigidity functions

    DOE PAGES [OSTI]

    Mu, Lin; Xia, Kelin; Wei, Guowei

    2017-03-01

    Geometric and electrostatic modeling is an essential component in computational biophysics and molecular biology. Commonly used geometric representations admit geometric singularities such as cusps, tips and self-intersecting facets that lead to computational instabilities in the molecular modeling. Our present work explores the use of flexibility and rigidity index (FRI), which has a proved superiority in protein B-factor prediction, for biomolecular geometric representation and associated electrostatic analysis. FRI rigidity surfaces are free of geometric singularities. We propose a rigidity based Poisson–Boltzmann equation for biomolecular electrostatic analysis. These approaches to surface and electrostatic modeling are validated by a set of 21 proteins.more » Our results are compared with those of established methods. Finally, being smooth and analytically differentiable, FRI rigidity functions offer excellent curvature analysis, which characterizes concave and convex regions on protein surfaces. Polarized curvatures constructed by using the product of minimum curvature and electrostatic potential is shown to predict potential protein–ligand binding sites.« less

  4. Biology and Medicine Division annual report, 1987

    SciTech Connect

    Not Available

    1988-04-01

    Modern biology is characterized by rapid change. The development of new tools and the results derived from their application to various biological systems require significant shifts in our concepts and the strategies that are adopted to analyze and elucidate mechanisms. In parallel with exciting new scientific developments our organizational structure and programmatic emphases have altered. These changes and developments have enabled the life sciences at LBL to be better positioned to create and respond to new opportunities. The work summarized in this annual report reflects a vital multifaceted research program that is in the vanguard of the areas represented. We are committed to justifying the confidence expressed by LBL through the new mission statement and reorganizational changes designed to give greater prominence to the life sciences.

  5. Monitoring Biological Activity at Geothermal Power Plants

    SciTech Connect

    Peter Pryfogle

    2005-09-01

    The economic impact of microbial growth in geothermal power plants has been estimated to be as high as $500,000 annually for a 100 MWe plant. Many methods are available to monitor biological activity at these facilities; however, very few plants have any on-line monitoring program in place. Metal coupon, selective culturing (MPN), total organic carbon (TOC), adenosine triphosphate (ATP), respirometry, phospholipid fatty acid (PLFA), and denaturing gradient gel electrophoresis (DGGE) characterizations have been conducted using water samples collected from geothermal plants located in California and Utah. In addition, the on-line performance of a commercial electrochemical monitor, the BIoGEORGE?, has been evaluated during extended deployments at geothermal facilities. This report provides a review of these techniques, presents data on their application from laboratory and field studies, and discusses their value in characterizing and monitoring biological activities at geothermal power plants.

  6. Scanning Probe Microscopy with Spectroscopic Molecular Recognition...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    capable of 5 nm Chemical differentiation of surface features Applications and Industries Atomic force microscopy to study biological and chemical samples Chemical differentiation...

  7. Dudley Herschbach: Chemical Reactions and Molecular Beams

    Office of Scientific and Technical Information (OSTI)

    As a co-recipient of the 1986 Nobel Prize in Chemistry, 'Dudley Herschbach was cited for ... Dudley R. Herschbach, Harvard Department of Chemistry and Chemical Biology Teaching ...

  8. Developing Biological Specifications for Fish Friendly Turbines

    SciTech Connect

    Neitzel, Duane A.

    2009-09-14

    This factsheet explains studies conducted in a highly reproducible manner to examine the biological effects to fish exposed to a shear environment in the laboratory. Strain rate was used as the index of intensity to describe the hydraulic force experienced by a fish in a shear environment. It was determined that no significant injuries occurred to any fish subjected to strain rates equal to or less than 500 cm/s/cm.

  9. Computational Tools to Assess Turbine Biological Performance

    SciTech Connect

    Richmond, Marshall C.; Serkowski, John A.; Rakowski, Cynthia L.; Strickler, Brad; Weisbeck, Molly; Dotson, Curtis L.

    2014-07-24

    Public Utility District No. 2 of Grant County (GCPUD) operates the Priest Rapids Dam (PRD), a hydroelectric facility on the Columbia River in Washington State. The dam contains 10 Kaplan-type turbine units that are now more than 50 years old. Plans are underway to refit these aging turbines with new runners. The Columbia River at PRD is a migratory pathway for several species of juvenile and adult salmonids, so passage of fish through the dam is a major consideration when upgrading the turbines. In this paper, a method for turbine biological performance assessment (BioPA) is demonstrated. Using this method, a suite of biological performance indicators is computed based on simulated data from a CFD model of a proposed turbine design. Each performance indicator is a measure of the probability of exposure to a certain dose of an injury mechanism. Using known relationships between the dose of an injury mechanism and frequency of injury (dose–response) from laboratory or field studies, the likelihood of fish injury for a turbine design can be computed from the performance indicator. By comparing the values of the indicators from proposed designs, the engineer can identify the more-promising alternatives. We present an application of the BioPA method for baseline risk assessment calculations for the existing Kaplan turbines at PRD that will be used as the minimum biological performance that a proposed new design must achieve.

  10. KPFM and PFM of Biological Systems

    SciTech Connect

    Rodriguez, Brian [University College, Dublin; Kalinin, Sergei V [ORNL

    2011-01-01

    Surface potentials and electrostatic interactions in biological systems are a key element of cellular regulation and interaction. Examples include cardiac and muscular activity, voltage-gated ion channels, protein folding and assembly, and electroactive cells and electrotransduction. The coupling between electrical, mechanical, and chemical signals and responses in cellular systems necessitates the development of tools capable of measuring the distribution of charged species, surface potentials, and mechanical responses to applied electrical stimuli and vice versa, ultimately under physiological conditions. In this chapter, applications of voltage-modulated atomic force microscopy (AFM) methods including Kelvin probe force microscopy (KPFM) and piezoresponse force microscopy (PFM) to biological systems are discussed. KPFM is a force-sensitive non-contact or intermittent-contact mode AFM technique that allows electrostatic interactions and surface potentials to be addressed. Beyond long-range electrostatic interactions, the application of bias can lead to a mechanical response, e.g., due to linear piezoelectric coupling in polar biopolymers or via more complex electrotransduction and redox pathways in other biosystems. The use and development of PFM, based on direct electromechanical detection, to biological systems will also be addressed. The similarities and limitations of measuring surface potentials and electromechanical coupling in solution will be outlined.

  11. Elasticity of crystalline molecular explosives

    DOE PAGES [OSTI]

    Hooks, Daniel E.; Ramos, Kyle J.; Bolme, C. A.; Cawkwell, Marc J.

    2015-04-14

    Crystalline molecular explosives are key components of engineered explosive formulations. In precision applications a high degree of consistency and predictability is desired under a range of conditions to a variety of stimuli. Prediction of behaviors from mechanical response and failure to detonation initiation and detonation performance of the material is linked to accurate knowledge of the material structure and first stage of deformation: elasticity. The elastic response of pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), and cyclotetramethylene tetranitramine (HMX), including aspects of material and measurement variability, and computational methods are described in detail. Experimental determinations of elastic tensors are compared, andmore » an evaluation of sources of error is presented. Furthermore, computed elastic constants are also compared for these materials and for triaminotrinitrobenzene (TATB), for which there are no measurements.« less

  12. Elasticity of crystalline molecular explosives

    SciTech Connect

    Hooks, Daniel E.; Ramos, Kyle J.; Bolme, C. A.; Cawkwell, Marc J.

    2015-04-14

    Crystalline molecular explosives are key components of engineered explosive formulations. In precision applications a high degree of consistency and predictability is desired under a range of conditions to a variety of stimuli. Prediction of behaviors from mechanical response and failure to detonation initiation and detonation performance of the material is linked to accurate knowledge of the material structure and first stage of deformation: elasticity. The elastic response of pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), and cyclotetramethylene tetranitramine (HMX), including aspects of material and measurement variability, and computational methods are described in detail. Experimental determinations of elastic tensors are compared, and an evaluation of sources of error is presented. Furthermore, computed elastic constants are also compared for these materials and for triaminotrinitrobenzene (TATB), for which there are no measurements.

  13. Production of high molecular weight polylactic acid

    DOEpatents

    Bonsignore, P.V.

    1995-11-28

    A degradable high molecular weight poly(lactic acid) is described. The poly(lactic acid) has a terminal end group of one of carboxyl or hydroxyl groups with low molecular weight poly(lactic acid) units coupled with linking agents of di-isocyanates, bis-epoxides, bis-oxazolines and bis-ortho esters. The resulting high molecular weight poly(lactic acid) can be used for applications taking advantage of the improved physical properties.

  14. Towards Using Molecular States as Qubits

    SciTech Connect

    Goswami, Debabrata; Goswami, Tapas; Kumar, S. K. Karthick; Das, Dipak K.

    2011-09-23

    Molecular systems are presented as possible qubit systems by exploring non-resonant molecular fragmentation of n-propyl benzene with femtosecond laser pulses as a model case. We show that such laser fragmentation process is dependent on the phase and polarization characteristics of the laser. The effect of the chirp and polarization of the femtosecond pulse when applied simultaneously is mutually independent of each other, which makes chirp and polarization as useful 'logic' implementing parameters for such molecular qubits.

  15. Production of high molecular weight polylactic acid

    DOEpatents

    Bonsignore, Patrick V.

    1995-01-01

    A degradable high molecular weight poly(lactic acid). A poly(lactic acid) has a terminal end group of one of carboxyl or hydroxyl groups with low molecular weight poly(lactic acid) units coupled with linking agents of di-isocyanates, bis-epoxides, bis-oxazolines and bis-ortho esters. The resulting high molecular weight poly(lactic acid) can be used for applications taking advantage of the improved physical properties.

  16. Parallel Molecular Dynamics Program for Molecules

    Energy Science and Technology Software Center

    1995-03-07

    ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.

  17. Biologically produced acid precipitable polymeric lignin

    DOEpatents

    Crawford, Don L.; Pometto, III, Anthony L.

    1984-01-01

    A water soluble, acid precipitable polymeric degraded lignin (APPL), having a molecular weight of at least 12,000 daltons, and comprising, by percentage of total weight, at least three times the number of phenolic hydroxyl groups and carboxylic acid groups present in native lignin. The APPL may be modified by chemical oxidation and reduction to increase its phenolic hydroxyl content and reduce the number of its antioxidant inhibitory side chains, thereby improving antioxidant properties.

  18. Molecular Manipulations of Symmetry | The Ames Laboratory

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Molecular Manipulations of Symmetry Researchers have studied the effect of concentration on the activity and selectivity in a zirconium-catalyzed hydroamination reaction. In this...

  19. PNNL: Center for Molecular Electrocatalysis - Energy Frontier...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Related Links Center for Molecular Electrocatalysis Members Pacific Northwest National Laboratory University of Illinois Yale University U.S. Department of Energy U.S. Department...

  20. Nanocrystal and Molecular Precursors for Photovoltaic Applications...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Nanocrystal and Molecular Precursors for Photovoltaic Applications The objective in this proposal is to identify factors that limit the efficiency of nanocrystal based solar cells...

  1. Molecular catalytic coal liquid conversion. Quarterly report...

    Office of Scientific and Technical Information (OSTI)

    report Citation Details In-Document Search Title: Molecular catalytic coal liquid ... It was found that the rhodium catalyst works well under biphase conditions rather than ...

  2. PNNL: Center for Molecular Electrocatalysis About Us

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    To improve reactions important for solar energy storage and fuel cells, the Center for Molecular Electrocatalysis seeks to transform our ability to design electrocatalysts that ...

  3. Nanoscopic Electrode Molecular Probes - Energy Innovation Portal

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    other molecular sensing Applications and Industries Cancer genome sequencing Comparative genome sequencing Human genotyping Medical sequencing Model systems Parasite and vector...

  4. Molecular catalytic coal liquid conversion. Quarterly status...

    Office of Scientific and Technical Information (OSTI)

    July--September 1995 Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. Quarterly status report, July--September 1995 You are accessing...

  5. Communication: Quantum molecular dynamics simulation of liquid...

    Office of Scientific and Technical Information (OSTI)

    Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach Citation Details In-Document Search Title: Communication:...

  6. Molecular catalytic coal liquid conversion. Quarterly status...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. ... organic base catalysts for arene hydrogenation and the hydrotreating of the coal liquids. ...

  7. Molecular catalytic coal liquid conversion. Quarterly report...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. ... organic base catalysts for arene hydrogenation and the hydrotreating of the coal liquids. ...

  8. Molecular catalytic coal liquid conversion. Quarterly report...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. ... Task 2, organic base-catalyzed arene hydrogenation and hydrotreating of the coal liquids. ...

  9. Molecular catalytic hydrogenation of aromatic hydrocarbons and...

    Office of Scientific and Technical Information (OSTI)

    and hydrotreating of coal liquids. Citation Details In-Document Search Title: Molecular catalytic hydrogenation of aromatic hydrocarbons and hydrotreating of coal liquids. ...

  10. Dynamics of Molecular Clouds: Observations, Simulations, and...

    Office of Scientific and Technical Information (OSTI)

    Simulations, and NIF Experiments Citation Details In-Document Search Title: Dynamics of Molecular Clouds: Observations, Simulations, and NIF Experiments You are ...

  11. Nonequilibrium molecular dynamics simulations of confined fluids...

    Office of Scientific and Technical Information (OSTI)

    A nonequilibrium molecular dynamics (MD) ... in a single simulation upon compression, whereas fluid molecules in the bulk ... for weak fluid -- wall interactions. ...

  12. PNNL: Center for Molecular Electrocatalysis - Using Hydrogenase...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    and Efficient Molecular Electrocatalysts January 2011 To create solar assemblies that use sunlight to split water and create hydrogen fuel requires designing fast, efficient ...

  13. Molecular interactions with ice: Molecular embedding, adsorption, detection, and release

    SciTech Connect

    Gibson, K. D.; Langlois, Grant G.; Li, Wenxin; Sibener, S. J.; Killelea, Daniel R.

    2014-11-14

    The interaction of atomic and molecular species with water and ice is of fundamental importance for chemistry. In a previous series of publications, we demonstrated that translational energy activates the embedding of Xe and Kr atoms in the near surface region of ice surfaces. In this paper, we show that inert molecular species may be absorbed in a similar fashion. We also revisit Xe embedding, and further probe the nature of the absorption into the selvedge. CF{sub 4} molecules with high translational energies (?3 eV) were observed to embed in amorphous solid water. Just as with Xe, the initial adsorption rate is strongly activated by translational energy, but the CF{sub 4} embedding probability is much less than for Xe. In addition, a larger molecule, SF{sub 6}, did not embed at the same translational energies that both CF{sub 4} and Xe embedded. The embedding rate for a given energy thus goes in the order Xe > CF{sub 4} > SF{sub 6}. We do not have as much data for Kr, but it appears to have a rate that is between that of Xe and CF{sub 4}. Tentatively, this order suggests that for Xe and CF{sub 4}, which have similar van der Waals radii, the momentum is the key factor in determining whether the incident atom or molecule can penetrate deeply enough below the surface to embed. The more massive SF{sub 6} molecule also has a larger van der Waals radius, which appears to prevent it from stably embedding in the selvedge. We also determined that the maximum depth of embedding is less than the equivalent of four layers of hexagonal ice, while some of the atoms just below the ice surface can escape before ice desorption begins. These results show that energetic ballistic embedding in ice is a general phenomenon, and represents a significant new channel by which incident species can be trapped under conditions where they would otherwise not be bound stably as surface adsorbates. These findings have implications for many fields including environmental science, trace gas

  14. A review on nanomechanical resonators and their applications in sensors and molecular transportation

    SciTech Connect

    Arash, Behrouz; Rabczuk, Timon; Jiang, Jin-Wu

    2015-06-15

    Nanotechnology has opened a new area in science and engineering, leading to the development of novel nano-electromechanical systems such as nanoresonators with ultra-high resonant frequencies. The ultra-high-frequency resonators facilitate wide-ranging applications such as ultra-high sensitive sensing, molecular transportation, molecular separation, high-frequency signal processing, and biological imaging. This paper reviews recent studies on dynamic characteristics of nanoresonators. A variety of theoretical approaches, i.e., continuum modeling, molecular simulations, and multiscale methods, in modeling of nanoresonators are reviewed. The potential application of nanoresonators in design of sensor devices and molecular transportation systems is introduced. The essence of nanoresonator sensors for detection of atoms and molecules with vibration and wave propagation analyses is outlined. The sensitivity of the resonator sensors and their feasibility in detecting different atoms and molecules are particularly discussed. Furthermore, the applicability of molecular transportation using the propagation of mechanical waves in nanoresonators is presented. An extended application of the transportation methods for building nanofiltering systems with ultra-high selectivity is surveyed. The article aims to provide an up-to-date review on the mechanical properties and applications of nanoresonators, and inspire additional potential of the resonators.

  15. Biological Imaging by Soft X-Ray Diffraction Microscopy

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biological Imaging by Soft X-Ray Diffraction Microscopy Biological Imaging by Soft X-Ray Diffraction Microscopy Print Wednesday, 30 November 2005 00:00 Electron and x-ray...

  16. Sharpening Our Tools: Algal Biology Toolbox Workshop | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Sharpening Our Tools: Algal Biology Toolbox Workshop Sharpening Our Tools: Algal Biology Toolbox Workshop May 24, 2016 8:00AM PDT to May 25, 2016 4:00PM PDT Hard Rock Hotel San ...

  17. Algal Biology Program at Los Alamos gets a star

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Algal Biology Program gets a star Algal Biology Program at Los Alamos gets a star Richard Sayre, one of the nation's top specialists in algae and energy-producing plant research, ...

  18. BioLogical Capital BLC | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    BioLogical Capital BLC Jump to: navigation, search Name: BioLogical Capital (BLC) Place: Denver, Colorado Zip: 80202 Product: Denver Colorado-based group focusing on generating...

  19. Generation and characterization of biological aerosols for laser measurements

    SciTech Connect

    Cheng, Yung-Sung; Barr, E.B.

    1995-12-01

    Concerns for proliferation of biological weapons including bacteria, fungi, and viruses have prompted research and development on methods for the rapid detection of biological aerosols in the field. Real-time instruments that can distinguish biological aerosols from background dust would be especially useful. Sandia National Laboratories (SNL) is developing a laser-based, real-time instrument for rapid detection of biological aerosols, and ITRI is working with SNL scientists and engineers to evaluate this technology for a wide range of biological aerosols. This paper describes methods being used to generate the characterize the biological aerosols for these tests. In summary, a biosafe system has been developed for generating and characterizing biological aerosols and using those aerosols to test the SNL laser-based real-time instrument. Such tests are essential in studying methods for rapid detection of airborne biological materials.

  20. Biological Conversion of Sugars to Hydrocarbons Technology Pathway

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    ... to leverage experience in biochemical processing, specifically cellulose and ... in downstream biological conversion and improving overall process integration. ...

  1. 2013 Biological Hydrogen Production Workshop Summary Report | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Energy Biological Hydrogen Production Workshop Summary Report 2013 Biological Hydrogen Production Workshop Summary Report November 2013 summary report for the 2013 Biological Hydrogen Production Workshop. bio_h2_workshop_final_report.pdf (1.55 MB) More Documents & Publications The Hydrogen Program at NREL: A Brief Overview Hydrogenases and Barriers for Biotechnological Hydrogen Production Technologies Renewable Hydrogen Production from Biological Systems

  2. Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 |

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Department of Energy Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 b2blowres63006.pdf (8.11 MB) More Documents & Publications Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 Cellulosic Sugar and Lignin Production Capabilities RFI Responses Review of Recent Pilot Scale Cellulosic Ethanol Demonstration

  3. National Association of Biology Teachers Conference | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Association of Biology Teachers Conference National Association of Biology Teachers Conference November 3, 2016 8:00AM MST to November 6, 2016 12:00PM MST Denver Sheraton-Downtown 1550 Court Pl Denver, Colorado 80202 The National Association of Biology Teachers Conference will be hosted in Denver, Colorado, November 3-6, 2016. The conference will provide an opportunity for leaders in biology and life science education to participate in hands-on workshops and informational sessions. Bioenergy

  4. Hydro Review: Computational Tools to Assess Turbine Biological Performance

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    | Department of Energy Hydro Review: Computational Tools to Assess Turbine Biological Performance Hydro Review: Computational Tools to Assess Turbine Biological Performance This review covers the BioPA method used to analyze the biological performance of proposed designs to help ensure the safety of fish passing through the turbines at the Priest Rapids Dam in Grant County, Washington. Computational Tools to Assess Turbine Biological Performance (483.71 KB) More Documents & Publications

  5. Measurement of Beryllium in Biological Samples by Accelerator Mass Spectrometry: Applications for Studying Chronic Beryllium Disease

    SciTech Connect

    Chiarappa-Zucca, M L; Finkel, R C; Martinelli, R E; McAninch, J E; Nelson, D O; Turtletaub, K W

    2004-04-15

    A method using accelerator mass spectrometry (AMS) has been developed for quantifying attomoles of beryllium (Be) in biological samples. This method provides the sensitivity to trace Be in biological samples at very low doses with the purpose of identifying the molecular targets involved in chronic beryllium disease. Proof of the method was tested by administering 0.001, 0.05, 0.5 and 5.0 {micro}g {sup 9}Be and {sup 10}Be by intraperitoneal injection to male mice and removing spleen, liver, femurs, blood, lung, and kidneys after 24 h exposure. These samples were prepared for AMS analysis by tissue digestion in nitric acid, followed by further organic oxidation with hydrogen peroxide and ammonium persulfate and lastly, precipitation of Be with ammonium hydroxide, and conversion to beryllium oxide at 800 C. The {sup 10}Be/{sup 9}Be ratio of the extracted beryllium oxide was measured by AMS and Be in the original sample was calculated. Results indicate that Be levels were dose-dependent in all tissues and the highest levels were measured in the spleen and liver. The measured {sup 10}Be/{sup 9}Be ratios spanned 4 orders of magnitude, from 10{sup -10} to 10{sup -14}, with a detection limit of 3.0 x 10{sup -14}, which is equivalent to 0.8 attomoles of {sup 10}Be. These results show that routine quantification of nanogram levels of Be in tissues is possible and that AMS is a sensitive method that can be used in biological studies to understand the molecular dosimetry of Be and mechanisms of toxicity.

  6. Signature molecular descriptor : advanced applications.

    SciTech Connect

    Visco, Donald Patrick, Jr.

    2010-04-01

    In this work we report on the development of the Signature Molecular Descriptor (or Signature) for use in the solution of inverse design problems as well as in highthroughput screening applications. The ultimate goal of using Signature is to identify novel and non-intuitive chemical structures with optimal predicted properties for a given application. We demonstrate this in three studies: green solvent design, glucocorticoid receptor ligand design and the design of inhibitors for Factor XIa. In many areas of engineering, compounds are designed and/or modified in incremental ways which rely upon heuristics or institutional knowledge. Often multiple experiments are performed and the optimal compound is identified in this brute-force fashion. Perhaps a traditional chemical scaffold is identified and movement of a substituent group around a ring constitutes the whole of the design process. Also notably, a chemical being evaluated in one area might demonstrate properties very attractive in another area and serendipity was the mechanism for solution. In contrast to such approaches, computer-aided molecular design (CAMD) looks to encompass both experimental and heuristic-based knowledge into a strategy that will design a molecule on a computer to meet a given target. Depending on the algorithm employed, the molecule which is designed might be quite novel (re: no CAS registration number) and/or non-intuitive relative to what is known about the problem at hand. While CAMD is a fairly recent strategy (dating to the early 1980s), it contains a variety of bottlenecks and limitations which have prevented the technique from garnering more attention in the academic, governmental and industrial institutions. A main reason for this is how the molecules are described in the computer. This step can control how models are developed for the properties of interest on a given problem as well as how to go from an output of the algorithm to an actual chemical structure. This report

  7. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    SciTech Connect

    JOHNSON AR; CAUDILL JG; GIDDINGS RF; RODRIGUEZ JM; ROOS RC; WILDE JW

    2010-02-11

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimated spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  8. Computational Cell Environment: A Problem Solving Environment for integrating diverse biological data

    SciTech Connect

    Klicker, Kyle R.; Singhal, Mudita; Stephan, Eric G.; Trease, Lynn L.; Gracio, Deborah K.

    2004-06-22

    Biologists and bioinformaticists face the ever-increasing challenge of managing large datasets queried from diverse data sources. Genomics and proteomics databases such as the National Center for Biotechnology (NCBI), Kyoto Encyclopedia of Genes and Genomes (KEGG), and the European Molecular Biology Laboratory (EMBL) are becoming the standard biological data department stores that biologists visit on a regular basis to obtain the supplies necessary for conducting their research. However, much of the data that biologists retrieve from these databases needs to be further managed and organized in a meaningful way so that the researcher can focus on the problem that they are trying to investigate and share their data and findings with other researchers. We are working towards developing a problem-solving environment called the Computational Cell Environment (CCE) that provides connectivity to these diverse data stores and provides data retrieval, management, and analysis through all aspects of biological study. In this paper we discuss the system and database design of CCE. We also outline a few problems encountered at various stages of its development and the design decisions taken to resolve them.

  9. Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

    DOE PAGES [OSTI]

    Unkefer, Clifford Jay; Sayre, Richard Thomas; Magnuson, Jon K.; Anderson, Daniel B.; Baxter, Ivan; Blaby, Ian K.; Brown, Judith K.; Carleton, Michael; Cattolico, Rose Ann; Dale, Taraka T.; et al

    2016-06-21

    In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oilmore » yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. Our review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.« less

  10. Historical Information H.2 Biological Studies

    Office of Legacy Management (LM)

    _-_ . - H.2 Biological Studies (0 \ j ; : : j Book . l Ad Hoc Rulison Review Panel Comments Regarding Re-Entry , and Testing Operations, December 22, 1969 This page intentionally left blank December 22, 1969 M r . Robert E. Miller, Manager Nevada Operations Office U. S. Atomic Energy Commission Post Office Box 14100 Las Vegas, Nevada 89114 Dear M r . Miller: F4cmbers of t h e A d Hoc Rulison Review Panel reconvened on December 22, 1969, t o hear and discuss comments r e s u l t i n g from our

  11. Synchronous Behavior of Two Coupled Biological Neurons

    SciTech Connect

    Elson, R.C.; Selverston, A.I.; Elson, R.C.; Selverston, A.I.; Huerta, R.; Rulkov, N.F.; Rabinovich, M.I.; Abarbanel, H.D.; Selverston, A.I.; Huerta, R.; Abarbanel, H.D.

    1998-12-01

    We report experimental studies of synchronization phenomena in a pair of biological neurons that interact through naturally occurring, electrical coupling. When these neurons generate irregular bursts of spikes, the natural coupling synchronizes slow oscillations of membrane potential, but not the fast spikes. By adding artificial electrical coupling we studied transitions between synchrony and asynchrony in both slow oscillations and fast spikes. We discuss the dynamics of bursting and synchronization in living neurons with distributed functional morphology. {copyright} {ital 1998} {ital The American Physical Society}

  12. LANSCE | Lujan Center | Biology Preparation Laboratory

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biology Preparation Laboratory The Lujan Center Biolab offers a variety of capabilities. 1) Biodeuteration Lab (BDL) We run a protein expression lab for perdeuteration of user proteins. We offer full perdeuteration (~99%) using our algal-based media for bacterial growth. We also have M9 minimal media made in D2O for expression of up to ~85% perdeuteration. Users can use our lab in person or mail-in a plasmid for us to express for them. We also have standard protein expression equipment:

  13. 08-ERD-071 Final Report: New Molecular Probes and Catalysts for Bioenergy Research

    SciTech Connect

    Thelen, M P; Rowe, A A; Siebers, A K; Jiao, Y

    2011-03-07

    A major thrust in bioenergy research is to develop innovative methods for deconstructing plant cell wall polymers, such as cellulose and lignin, into simple monomers that can be biologically converted to ethanol and other fuels. Current techniques for monitoring a broad array of cell wall materials and specific degradation products are expensive and time consuming. To monitor various polymers and assay their breakdown products, molecular probes for detecting specific carbohydrates and lignins are urgently needed. These new probes would extend the limited biochemical techniques available, and enable realtime imaging of ultrastructural changes in plant cells. Furthermore, degradation of plant biomass could be greatly accelerated by the development of catalysts that can hydrolyze key cell wall polysaccharides and lignin. The objective of this project was to develop cheap and efficient DNA reagents (aptamers) used to detect and quantify polysaccharides, lignin, and relevant products of their breakdown. A practical goal of the research was to develop electrochemical aptamer biosensors, which could be integrated into microfluidic devices and used for high-throughput screening of enzymes or biological systems that degrade biomass. Several important model plant cell wall polymers and compounds were targeted for specific binding and purification of aptamers, which were then tested by microscopic imaging, circular dichroism, surface plasmon resonance, fluorescence anisotropy, and electrochemical biosensors. Using this approach, it was anticiated that we could provide a basis for more efficient and economically viable biofuels, and the technologies established could be used to design molecular tools that recognize targets sought in medicine or chemical and biological defense projects.

  14. Carbon fiber composite molecular sieves

    SciTech Connect

    Burchell, T.D.; Rogers, M.R.; Williams, A.M.

    1996-06-01

    The removal of CO{sub 2} is of significance in several energy applications. The combustion of fossil fuels, such as coal or natural gas, releases large volumes of CO{sub 2} to the environment. Several options exist to reduce CO{sub 2} emissions, including substitution of nuclear power for fossil fuels, increasing the efficiency of fossil plants and capturing the CO{sub 2} prior to emission to the environment. All of these techniques have the attractive feature of limiting the amount of CO{sub 2} emitted to the atmosphere, but each has economic, technical, or societal limitations. In the production of natural gas, the feed stream from the well frequently contains contaminants and diluents which must be removed before the gas can enter the pipeline distribution system. Notable amongst these diluent gasses is CO{sub 2}, which has no calorific value. Currently, the pipeline specification calls for <2 mol % CO{sub 2} in the gas. Gas separation is thus a relevant technology in the field of energy production. A novel separation system based on a parametric swing process has been developed that utilizes the unique combination of properties exhibited by our carbon fiber composite molecular sieve (CFCMS).

  15. Reactions of small molecular systems

    SciTech Connect

    Wittig, C.

    1993-12-01

    This DOE program remains focused on small molecular systems relevant to combustion. Though a number of experimental approaches and machines are available for this research, the authors` activities are centered around the high-n Rydberg time-of-flight (HRTOF) apparatus in this laboratory. One student and one postdoc carry out experiments with this machine and also engage in small intra-group collaborations involving shared equipment. This past year was more productive than the previous two, due to the uninterrupted operation of the HRTOF apparatus. Results were obtained with CH{sub 3}OH, CH{sub 3}SH, Rg-HX complexes, HCOOH, and their deuterated analogs where appropriate. One paper is in print, three have been accepted for publication, and one is under review. Many preliminary results that augur well for the future were obtained with other systems such as HNO{sub 3}, HBr-HI complexes, toluene, etc. Highlights from the past year are presented below that display some of the features of this program.

  16. Molecular dynamics of membrane proteins.

    SciTech Connect

    Woolf, Thomas B.; Crozier, Paul Stewart; Stevens, Mark Jackson

    2004-10-01

    Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.

  17. Acceptance Criteria Framework for Autonomous Biological Detectors

    SciTech Connect

    Dzenitis, J M

    2006-12-12

    The purpose of this study was to examine a set of user acceptance criteria for autonomous biological detection systems for application in high-traffic, public facilities. The test case for the acceptance criteria was the Autonomous Pathogen Detection System (APDS) operating in high-traffic facilities in New York City (NYC). However, the acceptance criteria were designed to be generally applicable to other biological detection systems in other locations. For such detection systems, ''users'' will include local authorities (e.g., facility operators, public health officials, and law enforcement personnel) and national authorities [including personnel from the Department of Homeland Security (DHS), the BioWatch Program, the Centers for Disease Control and Prevention (CDC), and the Federal Bureau of Investigation (FBI)]. The panel members brought expertise from a broad range of backgrounds to complete this picture. The goals of this document are: (1) To serve as informal guidance for users in considering the benefits and costs of these systems. (2) To serve as informal guidance for developers in understanding the needs of users. In follow-up work, this framework will be used to systematically document the APDS for appropriateness and readiness for use in NYC.

  18. Biological and Environmental Research Network Requirements

    SciTech Connect

    Balaji, V.; Boden, Tom; Cowley, Dave; Dart, Eli; Dattoria, Vince; Desai, Narayan; Egan, Rob; Foster, Ian; Goldstone, Robin; Gregurick, Susan; Houghton, John; Izaurralde, Cesar; Johnston, Bill; Joseph, Renu; Kleese-van Dam, Kerstin; Lipton, Mary; Monga, Inder; Pritchard, Matt; Rotman, Lauren; Strand, Gary; Stuart, Cory; Tatusova, Tatiana; Tierney, Brian; Thomas, Brian; Williams, Dean N.; Zurawski, Jason

    2013-09-01

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy (DOE) Office of Science (SC), the single largest supporter of basic research in the physical sciences in the United States. In support of SC programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet be a highly successful enabler of scientific discovery for over 25 years. In November 2012, ESnet and the Office of Biological and Environmental Research (BER) of the DOE SC organized a review to characterize the networking requirements of the programs funded by the BER program office. Several key findings resulted from the review. Among them: 1) The scale of data sets available to science collaborations continues to increase exponentially. This has broad impact, both on the network and on the computational and storage systems connected to the network. 2) Many science collaborations require assistance to cope with the systems and network engineering challenges inherent in managing the rapid growth in data scale. 3) Several science domains operate distributed facilities that rely on high-performance networking for success. Key examples illustrated in this report include the Earth System Grid Federation (ESGF) and the Systems Biology Knowledgebase (KBase). This report expands on these points, and addresses others as well. The report contains a findings section as well as the text of the case studies discussed at the review.

  19. B13+: Photodriven Molecular Wankel Engine

    SciTech Connect

    Zhang, Jin; Sergeeva, Alina P.; Sparta, Manuel; Alexandrova, Anastassia N.

    2012-07-09

    Synthetic molecular motors that are capable of delivering controlled movement upon energy input are one of the key building blocks in nanomachinery. The major energy sources of molecular motors are from chemical reactions, photon beams, or electric current, which are converted into mechanical forces through the excitation of the electronic states of the molecule. The energy scale of the electronic excitation is normally two orders of magnitude larger than the molecular vibrational frequencies. To reduce the heat dissipation and increase the energy utilization efficiency, a motor running purely on the electronic ground-state (GS) potential energy surfaces is highly desirable.

  20. Niobate-based octahedral molecular sieves

    DOEpatents

    Nenoff, Tina M.; Nyman, May D.

    2003-07-22

    Niobate-based octahedral molecular sieves having significant activity for multivalent cations and a method for synthesizing such sieves are disclosed. The sieves have a net negatively charged octahedral framework, comprising niobium, oxygen, and octahedrally coordinated lower valence transition metals. The framework can be charge balanced by the occluded alkali cation from the synthesis method. The alkali cation can be exchanged for other contaminant metal ions. The ion-exchanged niobate-based octahedral molecular sieve can be backexchanged in acidic solutions to yield a solution concentrated in the contaminant metal. Alternatively, the ion-exchanged niobate-based octahedral molecular sieve can be thermally converted to a durable perovskite phase waste form.

  1. Niobate-based octahedral molecular sieves

    DOEpatents

    Nenoff, Tina M.; Nyman, May D.

    2006-10-17

    Niobate-based octahedral molecular sieves having significant activity for multivalent cations and a method for synthesizing such sieves are disclosed. The sieves have a net negatively charged octahedral framework, comprising niobium, oxygen, and octahedrally coordinated lower valence transition metals. The framework can be charge balanced by the occluded alkali cation from the synthesis method. The alkali cation can be exchanged for other contaminant metal ions. The ion-exchanged niobate-based octahedral molecular sieve can be backexchanged in acidic solutions to yield a solution concentrated in the contaminant metal. Alternatively, the ion-exchanged niobate-based octahedral molecular sieve can be thermally converted to a durable perovskite phase waste form.

  2. Molecular replacement and model-building using distant homology...

    Office of Scientific and Technical Information (OSTI)

    Research Org: Los Alamos National Laboratory (LANL) Sponsoring Org: NIH Country of Publication: United States Language: English Subject: Basic Biological Sciences(59) Biological ...

  3. 2010 Diffraction Methods in Structural Biology

    SciTech Connect

    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.

  4. Documentation of TRU biological transport model (BIOTRAN)

    SciTech Connect

    Gallegos, A.F.; Garcia, B.J.; Sutton, C.M.

    1980-01-01

    Inclusive of Appendices, this document describes the purpose, rationale, construction, and operation of a biological transport model (BIOTRAN). This model is used to predict the flow of transuranic elements (TRU) through specified plant and animal environments using biomass as a vector. The appendices are: (A) Flows of moisture, biomass, and TRU; (B) Intermediate variables affecting flows; (C) Mnemonic equivalents (code) for variables; (D) Variable library (code); (E) BIOTRAN code (Fortran); (F) Plants simulated; (G) BIOTRAN code documentation; (H) Operating instructions for BIOTRAN code. The main text is presented with a specific format which uses a minimum of space, yet is adequate for tracking most relationships from their first appearance to their formulation in the code. Because relationships are treated individually in this manner, and rely heavily on Appendix material for understanding, it is advised that the reader familiarize himself with these materials before proceeding with the main text.

  5. Quantifying evolvability in small biological networks

    SciTech Connect

    Nemenman, Ilya; Mugler, Andrew; Ziv, Etay; Wiggins, Chris H

    2008-01-01

    The authors introduce a quantitative measure of the capacity of a small biological network to evolve. The measure is applied to a stochastic description of the experimental setup of Guet et al. (Science 2002, 296, pp. 1466), treating chemical inducers as functional inputs to biochemical networks and the expression of a reporter gene as the functional output. The authors take an information-theoretic approach, allowing the system to set parameters that optimise signal processing ability, thus enumerating each network's highest-fidelity functions. All networks studied are highly evolvable by the measure, meaning that change in function has little dependence on change in parameters. Moreover, each network's functions are connected by paths in the parameter space along which information is not significantly lowered, meaning a network may continuously change its functionality without completely losing it along the way. This property further underscores the evolvability of the networks.

  6. Recovery from chemical, biological, and radiological incidents :

    SciTech Connect

    Franco, David Oliver; Yang, Lynn I.; Hammer, Ann E.

    2012-06-01

    To restore regional lifeline services and economic activity as quickly as possible after a chemical, biological or radiological incident, emergency planners and managers will need to prioritize critical infrastructure across many sectors for restoration. In parallel, state and local governments will need to identify and implement measures to promote reoccupation and economy recovery in the region. This document provides guidance on predisaster planning for two of the National Disaster Recovery Framework Recovery Support Functions: Infrastructure Systems and Economic Recovery. It identifies key considerations for infrastructure restoration, outlines a process for prioritizing critical infrastructure for restoration, and identifies critical considerations for promoting regional economic recovery following a widearea disaster. Its goal is to equip members of the emergency preparedness community to systematically prioritize critical infrastructure for restoration, and to develop effective economic recovery plans in preparation for a widearea CBR disaster.

  7. Biological Systems for Hydrogen Photoproduction (Presentation)

    SciTech Connect

    Ghirardi, M. L.

    2012-05-01

    This presentation summarizes NREL biological systems for hydrogen photoproduction work for the DOE Hydrogen and Fuel Cells Program Annual Merit Review and Peer Evaluation Meeting, May 14-18, 2012. General goal is develop photobiological systems for large-scale, low cost and efficient H{sub 2} production from water (barriers AH, AI and AJ). Specific tasks are: (1) Address the O{sub 2} sensitivity of hydrogenases that prevent continuity of H{sub 2} photoproduction under aerobic, high solar-to-hydrogen (STH) light conversion efficiency conditions; and (2) Utilize a limited STH H{sub 2}-producing method (sulfur deprivation) as a platform to address or test other factors limiting commercial algal H{sub 2} photoproduction, including low rates due to biochemical and engineering mechanisms.

  8. Biological effects of electric fields: EPRI's role

    SciTech Connect

    Kavet, R.

    1982-07-01

    Since 1973 the Electric Power Research Institute (EPRI) has supported research to evaluate the biological effects which may result from exposure to electric fields produced by AC overhead transmission lines; more recently, EPRI has also begun DC research. Through 1981 EPRI will have expended $8.7M on these efforts. Ongoing AC projects are studying a variety of lifeforms exposed to electric fields; these include humans, miniature swine, rats, honeybees, chick embryos, and crops. The status of these projects is discussed. The DC program has not as yet produced data. These studies will add to the current data base so as to enable a more complete assessment of health risks which may be associated with exposure to electric fields at power frequencies.

  9. Biology and Medicine Division annual report, 1985

    SciTech Connect

    Not Available

    1986-04-01

    This book briefly describes the activities of the Biology and Medicine Division of the Lawrence Berkeley Laboratory. During the past year the Donner Pavilion program on the treatment of arteriovenous malformations in the brain has chalked up very significant successes. The disease control rate has been high and objective measures of success using cerebral angiography have been established. The new high resolution positron emitting tomographic imager has been demonstrated to operate successfully. In the Radiation Biophysics program, the availability of higher mass ions up to uranium has allowed us cell and tissue studies in a radiation domain that is entirely new. Using uranium beams, investigators have already made new and exciting findings that are described in the body of the report.

  10. Molecular Characterization of Bacterial Respiration on Minerals

    SciTech Connect

    Blake, Robert C.

    2013-04-26

    The overall aim of this project was to contribute to our fundamental understanding of proteins and biological processes under extreme environmental conditions. We sought to define the biochemical and physiological mechanisms that underlie biodegradative and other cellular processes in normal, extreme, and engineered environments. Toward that end, we sought to understand the substrate oxidation pathways, the electron transport mechanisms, and the modes of energy conservation employed during respiration by bacteria on soluble iron and insoluble sulfide minerals. In accordance with these general aims, the specific aims were two-fold: To identify, separate, and characterize the extracellular biomolecules necessary for aerobic respiration on iron under strongly acidic conditions; and to elucidate the molecular principles whereby these bacteria recognize and adhere to their insoluble mineral substrates under harsh environmental conditions. The results of these studies were described in a total of nineteen manuscripts. Highlights include the following: 1. The complete genome of Acidithiobacillus ferrooxidans ATCC 23270 (type strain) was sequenced in collaboration with the DOE Joint Genome Institute; 2. Genomic and mass spectrometry-based proteomic methods were used to evaluate gene expression and in situ microbial activity in a low-complexity natural acid mine drainage microbial biofilm community. This was the first effort to successfully analyze a natural community using these techniques; 3. Detailed functional and structural studies were conducted on rusticyanin, an acid-stable electron transfer protein purified from cell-free extracts of At. ferrooxidans. The three-dimensional structure of reduced rusticyanin was determined from a combination of homonuclear proton and heteronuclear 15N- and 13C-edited NMR spectra. Concomitantly, the three-dimensional structure of oxidized rusticyanin was determined by X-ray crystallography to a resolution of 1.9 A by multiwavelength

  11. A systems biology, whole-genome association analysis of the molecular regulation of biomass growth and composition in Populus deltoides

    SciTech Connect

    Kirst, Matias

    2014-04-14

    Poplars trees are well suited for biofuel production due to their fast growing habit, favorable wood composition and adaptation to a broad range of environments. The availability of a reference genome sequence, ease of vegetative propagation and availability of transformation methods also make poplar an ideal model for the study of wood formation and biomass growth in woody, perennial plants. The objective of this project was to conduct a genome-wide association genetics study to identify genes that regulate bioenergy traits in Populus deltoides (eastern cottonwood). Populus deltoides is a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits and common and low-frequency single-nucleotide polymorphisms (SNPs) detected by targeted resequencing of 18,153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. These polymorphism are critical tools for the development of specialized plant feedstocks for bioenergy.

  12. A systems biology, whole-genome association analysis of the molecular regulation of biomass growth and composition in Populus deltoides

    SciTech Connect

    Kirst, Matias

    2015-04-15

    Poplars trees are well suited for biofuel production due to their fast growing habit, favorable wood composition and adaptation to a broad range of environments. The availability of a reference genome sequence, ease of vegetative propagation and availability of transformation methods also make poplar an ideal model for the study of wood formation and biomass growth in woody, perennial plants. The objective of this project was to conduct a genome-wide association genetics study to identify genes that regulate bioenergy traits in Populus deltoides (eastern cottonwood). Populus deltoides is a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits and common and low-frequency single-nucleotide polymorphisms (SNPs) detected by targeted resequencing of 18,153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. These polymorphism are critical tools for the development of specialized plant feedstocks for bioenergy.

  13. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

    SciTech Connect

    Taylor, R.C.

    1991-11-01

    This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese's group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

  14. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

    SciTech Connect

    Taylor, R.C.

    1991-11-01

    This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese`s group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

  15. Plant biology research and training for the 21st century

    SciTech Connect

    Kelly, K.

    1992-01-01

    The committee was assembled in response to a request from the National Science Foundation (NSF), the US Department of Agriculture (USDA), and the US Department of Energy (DoE). The leadership of these agencies asked the National Academy of Sciences through the National Research Council (NRC) to assess the status of plant-science research in the United States in light of the opportunities arising from advances inother areas of biology. NRC was asked to suggest ways of accelerating the application of these new biologic concepts and tools to research in plant science with the aim of enhancing the acquisition of new knowledge about plants. The charge to the committee was to examine the following: Organizations, departments, and institutions conducting plant biology research; human resources involved in plant biology research; graduate training programs in plant biology; federal, state, and private sources of support for plant-biology research; the role of industry in conducting and supporting plant-biology research; the international status of US plant-biology research; and the relationship of plant biology to leading-edge research in biology.

  16. Plant biology research and training for the 21st century

    SciTech Connect

    Kelly, K.

    1992-12-31

    The committee was assembled in response to a request from the National Science Foundation (NSF), the US Department of Agriculture (USDA), and the US Department of Energy (DoE). The leadership of these agencies asked the National Academy of Sciences through the National Research Council (NRC) to assess the status of plant-science research in the United States in light of the opportunities arising from advances inother areas of biology. NRC was asked to suggest ways of accelerating the application of these new biologic concepts and tools to research in plant science with the aim of enhancing the acquisition of new knowledge about plants. The charge to the committee was to examine the following: Organizations, departments, and institutions conducting plant biology research; human resources involved in plant biology research; graduate training programs in plant biology; federal, state, and private sources of support for plant-biology research; the role of industry in conducting and supporting plant-biology research; the international status of US plant-biology research; and the relationship of plant biology to leading-edge research in biology.

  17. Ultra-spatial synchrotron radiation for imaging molecular chemical structure: Applications in plant and animal studies

    DOE PAGES [OSTI]

    Yu, Peiqiang

    2007-01-01

    Synchrotron-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical features and make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced synchrotron technique to the study of plant and animal tissues' inherent structure at a cellular or subcellular level. In this article, a novel approach was introduced to show the potential of themore » newly developed, advanced synchrotron-based analytical technology, which can be used to reveal molecular structural-chemical features of various plant and animal tissues.« less

  18. SECTION IV: ATOMIC AND MOLECULAR SCIENCE

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    IV: ATOMIC AND MOLECULAR SCIENCE A Pyroelectric Crystal Particle Accelerator ....................................................................................................................................................IV-1 J. Kalodimos and R.L. Watson Polarization of Ka Satellite Transitions in Potassium .....................................................................................................................................IV-4 K. S. Fruchey, R.L. Watson, V. Horvat, and Yong

  19. SECTION IV: ATOMIC, MOLECULAR AND MATERIALS SCIENCE

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    ATOMIC, MOLECULAR AND MATERIALS SCIENCE A semiempirical scaling law for target K x-ray production in heavy ion collisions...... IV-1 R. L. Watson, Y. Peng, V. Horvat, and A. ...

  20. Molecular photoemission studies using synchrotron radiation

    SciTech Connect

    Truesdale, C.M.

    1983-04-01

    The angular distributions of photoelectrons and Auger electrons were measured by electron spectroscopy using synchrotron radiation. The experimental results are compared with theoretical calculations to interpret the electronic behavior of photoionization for molecular systems.

  1. Evaluating mixture adsorption models using molecular simulation...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    molecular simulation Previous Next List Joseph A. Swisher, Li-Chiang Lin, Jihan Kim, Berend Smit, AICHE J., 59, 3054-3064 (2013) DOI: 10.1002aic.14058 Abstract: The design of ...

  2. Environmental Molecular Sciences Laboratory 2007 Annual Report

    SciTech Connect

    Showalter, Mary Ann; Foster, Nancy S.

    2008-03-19

    This annual report provides details on the research conducted at the Environmental Molecular Sciences Laboratory in Fiscal Year 2007 and path forward for capability upgrades in Fiscal Year 2008.

  3. Production of Ultracold Trapped Molecular Hydrogen Ions

    SciTech Connect

    Blythe, P.; Roth, B.; Froehlich, U.; Wenz, H.; Schiller, S.

    2005-10-28

    We have cooled ensembles of the molecular hydrogen ions H{sub 2}{sup +}, H{sub 3}{sup +}, and all their deuterated variants to temperatures of a few mK in a radio frequency trap, by sympathetic cooling with laser-cooled beryllium ions. The molecular ions are embedded in the central regions of Coulomb crystals. Mass spectroscopy and molecular dynamics simulations were used to accurately characterize the properties of the ultracold multispecies crystals. We demonstrate species-selective purification of multispecies ensembles. These molecules are of fundamental importance as the simplest of all molecules, and have the potential to be used for precision tests of molecular structure theory, tests of Lorentz invariance, and measurements of electron to nuclear mass ratios and their time variation.

  4. Microdialysis unit for molecular weight separation

    DOEpatents

    Smith, Richard D. (Richland, WA); Liu, Chuanliang (Richland, WA)

    1999-01-01

    The present invention relates generally to an apparatus and method for separating high molecular weight molecules from low molecular weight molecules. More specifically, the invention relates to the use of microdialysis for removal of the salt (low molecular weight molecules) from a nucleotide sample (high molecular weight molecules) for ESI-MS analysis. The dialysis or separation performance of the present invention is improved by (1) increasing dialysis temperature thereby increasing desalting efficiency and improving spectrum quality; (2) adding piperidine and imidazole to the dialysis buffer solution and reducing charge states and further increasing detection sensitivity for DNA; (3) using low concentrations (0-2.5 mM NH4OAc) of dialysis buffer and shifting the DNA negative ions to higher charge states, producing a nearly 10-fold increase in detection sensitivity and a slightly decreased desalting efficiency, or (4) any combination of (1), (2), and (3).

  5. Molecular dynamics simulation studies of electrolytes andelectrolyte...

    Energy.gov [DOE] (indexed site)

    Merit Review and Peer Evaluation Meeting, May 18-22, 2009 -- Washington D.C. es40smith.pdf (4 MB) More Documents & Publications Molecular Dynamics Simulation Studies of ...

  6. Yuan T. Lee's Crossed Molecular Beam Experiment

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Yuan T. Lee's Crossed Molecular Beam Experiment http:web.archive.orgweb20000902074635www.er.doe.govproductionbesYuanLeeExp.html (1 of 4)472006 2:46:13 PM Yuan T. ...

  7. Molecular Characterizations of Surface Proteins Hemagglutinin and

    Office of Scientific and Technical Information (OSTI)

    Neuraminidase from Recent H5Nx Avian Influenza Viruses (Journal Article) | SciTech Connect Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses Citation Details In-Document Search Title: Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses During 2014, a subclade 2.3.4.4 highly pathogenic avian influenza (HPAI) A(H5N8) virus caused poultry outbreaks around

  8. MEIS: Molecular Environmental & Interface Science

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    People BL 11-2 Reports &Publications Model Compound Library SixPACK Glitch Curves MES User Resources & Instrumentation Environmental Remediation Science at SSRL MEIS Home SSRL Stanford EMSI SLAC Beam line resources and instrumentation Fundamental and applied research Why synchrotrons for environmental science? Molecular Environmental Science (MES) research at SSRL focuses on the fundamental interfacial, molecular- and nano-scale processes that control contaminant and nutrient cycling in

  9. Reliable Viscosity Calculation from Equilibrium Molecular Dynamics

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Simulations: A Time Decomposition Method - Joint Center for Energy Storage Research July 7, 2015, Research Highlights Reliable Viscosity Calculation from Equilibrium Molecular Dynamics Simulations: A Time Decomposition Method Schematic demonstration of the time decomposition method Scientific Achievement An equilibrium molecular dynamics-based computational method is developed and tested for the reliable calculation of viscosity. Significance and Impact Viscosity is one of the key properties

  10. PNNL: Center for Molecular Electrocatalysis: About Us

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Dr. Morris Bullock, CME Director About Us About the Center for Molecular Electrocatalysis To improve reactions important for solar energy storage and fuel cells, the Center for Molecular Electrocatalysis seeks to transform our ability to design electrocatalysts that convert electrical energy into the chemical bonds of fuels, or the reverse, convert chemical energy into electrical energy. Our researchers seek to understand, predict, and control the intra- and intermolecular flow of protons in

  11. Molecular gearing systems (Journal Article) | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    Molecular gearing systems Title: Molecular gearing systems The race to create smaller devices is fueling much of the research in electronics. The competition has intensified with the advent of microelectromechanical systems (MEMS), in which miniaturization is already reaching the dimensional limits imposed by physics of current lithographic techniques. Also, in the realm of biochemistry, evidence is accumulating that certain enzyme complexes are capable of very sophisticated modes of motion.

  12. Rigorous theory of molecular orientational nonlinear optics

    SciTech Connect

    Kwak, Chong Hoon Kim, Gun Yeup

    2015-01-15

    Classical statistical mechanics of the molecular optics theory proposed by Buckingham [A. D. Buckingham and J. A. Pople, Proc. Phys. Soc. A 68, 905 (1955)] has been extended to describe the field induced molecular orientational polarization effects on nonlinear optics. In this paper, we present the generalized molecular orientational nonlinear optical processes (MONLO) through the calculation of the classical orientational averaging using the Boltzmann type time-averaged orientational interaction energy in the randomly oriented molecular system under the influence of applied electric fields. The focal points of the calculation are (1) the derivation of rigorous tensorial components of the effective molecular hyperpolarizabilities, (2) the molecular orientational polarizations and the electronic polarizations including the well-known third-order dc polarization, dc electric field induced Kerr effect (dc Kerr effect), optical Kerr effect (OKE), dc electric field induced second harmonic generation (EFISH), degenerate four wave mixing (DFWM) and third harmonic generation (THG). We also present some of the new predictive MONLO processes. For second-order MONLO, second-order optical rectification (SOR), Pockels effect and difference frequency generation (DFG) are described in terms of the anisotropic coefficients of first hyperpolarizability. And, for third-order MONLO, third-order optical rectification (TOR), dc electric field induced difference frequency generation (EFIDFG) and pump-probe transmission are presented.

  13. Molecular Simulation of Carbon Dioxide, Brine, and Clay Mineral...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Molecular Simulation of Carbon Dioxide, Brine, and Clay Mineral Citation Details In-Document Search Title: Molecular Simulation of Carbon Dioxide, Brine, and Clay ...

  14. Controlling Motion at the Nanoscale: Rise of the Molecular Machines...

    Office of Scientific and Technical Information (OSTI)

    Published Article: Controlling Motion at the Nanoscale: Rise of the Molecular Machines Title: Controlling Motion at the Nanoscale: Rise of the Molecular Machines Authors: ...

  15. Molecular Weight Effects on Particle and Polymer Microstructure...

    Office of Scientific and Technical Information (OSTI)

    Molecular Weight Effects on Particle and Polymer Microstructure in Concentrated Polymer Solutions Citation Details In-Document Search Title: Molecular Weight Effects on Particle ...

  16. Analysis of Molecular Clusters in Simulations of Lithium-Ion...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Analysis of Molecular Clusters in Simulations of Lithium-Ion Battery Electrolytes. Citation Details In-Document Search Title: Analysis of Molecular Clusters in ...

  17. Applications of molecular replacement to G protein-coupled receptors...

    Office of Scientific and Technical Information (OSTI)

    Applications of molecular replacement to G protein-coupled receptors Citation Details In-Document Search Title: Applications of molecular replacement to G protein-coupled receptors ...

  18. Validation of Hydrogen Exchange Methodology on Molecular Sieves...

    Office of Environmental Management (EM)

    Validation of Hydrogen Exchange Methodology on Molecular Sieves for Tritium Removal from Contaminated Water Validation of Hydrogen Exchange Methodology on Molecular Sieves for ...

  19. PNNL: Center for Molecular Electrocatalysis - Research: An Assessment...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    December 2010 molecular-level understanding of the energetic and mechanistic factors The rational design of improved catalysts requires a detailed molecular-level understanding of ...

  20. The Influence of Molecular Structure of Distillate Fuels on HFRR...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    The Influence of Molecular Structure of Distillate Fuels on HFRR Lubricity The Influence of Molecular Structure of Distillate Fuels on HFRR Lubricity Presentation given at 2007 ...

  1. Final Report: Ionization chemistry of high temperature molecular...

    Office of Scientific and Technical Information (OSTI)

    Final Report: Ionization chemistry of high temperature molecular fluids Citation Details In-Document Search Title: Final Report: Ionization chemistry of high temperature molecular ...

  2. Molecular replacement and model-building using distant homology...

    Office of Scientific and Technical Information (OSTI)

    Molecular replacement and model-building using distant homology models as templates Citation Details In-Document Search Title: Molecular replacement and model-building using...

  3. Molecular Structure and Ion Transport near Electrode-Electrolyte...

    Office of Scientific and Technical Information (OSTI)

    Molecular Structure and Ion Transport near Electrode-Electrolyte Interfaces in Lithium-Ion Batteries Citation Details In-Document Search Title: Molecular Structure and Ion ...

  4. Remarkable Effect of Molecular Architecture on Chain Exchange...

    Office of Scientific and Technical Information (OSTI)

    Remarkable Effect of Molecular Architecture on Chain Exchange in Triblock Copolymer Micelles Citation Details In-Document Search Title: Remarkable Effect of Molecular Architecture...

  5. Accuracy of density functionals for molecular electronics: The...

    Office of Scientific and Technical Information (OSTI)

    Accuracy of density functionals for molecular electronics: The Anderson junction Title: Accuracy of density functionals for molecular electronics: The Anderson junction Authors: ...

  6. Molecular adsorption on metal surfaces with van der Waals density...

    Office of Scientific and Technical Information (OSTI)

    Molecular adsorption on metal surfaces with van der Waals density functionals Title: Molecular adsorption on metal surfaces with van der Waals density functionals Authors: Li, Guo ...

  7. Sandia Energy - Molecular Dynamics Simulations Predict Fate of...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Molecular Dynamics Simulations Predict Fate of Uranium in Sediments Home Highlights - Energy Research Molecular Dynamics Simulations Predict Fate of Uranium in Sediments Previous...

  8. Molecular catalytic coal liquid conversion (Conference) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    Conference: Molecular catalytic coal liquid conversion Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion This research, which is relevant to the ...

  9. A molecular basis for advanced materials in water treatment....

    Office of Scientific and Technical Information (OSTI)

    A molecular basis for advanced materials in water treatment. Citation Details In-Document Search Title: A molecular basis for advanced materials in water treatment. Authors: Rempe, ...

  10. Rotating fiber array molecular driver and molecular momentum transfer device constructed therewith

    DOEpatents

    Milleron, Norman

    1983-01-01

    A rotating fiber array molecular driver is disclosed which includes a magnetically suspended and rotated central hub to which is attached a plurality of elongated fibers extending radially therefrom. The hub is rotated so as to straighten and axially extend the fibers and to provide the fibers with a tip speed which exceeds the average molecular velocity of fluid molecules entering between the fibers. Molecules colliding with the sides of the rotating fibers are accelerated to the tip speed of the fiber and given a momentum having a directional orientation within a relatively narrow distribution angle at a point radially outward of the hub, which is centered and peaks at the normal to the fiber sides in the direction of fiber rotation. The rotating fiber array may be used with other like fiber arrays or with other stationary structures to form molecular momentum transfer devices such as vacuum pumps, molecular separators, molecular coaters, or molecular reactors.

  11. OSTIblog Articles in the Office of Biological and Environmental Research

    Office of Scientific and Technical Information (OSTI)

    (OBER) Abstracts Database Topic | OSTI, US Dept of Energy Office of Scientific and Technical Information Biological and Environmental Research (OBER) Abstracts Database Topic Managing the Department of Energy's Office of Biological and Environmental Research (BER) Project Information by Lorrie Johnson 02 Aug, 2011 in Science Communications 4339 BER%20banner.jpg Managing the Department of Energy's Office of Biological and Environmental Research (BER) Project Information Read more about 4339

  12. Biological and Environmental Research Advisory Committee (BERAC) meeting

    Office of Science (SC)

    October 27-28, 2016| U.S. DOE Office of Science (SC) Biological and Environmental Research Advisory Committee (BERAC) meeting October 27-28, 2016 Rockville, Md. Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (135KB) BER Committees of Visitors Federal Advisory Committees BER Home Meetings Biological and Environmental Research Advisory Committee (BERAC) meeting October 27-28,

  13. California Valley Solar Ranch Biological Assessment | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    California Valley Solar Ranch Biological Assessment California Valley Solar Ranch Biological Assessment Biological Assessment for the California Valley Solar Ranch Project San Luis Obispo County, California High Plains Ranch II, LLC (HPR II), a wholly owned subsidiary of SunPower Corporation, Systems ("SunPower") proposes to construct a 250-megawatt (MW) solar photovoltaic (PV) energy plant, the California Valley Solar Ranch Project (CVSR Project or Project), on a 4,747acre site in

  14. Damage-free vibrational spectroscopy of biological materials in the

    Office of Scientific and Technical Information (OSTI)

    electron microscope (Journal Article) | SciTech Connect Damage-free vibrational spectroscopy of biological materials in the electron microscope Citation Details In-Document Search Title: Damage-free vibrational spectroscopy of biological materials in the electron microscope Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy

  15. Synthetic biology and crop engineering | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Synthetic biology and crop engineering Synthetic biology and crop engineering Breakout Session 2: Frontiers and Horizons Session 2-A: Synthetic Biology and the Promise of Biofuels Jonathan Burbaum, Program Director, Department of Energy, Office of Science, ARPA-E b13_burbaum_2-a.pdf (1.63 MB) More Documents & Publications EIS-0481: Final Programmatic Environmental Impact Statement EIS-0481: Draft Programmatic Environmental Impact Statement EIS-0481: Notice of Intent to Prepare a Programmatic

  16. Browse by Discipline -- E-print Network Subject Pathways: Biology...

    Office of Scientific and Technical Information (OSTI)

    Biological, and Environmental Engineering, Oregon State University Williams, John M. (John M. Williams) - Petroleum Engineering program, Petroleum Institute (Abu Dhabi) Go ...

  17. Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen Production

    SciTech Connect

    James, B. D.; Baum, G. N.; Perez, J.; Baum, K. N.

    2009-09-01

    Report documenting the biological and engineering characteristics of five algal and bacterial hydrogen production systems selected by DOE and NREL for evaluation.

  18. Micro/nanofabricated environments for synthetic biology (Journal...

    Office of Scientific and Technical Information (OSTI)

    Artificial micro- and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when ...

  19. Most Viewed Documents for Biology and Medicine: September 2014...

    Office of Scientific and Technical Information (OSTI)

    for Biology and Medicine: September 2014 Modification to the Monte Carlo N-Particle (MCNP) Visual Editor (MCNPVised) to Read in Computer Aided Design (CAD) Files Randolph Schwarz; ...

  20. Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen Production

    Energy.gov [DOE]

    Report documenting the biological and engineering characteristics of five algal and bacterial hydrogen production systems selected by DOE and NREL for evaluation.

  1. March 2014 Most Viewed Documents for Biology And Medicine | OSTI...

    Office of Scientific and Technical Information (OSTI)

    March 2014 Most Viewed Documents for Biology And Medicine Carbon Dioxide Sequestering Using Microalgal Systems Daniel J. Stepan; Richard E. Shockey; Thomas A. Moe; Ryan Dorn (2002) ...

  2. September 2015 Most Viewed Documents for Biology And Medicine...

    Office of Scientific and Technical Information (OSTI)

    September 2015 Most Viewed Documents for Biology And Medicine Measuring dopamine release in the human brain with PET Volkow, N.D. Brookhaven National Lab., Upton, NY (United ...

  3. DOE Issues Request for Information on Biological Hydrogen Production

    Energy.gov [DOE]

    The Fuel Cell Technologies Office has issued a request for information seeking feedback from interested stakeholders regarding biological hydrogen production research and development.

  4. April 2013 Most Viewed Documents for Biology And Medicine | OSTI...

    Office of Scientific and Technical Information (OSTI)

    April 2013 Most Viewed Documents for Biology And Medicine Publications in biomedical and environmental sciences programs, 1981 Moody, J.B. (comp.) (1982) 306 Drug Retention Times ...

  5. Most Viewed Documents - Biology and Medicine | OSTI, US Dept...

    Office of Scientific and Technical Information (OSTI)

    - Biology and Medicine Drug Retention Times Center for Human Reliability Studies (2007) External dose-rate conversion factors for calculation of dose to the public Not Available ...

  6. June 2015 Most Viewed Documents for Biology And Medicine | OSTI...

    Office of Scientific and Technical Information (OSTI)

    June 2015 Most Viewed Documents for Biology And Medicine Measuring dopamine release in the human brain with PET Volkow, N.D. Brookhaven National Lab., Upton, NY (United ...

  7. Most Viewed Documents for Biology and Medicine: December 2014...

    Office of Scientific and Technical Information (OSTI)

    Most Viewed Documents for Biology and Medicine: December 2014 Dose and volume specification for reporting interstitial therapy NONE (1997) 38 Modification to the Monte Carlo ...

  8. June 2016 Most Viewed Documents for Biology And Medicine | OSTI...

    Office of Scientific and Technical Information (OSTI)

    Biology And Medicine Drug Retention Times Center for Human Reliability Studies (2007) 133 Modification to the Monte Carlo N-Particle (MCNP) Visual Editor (MCNPVised) to Read in ...

  9. July 2013 Most Viewed Documents for Biology And Medicine | OSTI...

    Office of Scientific and Technical Information (OSTI)

    July 2013 Most Viewed Documents for Biology And Medicine Carbon Dioxide Sequestering Using Microalgal Systems Daniel J. Stepan; Richard E. Shockey; Thomas A. Moe; Ryan Dorn (2002) ...

  10. September 2013 Most Viewed Documents for Biology And Medicine...

    Office of Scientific and Technical Information (OSTI)

    September 2013 Most Viewed Documents for Biology And Medicine Drug Retention Times Center for Human Reliability Studies (2007) 29 Oleoresin Capsicum toxicology evaluation and ...

  11. December 2015 Most Viewed Documents for Biology And Medicine...

    Office of Scientific and Technical Information (OSTI)

    December 2015 Most Viewed Documents for Biology And Medicine Measuring dopamine release in the human brain with PET Volkow, N.D. Brookhaven National Lab., Upton, NY (United ...

  12. Functionalized apertures for the detection of chemical and biological materials

    DOEpatents

    Letant, Sonia E.; van Buuren, Anthony W.; Terminello, Louis J.; Thelen, Michael P.; Hope-Weeks, Louisa J.; Hart, Bradley R.

    2010-12-14

    Disclosed are nanometer to micron scale functionalized apertures constructed on a substrate made of glass, carbon, semiconductors or polymeric materials that allow for the real time detection of biological materials or chemical moieties. Many apertures can exist on one substrate allowing for the simultaneous detection of numerous chemical and biological molecules. One embodiment features a macrocyclic ring attached to cross-linkers, wherein the macrocyclic ring has a biological or chemical probe extending through the aperture. Another embodiment achieves functionalization by attaching chemical or biological anchors directly to the walls of the apertures via cross-linkers.

  13. Speciation of Uranium in Biologically Reduced Sediments in the...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Speciation of Uranium in Biologically Reduced Sediments in the Old Rifle Aquifer ... Juan S. Lezama Pacheco The speciation and dynamics of Uranium(IV) in naturally and ...

  14. Biological Conversion of Sugars to Hydrocarbons Technology Pathway...

    Office of Scientific and Technical Information (OSTI)

    This technology pathway case investigates the biological conversion of biomass-derived ... Sponsoring Org: USDOE Office of Energy Efficiency and Renewable Energy Biomass Program ...

  15. Methods for isolation and viability assessment of biological organisms

    DOEpatents

    Letant, Sonia Edith; Baker, Sarah Elyse; Bond, Tiziana; Chang, Allan Shih-Ping

    2015-02-03

    Isolation of biological or chemical organisms can be accomplished using a surface enhanced Raman scattering (SERS) system. The SERS system can be a single or a stacked plurality of photonic crystal membranes with noble-metal lined through pores for flowing analyte potentially containing the biological or chemical organisms. The through pores can be adapted to trap individual biological or chemical organisms and emit SERS spectra, which can then be detected by a detector and further analyzed for viability of the biological or chemical organism.

  16. Linqu Qinchi Biological Co Ltd | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    City, Shandong Province, China Zip: 262600 Product: Shandong-based developer of a biogas plant that registered as a CDM project. References: Linqu Qinchi Biological Co.,...

  17. Synthetic biology for microbial production of lipid-based biofuels...

    Office of Scientific and Technical Information (OSTI)

    Synthetic biology for microbial production of lipid-based biofuels Citation Details In-Document Search This content will become publicly available on October 22, 2017 Title: ...

  18. March 2016 Most Viewed Documents for Biology And Medicine | OSTI...

    Office of Scientific and Technical Information (OSTI)

    March 2016 Most Viewed Documents for Biology And Medicine Measuring dopamine release in the human brain with PET Volkow, N.D. Brookhaven National Lab., Upton, NY (United ...

  19. January 2013 Most Viewed Documents for Biology And Medicine ...

    Office of Scientific and Technical Information (OSTI)

    January 2013 Most Viewed Documents for Biology And Medicine Nevada Test Site Radiological Control Manual Radiological Control Managers' Council Nevada Test Site Effects of ionizing ...

  20. Integration of hyperspectral imagery and biosensors for biological...

    Office of Scientific and Technical Information (OSTI)

    facility classification Citation Details In-Document Search Title: Integration of hyperspectral imagery and biosensors for biological and chemical facility classification Authors: ...

  1. Integration of hyperspectral imagery and biosensors for biological...

    Office of Scientific and Technical Information (OSTI)

    facility classification Citation Details In-Document Search Title: Integration of hyperspectral imagery and biosensors for biological and chemical facility classification You ...

  2. Integration of Hyperspectral Imagery and Biosensors for Biological...

    Office of Scientific and Technical Information (OSTI)

    Facility Classification Citation Details In-Document Search Title: Integration of Hyperspectral Imagery and Biosensors for Biological and Chemical Facility Classification You ...

  3. OSTIblog Articles in the Office of Biological and Environmental...

    Office of Scientific and Technical Information (OSTI)

    Biological and Environmental Research (OBER) Abstracts Database Topic Managing the Department of ... on two main areas: the Nation's Energy Security (developing cost-effective ...

  4. Genomics and Systems Biology of Tuberculosis (2009 JGI User Meeting)

    ScienceCinema

    Galagan, James

    2016-07-12

    James Galagan from the Broad Institute spoke about the "Genomics and Systems Biology of TB" on March 26, 2009 during the 4th Annual User Meeting

  5. Biological interactions of extremely-low-frequency electric and magnetic fields

    SciTech Connect

    Tenforde, T.S.

    1990-03-01

    A description is given of the fundamental physical properties of extremely-low frequency (ELF) electromagnetic fields, and the mechanisms through which these fields interact with the human body at a macroscopic level. the mechanisms through which ELF electric and magnetic fields induce currents in humans and other living objects are described. Evidence is presented that cell membranes play an important role in transducing ELF signals. Both experimental evidence and theoretical models are described that relate pericellular currents and electrochemical events at the outer membrane surface to transmembrane signaling pathways and cytoplasmic responses. Biological responses to ELF fields at the tissue, cellular and molecular levels are summarized, including new evidence that ELF field exposure produces alterations in messenger RNA synthesis, gene expression and the cytoplasmic concentrations of specific proteins. 50 refs., 9 figs., 2 tabs.

  6. Scalable Computational Methods for the Analysis of High-Throughput Biological Data

    SciTech Connect

    Langston, Michael A

    2012-09-06

    This primary focus of this research project is elucidating genetic regulatory mechanisms that control an organism?¢????s responses to low-dose ionizing radiation. Although low doses (at most ten centigrays) are not lethal to humans, they elicit a highly complex physiological response, with the ultimate outcome in terms of risk to human health unknown. The tools of molecular biology and computational science will be harnessed to study coordinated changes in gene expression that orchestrate the mechanisms a cell uses to manage the radiation stimulus. High performance implementations of novel algorithms that exploit the principles of fixed-parameter tractability will be used to extract gene sets suggestive of co-regulation. Genomic mining will be performed to scrutinize, winnow and highlight the most promising gene sets for more detailed investigation. The overall goal is to increase our understanding of the health risks associated with exposures to low levels of radiation.

  7. Final Report - Phylogenomic tools and web resources for the Systems Biology Knowledgebase

    SciTech Connect

    Sjolander, Kimmen

    2014-11-07

    The major advance during this last reporting period (8/15/12 to present) is our release of data on the PhyloFacts website: phylogenetic trees, multiple sequence alignments and other data for protein families are now available for download from http://phylogenomics.berkeley.edu/data/. This project as a whole aimed to develop high-throughput functional annotation systems that exploit information from protein 3D structure and evolution to provide highly precise inferences of various aspects of gene function, including molecular function, biological process, pathway association, Pfam domains, cellular localization and so on. We accomplished these aims by developing and testing different systems on a database of protein family trees: the PhyloFacts Phylogenomic Encyclopedia (at http://phylogenomics.berkeley.edu/phylofacts/ ).

  8. Combined LIBS-Raman for remote detection and characterization of biological samples

    SciTech Connect

    Anderson, Aaron S.; Mukundan, Harshini; Mcinroy, Rhonda E.; Clegg, Samuel M.

    2015-02-07

    Laser-Induced Breakdown Spectroscopy (LIBS) and Raman Spectroscopy have rich histories in the analysis of a wide variety of samples in both in situ and remote configurations. Our team is working on building a deployable, integrated Raman and LIBS spectrometer (RLS) for the parallel elucidation of elemental and molecular signatures under Earth and Martian surface conditions. Herein, results from remote LIBS and Raman analysis of biological samples such as amino acids, small peptides, mono- and disaccharides, and nucleic acids acquired under terrestrial and Mars conditions are reported, giving rise to some interesting differences. A library of spectra and peaks of interest were compiled, and will be used to inform the analysis of more complex systems, such as large peptides, dried bacterial spores, and biofilms. Lastly, these results will be presented and future applications will be discussed, including the assembly of a combined RLS spectroscopic system and stand-off detection in a variety of environments.

  9. Combined LIBS-Raman for remote detection and characterization of biological samples

    DOE PAGES [OSTI]

    Anderson, Aaron S.; Mukundan, Harshini; Mcinroy, Rhonda E.; Clegg, Samuel M.

    2015-02-07

    Laser-Induced Breakdown Spectroscopy (LIBS) and Raman Spectroscopy have rich histories in the analysis of a wide variety of samples in both in situ and remote configurations. Our team is working on building a deployable, integrated Raman and LIBS spectrometer (RLS) for the parallel elucidation of elemental and molecular signatures under Earth and Martian surface conditions. Herein, results from remote LIBS and Raman analysis of biological samples such as amino acids, small peptides, mono- and disaccharides, and nucleic acids acquired under terrestrial and Mars conditions are reported, giving rise to some interesting differences. A library of spectra and peaks of interestmore » were compiled, and will be used to inform the analysis of more complex systems, such as large peptides, dried bacterial spores, and biofilms. Lastly, these results will be presented and future applications will be discussed, including the assembly of a combined RLS spectroscopic system and stand-off detection in a variety of environments.« less

  10. Method and apparatus for biological sequence comparison

    DOEpatents

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  11. Method and apparatus for biological sequence comparison

    DOEpatents

    Marr, Thomas G.; Chang, William I-Wei

    1997-01-01

    A method and apparatus for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence.

  12. Speeding up biomolecular interactions by molecular sledding

    SciTech Connect

    Turkin, Alexander; Zhang, Lei; Marcozzi, Alessio; Mangel, Walter F.; Herrmann, Andreas; van Oijen, Antoine M.

    2015-10-07

    In numerous biological processes associations involve a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Moreover, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We also demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptide and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.

  13. Speeding up biomolecular interactions by molecular sledding

    DOE PAGES [OSTI]

    Turkin, Alexander; Zhang, Lei; Marcozzi, Alessio; Mangel, Walter F.; Herrmann, Andreas; van Oijen, Antoine M.

    2015-10-07

    In numerous biological processes associations involve a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Moreover, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We also demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptidemore » and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.« less

  14. Determining the Overpotential for a Molecular Electrocatalyst

    SciTech Connect

    Appel, Aaron M.; Helm, Monte L.

    2014-02-07

    “The additional potential (beyond the thermodynamic requirement) needed to drive a reaction at a certain rate is called the overpotential.”1 Over the last decade there has been considerable interest in the design and testing of molecular electrocatalysis for the interconversion of renewable energy and chemical fuels.2-5 One of the primary motivations for such research is the replacement of expensive and rare precious metal catalysts, such as platinum, with cheaper, more abundant metals.2,6-8 To become competitive with current electrocatalytic energy conversion technologies, new catalysts must be robust, fast, and energy-efficient. This last feature, the energy-efficiency, is dependent upon the overpotential. For molecular catalysts, the determination and reporting of overpotentials can be complicated by the frequent dependence on assumptions, especially when working in nonaqueous solvents. As overpotentials become lower, the meaningful comparison of molecular catalysts will require improved accuracy and precision. The intended purpose of this viewpoint is to provide a clear and concise description of overpotential and recommendation for its determination in molecular electrocatalysis. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

  15. Reversibly immobilized biological materials in monolayer films on electrodes

    DOEpatents

    Weaver, P.F.; Frank, A.J.

    1993-05-04

    Methods and techniques are described for reversibly binding charged biological particles in a fluid medium to an electrode surface. The methods are useful in a variety of applications. The biological materials may include microbes, proteins, and viruses. The electrode surface may consist of reversibly electroactive materials such as polyvinylferrocene, silicon-linked ferrocene or quinone.

  16. Reversibly immobilized biological materials in monolayer films on electrodes

    DOEpatents

    Weaver, Paul F. (Golden, CO); Frank, Arthur J. (Lakewood, CO)

    1993-01-01

    Methods and techniques are described for reversibly binding charged biological particles in a fluid medium to an electrode surface. The methods are useful in a variety of applications. The biological materials may include microbes, proteins, and viruses. The electrode surface may consist of reversibly electroactive materials such as polyvinylferrocene, silicon-linked ferrocene or quinone.

  17. Method of making molecularly doped composite polymer material

    SciTech Connect

    Affinito, John D; Martin, Peter M; Graff, Gordon L; Burrows, Paul E; Gross, Mark E. , Sapochak, Linda S.

    2005-06-21

    A method of making a composite polymer of a molecularly doped polymer. The method includes mixing a liquid polymer precursor with molecular dopant forming a molecularly doped polymer precursor mixture. The molecularly doped polymer precursor mixture is flash evaporated forming a composite vapor. The composite vapor is cryocondensed on a cool substrate forming a composite molecularly doped polymer precursor layer, and the cryocondensed composite molecularly doped polymer precursor layer is cross linked thereby forming a layer of the composite polymer layer of the molecularly doped polymer.

  18. Opportunities for Materials Science and Biological Research at the OPAL Research Reactor

    SciTech Connect

    Kennedy, S. J.

    2008-03-17

    Neutron scattering techniques have evolved over more than 1/2 century into a powerful set of tools for determination of atomic and molecular structures. Modern facilities offer the possibility to determine complex structures over length scales from {approx}0.1 nm to {approx}500 nm. They can also provide information on atomic and molecular dynamics, on magnetic interactions and on the location and behaviour of hydrogen in a variety of materials. The OPAL Research Reactor is a 20 megawatt pool type reactor using low enriched uranium fuel, and cooled by water. OPAL is a multipurpose neutron factory with modern facilities for neutron beam research, radioisotope production and irradiation services. The neutron beam facility has been designed to compete with the best beam facilities in the world. After six years in construction, the reactor and neutron beam facilities are now being commissioned, and we will commence scientific experiments later this year. The presentation will include an outline of the strengths of neutron scattering and a description of the OPAL research reactor, with particular emphasis on it's scientific infrastructure. It will also provide an overview of the opportunities for research in materials science and biology that will be possible at OPAL, and mechanisms for accessing the facilities. The discussion will emphasize how researchers from around the world can utilize these exciting new facilities.

  19. Management of Biological Materials in Wastewater from Research & Development Facilities

    SciTech Connect

    Raney, Elizabeth A.; Moon, Thomas W.; Ballinger, Marcel Y.

    2011-04-01

    PNNL has developed and instituted a systematic approach to managing work with biological material that begins in the project planning phase and carries through implementation to waste disposal. This paper describes two major processes used at PNNL to analyze and mitigate the hazards associated with working with biological materials and evaluate them for disposal to the sewer, ground, or surface water in a manner that protects human health and the environment. The first of these processes is the Biological Work Permit which is used to identify requirements for handling, storing, and working with biological materials and the second is the Sewer Approval process which is used to evaluate discharges of wastewaters containing biological materials to assure they meet industrial wastewater permits and other environmental regulations and requirements.

  20. Developing Enzyme and Biomimetic Catalysts for Upgrading Heavy Crudes via Biological Hydrogenation and Hydrodesulfurization

    SciTech Connect

    Borole, A P

    2006-08-22

    The recovery and conversion of heavy oils is limited due to the high viscosity of these crudes and their high heteroatom content. Conventional technology relies on thermochemical hydrogenation and hydrodesulfurization to address these problems and is energy intensive due to the high operating temperature and pressure. This project was initiated to explore biological catalysts for adding hydrogen to the heavy oil molecules. Biological enzymes are efficient at hydrogen splitting at very mild conditions such as room temperature and pressure, however, they are very specific in terms of the substrates they hydrogenate. The goal of the project was to investigate how the specificity of these enzymes can be altered to develop catalysts for oil upgrading. Three approaches were used. First was to perform chemical modification of the enzyme surface to improve binding of other non-natural substrates. Second approach was to expose the deeply buried catalytic active site of the enzyme by removal of protein scaffolding to enable better interaction with other substrates. The third approach was based on molecular biology to develop genetically engineered systems for enabling targeted structural changes in the enzyme. The first approach was found to be limited in success due to the non-specificity of the chemical modification and inability to target the region near the active site or the site of substrate binding. The second approach produced a smaller catalyst capable of catalyzing hydrogen splitting, however, further experimentation is needed to address reproducibility and stability issues. The third approach which targeted cloning of hydrogenase in alternate hosts demonstrated progress, although further work is necessary to complete the cloning process. The complex nature of the hydrogenase enzyme structure-function relationship and role of various ligands in the protein require significant more research to better understand the enzyme and to enable success in strategies in

  1. Towards reproducible, scalable lateral molecular electronic devices

    SciTech Connect

    Durkan, Colm Zhang, Qian

    2014-08-25

    An approach to reproducibly fabricate molecular electronic devices is presented. Lateral nanometer-scale gaps with high yield are formed in Au/Pd nanowires by a combination of electromigration and Joule-heating-induced thermomechanical stress. The resulting nanogap devices are used to measure the electrical properties of small numbers of two different molecular species with different end-groups, namely 1,4-butane dithiol and 1,5-diamino-2-methylpentane. Fluctuations in the current reveal that in the case of the dithiol molecule devices, individual molecules conduct intermittently, with the fluctuations becoming more pronounced at larger biases.

  2. Physics with fast molecular-ion beams

    SciTech Connect

    Kanter, E.P.

    1980-01-01

    Fast (MeV) molecular-ion beams provide a unique source of energetic projectile nuclei which are correlated in space and time. The recognition of this property has prompted several recent investigations of various aspects of the interactions of these ions with matter. High-resolution measurements on the fragments resulting from these interactions have already yielded a wealth of new information on such diverse topics as plasma oscillations in solids and stereochemical structures of molecular ions as well as a variety of atomic collision phenomena. The general features of several such experiments will be discussed and recent results will be presented.

  3. On the emergence of molecular structure

    SciTech Connect

    Matyus, Edit; Reiher, Markus; Hutter, Juerg; Mueller-Herold, Ulrich

    2011-05-15

    The structure of (a{sup {+-}},a{sup {+-}},b{sup {+-}})-type Coulombic systems is characterized by the effective ground-state density of the a-type particles, computed via nonrelativistic quantum mechanics without introduction of the Born-Oppenheimer approximation. A structural transition is observed when varying the relative mass of the a- and b-type particles, e.g., between atomic H{sup -} and molecular H{sub 2}{sup +}. The particle-density profile indicates a molecular-type behavior for the positronium ion, Ps{sup -}.

  4. 1982 bibliography of atomic and molecular processes

    SciTech Connect

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A.

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  5. Committee on Atomic, Molecular and Optical Sciences

    SciTech Connect

    Lancaster, James

    2015-06-30

    The Committee on Atomic, Molecular, and Optical Sciences (CAMOS) is a standing activity of the National Research Council (NRC) that operates under the auspices of the Board on Physics and Astronomy. CAMOS is one of five standing committees of the BPA that are charged with assisting it in achieving its goals—monitoring the health of physics and astronomy, identifying important new developments at the scientific forefronts, fostering interactions with other fields, strengthening connections to technology, facilitating effective service to the nation, and enhancing education in physics. CAMOS provides these capabilities for the atomic, molecular and optical (AMO) sciences.

  6. Optically pumped molecular bromine laser. Master's thesis

    SciTech Connect

    Morrison, J.W.

    1990-12-01

    An optically pumped molecular bromine laser was studied to investigate the quenching kinetics state of Br2. This included characterization of the pressure dependence of the laser output power. The approach was to excite molecular bromine in a sealed cell with a Nd:YAG pumped dye laser. Unresolved side fluorescence and amplified stimulated emission (ASE) spectra were recorded. ASE offered the advantage of a simpler optical system with no externally induced wavelength dependencies. Stimulated emission as a signal monitor offered greater resolution than side fluorescence spectra and facilitated spectroscopic assignment. (JS)

  7. A New Biology for the 21st Century; Ensuring the United States Leads the Coming Biology Revolution. Final committee report

    SciTech Connect

    None None

    2012-05-10

    In July, 2008, the National Institutes of Health (NIH), National Science Foundation (NSF), and Department of Energy (DOE) asked the National Research Council’s Board on Life Sciences to convene a committee to examine the current state of biological research in the United States and recommend how best to capitalize on recent technological and scientific advances that have allowed biologists to integrate biological research findings, collect and interpret vastly increased amounts of data, and predict the behavior of complex biological systems. From September 2008 through July of 2009, a committee of 16 experts from the fields of biology, engineering and computational science undertook to delineate those scientific and technological advances and come to a consensus on how the U.S. might best capitalize on them. This report, authored by the Committee on a New Biology for the 21st Century, describes the committee’s work and conclusions.

  8. Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

    SciTech Connect

    Gregurick, S.; Fredrickson, J. K.; Stevens, R.

    2009-03-01

    Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

  9. Biologically based multistage modeling of radiation effects

    SciTech Connect

    William Hazelton; Suresh Moolgavkar; E. Georg Luebeck

    2005-08-30

    This past year we have made substantial progress in modeling the contribution of homeostatic regulation to low-dose radiation effects and carcinogenesis. We have worked to refine and apply our multistage carcinogenesis models to explicitly incorporate cell cycle states, simple and complex damage, checkpoint delay, slow and fast repair, differentiation, and apoptosis to study the effects of low-dose ionizing radiation in mouse intestinal crypts, as well as in other tissues. We have one paper accepted for publication in ''Advances in Space Research'', and another manuscript in preparation describing this work. I also wrote a chapter describing our combined cell-cycle and multistage carcinogenesis model that will be published in a book on stochastic carcinogenesis models edited by Wei-Yuan Tan. In addition, we organized and held a workshop on ''Biologically Based Modeling of Human Health Effects of Low dose Ionizing Radiation'', July 28-29, 2005 at Fred Hutchinson Cancer Research Center in Seattle, Washington. We had over 20 participants, including Mary Helen Barcellos-Hoff as keynote speaker, talks by most of the low-dose modelers in the DOE low-dose program, experimentalists including Les Redpath (and Mary Helen), Noelle Metting from DOE, and Tony Brooks. It appears that homeostatic regulation may be central to understanding low-dose radiation phenomena. The primary effects of ionizing radiation (IR) are cell killing, delayed cell cycling, and induction of mutations. However, homeostatic regulation causes cells that are killed or damaged by IR to eventually be replaced. Cells with an initiating mutation may have a replacement advantage, leading to clonal expansion of these initiated cells. Thus we have focused particularly on modeling effects that disturb homeostatic regulation as early steps in the carcinogenic process. There are two primary considerations that support our focus on homeostatic regulation. First, a number of epidemiologic studies using multistage

  10. Molecular sieving silica membrane fabrication process

    DOEpatents

    Raman, N.K.; Brinker, C.J.

    1999-08-10

    A process is described for producing a molecular sieve silica membrane comprising depositing a hybrid organic-inorganic polymer comprising at least one organic constituent and at least one inorganic constituent on a porous substrate material and removing at least a portion of the at least one organic constituent of the hybrid organic-inorganic polymer, forming a porous film. 11 figs.

  11. Molecular sieving silica membrane fabrication process

    DOEpatents

    Raman, Narayan K. (Monroeville, PA); Brinker, Charles Jeffrey (Albuquerque, NM)

    1999-01-01

    A process for producing a molecular sieve silica membrane comprising depositing a hybrid organic-inorganic polymer comprising at least one organic constituent and at least one inorganic constituent on a porous substrate material and removing at least a portion of the at least one organic constituent of the hybrid organic-inorganic polymer, forming a porous film.

  12. Reaction dynamics in polyatomic molecular systems

    SciTech Connect

    Miller, W.H.

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  13. Geochemical Reaction Mechanism Discovery from Molecular Simulation

    SciTech Connect

    Stack, Andrew G.; Kent, Paul R. C.

    2014-11-10

    Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineral surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.

  14. Berkeley Lab Scientists Create Molecular Paper

    SciTech Connect

    2010-01-01

    These fluorescence microscope images show free-floating peptoid nanosheets in liquid. Each peptoid sheet is just two molecules thick yet up to hundreds of square micrometers in areaa molecular paper large enough to be visible to the naked eye.

  15. Geochemical Reaction Mechanism Discovery from Molecular Simulation

    DOE PAGES [OSTI]

    Stack, Andrew G.; Kent, Paul R. C.

    2014-11-10

    Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less

  16. Molecular sieving silica membrane fabrication process

    DOEpatents

    Raman, Narayan K.; Brinker, Charles Jeffrey

    1998-01-01

    A process for producing a molecular sieve silica membrane comprising depositing a hybrid organic-inorganic polymer comprising at least one organic constituent and at least one inorganic constituent on a porous substrate material and removing at least a portion of the at least one organic constituent of the hybrid organic-inorganic polymer, forming a porous film.

  17. Biological applications of ultraviolet free-electron lasers

    SciTech Connect

    Sutherland, J.C.

    1997-10-01

    This review examines the possibilities for biological research using the three ultraviolet free-electron lasers that are nearing operational status in the US. The projected operating characteristics of major interest in biological research of the free-electron lasers at Brookhaven National Laboratory, the Thomas Jefferson National Accelerator Facility, and Duke University are presented. Experimental applications in the areas of far- and vacuum ultraviolet photophysics and photochemistry, structural biology, environmental photobiology, and medical research are discussed and the prospects for advances in these areas, based upon the characteristics of the new ultraviolet free-electron lasers, are evaluated.

  18. Kinetic model for anaerobic digestion of biogas biological sludge

    SciTech Connect

    Pavlostathis, S.G.; Gossett, J.M.

    1986-10-01

    The principal objective of this study was the development and evaluation of a comprehensive kinetic model capable of predicting digester performance when fed biological sludge. Preliminary conversion mechanisms such as cell deaths, lysis, and hydrolysis responsible for rendering viable biological sludge organisms to available substrate were studied in depth. The results of this study indicate that hydrolysis of the dead, particulate biomass - primarily consisting of protein - is the slowest step, and therefore kinetically controls the overall process of an anaerobic digestion of biological sludge. A kinetic model was developed which could accurately describe digester performance and predict effluent quality.

  19. Detection of Chemical/Biological Agents and Stimulants using Quadrupole Ion Trap Mass Spectrometry

    SciTech Connect

    Harmon, S.H.; Hart, K.J.; Vass, A.A.; Wise, M.B.; Wolf, D.A.

    1999-06-14

    Detection of Chemical/Biological Agents and Simulants A new detector for chemical and biological agents is being developed for the U. S. Army under the Chemical and Biological Mass Spectrometer Block II program. The CBMS Block II is designed to optimize detection of both chemical and biological agents through the use of direct sampling inlets [I], a multi- ported sampling valve and a turbo- based vacuum system to support chemical ionization. Unit mass resolution using air as the buffer gas [2] has been obtained using this design. Software to control the instrument and to analyze the data generated from the instrument has also been newly developed. Detection of chemical agents can be accomplished. using the CBMS Block II design via one of two inlets - a l/ I 6'' stainless steel sample line -Chemical Warfare Air (CW Air) or a ground probe with enclosed capillary currently in use by the US Army - CW Ground. The Block II design is capable of both electron ionization and chemical ionization. Ethanol is being used as the Cl reagent based on a study indicating best performance for the Biological Warfare (BW) detection task (31). Data showing good signal to noise for 500 pg of methyl salicylate injected into the CW Air inlet, 50 ng of dimethylmethylphosphonate exposed to the CW Ground probe and 5 ng of methyl stearate analyzed using the pyrolyzer inlet were presented. Biological agents are sampled using a ''bio-concentrator'' unit that is designed to concentrate particles in the low micron range. Particles are collected in the bottom of a quartz pyrolyzer tube. An automated injector is being developed to deliver approximately 2 pL of a methylating reagent, tetramethylamonium- hydroxide to 'the collected particles. Pyrolysis occurs by rapid heating to ca. 55OOC. Biological agents are then characterized by their fatty acid methyl ester profiles and by other biomarkers. A library of ETOH- Cl/ pyrolysis MS data of microorganisms used for a recently published study [3] has been

  20. Designing π-stacked molecular structures to control heat transport through molecular junctions

    SciTech Connect

    Kiršanskas, Gediminas; Li, Qian; Solomon, Gemma C.; Flensberg, Karsten; Leijnse, Martin

    2014-12-08

    We propose and analyze a way of using π stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly desirable in thermoelectric energy converters, as well as in other electronic components where heat dissipation should be minimized or maximized. We suggest a molecular design consisting of two masses coupled to each other with one mass coupled to each lead. By having a small coupling (spring constant) between the masses, it is possible to either reduce or perhaps more surprisingly enhance the phonon conductance. We investigate a simple model system to identify optimal parameter regimes and then use first principle calculations to extract model parameters for a number of specific molecular realizations, confirming that our proposal can indeed be realized using standard molecular building blocks.

  1. Microsoft Word - DOE GTL grant - biological hydrogen production...

    Office of Scientific and Technical Information (OSTI)

    ... PLoS Computational Biology (2010), 6(11): e1001002. Miriam A. Rosenbaum, Haim Y. Bar, Qasim K. Beg, Daniel Segre, James Booth, Michael Cotta, Largus T. Angenent: Transcriptional ...

  2. Biological Imaging by Soft X-Ray Diffraction Microscopy

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biological Imaging by Soft X-Ray Diffraction Microscopy Print Electron and x-ray microscopes are a valuable tool for both the life and materials sciences, but they are limited in...

  3. EA-2011: Proposed Release of Three Parasitoids for the Biological...

    Energy.gov [DOE] (indexed site)

    the continental U.S. for the biological control of the emerald ash borer, a nonnative invasive beetle. The DOE Oak Ridge Office reviewed the EA, adopted it, and issued a FONSI for...

  4. June 2014 Most Viewed Documents for Biology And Medicine | OSTI...

    Office of Scientific and Technical Information (OSTI)

    June 2014 Most Viewed Documents for Biology And Medicine Modification to the Monte Carlo N-Particle (MCNP) Visual Editor (MCNPVised) to Read in Computer Aided Design (CAD) Files ...

  5. Biology Chemistry & Material Science Laboratory 1 | Sample Preparation...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    1 Cynthia Patty | (650) 926-3925 Biology Chemistry & Material Science Laboratory 1 Inventory The BioChemMat Lab 1 at SSRL is dedicated to researcher experiments, including x-ray ...

  6. John Marohn > ProfessorChemistry and Chemical Biology > Faculty...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Marohn Professor Chemistry and Chemical Biology Research Group Webpage jam99@cornell.edu John Marohn earned a B.S. in Chemistry and a B.A. in Physics from the University of ...

  7. March 2015 Most Viewed Documents for Biology And Medicine | OSTI...

    Office of Scientific and Technical Information (OSTI)

    5 Most Viewed Documents for Biology And Medicine Measuring dopamine release in the human brain with PET Volkow, N.D. Brookhaven National Lab., Upton, NY (United States)|State ...

  8. Biology Chemistry & Material Science Laboratory 2 | Sample Preparation...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    2 Cynthia Patty | (650) 926-3925 Biology Chemistry & Material Science Laboratory 2 Inventory The BioChemMat Lab 2 (BCM 2) at SSRL is dedicated to researcher experiments, including ...

  9. Methods of increasing secretion of polypeptides having biological activity

    DOEpatents

    Merino, Sandra

    2015-04-14

    The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

  10. Methods of increasing secretion of polypeptides having biological activity

    DOEpatents

    Merino, Sandra

    2014-05-27

    The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

  11. Methods of increasing secretion of polypeptides having biological activity

    DOEpatents

    Merino, Sandra

    2013-10-01

    The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

  12. Methods of increasing secretion of polypeptides having biological activity

    DOEpatents

    Merino, Sandra

    2014-10-28

    The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

  13. Biological assessments for the low energy demonstration accelerator, 1996

    SciTech Connect

    Cross, S.

    1997-03-01

    This report discusses the biological impact to the area around the Los Alamos National Laboratory of the Low Energy Demonstration Accelerator. In particular the impact to the soils, water quality, vegetation, and wildlife are discussed.

  14. Biological Imaging by Soft X-Ray Diffraction Microscopy

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Biological Imaging by Soft X-Ray Diffraction Microscopy Print Electron and x-ray microscopes are a valuable tool for both the life and materials sciences, but they are limited in ...

  15. Investigations of biological processes in Austrian MBT plants

    SciTech Connect

    Tintner, J.; Smidt, E.; Boehm, K.; Binner, E.

    2010-10-15

    Mechanical biological treatment (MBT) of municipal solid waste (MSW) has become an important technology in waste management during the last decade. The paper compiles investigations of mechanical biological processes in Austrian MBT plants. Samples from all plants representing different stages of degradation were included in this study. The range of the relevant parameters characterizing the materials and their behavior, e.g. total organic carbon, total nitrogen, respiration activity and gas generation sum, was determined. The evolution of total carbon and nitrogen containing compounds was compared and related to process operation. The respiration activity decreases in most of the plants by about 90% of the initial values whereas the ammonium release is still ongoing at the end of the biological treatment. If the biogenic waste fraction is not separated, it favors humification in MBT materials that is not observed to such extent in MSW. The amount of organic carbon is about 15% dry matter at the end of the biological treatment.

  16. Arms Control: US and International efforts to ban biological weapons

    SciTech Connect

    Not Available

    1992-12-01

    The Bacteriological (Biological) and Toxin Weapons Convention, the treaty that bans the development, production, and stockpiling and acquisition of biological weapons was opened for signature in 1972 and came into force in 1975 after being ratified by 22 governments, including the depository nations of the USA, the United Kingdom, and the former Soviet Union. In support of the Convention, the USA later established export controls on items used to make biological weapons. Further, in accordance with the 1990 President`s Enhanced Proliferation Control Initiative, actions were taken to redefine and expand US export controls, as well as to encourage multilateral controls through the Australia Group. Thus far, the Convention has not been effective in stopping the development of biological weapons. The principal findings as to the reasons of the failures of the Convention are found to be: the Convention lacks universality, compliance measures are effective, advantage of verification may outweigh disadvantages. Recommendations for mitigating these failures are outlined in this report.

  17. Browse by Discipline -- E-print Network Subject Pathways: Biology...

    Office of Scientific and Technical Information (OSTI)

    L M N O P Q R S T U V W X Y Z Keller, Christopher (Christopher Keller) - Department of Biology, Minot State University Go back to Individual Researchers Collections: A B C D E F G ...

  18. The Biological Implications of the PP2A Crystal Structure

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    The Biological Implications of the PP2A Crystal Structure Print Phosphatases, enzymes that remove a phosphate group from amino-acid substrates, can be subdivided according to their...

  19. Measuring Real-time Biological and Abiotic Manganese Oxide Reduction |

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Stanford Synchrotron Radiation Lightsource Measuring Real-time Biological and Abiotic Manganese Oxide Reduction Tuesday, May 31, 2016 Manganese(IV) oxides are powerful scavengers of toxins and trace metals, but they are also strong oxidants in the environment (1). Certain common microbes can also 'breathe' manganese oxides, in a process known as anaerobic respiration (2). During these environmental -commonly with sulfur or iron species- and biological interactions, manganese oxides are often

  20. Division of Chemical & Biological Sciences | The Ames Laboratory

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Chemical & Biological Sciences [PHOTO]Theory and modeling Researchers from the Ames Laboratory's Division of Chemical and Biological Sciences are developing computational tools to understand diffusion and reactivity in porous materials. Read more [PHOTO]Dynamic Nuclear Polarization The Ames Laboratory is home to the United States' first dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance (NMR) spectrometer dedicated to the study of materials science and chemistry. Read