National Library of Energy BETA

Sample records for link biological systems

  1. Enhancing the role of veterinary vaccines reducing zoonotic diseases of humans: Linking systems biology with vaccine development

    SciTech Connect (OSTI)

    Adams, Leslie G.; Khare, Sangeeta; Lawhon, Sara D.; Rossetti, Carlos A.; Lewin, Harris A.; Lipton, Mary S.; Turse, Joshua E.; Wylie, Dennis C.; Bai, Yu; Drake, Kenneth L.

    2011-09-22

    The aim of research on infectious diseases is their prevention, and brucellosis and salmonellosis as such are classic examples of worldwide zoonoses for application of a systems biology approach for enhanced rational vaccine development. When used optimally, vaccines prevent disease manifestations, reduce transmission of disease, decrease the need for pharmaceutical intervention, and improve the health and welfare of animals, as well as indirectly protecting against zoonotic diseases of people. Advances in the last decade or so using comprehensive systems biology approaches linking genomics, proteomics, bioinformatics, and biotechnology with immunology, pathogenesis and vaccine formulation and delivery are expected to enable enhanced approaches to vaccine development. The goal of this paper is to evaluate the role of computational systems biology analysis of host:pathogen interactions (the interactome) as a tool for enhanced rational design of vaccines. Systems biology is bringing a new, more robust approach to veterinary vaccine design based upon a deeper understanding of the host pathogen interactions and its impact on the host's molecular network of the immune system. A computational systems biology method was utilized to create interactome models of the host responses to Brucella melitensis (BMEL), Mycobacterium avium paratuberculosis (MAP), Salmonella enterica Typhimurium (STM), and a Salmonella mutant (isogenic *sipA, sopABDE2) and linked to the basis for rational development of vaccines for brucellosis and salmonellosis as reviewed by Adams et al. and Ficht et al. [1,2]. A bovine ligated ileal loop biological model was established to capture the host gene expression response at multiple time points post infection. New methods based on Dynamic Bayesian Network (DBN) machine learning were employed to conduct a comparative pathogenicity analysis of 219 signaling and metabolic pathways and 1620 gene ontology (GO) categories that defined the host's biosignatures

  2. Genomics and Systems Biology

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

    Genomics and Systems Biology LANL leads the world in computational finishing of microbial ... and experimental biology as the foundation of a dynamic systems biology capability. ...

  3. Genomics and Systems Biology

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

  4. Biological conversion system

    DOE Patents [OSTI]

    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. Genomics and Systems Biology

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

  6. Genomics and Systems Biology

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

    Genomics and Systems Biology LANL 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 biology capability. Systems

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

    SciTech Connect (OSTI)

    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."

  8. Adjustable link for kinematic mounting systems

    DOE Patents [OSTI]

    Hale, L.C.

    1997-07-01

    An adjustable link for kinematic mounting systems is disclosed. The adjustable link is a low-cost, passive device that provides backlash-free adjustment along its single constraint direction and flexural freedom in all other directions. The adjustable link comprises two spheres, two sockets in which the spheres are adjustable retain, and a connection link threadly connected at each end to the spheres, to provide a single direction of restraint and to adjust the length or distance between the sockets. Six such adjustable links provide for six degrees of freedom for mounting an instrument on a support. The adjustable link has applications in any machine or instrument requiring precision adjustment in six degrees of freedom, isolation from deformations of the supporting platform, and/or additional structural damping. The damping is accomplished by using a hollow connection link that contains an inner rod and a viscoelastic separation layer between the two. 3 figs.

  9. Adjustable link for kinematic mounting systems

    DOE Patents [OSTI]

    Hale, Layton C.

    1997-01-01

    An adjustable link for kinematic mounting systems. The adjustable link is a low-cost, passive device that provides backlash-free adjustment along its single constraint direction and flexural freedom in all other directions. The adjustable link comprises two spheres, two sockets in which the spheres are adjustable retain, and a connection link threadly connected at each end to the spheres, to provide a single direction of restraint and to adjust the length or distance between the sockets. Six such adjustable links provide for six degrees of freedom for mounting an instrument on a support. The adjustable link has applications in any machine or instrument requiring precision adjustment in six degrees of freedom, isolation from deformations of the supporting platform, and/or additional structural damping. The damping is accomplished by using a hollow connection link that contains an inner rod and a viscoelastic separation layer between the two.

  10. Links

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

    Useful Links BIOSYNC: Structural Biology Synchrotron Users Organization X-ray Anomalous Scattering Going MAD at CHESS Protein Data Bank Protein Data Bank Search International Union of Crystallography American Crystallographic Association Crystallography 101 Teaching Crystallography Periodic Table Periodic Table and X-ray Properties X-ray data booklet Merohedral crystal twinning server Software Links CCP4 MOSFLM HKL Research, Inc. homepage Solve/Resolve The O-files - Useful reference to the O

  11. Systems biology approach to bioremediation

    SciTech Connect (OSTI)

    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’.

  12. Method of measurement in biological systems

    DOE Patents [OSTI]

    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.

  13. Systems Biology in Prokaryote - Eukaryote Symbiosis | Stanford Synchrotron

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

    Radiation Lightsource Systems Biology in Prokaryote - Eukaryote Symbiosis Monday, June 25, 2012 - 12:00pm SLAC, SSRL Main Conference Room, 137-322 Allen M. Orville, Brookhaven National Laboratory Frontier challenges for macromolecular crystallography (MX) now include determining structures of trapped reactive intermediates, large macromolecules and viruses, membrane proteins, protein-protein complexes, and protein-nucleic acid complexes. Although structure and function are intimately linked,

  14. Method of measurement in biological systems

    DOE Patents [OSTI]

    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.

  15. Method of measurement in biological systems

    DOE Patents [OSTI]

    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.

  16. Method of measurement in biological systems

    DOE Patents [OSTI]

    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.

  17. 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 ...

  18. 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 ...

  19. A Systems Biology Platform for Characterizing Regulatory and...

    Office of Scientific and Technical Information (OSTI)

    Technical Report: A Systems Biology Platform for Characterizing Regulatory and Metabolic ... Citation Details In-Document Search Title: A Systems Biology Platform for Characterizing ...

  20. 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 ...

  1. Document creation, linking, and maintenance system

    DOE Patents [OSTI]

    Claghorn, Ronald

    2011-02-15

    A document creation and citation system designed to maintain a database of reference documents. The content of a selected document may be automatically scanned and indexed by the system. The selected documents may also be manually indexed by a user prior to the upload. The indexed documents may be uploaded and stored within a database for later use. The system allows a user to generate new documents by selecting content within the reference documents stored within the database and inserting the selected content into a new document. The system allows the user to customize and augment the content of the new document. The system also generates citations to the selected content retrieved from the reference documents. The citations may be inserted into the new document in the appropriate location and format, as directed by the user. The new document may be uploaded into the database and included with the other reference documents. The system also maintains the database of reference documents so that when changes are made to a reference document, the author of a document referencing the changed document will be alerted to make appropriate changes to his document. The system also allows visual comparison of documents so that the user may see differences in the text of the documents.

  2. Radiological/biological/aerosol removal system

    DOE Patents [OSTI]

    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.

  3. Modular microfluidic system for biological sample preparation

    DOE Patents [OSTI]

    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.

  4. KPFM and PFM of Biological Systems

    SciTech Connect (OSTI)

    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.

  5. Links

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

    Links: CAMD's SAXS beamline sister page By Derek Dorman General Reference: Glatter and Kratky Small Angle X-ray Scattering Book (subject to the permission letter and terms of use) SAXS Presentation by Jianhua Li SAXS Presentation by John Pople Dr. Brian Grady's Polymer Characterization Group SAXS page Jun, Y., Waychunas, G. "Molecular-Level Investigations of Nucleation Mechanisms and Kinetics of Formation of Environmental Nanoparticles" Poster SAXS Analysis/Simulation: Paul Scherrer

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

    DOE Patents [OSTI]

    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.

  7. Cross-Linking and Mass Spectrometry Methodologies to Facilitate Structural Biology: Finding a Path through the Maze

    SciTech Connect (OSTI)

    Merkley, Eric D.; Cort, John R.; Adkins, Joshua N.

    2013-09-01

    Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature. These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.

  8. 6th Annual Systems Biology Symposium: Systems Biology and the Environment

    SciTech Connect (OSTI)

    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

  9. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    SciTech Connect (OSTI)

    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.

  10. Genomics and Systems Biology of Tuberculosis (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Galagan, James

    2011-04-25

    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

  11. Renewable Hydrogen Production from Biological Systems

    Broader source: Energy.gov [DOE]

    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.

  12. Adding Links in Energy.gov Content Management System | Department of Energy

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

    Energy.gov Content Management System » Adding Links in Energy.gov Content Management System Adding Links in Energy.gov Content Management System For Office of Energy Efficiency and Renewable Energy (EERE) websites, to add a link in the Energy.gov Drupal content management system (CMS), follow these steps: Edit the page (also called a node) that you want to add a link to. Select the text you want to link. Click the "Link" button. Then: If you are linking to a page on Energy.gov, select

  13. Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-Energy Physics

    SciTech Connect (OSTI)

    Ruebel, Oliver

    2009-12-01

    Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research covered in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation becomes possible. The analysis framework MATLAB and the visualization have been integrated, making advanced analysis tools accessible to biologist and enabling bioinformatic researchers to directly integrate their analysis with the visualization. Laser wakefield particle accelerators (LWFAs) promise to be a new compact source of high-energy particles and radiation, with wide applications ranging from medicine to physics. To gain insight into the complex physical processes of particle

  14. A Systems Biology Platform for Characterizing Regulatory and Metabolic

    Office of Scientific and Technical Information (OSTI)

    Pathways that Influence and Control Microbial Hydrogen Production (Technical Report) | SciTech Connect Technical Report: A Systems Biology Platform for Characterizing Regulatory and Metabolic Pathways that Influence and Control Microbial Hydrogen Production Citation Details In-Document Search Title: A Systems Biology Platform for Characterizing Regulatory and Metabolic Pathways that Influence and Control Microbial Hydrogen Production Authors: Collins, James J [1] + Show Author Affiliations

  15. Chemical Biological Emergency Management Information System

    Energy Science and Technology Software Center (OSTI)

    2004-06-15

    CB-EMIS is designed to provide information and analysis to transit system operators and emergency responders in the event of a chemical attack on a subway system. The software inforporates detector data, video images, train data, meteorological data, and above- and below-ground plume dispersion models, hight of the liquid level.

  16. Computational Proteomics: High-throughput Analysis for Systems Biology

    SciTech Connect (OSTI)

    Cannon, William R.; Webb-Robertson, Bobbie-Jo M.

    2007-01-03

    High-throughput (HTP) proteomics is a rapidly developing field that offers the global profiling of proteins from a biological system. The HTP technological advances are fueling a revolution in biology, enabling analyses at the scales of entire systems (e.g., whole cells, tumors, or environmental communities). However, simply identifying the proteins in a cell is insufficient for understanding the underlying complexity and operating mechanisms of the overall system. Systems level investigations are relying more and more on computational analyses, especially in the field of proteomics generating large-scale global data.

  17. Behavior of REE in geological and biological systems

    SciTech Connect (OSTI)

    Laul, J.C.; Weimer, W.C.

    1981-05-01

    The REE abundances when normalized to primordial (chondritic) abundances behave as a smooth function of the REE ionic radii in both the geological and biological systems. The REE are hardly fractionated chemically through various stages of their transformation from soil-soil extract-plant-geological systems.

  18. Enabling a Systems Biology Knowledgebase with Gaggle and Firegoose

    SciTech Connect (OSTI)

    Baliga, Nitin S.

    2014-12-12

    The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is an open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and

  19. Request for Travel Funds for Systems Radiation Biology Workshop

    SciTech Connect (OSTI)

    Barcellos-Hoff, Mary Helen

    2014-03-22

    The 3rd International Systems Radiation Biology Workshop brought together the major European, US and Japanese research programs on radiation risk as well as selected experts representing systems biological approaches to discuss how the new methodologies could be best exploited for low dose research. A significant part of the workshop was devoted to discussions organised as breakout group sessions. To facilitate discussions number of participants was limited to 60 persons. To achieve the goals of this symposium in this international conference, support from DOE is vital. Hence, this proposal requested support in the amount of $15,000 to cover the travel expenses of international experts and radiation biology scientists from the United States. This supporting mechanism was clearly identified to the selected US participants as a conference support award from the DOE (See attached PDF). The workshop was an outstanding opportunity to strengthen interactions between leading experts in the emerging areas of radiation sciences, and will also provide opportunities for younger scientists to meet with experts and discuss their results. This workshop was designed to endorse active engagement in international collaboration. A major objective of this conference was to effectively communicate research results, in order to ensure that current thinking reflects sound science of radiation biology. Further, this international event addressed the use and success of scientific initiatives in radiation biology for policymakers, standard-setters, and the general public.

  20. EIA - Natural Gas Pipeline System - Links to U.S. Natural Gas Pipeline

    U.S. Energy Information Administration (EIA) Indexed Site

    Systems Links About U.S. Natural Gas Pipelines - Transporting Natural Gas based on data through 2007/2008 with selected updates Links to U.S. Natural Gas Pipeline Information - The links below will either direct the user to a narrative describing the system, a pipeline system map, a FERC prescribed "Informational Postings" page, or a FERC Tariff Sheet. Pipeline Name Type of System Regions of Operations Acadian Gas Pipeline System Intrastate Southwest Algonquin Gas Transmission Co

  1. Biological optimization systems for enhancing photosynthetic efficiency and methods of use

    DOE Patents [OSTI]

    Hunt, Ryan W; Chinnasamy, Senthil; Das, Keshav C; Rolim de Mattos, Erico

    2014-02-25

    The present disclosure relates to biological optimization systems for enhancing photosynthetic efficiency and methods of use.

  2. Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

    SciTech Connect (OSTI)

    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.

  3. FRAMES Software System: Linking to the Statistical Package R

    SciTech Connect (OSTI)

    Castleton, Karl J.; Whelan, Gene; Hoopes, Bonnie L.

    2006-12-11

    This document provides requirements, design, data-file specifications, test plan, and Quality Assurance/Quality Control protocol for the linkage between the statistical package R and the Framework for Risk Analysis in Multimedia Environmental Systems (FRAMES) Versions 1.x and 2.0. The requirements identify the attributes of the system. The design describes how the system will be structured to meet those requirements. The specification presents the specific modifications to FRAMES to meet the requirements and design. The test plan confirms that the basic functionality listed in the requirements (black box testing) actually functions as designed, and QA/QC confirms that the software meets the client’s needs.

  4. Biology

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

    Biology @WIPP Life Begins at 250,000,000 Years WIPP's underground isn't just suited for physics experiments aiming to unlock the mysteries of the Universe, it is also a perfect "dig site" for biologists wanting to chronicle the history of life. 250 million years ago, the area around WIPP was all part of the Permian Sea. Today, the salt beds that make up the WIPP underground provide a time capsule, of sorts, to this ancient era. Researchers have uncovered ancient bacteria, cellulose and

  5. Embedded calibration system for the DIII-D Langmuir probe analog fiber optic links

    SciTech Connect (OSTI)

    Watkins, J. G. [Sandia National Laboratories, Livermore, California (United States); Rajpal, R.; Mandaliya, H. [Institute for Plasma Research, Bhat, Gandhinagar, Gujarat (India); Watkins, M.; Boivin, R. L. [General Atomics, San Diego, California (United States)

    2012-10-15

    This paper describes a generally applicable technique for simultaneously measuring offset and gain of 64 analog fiber optic data links used for the DIII-D fixed Langmuir probes by embedding a reference voltage waveform in the optical transmitted signal before every tokamak shot. The calibrated data channels allow calibration of the power supply control fiber optic links as well. The array of fiber optic links and the embedded calibration system described here makes possible the use of superior modern data acquisition electronics in the control room.

  6. Protecting a HVDC link against accidental isolation from its receiving AC system

    SciTech Connect (OSTI)

    Whitehouse, R.S. )

    1993-07-01

    When an HVdc scheme is isolated from its receiving ac system, the inverter may continue to operate, generating its own ac bus voltages; this is defined here as islanding. If islanding is allowed to continue unrestricted, then main circuit components may in some conditions be damaged and it is therefore necessary to provide a suitable protection system. This paper outlines the protection scheme developed for the McNeill Back-to-Back HVdc link in Alberta, Canada, to prevent damage due to islanding while still permitting the link to automatically restart on reclosure of the isolating breaker. Oscillograms showing the protection in operation on both the GEC ALSTHOM HVdc simulator and during tests carried out as part of the commissioning of the McNeill HV dc link are included.

  7. Improving Power System Modeling. A Tool to Link Capacity Expansion and Production Cost Models

    SciTech Connect (OSTI)

    Diakov, Victor; Cole, Wesley; Sullivan, Patrick; Brinkman, Gregory; Margolis, Robert

    2015-11-01

    Capacity expansion models (CEM) provide a high-level long-term view at the prospects of the evolving power system. In simulating the possibilities of long-term capacity expansion, it is important to maintain the viability of power system operation in the short-term (daily, hourly and sub-hourly) scales. Production-cost models (PCM) simulate routine power system operation on these shorter time scales using detailed load, transmission and generation fleet data by minimizing production costs and following reliability requirements. When based on CEM 'predictions' about generating unit retirements and buildup, PCM provide more detailed simulation for the short-term system operation and, consequently, may confirm the validity of capacity expansion predictions. Further, production cost model simulations of a system that is based on capacity expansion model solution are 'evolutionary' sound: the generator mix is the result of logical sequence of unit retirement and buildup resulting from policy and incentives. The above has motivated us to bridge CEM with PCM by building a capacity expansion - to - production cost model Linking Tool (CEPCoLT). The Linking Tool is built to onset capacity expansion model prescriptions onto production cost model inputs. NREL's ReEDS and Energy Examplar's PLEXOS are the capacity expansion and the production cost models, respectively. Via the Linking Tool, PLEXOS provides details of operation for the regionally-defined ReEDS scenarios.

  8. The OME Framework for genome-scale systems biology

    SciTech Connect (OSTI)

    Palsson, Bernhard O.; Ebrahim, Ali; Federowicz, Steve

    2014-12-19

    The life sciences are undergoing continuous and accelerating integration with computational and engineering sciences. The biology that many in the field have been trained on may be hardly recognizable in ten to twenty years. One of the major drivers for this transformation is the blistering pace of advancements in DNA sequencing and synthesis. These advances have resulted in unprecedented amounts of new data, information, and knowledge. Many software tools have been developed to deal with aspects of this transformation and each is sorely needed [1-3]. However, few of these tools have been forced to deal with the full complexity of genome-scale models along with high throughput genome- scale data. This particular situation represents a unique challenge, as it is simultaneously necessary to deal with the vast breadth of genome-scale models and the dizzying depth of high-throughput datasets. It has been observed time and again that as the pace of data generation continues to accelerate, the pace of analysis significantly lags behind [4]. It is also evident that, given the plethora of databases and software efforts [5-12], it is still a significant challenge to work with genome-scale metabolic models, let alone next-generation whole cell models [13-15]. We work at the forefront of model creation and systems scale data generation [16-18]. The OME Framework was borne out of a practical need to enable genome-scale modeling and data analysis under a unified framework to drive the next generation of genome-scale biological models. Here we present the OME Framework. It exists as a set of Python classes. However, we want to emphasize the importance of the underlying design as an addition to the discussions on specifications of a digital cell. A great deal of work and valuable progress has been made by a number of communities [13, 19-24] towards interchange formats and implementations designed to achieve similar goals. While many software tools exist for handling genome

  9. Biologically-based signal processing system applied to noise removal for signal extraction

    DOE Patents [OSTI]

    Fu, Chi Yung; Petrich, Loren I.

    2004-07-13

    The method and system described herein use a biologically-based signal processing system for noise removal for signal extraction. A wavelet transform may be used in conjunction with a neural network to imitate a biological system. The neural network may be trained using ideal data derived from physical principles or noiseless signals to determine to remove noise from the signal.

  10. Enhanced visible and near-infrared capabilities of the JET mirror-linked divertor spectroscopy system

    SciTech Connect (OSTI)

    Lomanowski, B. A. Sharples, R. M.; Meigs, A. G.; Conway, N. J.; Zastrow, K.-D.; Heesterman, P.; Kinna, D. [EURATOM Collaboration: JET-EFDA Team

    2014-11-15

    The mirror-linked divertor spectroscopy diagnostic on JET has been upgraded with a new visible and near-infrared grating and filtered spectroscopy system. New capabilities include extended near-infrared coverage up to 1875 nm, capturing the hydrogen Paschen series, as well as a 2 kHz frame rate filtered imaging camera system for fast measurements of impurity (Be II) and deuterium D?, D?, D? line emission in the outer divertor. The expanded system provides unique capabilities for studying spatially resolved divertor plasma dynamics at near-ELM resolved timescales as well as a test bed for feasibility assessment of near-infrared spectroscopy.

  11. Reliability of unstable periodic orbit based control strategies in biological systems

    SciTech Connect (OSTI)

    Mishra, Nagender; Singh, Harinder P.; Hasse, Maria; Biswal, B.

    2015-04-15

    Presence of recurrent and statistically significant unstable periodic orbits (UPOs) in time series obtained from biological systems is now routinely used as evidence for low dimensional chaos. Extracting accurate dynamical information from the detected UPO trajectories is vital for successful control strategies that either aim to stabilize the system near the fixed point or steer the system away from the periodic orbits. A hybrid UPO detection method from return maps that combines topological recurrence criterion, matrix fit algorithm, and stringent criterion for fixed point location gives accurate and statistically significant UPOs even in the presence of significant noise. Geometry of the return map, frequency of UPOs visiting the same trajectory, length of the data set, strength of the noise, and degree of nonstationarity affect the efficacy of the proposed method. Results suggest that establishing determinism from unambiguous UPO detection is often possible in short data sets with significant noise, but derived dynamical properties are rarely accurate and adequate for controlling the dynamics around these UPOs. A repeat chaos control experiment on epileptic hippocampal slices through more stringent control strategy and adaptive UPO tracking is reinterpreted in this context through simulation of similar control experiments on an analogous but stochastic computer model of epileptic brain slices. Reproduction of equivalent results suggests that far more stringent criteria are needed for linking apparent success of control in such experiments with possible determinism in the underlying dynamics.

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

    Office of Science (SC) Website

    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

  13. Linking home energy rating systems with energy efficiency financing: Progress on national and state programs

    SciTech Connect (OSTI)

    Farhar, B.C.; Collins, N.E.; Walsh, R.W.

    1996-10-01

    In 1991 and early 1992, the U.S. Department of Energy (DOE), in cooperation with the U.S. Department of Housing and Urban Development (HUD), established a National Collaborative on Home Energy Rating Systems (HERS) and Energy Efficient Mortgages (EEMs). The Collaborative's purpose was to involve stakeholders at a national policy level to develop a plan leading the nation toward a voluntary system linking HERS with EEMs. The National Renewable Energy Laboratory (NREL) coordinated the National Collaborative's meetings for DOE. Composed of representatives from 25 stakeholder organizations, the Collaborative, after some 14 meetings, reached consensus on two documents, both published by NREL in mg 1992: A National Program for Energy-Efficient Mortgages and Home Energy Rating Systems: A Blueprint for Action and Going National with HERS and EEMs: Issues and Impacts, The Collected Papers of the National Collaborative.

  14. Theoretical Biology and Biophysics

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

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

  15. DOE Systems Biology Knowledgebase (KBASE) (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Arkin, Adam [LBNL

    2013-01-15

    Adam Arkin from Berkeley Lab on the DOE Systems Biology Knowledgebase (KBASE) at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  16. Building the DOE Systems Biology Knowledgebase (KBase) ( 7th Annual SFAF Meeting, 2012)

    ScienceCinema (OSTI)

    Brettin, Tom [Oak Ridge National Laboratory

    2013-03-22

    Tom Brettin on "Building the DOE Systems Biology Knowledgebase (KBase)" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  17. DOE Systems Biology Knowledgebase (KBASE) (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Arkin, Adam [LBNL] [LBNL

    2012-03-21

    Adam Arkin from Berkeley Lab on the DOE Systems Biology Knowledgebase (KBASE) at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

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

    SciTech Connect (OSTI)

    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.

  19. Modular Automated Processing System (MAPS) for analysis of biological samples.

    SciTech Connect (OSTI)

    Gil, Geun-Cheol; Chirica, Gabriela S.; Fruetel, Julia A.; VanderNoot, Victoria A.; Branda, Steven S.; Schoeniger, Joseph S.; Throckmorton, Daniel J.; Brennan, James S.; Renzi, Ronald F.

    2010-10-01

    We have developed a novel modular automated processing system (MAPS) that enables reliable, high-throughput analysis as well as sample-customized processing. This system is comprised of a set of independent modules that carry out individual sample processing functions: cell lysis, protein concentration (based on hydrophobic, ion-exchange and affinity interactions), interferent depletion, buffer exchange, and enzymatic digestion of proteins of interest. Taking advantage of its unique capacity for enclosed processing of intact bioparticulates (viruses, spores) and complex serum samples, we have used MAPS for analysis of BSL1 and BSL2 samples to identify specific protein markers through integration with the portable microChemLab{trademark} and MALDI.

  20. System for monitoring an industrial or biological process

    DOE Patents [OSTI]

    Gross, K.C.; Wegerich, S.W.; Vilim, R.B.; White, A.M.

    1998-06-30

    A method and apparatus are disclosed for monitoring and responding to conditions of an industrial process. Industrial process signals, such as repetitive manufacturing, testing and operational machine signals, are generated by a system. Sensor signals characteristic of the process are generated over a time length and compared to reference signals over the time length. The industrial signals are adjusted over the time length relative to the reference signals, the phase shift of the industrial signals is optimized to the reference signals and the resulting signals output for analysis by systems such as SPRT. 49 figs.

  1. System for monitoring an industrial or biological process

    DOE Patents [OSTI]

    Gross, Kenneth C.; Wegerich, Stephan W.; Vilim, Rick B.; White, Andrew M.

    1998-01-01

    A method and apparatus for monitoring and responding to conditions of an industrial process. Industrial process signals, such as repetitive manufacturing, testing and operational machine signals, are generated by a system. Sensor signals characteristic of the process are generated over a time length and compared to reference signals over the time length. The industrial signals are adjusted over the time length relative to the reference signals, the phase shift of the industrial signals is optimized to the reference signals and the resulting signals output for analysis by systems such as SPRT.

  2. Optimiziing the laboratory monitoring of biological wastewater-purification systems

    SciTech Connect (OSTI)

    S.V. Gerasimov

    2009-05-15

    Optimization of the laboratory monitoring of biochemical wastewater-treatment systems at coke plants is considered, for the example of OAO Koks. By adopting a methodological approach to determine the necessary data from chemical analysis, it is possible to reduce the time, labor, and materials required for monitoring, without impairing the purification process or compromising the plant's environmental policies.

  3. Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.

    DOE Patents [OSTI]

    Alfano, Robert R.; Wang, Wubao

    2003-05-06

    A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. A low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic transaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively.

  4. Systems-Level Synthetic Biology for Advanced Biofuel Production

    SciTech Connect (OSTI)

    Ruffing, Anne; Jensen, Travis J.; Strickland, Lucas Marshall; Meserole, Stephen; Tallant, David

    2015-03-01

    Cyanobacteria have been shown to be capable of producing a variety of advanced biofuels; however, product yields remain well below those necessary for large scale production. New genetic tools and high throughput metabolic engineering techniques are needed to optimize cyanobacterial metabolisms for enhanced biofuel production. Towards this goal, this project advances the development of a multiple promoter replacement technique for systems-level optimization of gene expression in a model cyanobacterial host: Synechococcus sp. PCC 7002. To realize this multiple-target approach, key capabilities were developed, including a high throughput detection method for advanced biofuels, enhanced transformation efficiency, and genetic tools for Synechococcus sp. PCC 7002. Moreover, several additional obstacles were identified for realization of this multiple promoter replacement technique. The techniques and tools developed in this project will help to enable future efforts in the advancement of cyanobacterial biofuels.

  5. External Links

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

    External Links External Links This page contains links to web sites and pages having to do with the Federal Energy Technology Network, Department of Energy, and Energy related ...

  6. Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.

    DOE Patents [OSTI]

    Alfano, Robert R.; Wang, Wubao

    2000-11-21

    A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. In accordance with the teachings of the invention, a low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic tansaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively. For example, it may also be used to diagnose diseases associated with the concentration of Raman-active constituents in urine, lymph and saliva It may be used to identify cancer in the breast, cervix, uterus, ovaries and the like by measuring the fingerprint excitation Raman spectra of these tissues. It may also be used to reveal the growing of tumors or cancers by measuring the levels of nitric oxide in tissue.

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

    SciTech Connect (OSTI)

    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.

  8. MIDC: Links

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

    Links Other Data Collection Activities Baseline Surface Radiation Network (BSRN) Clear Sky Forcast for NREL/SRRL (or other locations) Colorado Dept. of Public Health & Environment: Air Quality Index (AQI) Reporting System Colorado State University: USDA UV-B Monitoring and Research Program European Skynet Radiometers network (ESR) Jefferson County, Colorado: Jeffco Weather Station NOAA: Climate Monitoring & Diagnostics Laboratory (CMDL) NREL OTF: Reference Meteorological and Irradiance

  9. Interaction of biological systems with static and ELF electric and magnetic fields

    SciTech Connect (OSTI)

    Anderson, L.E.; Kelman, B.J.; Weigel, R.J.

    1987-01-01

    Although background levels of atmospheric electric and geomagnetic field levels are extremely low, over the past several decades, human beings and other life forms on this planet have been subjected to a dramatically changing electromagnetic milieu. An exponential increase in exposure to electromagnetic fields has occurred, largely because of such technological advances as the growth of electrical power generation and transmission systems, the increased use of wireless communications, and the use of radar. In addition, electromagnetic field generating devices have proliferated in industrial plants, office buildings, homes, public transportation systems, and elsewhere. Although significant increases have occurred in electromagnetic field strenghths spanning all frequency ranges, this symposium addresses only the impact of these fields at static and extremely low frequencies (ELF), primarily 50 and 60 Hz. This volume contains the proceedings of the symposium entitled /open quotes/Interaction of biological systems with static and ELF electric and magnetic fields/close quotes/. The purpose of the symposium was to provide a forum for discussions of all aspects of research on the interaction of static and ELF electromagnetic fields with biological systems. These systems include simple biophysical models, cell and organ preparations, whole animals, and man. Dosimetry, exposure system design, and artifacts in ELF bioeffects research were also addressed, along with current investigations that examine fundamental mechanisms of interactions between the fields and biological processes. Papers are indexed separately.

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

    SciTech Connect (OSTI)

    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.

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

    SciTech Connect (OSTI)

    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

  12. Biological optimization systems for enhancing photosynthetic efficiency and methods of use

    DOE Patents [OSTI]

    Hunt, Ryan W.; Chinnasamy, Senthil; Das, Keshav C.; de Mattos, Erico Rolim

    2012-11-06

    Biological optimization systems for enhancing photosynthetic efficiency and methods of use. Specifically, methods for enhancing photosynthetic efficiency including applying pulsed light to a photosynthetic organism, using a chlorophyll fluorescence feedback control system to determine one or more photosynthetic efficiency parameters, and adjusting one or more of the photosynthetic efficiency parameters to drive the photosynthesis by the delivery of an amount of light to optimize light absorption of the photosynthetic organism while providing enough dark time between light pulses to prevent oversaturation of the chlorophyll reaction centers are disclosed.

  13. Grid-Interactive Electric Vehicle DC-Link Photovoltaic Charging System -

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

    Grid-Connected Renewable Energy Systems Grid-Connected Renewable Energy Systems When connecting a home energy system to the electric grid, research and consider equipment required as well as your power provider’s requirements and agreements. | Photo courtesy of Solar Design Associates, Inc. When connecting a home energy system to the electric grid, research and consider equipment required as well as your power provider's requirements and agreements. | Photo courtesy of Solar Design

  14. Meteorological Integration for the Biological Warning and Incident Characterization (BWIC) System: General Guidance for BWIC Cities

    SciTech Connect (OSTI)

    Shaw, William J.; Wang, Weiguo; Rutz, Frederick C.; Chapman, Elaine G.; Rishel, Jeremy P.; Xie, YuLong; Seiple, Timothy E.; Allwine, K Jerry

    2007-02-16

    The U.S. Department of Homeland Security (DHS) is responsible for developing systems to detect the release of aerosolized bioagents in urban environments. The system that accomplishes this, known as BioWatch, is a robust first-generation monitoring system. In conjunction with the BioWatch detection network, DHS has also developed a software tool for cities to use to assist in their response when a bioagent is detected. This tool, the Biological Warning and Incident Characterization (BWIC) System, will eventually be deployed to all BioWatch cities to aid in the interpretation of the public health significance of indicators from the BioWatch networks. BWIC consists of a set of integrated modules, including meteorological models, that estimate the effect of a biological agent on a city’s population once it has been detected. For the meteorological models in BWIC to successfully calculate the distribution of biological material, they must have as input accurate meteorological data, and wind fields in particular. The purpose of this document is to provide guidance for cities to use in identifying sources of good-quality local meteorological data that BWIC needs to function properly. This process of finding sources of local meteorological data, evaluating the data quality and gaps in coverage, and getting the data into BWIC, referred to as meteorological integration, is described. The good news for many cities is that meteorological measurement networks are becoming increasingly common. Most of these networks allow their data to be distributed in real time via the internet. Thus, cities will often only need to evaluate the quality of available measurements and perhaps add a modest number of stations where coverage is poor.

  15. Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options

    SciTech Connect (OSTI)

    Carter, Sarah R.; Rodemeyer, Michael; Garfinkel, Michele S.; Friedman, Robert M

    2014-05-01

    Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options Sarah R. Carter, Ph.D., J. Craig Venter Institute; Michael Rodemeyer, J.D., University of Virginia; Michele S. Garfinkel, Ph.D., EMBO; Robert M. Friedman, Ph.D., J. Craig Venter Institute In recent years, a range of genetic engineering techniques referred to as “synthetic biology” has significantly expanded the tool kit available to scientists and engineers, providing them with far greater capabilities to engineer organisms than previous techniques allowed. The field of synthetic biology includes the relatively new ability to synthesize long pieces of DNA from chemicals, as well as improved methods for genetic manipulation and design of genetic pathways to achieve more precise control of biological systems. These advances will help usher in a new generation of genetically engineered microbes, plants, and animals. The JCVI Policy Center team, along with researchers at the University of Virginia and EMBO, examined how well the current U.S. regulatory system for genetically engineered products will handle the near-term introduction of organisms engineered using synthetic biology. In particular, the focus was on those organisms intended to be used or grown directly in the environment, outside of a contained facility. The study concludes that the U.S. regulatory agencies have adequate legal authority to address most, but not all, potential environmental, health and safety concerns posed by these organisms. Such near-term products are likely to represent incremental changes rather than a marked departure from previous genetically engineered organisms. However, the study also identified two key challenges for the regulatory system, which are detailed in the report. First, USDA’s authority over genetically engineered plants depends on the use of an older engineering technique that is no longer necessary for many applications. The shift to synthetic biology and other newer genetic

  16. A Fish-eye View of Riverine Hydropower Systems: Understanding the Biological Response to Turbine Passage

    SciTech Connect (OSTI)

    Pracheil, Brenda M; DeRolph, Christopher R; Schramm, Michael P; Bevelhimer, Mark S

    2016-01-01

    Fish populations that have been traditionally thought of as completely fragmented by dams still maintain limited, one-way connectivity from upstream to downstream reaches via downstream turbine passage. This one-way connectivity may be important to population dynamics, but can also introduce a new and significant source of mortality due to turbine-induced fish injury and mortality. Mechanistically, fish injury and mortality associated with downstream turbine passage can come from several sources including blade strike, shear forces, cavitation, or pressure decreases, and parsing the contributions of these individual forces is important for advancing and deploying turbines that minimize these impacts to fishes. The overarching goals of this project are two-fold: 1. To inform biological limitations of fish for use in creating and testing advanced turbine designs (e.g., research and development) and 2. To provide insight into locations that would be good initial locations for deploying advanced turbines (e.g., marketing). This report is an initial step in linking physical forces to injury and mortality rates to provide a better understanding turbine-associated injury and mortality rates for turbine designers and manufacturers and examine the spatial distribution of hydropower, turbines, and fishes across the U.S.A. to determine locations that may be good candidates for advanced turbine designs. We also use this report to present an initial approach for selecting species for further laboratory and field studies that examine the impacts of hydropower on fishes.

  17. Towards Composing Data Aware Systems Biology Workflows on Cloud Platforms: A MeDICi-based Approach

    SciTech Connect (OSTI)

    Gorton, Ian; Liu, Yan; Yin, Jian; Kulkarni, Anand V.; Wynne, Adam S.

    2011-09-08

    Cloud computing is being increasingly adopted for deploying systems biology scientific workflows. Scientists developing these workflows use a wide variety of fragmented and competing data sets and computational tools of all scales to support their research. To this end, the synergy of client side workflow tools with cloud platforms is a promising approach to share and reuse data and workflows. In such systems, the location of data and computation is essential consideration in terms of quality of service for composing a scientific workflow across remote cloud platforms. In this paper, we describe a cloud-based workflow for genome annotation processing that is underpinned by MeDICi - a middleware designed for data intensive scientific applications. The workflow implementation incorporates an execution layer for exploiting data locality that routes the workflow requests to the processing steps that are colocated with the data. We demonstrate our approach by composing two workflowswith the MeDICi pipelines.

  18. Final Report - Phylogenomic tools and web resources for the Systems Biology Knowledgebase

    SciTech Connect (OSTI)

    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/ ).

  19. How sulphate-reducing microorganisms cope with stress: Lessons from systems biology

    SciTech Connect (OSTI)

    Zhou, J.; He, Q.; Hemme, C.L.; Mukhopadhyay, A.; Hillesland, K.; Zhou, A.; He, Z.; Nostrand, J.D. Van; Hazen, T.C.; Stahl, D.A.; Wall, J.D.; Arkin, A.P.

    2011-04-01

    Sulphate-reducing microorganisms (SRMs) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. As SRMs have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. In this Review, we highlight recent applications of systems biology tools in studying the stress responses of SRMs, particularly Desulfovibrio spp., at the cell, population, community and ecosystem levels. The syntrophic lifestyle of SRMs is also discussed, with a focus on system-level analyses of adaptive mechanisms. Such information is important for understanding the microbiology of the global sulphur cycle and for developing biotechnological applications of SRMs for environmental remediation, energy production, biocorrosion control, wastewater treatment and mineral recovery.

  20. A NEW ACCRETION DISK AROUND THE MISSING LINK BINARY SYSTEM PSR J1023+0038

    SciTech Connect (OSTI)

    Patruno, A.; Archibald, A. M.; Hessels, J. W. T.; Bassa, C. G.; Janssen, G. H.; Bogdanov, S.; Stappers, B. W.; Lyne, A. G.; Kaspi, V. M.; Tendulkar, S.

    2014-01-20

    PSR J1023+0038 is an exceptional system for understanding how slowly rotating neutron stars are spun up to millisecond rotational periods through accretion from a companion star. Observed as a radio pulsar from 2007-2013, optical data showed that the system had an accretion disk in 2000/2001. Starting at the end of 2013 June, the radio pulsar has become undetectable, suggesting a return to the previous accretion-disk state, where the system more closely resembles an X-ray binary. In this Letter we report the first targeted X-ray observations ever performed of the active phase and complement them with UV/optical and radio observations collected in 2013 October. We find strong evidence that indeed an accretion disk has recently formed in the system and we report the detection of fast X-ray changes spanning about two orders of magnitude in luminosity. No radio pulsations are seen during low flux states in the X-ray light curve or at any other times.

  1. DANDE: a linked code system for core neutronics/depletion analysis

    SciTech Connect (OSTI)

    LaBauve, R.J.; England, T.R.; George, D.C.; MacFarlane, R.E.; Wilson, W.B.

    1985-06-01

    This report describes DANDE - a modular neutronics, depletion code system for reactor analysis. It consists of nuclear data processing, core physics, and fuel depletion modules, and allows one to use diffusion and transport methods interchangeably in core neutronics calculations. This latter capability is especially important in the design of small modular cores. Additional unique features include the capability of updating the nuclear data file during a calculation; a detailed treatment of depletion, burnable poisons as well as fuel; and the ability to make geometric changes such as control rod repositioning and fuel relocation in the course of a calculation. The detailed treatment of reactor fuel burnup, fission-product creation and decay, as well as inventories of higher-order actinides is a necessity when predicting the behavior of reactor fuel under increased burn conditions. The operation of the code system is made clear in this report by following a sample problem.

  2. Controlling harmonic instability of HVDC links connected to weak ac systems

    SciTech Connect (OSTI)

    Bodger, P.S. ); Irwin, G.D.; Woodford, D.A. )

    1990-10-01

    Time domain digital simulation of HVDC transmission enables harmonic stability of a system to be studied. This paper reports two alternative measures of controlling harmonic instability were investigated; the use of C-type ac filters and a simple addition of a harmonic damping circuit in the rectifier converter control. The design of a C-type filter is described and its effectiveness presented. Harmonic damping by controls consists of taking the output from a fast response dc current transducer, passing it through a filter and a gain and adding the output to the firing angle order. Both methods result in stable recovery from faults at both rectifier and inverter terminal busbars for a dc system inherently harmonically unstable.

  3. Ultrashort pulse high repetition rate laser system for biological tissue processing

    DOE Patents [OSTI]

    Neev, J.; Da Silva, L.B.; Matthews, D.L.; Glinsky, M.E.; Stuart, B.C.; Perry, M.D.; Feit, M.D.; Rubenchik, A.M.

    1998-02-24

    A method and apparatus are disclosed for fast, efficient, precise and damage-free biological tissue removal using an ultrashort pulse duration laser system operating at high pulse repetition rates. The duration of each laser pulse is on the order of about 1 fs to less than 50 ps such that energy deposition is localized in a small depth and occurs before significant hydrodynamic motion and thermal conduction, leading to collateral damage, can take place. The depth of material removed per pulse is on the order of about 1 micrometer, and the minimal thermal and mechanical effects associated with this ablation method allows for high repetition rate operation, in the region 10 to over 1000 Hertz, which, in turn, achieves high material removal rates. The input laser energy per ablated volume of tissue is small, and the energy density required to ablate material decreases with decreasing pulse width. The ablation threshold and ablation rate are only weakly dependent on tissue type and condition, allowing for maximum flexibility of use in various biological tissue removal applications. The use of a chirped-pulse amplified Titanium-doped sapphire laser is disclosed as the source in one embodiment. 8 figs.

  4. Ultrashort pulse high repetition rate laser system for biological tissue processing

    DOE Patents [OSTI]

    Neev, Joseph; Da Silva, Luiz B.; Matthews, Dennis L.; Glinsky, Michael E.; Stuart, Brent C.; Perry, Michael D.; Feit, Michael D.; Rubenchik, Alexander M.

    1998-01-01

    A method and apparatus is disclosed for fast, efficient, precise and damage-free biological tissue removal using an ultrashort pulse duration laser system operating at high pulse repetition rates. The duration of each laser pulse is on the order of about 1 fs to less than 50 ps such that energy deposition is localized in a small depth and occurs before significant hydrodynamic motion and thermal conduction, leading to collateral damage, can take place. The depth of material removed per pulse is on the order of about 1 micrometer, and the minimal thermal and mechanical effects associated with this ablation method allows for high repetition rate operation, in the region 10 to over 1000 Hertz, which, in turn, achieves high material removal rates. The input laser energy per ablated volume of tissue is small, and the energy density required to ablate material decreases with decreasing pulse width. The ablation threshold and ablation rate are only weakly dependent on tissue type and condition, allowing for maximum flexibility of use in various biological tissue removal applications. The use of a chirped-pulse amplified Titanium-doped sapphire laser is disclosed as the source in one embodiment.

  5. Designing Biological Systems for Sustainability and Programmed Environmental Interface (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Silver, Pam [Harvard University

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Pam Silver of Harvard University gives a presentation on "Designing Biological Systems for Sustainability and Programmed Environmental Interface" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  6. Designing Biological Systems for Sustainability and Programmed Environmental Interface (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Silver, Pam [Harvard University] [Harvard University

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Pam Silver of Harvard University gives a presentation on "Designing Biological Systems for Sustainability and Programmed Environmental Interface" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  7. Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses

    SciTech Connect (OSTI)

    Yang, Shihui; Pan, Chongle; Tschaplinski, Timothy J; Hurst, Gregory {Greg} B; Engle, Nancy L; Zhou, Wen; Dam, Phuongan; Xu, Ying; Dice, Lezlee T; Davison, Brian H; Brown, Steven D

    2013-01-01

    Zymomonas mobilis ZM4 is a capable ethanogenic bacterium with high ethanol productivity and high level of ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of ethanol stress response have not been elucidated fully. In this study, ethanol stress responses were investigated using systems biology tools. Medium supplementation with an initial 47.3 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. Metabolomic profiling showed that ethanol-treated ZM4 cells accumulated greater amounts of glycerol during the entire fermentation process, which may indicate an important role for this metabolite. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 56% of the predicted ZM4 proteome. Proteins related to metabolism and stress response such as chaperones and key regulators were more abundant in the early ethanol stress condition. Transcriptomic studies indicated the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. There were fewer genes significantly differentially expressed in the exponential phase compared to that of stationary phase and early stationary phase. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Correlations among the transcriptomics, proteomics and metabolism were examined and among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher. This systems biology study elucidates key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to

  8. On linking an Earth system model to the equilibrium carbon representation of an economically optimizing land use model

    SciTech Connect (OSTI)

    Bond-Lamberty, Benjamin; Calvin, Katherine V.; Jones, Andrew D.; Mao, Jiafu; Patel, Pralit L.; Shi, Xiaoying; Thomson, Allison M.; Thornton, Peter E.; Zhou, Yuyu

    2014-01-01

    Human activities are significantly altering biogeochemical cycles at the global scale, posing a significant problem for earth system models (ESMs), which may incorporate static land-use change inputs but do not actively simulate policy or economic forces. One option to address this problem is a to couple an ESM with an economically oriented integrated assessment model. Here we have implemented and tested a coupling mechanism between the carbon cycles of an ESM (CLM) and an integrated assessment (GCAM) model, examining the best proxy variables to share between the models, and quantifying our ability to distinguish climate- and land-use-driven flux changes. CLMs net primary production and heterotrophic respiration outputs were found to be the most robust proxy variables by which to manipulate GCAMs assumptions of long-term ecosystem steady state carbon, with short-term forest production strongly correlated with long-term biomass changes in climate-change model runs. By leveraging the fact that carbon-cycle effects of anthropogenic land-use change are short-term and spatially limited relative to widely distributed climate effects, we were able to distinguish these effects successfully in the model coupling, passing only the latter to GCAM. By allowing climate effects from a full earth system model to dynamically modulate the economic and policy decisions of an integrated assessment model, this work provides a foundation for linking these models in a robust and flexible framework capable of examining two-way interactions between human and earth system processes.

  9. Links - SRSCRO

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

    links Links Surplus Equipment Bolin Marketing Group | www.bmgsurplus.com Counties of the SRSCRO Region Aiken County | www.aikencounty.net Allendale County | www.allendalecounty.com Barnwell County | www.barnwellcounty.sc.gov Columbia County | www.columbiacountyga.gov Richmond County | www.augustaga.gov Chambers of Commerce Aiken SC | www.aikenchamber.net Augusta, GA | www.augustagausa.com Barnwell, SC | www.barnwellcountychamber.org Columbia County, GA | www.columbiacountychamber.com North

  10. A comprehensive collection of systems biology data characterizing the host response to viral infection

    SciTech Connect (OSTI)

    Aevermann, Brian D.; Pickett, Brett E.; Kumar, Sanjeev; Klem, Edward B.; Agnihothram, Sudhakar; Askovich, Peter S.; Bankhead, Armand; Bolles, Meagan; Carter, Victoria; Chang, Jean H.; Clauss, Therese R. W.; Dash, Pradyot; Diercks, Alan H.; Eisfeld, Amie J.; Ellis, Amy L.; Fan, Shufang; Ferris, Martin T.; Gralinski, Lisa; Green, Richard; Gritsenko, Marina A.; Hatta, Masato; Heegel, Robert A.; Jacobs, Jon M.; Jeng, Sophia; Josset, Laurence; Kaiser, Shari M.; Kelly, Sarah; Law, Gale Lynn; Li, Chengjun; Li, Jiangning; Long, Casey; Luna, Maria L.; Matzke, Melissa M.; McDermott, Jason E.; Menachery, Vineet; Metz, Thomas O.; Mitchell, Hugh D.; Monroe, Matthew E.; Navarro, Garnet; Neumann, Gabriele; Podyminogin, Rebecca L.; Purvine, Samuel O.; Rosenberger, Carrie; Sanders, Catherine J.; Schepmoes, Athena A.; Shukla, Anil K.; Sims, Amy; Sova, Pavel; Tam, Vincent C.; Tchitchek, Nicholas; Thomas, Paul G.; Tilton, Susan C.; Totura, Allison L.; Wang, Jing; Webb-Robertson, Bobbie-Jo M.; Wen, Ji; Weiss, Jeffrey M.; Yang, Feng; Yount, Boyd; Zhang, Qibin; Mcweeney, Shannon K.; Smith, Richard D.; Waters, Katrina M.; Kawaoka, Yoshihiro; Baric, Ralph; Aderem, Alan; Katze, Michael G.; Scheuermann, Richard H.

    2014-10-14

    The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archived at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). As a result, by comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.

  11. A comprehensive collection of systems biology data characterizing the host response to viral infection

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

    Aevermann, Brian D.; Pickett, Brett E.; Kumar, Sanjeev; Klem, Edward B.; Agnihothram, Sudhakar; Askovich, Peter S.; Bankhead, Armand; Bolles, Meagan; Carter, Victoria; Chang, Jean H.; et al

    2014-10-14

    The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archivedmore » at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). As a result, by comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.« less

  12. Department of Energy's Biological and Environmental Research Strategic Data Roadmap for Earth System Science

    SciTech Connect (OSTI)

    Williams, Dean N.; Palanisamy, Giri; Shipman, Galen; Boden, Thomas A.; Voyles, Jimmy W.

    2014-04-25

    Rapid advances in experimental, sensor, and computational technologies and techniques are driving exponential growth in the volume, acquisition rate, variety, and complexity of scientific data. This wealth of scientifically meaningful data has tremendous potential to lead to scientific discovery. However, to achieve scientific breakthroughs, these data must be exploitable—they must be analyzed effectively and efficiently and the results shared and communicated easily within the wider Department of Energy’s (DOE’s) Biological and Environmental Research (BER) Climate and Environmental Sciences Division (CESD) community. The explosion in data complexity and scale makes these tasks exceedingly difficult to achieve, particularly given that an increasing number of disciplines are working across techniques, integrating simulation and experimental or observational results (see Table 5 in Appendix 2). Consequently, we need new approaches to data management, analysis, and visualization that provide research teams with easy-to-use and scalable end-to-end solutions. These solutions must facilitate (and where feasible, automate and capture) every stage in the data lifecycle (shown in Figure 1), from collection to management, annotation, sharing, discovery, analysis, and visualization. In addition, the core functionalities are the same across climate science communities, but they require customization to adapt to specific needs and fit into research and analysis workflows. To this end, the mission of CESD’s Data and Informatics Program is to integrate all existing and future distributed CESD data holdings into a seamless and unified environment for the acceleration of Earth system science.

  13. System and method for preconcentrating, identifying, and quantifying chemical and biological substances

    DOE Patents [OSTI]

    Yu, Conrad M. (Antioch, CA); Koo, Jackson C. (San Ramon, CA)

    2000-01-01

    A system and method for preconcentrating, identifying, and quantifying chemical and biological substances is disclosed. An input valve directs a first volume of a sample gas to a surface acoustic wave (SAW) device. The SAW device preconcentrates and detects a mass of a substance within the sample gas. An output valve receives a second volume of the sample gas containing the preconcentrated substance from the SAW device and directs the second volume to a gas chromatograph (GC). The GC identifies the preconcentrated substance within the sample gas. A shunt valve exhausts a volume of the sample gas equal to the first volume minus the second volume away from the SAW device and the GC. The method of the present invention includes the steps of opening an input valve for passing a first volume of a sample gas to a SAW device; preconcentrating and detecting a mass of a substance within the sample gas using the SAW device; opening an output valve for passing a second volume of the sample gas containing the preconcentrated substance to a gas chromatograph (GC); and then identifying the preconcentrated substance within the sample gas using the GC.

  14. New wholesale power market design using linked forward markets : a study for the DOE energy storage systems program.

    SciTech Connect (OSTI)

    Silva Monroy, Cesar Augusto; Loose, Verne William; Ellison, James F.; Elliott, Ryan Thomas; Byrne, Raymond Harry; Guttromson, Ross; Tesfatsion, Leigh S.

    2013-04-01

    This report proposes a reformulation of U.S. ISO/RTO-managed wholesale electric power mar- kets for improved reliability and e ciency of system operations. Current markets do not specify or compensate primary frequency response. They also unnecessarily limit the participation of new technologies in reserve markets and o er insu cient economic inducements for new capacity invest- ment. In the proposed market reformulation, energy products are represented as physically-covered rm contracts and reserve products as physically-covered call option contracts. Trading of these products is supported by a backbone of linked ISO/RTO-managed forward markets with planning horizons ranging from multiple years to minutes ahead. A principal advantage of this reformulation is that reserve needs can be speci ed in detail, and resources can o er the services for which they are best suited, without being forced to conform to rigid reserve product de nitions. This should improve the business case for electric energy storage and other emerging technologies to provide reserve. In addition, the facilitation of price discovery should help to ensure e cient energy/reserve procurement and adequate levels of new capacity investment.

  15. Methods and systems for carrying out a pH-influenced chemical and/or biological reaction

    DOE Patents [OSTI]

    Stern, Michael C.; Simeon, Fritz; Hatton, Trevor Alan

    2016-04-05

    The present invention generally relates to methods and systems for carrying out a pH-influenced chemical and/or biological reaction. In some embodiments, the pH-influenced reaction involves the conversion of CO.sub.2 to a dissolved species.

  16. Chemical and biological warfare: Detection and warning systems. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect (OSTI)

    1995-03-01

    The bibliography contains citations concerning the detection, identification, verification, and warning systems of chemical and biological warfare agents. Citations discuss agents sampling, monitoring, and assessment. Techniques include chromotography, biosensing, chemical analysis, and DNA probes. Land pollution, soil tests, and skin protection are examined. (Contains a minimum of 244 citations and includes a subject term index and title list.)

  17. Chemical and biological warfare: Detection and warning systems. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect (OSTI)

    1996-10-01

    The bibliography contains citations concerning the detection, identification, verification, and warning systems of chemical and biological warfare agents. Citations discuss agents sampling, monitoring, and assessment. Techniques include chromotography, biosensing, chemical analysis, and DNA probes. Land pollution, soil tests, and skin protection are examined. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  18. Experimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production

    SciTech Connect (OSTI)

    Papoutsakis, Elefterios

    2015-04-30

    This is the final project report for project "Experimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production" for the funding period of 9/1/12 to 2/28/2015 (three years with a 6-month no-cost extension) OVERVIEW AND PROJECT GOALS The bottleneck of achieving higher rates and titers of toxic metabolites (such as solvents and carboxylic acids that can used as biofuels or biofuel precursors) can be overcome by engineering the stress response system. Thus, understanding and modeling the response of cells to toxic metabolites is a problem of great fundamental and practical significance. In this project, our goal is to dissect at the molecular systems level and build models (conceptual and quantitative) for the stress response of C. acetobutylicum (Cac) to its two toxic metabolites: butanol (BuOH) and butyrate (BA). Transcriptional (RNAseq and microarray based), proteomic and fluxomic data and their analysis are key requirements for this goal. Transcriptional data from mid-exponential cultures of Cac under 4 different levels of BuOH and BA stress was obtained using both microarrays (Papoutsakis group) and deep sequencing (RNAseq; Meyers and Papoutsakis groups). These two sets of data do not only serve to validate each other, but are also used for identification of stress-induced changes in transcript levels, small regulatory RNAs, & in transcriptional start sites. Quantitative proteomic data (Lee group), collected using the iTRAQ technology, are essential for understanding of protein levels and turnover under stress and the various protein-protein interactions that orchestrate the stress response. Metabolic flux changes (Antoniewicz group) of core pathways, which provide important information on the re-allocation of energy and carbon resources under metabolite stress, were examined using 13C-labelled chemicals. Omics data are integrated at different levels and scales. At the metabolic-pathway level, omics data are integrated into a 2nd generation genome

  19. Links - MST - UW Plasma Physics

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

    Links UW Madison Madison Symmetric Torus Links MST HomeGraduate Student InformationLinksTourControl and Auxiliary SystemsPhysics TopicsDeviceResearch MissionMST People mst logo CPLA Home Directory Publications Links Internal University of Wisconsin Physics Department Research funding includes support from: Department of Energy National Science Foundation Other Reversed Field Pinch Experiments around the world: RFX-mod in Padua, Italy Extrap-T2R in Stockhom, Sweden RELAX at Kyoto Institute of

  20. Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by dynamic global mapping of contended links

    DOE Patents [OSTI]

    Archer, Charles Jens; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

    2011-10-04

    A massively parallel nodal computer system periodically collects and broadcasts usage data for an internal communications network. A node sending data over the network makes a global routing determination using the network usage data. Preferably, network usage data comprises an N-bit usage value for each output buffer associated with a network link. An optimum routing is determined by summing the N-bit values associated with each link through which a data packet must pass, and comparing the sums associated with different possible routes.

  1. (Biological dosimetry)

    SciTech Connect (OSTI)

    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.

  2. Reducing Mortality from Terrorist Releases of Chemical and Biological Agents: I. Filtration for Ventilation Systems in Commercial Building

    SciTech Connect (OSTI)

    Thatcher, Tracy L.; Daisey, Joan M.

    1999-09-01

    There is growing concern about potential terrorist attacks involving releases of chemical and/or biological (CB) agents, such as sarin or anthrax, in and around buildings. For an external release, the CB agent can enter the building through the air intakes of a building's mechanical ventilation system and by infiltration through the building envelope. For an interior release in a single room, the mechanical ventilation system, which often recirculates some fraction of the air within a building, may distribute the released CB agent throughout the building. For both cases, installing building systems that remove chemical and biological agents may be the most effective way to protect building occupants. Filtration systems installed in the heating, ventilating and air-conditioning (HVAC) systems of buildings can significantly reduce exposures of building occupants in the event of a release, whether the release is outdoors or indoors. Reduced exposures can reduce the number of deaths from a terrorist attack. The purpose of this report is to provide information and examples of the design of filtration systems to help building engineers retrofit HVAC systems. The report also provides background information on the physical nature of CB agents and brief overviews of the basic principles of particle and vapor filtration.

  3. Biological Effects of Ionizing Radiation

    DOE R&D Accomplishments [OSTI]

    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.

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

    SciTech Connect (OSTI)

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

    2015-03-17

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

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

    SciTech Connect (OSTI)

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

    2015-03-17

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

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

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

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

    2015-03-17

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

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

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

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

    2015-03-17

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

  8. Protective link for superconducting coil

    DOE Patents [OSTI]

    Umans, Stephen D.

    2009-12-08

    A superconducting coil system includes a superconducting coil and a protective link of superconducting material coupled to the superconducting coil. A rotating machine includes first and second coils and a protective link of superconducting material. The second coil is operable to rotate with respect to the first coil. One of the first and second coils is a superconducting coil. The protective link is coupled to the superconducting coil.

  9. Development and Applications Of Photosensitive Device Systems To Studies Of Biological And Organic Materials

    SciTech Connect (OSTI)

    Gruner, Sol

    2012-01-20

    The primary focus of the grant is the development of new x-ray detectors for biological and materials work at synchrotron sources, especially Pixel Array Detectors (PADs), and the training of students via research applications to problems in biophysics and materials science using novel x-ray methods. This Final Progress Report provides a high-level overview of the most important accomplishments. These major areas of accomplishment include: (1) Development and application of x-ray Pixel Array Detectors; (2) Development and application of methods of high pressure x-ray crystallography as applied to proteins; (3) Studies on the synthesis and structure of novel mesophase materials derived from block co-polymers.

  10. E-Link - Disclaimer

    Office of Scientific and Technical Information (OSTI)

    Javascript Not Enabled OSTI Security Website Policies and Important Links

  11. Integrated Omics in Systems Biology: The New Frontier for Environmental Biotechnology

    SciTech Connect (OSTI)

    Hazen, Terry C.

    2008-08-12

    Environmental biotechnology encompasses a wide range of characterization, monitoring and control for bioenergy and bioremediation technologies that are based on biological processes. Recent breakthroughs in our understanding of biogeochemical processes and genomics are leading to exciting new and cost effective ways to monitor and manipulate the environment and potentially produce bioenergy fuels as we also cleanup the environment. Indeed, our ability to sequence an entire microbial genome in just a few hours is leading to similar breakthroughs in characterizing proteomes, metabolomes, phenotypes, and fluxes for organisms, populations, and communities. Understanding and modeling functional microbial community structure and stress responses in subsurface environments has tremendous implications for our fundamental understanding of biogeochemistry and the potential for making biofuel breakthroughs. Monitoring techniques that inventory and monitor terminal electron acceptors and electron donors, enzyme probes that measure functional activity in the environment, functional genomic microarrays, phylogenetic microarrays, metabolomics, proteomics, and quantitative PCR are also being rapidly adapted for studies in environmental biotechnology. Integration of all of these new high throughput techniques using the latest advances in bioinformatics and modeling will enable break-through science in environmental biotechnology. A review of these techniques with examples from field studies and lab simulations will be discussed.

  12. Proactive investigation of hydrocarbons released into a linked groundwater-surfacewater hydrologic system: Chevron Estero Marine Terminal

    SciTech Connect (OSTI)

    Tormey, D. ); Waldron, J. ); Culbertson, D. )

    1996-01-01

    When regulatory concern is high, it is critical to address potential ecological impacts early, and hence [open quotes]close the door[close quotes] on further unnecessary studies, as illustrated by the Chevron Estero Marine Terminal case study. Cutter stock (diesel-like hydrocarbons) leaked from a facility sump, reached the water table, and migrated laterally an unknown distance. Media reports led to heightened public and regulatory concern, and the information gap led to worst-case assumptions about the extent and impact of the release to the biota of a nearby creek (Toro Creek). Chevron undertook a rapid assessment with two goals: define the extent of cutter stock in soil and groundwater, and close the door on expensive biological studies of Toro Creek. The assessment consisted of installing a large number of small-diameter soil borings and temporary well points, monitor wells, and analyzing soil, groundwater, and hydraulic gradient. The information gap was very rapidly filled with the following comprehensive picture: (1) the cutter stock had mixed with heavy crude oil, was highly adsorptive to soil and practically insoluble in water; (2) the cutter stock had not reached Toro Creek; (3) Toro Creek is always a losing stream, hydraulically connected to groundwater beneath the Chevron facility; (4) the groundwater basin is isolated by bedrock boundaries. Early attention to Toro Creek and the Pacific Ocean, and open communication with concerned agencies effectively limited the investigation to soil and water.

  13. Proactive investigation of hydrocarbons released into a linked groundwater-surfacewater hydrologic system: Chevron Estero Marine Terminal

    SciTech Connect (OSTI)

    Tormey, D.; Waldron, J.; Culbertson, D.

    1996-12-31

    When regulatory concern is high, it is critical to address potential ecological impacts early, and hence {open_quotes}close the door{close_quotes} on further unnecessary studies, as illustrated by the Chevron Estero Marine Terminal case study. Cutter stock (diesel-like hydrocarbons) leaked from a facility sump, reached the water table, and migrated laterally an unknown distance. Media reports led to heightened public and regulatory concern, and the information gap led to worst-case assumptions about the extent and impact of the release to the biota of a nearby creek (Toro Creek). Chevron undertook a rapid assessment with two goals: define the extent of cutter stock in soil and groundwater, and close the door on expensive biological studies of Toro Creek. The assessment consisted of installing a large number of small-diameter soil borings and temporary well points, monitor wells, and analyzing soil, groundwater, and hydraulic gradient. The information gap was very rapidly filled with the following comprehensive picture: (1) the cutter stock had mixed with heavy crude oil, was highly adsorptive to soil and practically insoluble in water; (2) the cutter stock had not reached Toro Creek; (3) Toro Creek is always a losing stream, hydraulically connected to groundwater beneath the Chevron facility; (4) the groundwater basin is isolated by bedrock boundaries. Early attention to Toro Creek and the Pacific Ocean, and open communication with concerned agencies effectively limited the investigation to soil and water.

  14. Systems Biology Model of Interactions Between Tissue Growth Factors and DNA Damage Pathways: Low Dose Response and Cross-Talk in TGFbeta and ATM Signaling

    SciTech Connect (OSTI)

    O'Neill, Peter; Anderson, Jennifer

    2014-10-02

    The etiology of radiation carcinogenesis has been described in terms of aberrant changes that span several levels of biological organization. Growth factors regulate many important cellular and tissue functions including apoptosis, differentiation and proliferation. A variety of genetic and epigenetic changes of growth factors have been shown to contribute to cancer initiation and progression. It is known that cellular and tissue damage to ionizing radiation is in part initiated by the production of reactive oxygen species, which can activate cytokine signaling, and the DNA damage response pathways, most notably the ATM signaling pathway. Recently the transforming growth factor β (TGFβ) pathway has been shown to regulate or directly interact with the ATM pathway in the response to radiation. The relevance of this interaction with the ATM pathway is not known although p53 becomes phosphorylated and DNA damage responses are involved. However, growth factor interactions with DNA damage responses have not been elucidated particularly at low doses and further characterization of their relationship to cancer processes is warranted. Our goal will be to use a systems biology approach to mathematically and experimentally describe the low dose responses and cross-talk between the ATM and TGFβ pathways initiated by low and high LET radiation. We will characterize ATM and TGFβ signaling in epithelial and fibroblast cells using 2D models and ultimately extending to 3D organotypic cell culture models to begin to elucidate possible differences that may occur for different cell types and/or inter-cellular communication. We will investigate the roles of the Smad and Activating transcription factor 2 (ATF2) proteins as the potential major contributors to cross- talk between the TGFβ and ATM pathways, and links to cell cycle control and/or the DNA damage response, and potential differences in their responses at low and high doses. We have developed various experimental

  15. AlumniLink: June 2014

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

    Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit IN THIS ISSUE New science Neutrons provide new insights into human cell behavior Physics and biology intersect in breakthroughs Metallic glass could make your next cell phone harder to break Lab researcher works to rearrange the atoms in metals Alumni spotlight Shadi Dayeh: UCSD Former postdoc now an Associate Professor with the Jacobs School of Engineering at the UC

  16. A Study to Determine the Biological Feasibility of a New Fish-Tagging System : Annual Report 1998-1999.

    SciTech Connect (OSTI)

    Downing, Sandra L.; Prentice, Earl F.; Peterson, Bradley W.; Nunnallee, Edmund P.; Jonasson, Bruce F.

    2000-09-01

    This report covers our work during 1998 and 1999 (FY99) on a project to expand and improve technology for passive-integrated-transponder tags (PIT tags) throughout the Columbia River Basin. The National Marine Fisheries Service (NMFS) in cooperation with the Bonneville Power Administration (BPA) conducted the work. Timely and accurate information derived from PIT-tag technology is increasingly critical to resource stakeholders in assessing the effectiveness of efforts to enhance survival of juvenile and adult salmonids. Continued development of PIT-tag technology will enable researchers and fisheries managers to address issues expressed in the NMFS biological opinions for operation of the Federal Columbia River Power System (FCRPS) and the proposed Snake River Recovery Plan. The FY99 work was divided into individual projects that are covered separately in this report.

  17. An adaptive multi-level simulation algorithm for stochastic biological systems

    SciTech Connect (OSTI)

    Lester, C. Giles, M. B.; Baker, R. E.; Yates, C. A.

    2015-01-14

    Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics, SIAM Multiscale Model. Simul. 10(1), 146179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of ?. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where ? is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency

  18. Biology and management of insect pests in North American intensively managed hardwood forest systems.

    SciTech Connect (OSTI)

    Coyle, David R.; Nebeker, T., E.; Hart, E., R.; Mattson, W., J.

    2005-01-01

    Annu. Rev. Entomol. 50:1-29. Abstract Increasing demand for wood and wood products is putting stress on traditional forest production areas, leading to long-term economic and environmental concerns. Intensively managed hardwood forest systems (IMHFS), grown using conventional agricultural as well as forestry methods, can help alleviate potential problems in natural forest production areas. Although IMHFS can produce more biomass per hectare per year than natural forests, the ecologically simplified, monocultural systems may greatly increase the crops susceptibility to pests. Species in the genera Populus and Salix comprise the greatest acreage in IMHFS in North America, but other species, including Liquidambar styracifua and Platanus occidentalis, are also important. We discuss life histories, realized and potential damage, and management options for the most economically infuential pests that affect these hardwood species. The substantial inherent challenges associated with pest management in the monocultural environments created by IMHFS are reviewed. Finally, we discuss ways to design IMHFS that may reduce their susceptibility to pests, increase their growth and productivity potential, and create a more sustainable environment.

  19. Electro-mechanical energy conversion system having a permanent magnet machine with stator, resonant transfer link and energy converter controls

    DOE Patents [OSTI]

    Skeist, S. Merrill; Baker, Richard H.

    2006-01-10

    An electro-mechanical energy conversion system coupled between an energy source and an energy load comprising an energy converter device including a permanent magnet induction machine coupled between the energy source and the energy load to convert the energy from the energy source and to transfer the converted energy to the energy load and an energy transfer multiplexer to control the flow of power or energy through the permanent magnetic induction machine.

  20. A Study to Determine the Biological Feasability of a New Fish Tagging System : Annual Report, 1986-1987.

    SciTech Connect (OSTI)

    Prentice, Earl F.; Flagg, T.A.

    1987-12-01

    In 1983, a multi-year project to evaluate the technical and biological feasibility of adapting a new identification system to salmonids was established. The system is based upon a miniaturized passive integrated transponder (PIT) tag. This report discusses the work completed and is divided into laboratory studies, field studies, and systems development. All studies were conducted using a glass-encapsulated tag implanted into the body cavity of test fish via a 12-gauge hypodermic needle. Laboratory studies with juvenile chinook salmon, Oncorhynchus tshawytscha, showed that retention of glass-encapsulated PIT tags was 99-100% in fish weighing 3 g (mean weight) or larger. No adverse tissue response to the tag was noted. The survival of fish 5 g (mean weight) or larger was usually greater than 99%. However, fish ranging in weight from 2 to 4 g, or fish undergoing a physiological change such as smoltification may have a low mortality (usually less than 5.0%) after tagging. The mortality rate in the smaller fish was dependent upon tagging skill whereas mortality in smolting fish seemed dependent upon the level of stress. Growth comparisons between tagged and control fish indicated PIT-tagged fish had a slightly depressed growth rate at some measurement periods. The operational life of glass-encapsulated PIT tags implanted in fish was good, with 100% of the tags operating after 401 days. No tags were rejected from the fish during the observation period.

  1. Emerging semantics to link phenotype and environment

    SciTech Connect (OSTI)

    Thessen, Anne E.; Bunker, Daniel E.; Buttigieg, Pier Luigi; Cooper, Laurel D.; Dahdul, Wasila M.; Domisch, Sami; Franz, Nico M.; Jaiswal, Pankaj; Lawrence-Dill, Carolyn J.; Midford, Peter E.; Mungall, Christopher J.; Ramirez, Martin J.; Specht, Chelsea D.; Vogt, Lars; Vos, Rutger Aldo; Walls, Ramona L.; White, Jeffrey W.; Zhang, Guanyang; Deans, Andrew R.; Huala, Eva; Lewis, Suzanna E.; Mabee, Paula M.

    2015-12-14

    Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. Lastly, in this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.

  2. Emerging semantics to link phenotype and environment

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

    Thessen, Anne E.; Bunker, Daniel E.; Buttigieg, Pier Luigi; Cooper, Laurel D.; Dahdul, Wasila M.; Domisch, Sami; Franz, Nico M.; Jaiswal, Pankaj; Lawrence-Dill, Carolyn J.; Midford, Peter E.; et al

    2015-12-14

    Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies aremore » well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. Lastly, in this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.« less

  3. Preparation of a Magnetically Switchable Bioelectrocatalytic System Employing Cross-Linked Enzyme Aggregates in Magnetic Mesocellular Carbon Foam

    SciTech Connect (OSTI)

    Lee, Jinwoo; Lee, Dohun; Oh, Eunkeu; Kim, Jaeyun; Kim, Young-Pil; Jin, Sunmi; Kim, Hak Sung; Hwang, Yosun; Kwak, Ja Hun; Park, Je-Geun; Shin, Chae-Ho; Kim, Jungbae; Hyeon, Taeghwan

    2005-11-18

    Nanostructured magnetic materials (NMMs)[1] have attracted much attention recently because of their broad biotechnological applications including support matrices for enzyme immobilization,[2] immunoassays,[3] drug delivery,[4] and biosensors.[ 5] Specifically, the easy separation and controlled placement of NMMs by means of an external magnetic field enables their application in the development of immobilized enzyme processes[2] and the construction of magnetically controllable bio-electrocatalytic systems.[5, 6] Herein, we demonstrate the use of immobilized enzymes in NMMs for magnetically switchable bio-electrocatalysis.

  4. Energy Efficiency Links

    U.S. Energy Information Administration (EIA) Indexed Site

    Energy Efficiency Organizations Energy Efficiency Organizations Release Date: October 1999 Last Updated: Septembert 2009 EIA Links Disclaimer: These pages contain hypertext links...

  5. MicroLink Devices Inc | Open Energy Information

    Open Energy Info (EERE)

    search Name: MicroLink Devices, Inc. Place: Niles, Illinois Product: MicroLink Devices is a semiconductor manufacturer and system integrator that provides the latest...

  6. Feedstock Related Links | Department of Energy

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

    Research & Development » Feedstocks » Feedstock Related Links Feedstock Related Links There are a variety of other resources available for information on biomass feedstocks. We have organized some of those resources into the following categories: Other DOE Offices and Federal Agencies Department of Energy (DOE) Office of Science Biological and Environmental Research (BER) Biofuels Mission Focus DOE Office of Science BER Bioenergy Research Centers U.S. Department of Agriculture (USDA) 2007

  7. Website Policies / Important Links | Geothermal

    Office of Scientific and Technical Information (OSTI)

    Website Policies Important Links Website Policies Important Links Javascript Not Enabled OSTI Security Website Policies and Important Links

  8. Website Policies / Important Links | sciencecinema

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

    Website Policies / Important Links Website Policies / Important Links Javascript Not Enabled OSTI Security Website Policies and Important Links

  9. Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Glass, N Louise [UC Berkeley

    2013-01-25

    N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  10. Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Glass, N Louise [UC Berkeley] [UC Berkeley

    2012-03-22

    N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  11. Autofermentative Biological Hydrogen Production by Cyanobacteria...

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

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

  12. 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.

  13. Helpful Links - Hanford Site

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

    Helpful Links Helpful Links Helpful Links Hanford Staff Directory Hanford Site Wide Programs Energy Employees Occupational Illness Compensation Hanford Workers Compensation Projects & Facilities HERO PHOENIX Hanford Meteorological Station Definitions Abbreviations and Acronyms Visitor Control and Site Access Visitor Hanford Computer Access Request Helpful Links Email Email Page | Print Print Page | Text Increase Font Size Decrease Font Size Contact Us Do you have a question? Contact Hanford

  14. Links - 88-Inch Cyclotron

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

    Links Berkeley Lab Links: Nuclear Science Division Berkeley Lab Berkeley Lab Guest House Berkeley Lab Cafeteria Jobs at Berkeley Lab Today at Berkeley Lab Health and Safety Manual (PUB-3000) Science Links: Web Elements (Periodic Table) Science Daily News Sci Tech Daily News Space Weather Astronomy Picture of the Day The Cyclotron Kids Lawrence's Cyclotron Patent Science Fair Cyclotron Bay Area Links: Bay Area Traffic Bay Area Weather Bay Area Weather RADAR Bay Area Earthquakes

  15. FRAMES-2.0 Software System: Linking to the Groundwater Modeling System (GMS) RT3D and MT3DMS Models

    SciTech Connect (OSTI)

    Whelan, Gene; Castleton, Karl J.; Pelton, Mitch A.

    2007-08-08

    Linkages to the Groundwater Modeling System have been developed at Pacific Northwest National Laboratory to enable the Nuclear Regulatory Commission (NRC) to more realistically assess the risk to the public of radioactive contaminants at NRC-licensed sites. Common software tools presently in use are limited in that they cannot assess contaminant migration through complex natural environments. The purpose of this initiative is to provide NRC with a licensing safety-analysis tool with sufficient power, flexibility, and utility that it can serve as the primary software platform for analyzing the hazards associated with licensing actions at those complex sites at which the traditional tools are inappropriate. As a tool designed to realistically approximate prospective doses to the public, this initiative addresses NRCs safety-performance goal by confirming that licensing actions do not result in undue risk to the public.

  16. Development of an Implementation Plan Related to Biological Opinion on Operation of the Federal Columbia River Power System ; Step 1: Review and Critique of Implementation Plans.

    SciTech Connect (OSTI)

    Neitzel, Duane A.; Bunn, Amoret

    2000-12-01

    The Draft Biological Opinion on Operation of the Federal Columbia River Power System calls for the development of 1- and 5-year implementation plans. These plans will provide the roadmap for planning and subsequent implementation of actions intended to meet specific performance standards (i.e., biological objectives) in a timely manner. To develop implementation plans the key tasks and sequences of steps must be determined. Those responsible for specific tasks must be identified and they must understand what they need to do. There must be assurances that the resources (human, physical, and fiscal) to complete the tasks are available. Motivation and incentive systems should be set up. Systems to coordinate efforts and guide activity must be devised and installed. An information management system must be designed to manage and analyze data and ensure that appropriate data are collected. This will aid managers in assessing whether individual activities or actions are tracking with stated goals and objectives. Training programs to improve managerial and worker capability in making and implementing plans should be designed. Managerial leadership to guide the efforts of all individuals in achieving the goals of the anadromous and resident fish recovery must be developed. It is the entire process of managing fish recovery in relationship to the Biological Opinion that will guide, coordinate, motivate, and control work and determine the effectiveness and efficiency of plan implementation.

  17. AlumniLink: November 2014

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

    Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit IN THIS ISSUE New Science Climate, Earth system project draws on science powerhouses Three climate change drivers and corresponding questions for project's initial phase Collaboration drives achievement in protein structure research By tracking down how bacterial defense systems work, the scientists can potentially fight infectious diseases and genetic disorders Secure

  18. Biological and Environmental Research

    Broader source: All U.S. Department of Energy (DOE) Office 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 Cheryl Kuske (505) 665-4800 Email James Bossert (505) 667-3644 Email Manvendra Dubey (505) 665-3128 Email Kim Nitschke (505) 667-1186 Email Phil Jones (505) 667-6387 Email Cathy Wilson (505) 667-0202 Email Conducting

  19. Related Links - Hanford Site

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

    Related Links Hanford Advisory Board Convening Report SSAB Guidance Memorandum of Understanding Membership Nomination and Appointment Process Operating Ground Rules Calendars Advice and Responses Full Board Meeting Information Committee Meeting Information Outgoing Board Correspondence Key Board Products and Special Reports HAB Annual Report HAB and Committee Lists Points of Contact Related Links Related Links Email Email Page | Print Print Page | Text Increase Font Size Decrease Font Size

  20. ARM - Quick Links

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

    Links Related Links ISDAC Home AAF Home AVP Aircraft Instrumentation, October 14-16, 2008 ARM Data Discovery Browse Data Post-Campaign Data Sets Flight Summary Table (PDF, 440K) ISDAC Wiki Mission Summary Journal Deployment Resources NSA Site ARM Data Plots Quick Links Experiment Planning ISDAC Proposal Abstract Full Proposal (pdf, 1,735K) Science Questions Science Overview Document for ISDAC (pdf, 525K) ISDAC Flight Planning Document (PDF, 216K) Collaborations Logistics Measurements &

  1. AlumniLink

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

    AlumniLink Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit AlumniLink Bi-monthly publication connecting our alumni with news, information and former colleagues from the Lab. Alumni September 2015 September 2015 Neutrons find "missing" magnetism of plutonium Young, Jupiter-like planet discovered Four Los Alamos projects selected as R&D 100 Award finalists SHARE Alumni July 2015 July 2015 Mars Rover's

  2. Related Links | Department of Energy

    Energy Savers [EERE]

    Research & Development Algal Biofuels Related Links Related Links The links below ... Events Algal Biofuels Strategy Workshops Annual Biomass Conference Office-Attended ...

  3. Nuclear Data Links

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

    Links to Useful Online Nuclear Physics Journals Important Online Resources Science Direct ... Elsevier Physics Online: Nuclear Physics A, B, Physics Repots, Physics Letters B and more. ...

  4. Links (pbl/contracts)

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

    Implementation Links to related sites Regional Dialogue Transmission Regional Dialogue issues Team ASC Methodology 2012 BPA Rate Case Page content last modified on: April 06, 2010...

  5. Related Links - Hanford Site

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

    Links Tri-Party Agreement The Agreement Announcements List of Approved Changes TPA Project Manager's Lists Modifications for Public Comment Data Management MP-14 WIDS...

  6. 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...

  7. Biological and Chemical Security

    SciTech Connect (OSTI)

    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.

  8. Biological preconcentrator

    DOE Patents [OSTI]

    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.

  9. Carbon Cycling and Biosequestration Integrating Biology and Climate Through Systems Science Report from the March 2008 Workshop

    SciTech Connect (OSTI)

    Graber, J.; Amthor, J.; Dahlman, R.; Drell, D.; Weatherwax, S.

    2008-12-01

    One of the most daunting challenges facing science in the 21st Century is to predict how Earth's ecosystems will respond to global climate change. The global carbon cycle plays a central role in regulating atmospheric carbon dioxide (CO{sub 2}) levels and thus Earth's climate, but our basic understanding of the myriad of tightly interlinked biological processes that drive the global carbon cycle remains limited at best. Whether terrestrial and ocean ecosystems will capture, store, or release carbon is highly dependent on how changing climate conditions affect processes performed by the organisms that form Earth's biosphere. Advancing our knowledge of biological components of the global carbon cycle is thus crucial to predicting potential climate change impacts, assessing the viability of climate change adaptation and mitigation strategies, and informing relevant policy decisions. Global carbon cycling is dominated by the paired biological processes of photosynthesis and respiration. Photosynthetic plants and microbes of Earth's land-masses and oceans use solar energy to transform atmospheric CO{sub 2} into organic carbon. The majority of this organic carbon is rapidly consumed by plants or microbial decomposers for respiration and returned to the atmosphere as CO{sub 2}. Coupling between the two processes results in a near equilibrium between photosynthesis and respiration at the global scale, but some fraction of organic carbon also remains in stabilized forms such as biomass, soil, and deep ocean sediments. This process, known as carbon biosequestration, temporarily removes carbon from active cycling and has thus far absorbed a substantial fraction of anthropogenic carbon emissions.

  10. (Biological dosimetry)

    SciTech Connect (OSTI)

    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.

  11. ARM - Related Links

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

    Related Links Related Links TWP-ICE Home Tropical Western Pacific Home ARM Data Discovery Browse Data Post-Experiment Data Sets Weather Summary (pdf, 6M) New York Workshop Presentations Experiment Planning TWP-ICE Proposal Abstract Detailed Experiment Description Science Plan (pdf, 1M) Operations Plan (pdf, 321K) Maps Contact Info Related Links Daily Report Report Archives Press Media Coverage TWP-ICE Fact Sheet (pdf, 211K) Press Releases TWP-ICE Images ARM flickr site <=""

  12. AlumniLink: July 2015

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

    Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit IN THIS ISSUE New Science Project ATHENA creates surrogate human organ systems Uncovering the mysteries of cosmic explosions Portable MRI could aid wounded soldiers and children in the Third World Where former employees are now Alumni: Zoltán Toroczkai, University of Notre Dame Alumni: Sarah Nurre, University of Arkansas Funding opportunities Potential partnerships

  13. AlumniLink: March 2015

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

    Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit IN THIS ISSUE New Science One in five online scholarly articles affected by 'reference rot' Scientists call for antibody 'bar code' system to follow Human Genome Project Los Alamos develops new technique for growing high-efficiency perovskite solar cells Alumni spotlight Mark Jankowski: Minnesota Pollution Control Agency Madalina Furis: University of Vermont Funding

  14. AlumniLink: September 2014

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

    Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit IN THIS ISSUE New science Probing Fukushima with cosmic rays should speed cleanup Could reduce the time required for clean up Scientists uncover combustion mechanism to better predict warming by wildfires Scientists have uncovered key attributes of so-called "brown carbon" from wildfires High-performance computer system installed at Los Alamos National

  15. Biological Mass Spectrometry and Shotgun Proteomics of Microbial Systems: Methods for studying microbial physiology from isolates to environmental communities

    SciTech Connect (OSTI)

    Dill, Brian; Young, Jacque C; Carey, Patricia A; Verberkmoes, Nathan C

    2010-01-01

    Microbial ecology is currently experiencing a renaissance spurred by the rapid development of molecular techniques and omics technologies in particular. As never before, these tools have allowed researchers in the field to produce a massive amount of information through in situ measurements and analysis of natural microbial communities, both vital approaches to the goal of unraveling the interactions of microbes with their environment and with one another. While genomics can provide information regarding the genetic potential of microbes, proteomics characterizes the primary end-stage product, proteins, thus conveying functional information concerning microbial activity. Advances in mass spectrometry instrumentation and methodologies, along with bioinformatic approaches, have brought this analytic chemistry technique to relevance in the biological realm due to its powerful applications in proteomics. Mass spectrometry-enabled proteomics, including bottom-up and top-down approaches, is capable of supplying a wealth of biologically-relevant information, from simple protein cataloging of the proteome of a microbial community to identifying post-translational modifications of individual proteins.

  16. EEO Links | National Nuclear Security Administration | (NNSA)

    National Nuclear Security Administration (NNSA)

    Links DOE Office of Civil Rights Department Of Justice Civil Rights Division Department of Veterans Affairs Equal Employment Opportunity Commission Office of Personnel Management U.S. Merit Systems Protection Board U.S. Office of Special Counsel

  17. A New Link Between Human and Bacterial Signaling Machinery

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

    A New Link Between Human and Bacterial Signaling Machinery A New Link Between Human and Bacterial Signaling Machinery Print Tuesday, 19 August 2014 10:34 The human immune system...

  18. A Study to Determine the Biological Feasibility of a New Fish Tagging System : Annual Report 1990-1993.

    SciTech Connect (OSTI)

    Prentice, Earl F.; Maynard, D.J.; Downing, S.L. (and others)

    1994-01-01

    In 1983, the National Marine Fisheries Service (NMFS) began a multiyear cooperative research program with the Bonneville Power Administration (BPA) to evaluate a new miniaturized identification system that could be used with salmonids. The system is referred to as the passive-integrated-transponder (PIT) tagging and interrogation system. The program has focused on determining the effects of PIT tags on juvenile and adult salmonids, as well as the development and evaluation of tagging and interrogation methods. Earlier results of the program have been reported in annual reports and journal articles cited in this report. This report covers the work per formed from 1990 through 1993. For convenience, the report is divided into three sections: (1) Interrogation and separation systems at Columbia River Basin dams; (2) Systems development and evaluation; and (3) Information and technology transfer.

  19. MAJOR CONFORMED CONTRACTS LINKS Site/Project Contract Link Idaho

    Office of Environmental Management (EM)

    MAJOR CONFORMED CONTRACTS LINKS SiteProject Contract Link Idaho Idaho Cleanup Project http:www.id.doe.govdoeidICPContractICPContract.htm Advance Mixed Waste Treatment http:...

  20. 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.

  1. The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

    SciTech Connect (OSTI)

    Kolker, Eugene; Sansone, Susanna

    2011-09-11

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

  2. Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Robinson, Gene

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gene Robinson of the University of Illinois on "Genomic and Systems Biology Analyses of Social Behavior" at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011

  3. The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kolker, Eugene [Seattle Children's Hospital]; Sansone, Susanna [EBI

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

  4. Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Robinson, Gene

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gene Robinson of the University of Illinois on "Genomic and Systems Biology Analyses of Social Behavior" at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011

  5. 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...

  6. Balanced link for dry coal extrusion pumps

    DOE Patents [OSTI]

    Bebejian, Maral

    2013-10-22

    A link which defines a link body that includes a multiple of link plates integral with a link body, the link body disposed at least partially forward of a forward edge of the multiple of link plates.

  7. Nuclear Data Links

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

    Links to Other Useful Sites Online Journals Institutions and Programs Related to Nuclear Physics U.S. Nuclear Data Program: All evaluated nuclear data supported by the U.S. Department of Energy. National Nuclear Data Center: Brookhaven National Laboratory; Evaluated Nuclear Structure Data Files (ENSDF), Nuclear Science References (NSR) and other databases. Isotopes Project: (E.O.L. Berkeley National Laboratory) Table of Isotopes, Isotope Explorer, XUNDL, Nuclear Data Dissemination Homepage, and

  8. Page 11, Links

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

    11 of 11 Previous Page Links Information for Employees & In-Processing DOE Order 3792.3 - Drug-Free Federal Workplace Testing http://www.archives.gov/federal-register/codification/executive-order/12564.html Flexible Spending Accounts (FSA) https://www.fsafeds.com/fsafeds/index.asp Pay & Pay Scales http://www.opm.gov/a-z-index/ Benefits Facts on Leave Programs http://www.opm.gov/policy-data-oversight/pay-leave/leave-administration/ Health Benefits

  9. CAMD Nanofabrication Links

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

    Research :: Publications :: Infrastructure :: Links :: Nanofabrication Facility in News Nano 50TM Awards: The Nano 50TM Awards, presented by Nanotech Briefs magazine, recognize the top 50 technologies, products and innovators that have significantly impacted, or are expected to impact, the state of the art in nanotechnology. "The winners of the Nano 50 awards are the best of the best - the innovative people and technologies that will continue to move nanotechnology to key mainstream

  10. Conservation Standards Enforcement: Useful Links | Department of Energy

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

    Useful Links Conservation Standards Enforcement: Useful Links This page provides a variety of links to help manufacturers fulfill their compliance obligations under the energy conservation standards program for consumer products and industrial equipment. Under the applicable law (42 U.S.C. 6291-6317), an importer is a manufacturer; therefore, any material you read in the links below that references a "manufacturer" also applies to an importer. Certification Compliance Management System

  11. Website Policies / Important Links | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    Website Policies Important Links Website Policies Important Links Javascript Not Enabled OSTI Security Website Policies and Important Links

  12. Website Policies / Important Links | Data Explorer

    Office of Scientific and Technical Information (OSTI)

    Website Policies Important Links Website Policies Important Links Javascript Not Enabled OSTI Security Website Policies and Important Links

  13. Website Policies / Important Links | DOE Patents

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

    Website Policies / Important Links Website Policies / Important Links Javascript Not Enabled OSTI Security Website Policies and Important Links

  14. Acidbase bifunctional shell cross-linked micelle nanoreactor for one-pot tandem reaction

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

    Lee, Li -Chen; Lu, Jie; Weck, Marcus; Jones, Christopher W.

    2015-12-29

    Shell cross-linked micelles (SCMs) containing acid sites in the shell and base sites in the core are prepared from amphiphilic poly(2-oxazoline) triblock copolymers. The materials are utilized as two-chamber nanoreactors for a prototypical acid-base bifunctional tandem deacetalization-nitroaldol reaction. Furthermore, the acid and base sites are localized in different regions of the micelle, allowing the two steps in the reaction sequence to largely proceed in separate compartments, akin to the compartmentalization that occurs in biological systems.

  15. Acid–base bifunctional shell cross-linked micelle nanoreactor for one-pot tandem reaction

    SciTech Connect (OSTI)

    Lee, Li -Chen; Lu, Jie; Weck, Marcus; Jones, Christopher W.

    2015-12-29

    Shell cross-linked micelles (SCMs) containing acid sites in the shell and base sites in the core are prepared from amphiphilic poly(2-oxazoline) triblock copolymers. The materials are utilized as two-chamber nanoreactors for a prototypical acid-base bifunctional tandem deacetalization-nitroaldol reaction. Furthermore, the acid and base sites are localized in different regions of the micelle, allowing the two steps in the reaction sequence to largely proceed in separate compartments, akin to the compartmentalization that occurs in biological systems.

  16. Major Conformed Contract Links | Department of Energy

    Office of Environmental Management (EM)

    Conformed Contract Links Major Conformed Contract Links Links to conformed copies of EM's major contracts. Major Conformed Contract Links (302.59 KB) More Documents & Publications ...

  17. Subdiffraction instrumentation development and application to the elucidation of biological systems, thin films, and organic photovoltaic devices

    SciTech Connect (OSTI)

    Lesoine, Michael D

    2014-12-01

    Fluorescence and Raman instrumentation was developed to elucidate morphology, information on local environment, and material properties of target systems. Far-field fluorescence and luminescence spectroscopic measurements were performed using a pulsed super-continuum laser source and detector with high temporal resolution. With this arrangement morphologies of structures were coupled with time-correlated data. Polymeric beads and Alexa Fluor 594-phalloidin labeled cellular actin structures of cultured cells were imaged below the diffraction limit using stimulated emission depletion to resolve structures to ≈40nm. Lifetime imaging revealed a 2.0 ± 0.1 ns lifetime for fluorescently-labeled beads in confocal and depletion imaging modes. Depletion imaging was also able to display a change of 2.2 to 2.9 ns for different regions of the cellular actin network of cultured cells with a possible difference in lifetime caused by tryptophan quenching of the dye. Subdiffraction imaging with a resolution of ≈40 nm was also accomplished using luminescence depletion of photostable giant CdSe/14CdS nanocrystal quantum dots in air. Nanocrystal quantum dots, typically not prone to depletion, exhibited this phenomenon when excited with an energy of 50 pJ and 2 nJ of depletion energy. Luminescence depletion required half the energy compared to stimulated emission depletion to achieve the same resolution limit. The luminescence was depleted by as much as ≈92% with no observable photobleaching. Raman measurements of polymer films were performed with 532-nm laser illumination using scanning angle and conventional 180° backscattering modes to determine chemical information. The scanning angle mode achieved an angle resolution of 0.09° and was used to probe a thin layer of polystyrene as well as a diblock copolymer of polystyrene and poly(3-hexylthiophene-2,5-diyl). Enhancements to the Raman signals at selected angles lower than the critical angle for total internal reflection

  18. Link Alpha B

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

    b A B C D E F G H I J K L M N O P Q R S T U V W Y Z Filter by alpha... A B C D E F G H I J K L M N O P Q R S T U V W Y Z Back-Up Dependent (Child & Elder) Care Program Backups for Computers Backups for PC and Mac (self-service using Carbonite) Badge Office BASE (Berkeley Accelerator Space Effects) BELLA (Berkeley Lab Laser Accelerator) Benefits Berkeley Center for Structural Biology(BCSB) Berkeley Lab 75th Anniversary Site Berkeley Lab Energy and Environmental Research Blog Berkeley Lab

  19. Beryllium Related Links - Hanford Site

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

    Related Links About Us Hanford Cultural Resources Beryllium Program Beryllium Program Points of Contact Beryllium Facilities & Areas Beryllium Program Information Hanford CBDPP Committee Beryllium FAQs Beryllium Related Links Hanford Beryllium Awareness Group (BAG) Program Performance Assessments Beryllium Program Feedback Beryllium Health Advocates Primary Contractors/Employers Medical Testing and Surveillance Facilities General Resources Beryllium Related Links Email Email Page | Print

  20. Multilevel DC link inverter

    DOE Patents [OSTI]

    Su, Gui-Jia

    2003-06-10

    A multilevel DC link inverter and method for improving torque response and current regulation in permanent magnet motors and switched reluctance motors having a low inductance includes a plurality of voltage controlled cells connected in series for applying a resulting dc voltage comprised of one or more incremental dc voltages. The cells are provided with switches for increasing the resulting applied dc voltage as speed and back EMF increase, while limiting the voltage that is applied to the commutation switches to perform PWM or dc voltage stepping functions, so as to limit current ripple in the stator windings below an acceptable level, typically 5%. Several embodiments are disclosed including inverters using IGBT's, inverters using thyristors. All of the inverters are operable in both motoring and regenerating modes.

  1. Michael Levitt and Computational Biology

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

    Michael Levitt and Computational Biology Resources with Additional Information * Publications Michael Levitt Courtesy of Linda A. Cicero / Stanford News Service Michael Levitt, PhD, professor of structural biology at the Stanford University School of Medicine, has won the 2013 Nobel Prize in Chemistry. ... Levitt ... shares the ... prize with Martin Karplus ... and Arieh Warshel ... "for the development of multiscale models for complex chemical systems." Levitt's work focuses on

  2. Structural Molecular Biology, SSRL

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

    Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating ... major experimental driver for structural biology research, serving the needs of a large ...

  3. Work with Biological Materials

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

  4. Link Alpha P

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

    Particle Adventure: A Tour of the Atom & Tools for Discovery Particle Data Group (PDG) Password Reset Patent Group Payroll Department (CFO) PDSF: Parallel Distributed Systems ...

  5. Plant Vascular Biology 2010

    SciTech Connect (OSTI)

    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.

  6. Reversibly immobilized biological materials in monolayer films on electrodes

    DOE Patents [OSTI]

    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.

  7. Reversibly immobilized biological materials in monolayer films on electrodes

    DOE Patents [OSTI]

    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.

  8. Link Alpha F

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

    f A B C D E F G H I J K L M N O P Q R S T U V W Y Z Filter by alpha... A B C D E F G H I J K L M N O P Q R S T U V W Y Z Facilities Division Facilities Lockshop Facilities Project Status Facilities Safety and Hazardous Waste Facilities Work Request Center Family Member Eligibility Verification Project FAQ on Computing Topics Financial Compliance Financial Management System (FMS 8.8 - FY14 and Prior) Financial Management System (FMS 9.2 - FY15+) Financial Management System (FMS) Help &

  9. Links | National Nuclear Security Administration

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

    Links | National Nuclear Security Administration Facebook Twitter Youtube Flickr RSS People Mission Managing the Stockpile Preventing Proliferation Powering the Nuclear Navy...

  10. Linking Humans and Systems in Nuclear Power

    SciTech Connect (OSTI)

    Jacques Hugo

    2013-02-01

    Traditional engineering methods do not make provision for the integration of human considerations, while traditional human factors methods do not scale well to the complexity of large-scale nuclear power plant projects. Although the need for up-to-date human factors engineering processes and tools is recognised widely in industry, so far no formal guidance has been developed. This article proposes such a framework.

  11. Link Alpha T

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

    t A B C D E F G H I J K L M N O P Q R S T U V W Y Z Filter by alpha... A B C D E F G H I J K L M N O P Q R S T U V W Y Z Tax Services Technical Area Designation Technology Transfer Department (Innovation and Partnerships Office) Technology Transfer Ombudsman Telecommuting Telemetry Database Telephone Service Center Termination Termination Notification System (TNS) Today at Berkeley Lab Tours of Berkeley Lab for the Public Traffic Safety Training (Berkeley Lab Training) Transit Passes

  12. Link Alpha C

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

    c A B C D E F G H I J K L M N O P Q R S T U V W Y Z Filter by alpha... A B C D E F G H I J K L M N O P Q R S T U V W Y Z Cafeteria: Laboratory Cafeteria menu Calendar Calendar of Events Calendaring FAQ Cancer & Carcinogens: Carcinogenic Potency Database Project Carbon Cycle 2.0 Careers Carpooling Catalog: Berkeley Lab Scientific and Technical Reports Catalog (1989 to present) Catastrophic Leave Sharing Catering CATS (Corrective Action Tracking System) CCSE: Center for Computational Sciences

  13. Link Alpha H

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

    h A B C D E F G H I J K L M N O P Q R S T U V W Y Z Filter by alpha... A B C D E F G H I J K L M N O P Q R S T U V W Y Z Hands-on Universe (HOU) Program Harassment Prevention and Harassment Complaint Process HARP Hazard Management System (HMS) Hazardous Waste Requisition Health Services at the Lab (or call x6266) Heat Island Research Group Helios - harnessing the sun for a secure, sustainable, and prosperous future Help Desk (or call x4357) High Performance Computing Research Department Hire

  14. Link Alpha L

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

    l A B C D E F G H I J K L M N O P Q R S T U V W Y Z Filter by alpha... A B C D E F G H I J K L M N O P Q R S T U V W Y Z LabAlert - LabAlert Emergency Alerting Service Laboratory Counsel Laboratory Directed Research & Development Program (LDRD) Laboratory Property Review (LPR) Laboratory Support Services Lactation / Nursing Moms Lactation Accommodation Program Laser Ablation: Advanced Laser Technologies Lab Laser Management System (Laser Inventory) Laser Safety Web Page Lasers, Optical

  15. Electrostatic thin film chemical and biological sensor

    DOE Patents [OSTI]

    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.

  16. Neutron instrumentation for biology

    SciTech Connect (OSTI)

    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.

  17. Structural Molecular Biology, SSRL

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

  18. LTS Related Links - Hanford Site

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

    Related Links About Us Hanford Cultural Resources LTS Home Page LTS Project Management LTS Transition and Timeline LTS Execution LTS Background LTS Information Management LTS Fact Sheets / Briefings LTS In The News LTS Related Links LTS Contact Us LTS Related Links Email Email Page | Print Print Page | Text Increase Font Size Decrease Font Size Hanford Site Cleanup Completion Framework (DOE/RL 2009-10) (PDF) Hanford Long-Term Stewardship Program Plan (DOE/RL 2010-35) (PDF) DOE-EM LTS Site Legacy

  19. Multiple weak-link SQUID

    SciTech Connect (OSTI)

    Kroger, H.

    1980-09-23

    The disclosed SQUID (Superconducting quantum interference device) comprises two superposed superconductive layers with an insulating layer therebetween. A plurality of holes through the insulating layer filled with superconductive material form weak links between the superconductive layers. One or more control lines superposed with respect to the superconductive layers provide magnetic flux through the area between the weak links to control the zero voltage supercurrent flowing through the weak links from one of the superconductive layers to the other thereby providing the switching function for Josephson superconductive circuits.

  20. E-Link - User Account

    Office of Scientific and Technical Information (OSTI)

    Energy Link (E-LINK) Access Request FOR DOE MAJOR SITE/FACILITY MANAGEMENT CONTRACTOR AND DOE HEADQUARTERS AND FIELD OFFICE PERSONNEL ONLY (Financial Assistance Recipients/Non-Major Site/Facility Management Contractors, go to www.osti.gov/elink-2413/) Major Site/Facility Management Contractors and DOE Headquarters and Field personnel are required to obtain a user name and password to access E-Link submissions and related reports. The process to obtain a user name and password also requires the

  1. Cross-linked structure of network evolution

    SciTech Connect (OSTI)

    Bassett, Danielle S.; Wymbs, Nicholas F.; Grafton, Scott T.; Porter, Mason A.; Mucha, Peter J.

    2014-03-15

    We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice. Subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks.

  2. Related Links | Department of Energy

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

    Related Links Related Links Private, public, and nonprofit organizations around the country offer a wide range of courses and other services to help you either improve your current skills or learn new ones. The sites featured here can help you find courses of specific interest as well as other information about training requirements for certain energy jobs. DOE Related Advanced Manufacturing Office: Training Find training sessions in your area and learn how to save energy in your manufacturing

  3. Alternative Fuels Data Center: Biodiesel Related Links

    Alternative Fuels and Advanced Vehicles Data Center [Office of Energy Efficiency and Renewable Energy (EERE)]

    Biodiesel Printable Version Share this resource Send a link to Alternative Fuels Data Center: Biodiesel Related Links to someone by E-mail Share Alternative Fuels Data Center: Biodiesel Related Links on Facebook Tweet about Alternative Fuels Data Center: Biodiesel Related Links on Twitter Bookmark Alternative Fuels Data Center: Biodiesel Related Links on Google Bookmark Alternative Fuels Data Center: Biodiesel Related Links on Delicious Rank Alternative Fuels Data Center: Biodiesel Related Links

  4. Alternative Fuels Data Center: Ethanol Related Links

    Alternative Fuels and Advanced Vehicles Data Center [Office of Energy Efficiency and Renewable Energy (EERE)]

    Ethanol Printable Version Share this resource Send a link to Alternative Fuels Data Center: Ethanol Related Links to someone by E-mail Share Alternative Fuels Data Center: Ethanol Related Links on Facebook Tweet about Alternative Fuels Data Center: Ethanol Related Links on Twitter Bookmark Alternative Fuels Data Center: Ethanol Related Links on Google Bookmark Alternative Fuels Data Center: Ethanol Related Links on Delicious Rank Alternative Fuels Data Center: Ethanol Related Links on Digg Find

  5. Alternative Fuels Data Center: Hydrogen Related Links

    Alternative Fuels and Advanced Vehicles Data Center [Office of Energy Efficiency and Renewable Energy (EERE)]

    Hydrogen Printable Version Share this resource Send a link to Alternative Fuels Data Center: Hydrogen Related Links to someone by E-mail Share Alternative Fuels Data Center: Hydrogen Related Links on Facebook Tweet about Alternative Fuels Data Center: Hydrogen Related Links on Twitter Bookmark Alternative Fuels Data Center: Hydrogen Related Links on Google Bookmark Alternative Fuels Data Center: Hydrogen Related Links on Delicious Rank Alternative Fuels Data Center: Hydrogen Related Links on

  6. Alternative Fuels Data Center: Propane Related Links

    Alternative Fuels and Advanced Vehicles Data Center [Office of Energy Efficiency and Renewable Energy (EERE)]

    Propane Printable Version Share this resource Send a link to Alternative Fuels Data Center: Propane Related Links to someone by E-mail Share Alternative Fuels Data Center: Propane Related Links on Facebook Tweet about Alternative Fuels Data Center: Propane Related Links on Twitter Bookmark Alternative Fuels Data Center: Propane Related Links on Google Bookmark Alternative Fuels Data Center: Propane Related Links on Delicious Rank Alternative Fuels Data Center: Propane Related Links on Digg Find

  7. Alternative Fuels Data Center: Related Links

    Alternative Fuels and Advanced Vehicles Data Center [Office of Energy Efficiency and Renewable Energy (EERE)]

    Tools Printable Version Share this resource Send a link to Alternative Fuels Data Center: Related Links to someone by E-mail Share Alternative Fuels Data Center: Related Links on Facebook Tweet about Alternative Fuels Data Center: Related Links on Twitter Bookmark Alternative Fuels Data Center: Related Links on Google Bookmark Alternative Fuels Data Center: Related Links on Delicious Rank Alternative Fuels Data Center: Related Links on Digg Find More places to share Alternative Fuels Data

  8. Khovanov homology of graph-links

    SciTech Connect (OSTI)

    Nikonov, Igor M

    2012-08-31

    Graph-links arise as the intersection graphs of turning chord diagrams of links. Speaking informally, graph-links provide a combinatorial description of links up to mutations. Many link invariants can be reformulated in the language of graph-links. Khovanov homology, a well-known and useful knot invariant, is defined for graph-links in this paper (in the case of the ground field of characteristic two). Bibliography: 14 titles.

  9. Overview of How to Compile and Link | Argonne Leadership Computing...

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

    code for the BGQ system is too complex to cover in this document. What follows is a brief summary. All compile and link procedures are performed on login nodes with a ...

  10. Sharpening Our Tools: Algal Biology Toolbox Workshop

    Broader source: Energy.gov [DOE]

    The Bioenergy Technologies Office (BETO) will host the Algal Biology Toolbox Workshop on May 24-25, 2016, in San Diego, California. Because biological productivity is a key driver for the economic viability of algae-based biofuels, improving on the performance of native strains is a critical element of the research efforts funded by the Advanced Algal Systems program at BETO.

  11. Biological tracer method

    DOE Patents [OSTI]

    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.

  12. Biological tracer method

    DOE Patents [OSTI]

    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.

  13. Tobacco mosaic virus: A biological building block for micro/nano...

    Office of Scientific and Technical Information (OSTI)

    Tobacco mosaic virus: A biological building block for micronanobio systems Citation Details In-Document Search Title: Tobacco mosaic virus: A biological building block for micro...

  14. Links

    Broader source: Energy.gov [DOE]

    More Legal Research ResourcesEnergy Law NetLegal Citation Style GuideNuclear Regulatory LegislationOpen CRSPublic Library of LawTreatiesU.S. Code Classification TablesU.S. Congressional Documents...

  15. Links

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

    Related Sites National Nanotechnology Initiative Nano Technology Industries Advanced Materials Research Institute Institute of Physics Max-Planck Institute for Kohlenforschung The institute of nanotechnology Nanotechnology Now Nanotechnology - Education Nanojournals Chancellor's Distinguished Lectureship Series Patent Analytics and Patent Searching

  16. Biological detector and method

    DOE Patents [OSTI]

    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.

  17. Biological detector and method

    DOE Patents [OSTI]

    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.

  18. Biological detector and method

    DOE Patents [OSTI]

    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.

  19. ElectraLink | Open Energy Information

    Open Energy Info (EERE)

    ElectraLink Jump to: navigation, search Name: ElectraLink Place: London, United Kingdom Product: London-based ElectraLink specialises in technology to communicate data between the...

  20. Structural Molecular Biology, SSRL

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

  1. Alternative Fuels Data Center: Electricity Related Links

    Alternative Fuels and Advanced Vehicles Data Center [Office of Energy Efficiency and Renewable Energy (EERE)]

    Electricity Printable Version Share this resource Send a link to Alternative Fuels Data Center: Electricity Related Links to someone by E-mail Share Alternative Fuels Data Center: Electricity Related Links on Facebook Tweet about Alternative Fuels Data Center: Electricity Related Links on Twitter Bookmark Alternative Fuels Data Center: Electricity Related Links on Google Bookmark Alternative Fuels Data Center: Electricity Related Links on Delicious Rank Alternative Fuels Data Center: Electricity

  2. BizLink Technology | Open Energy Information

    Open Energy Info (EERE)

    BizLink Technology Jump to: navigation, search Name: BizLink Technology Place: Fremont, California Zip: 94538 Sector: Solar Product: California-based manufacturer of solar modules,...

  3. Help:Linked images | Open Energy Information

    Open Energy Info (EERE)

    Linked images Redirect page Jump to: navigation, search REDIRECT Manual:Linked images Retrieved from "http:en.openei.orgwindex.php?titleHelp:Linkedimages&oldid58478" ...

  4. Useful Links - Combustion Energy Frontier Research Center

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

    FAQ Useful Links Useful Links Detailed campus map with CEFRC summer school buildings highlighted (NEW) Schedule of Events (NEW) Campus Map with CEFRC-specific buildings...

  5. Voluntary Protection Program - Related Links | Department of...

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

    - Related Links Voluntary Protection Program - Related Links VPPPA - The Voluntary Protection Programs Participants' Association, a non- profit organization is leading the way in ...

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

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

  7. Integrated Biological Control

    SciTech Connect (OSTI)

    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.

  8. Integrated Biological Control

    SciTech Connect (OSTI)

    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.

  9. Biological sample collector

    DOE Patents [OSTI]

    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.

  10. OpenEI and Linked Open Data | Department of Energy

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

    OpenEI and Linked Open Data OpenEI and Linked Open Data OpenEI presentation by Jon Weers and Kate Young at the Geothermal Technologies Office 2013 Annual Peer Review in Colorado. openei_peerreview2013.pdf (4.95 MB) More Documents & Publications Web Coordinator Meetings - October 2014 Fueling Innovation and Adoption by Sharing Data on the DOE Geothermal Data Repository National Geothermal Data System (NGDS) Fact Sheet

  11. Reference Links | U.S. DOE Office of Science (SC)

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

    Reference Links Integrated Support Center (ISC) ISC Home About Services Freedom of Information Act (FOIA) Privacy Act Compilation of Systems of Records Energy Employees Occupational Illness Compensation Program Act (EEOICPA) How to Submit a Privacy Act Request Reference Links NEPA Documents Contact Information Integrated Support Center Roxanne Purucker U.S. Department of Energy 9800 S. Cass Avenue Argonne, IL 60439 P: (630) 252-2110 Kenneth Tarcza U.S. Department of Energy 200 Administration

  12. EIA - Natural Gas Pipeline Network - Regional Overview and Links

    U.S. Energy Information Administration (EIA) Indexed Site

    Overview and Links About U.S. Natural Gas Pipelines - Transporting Natural Gas based on data through 2007/2008 with selected updates Regional Overviews and Links to Pipeline Companies Through a series of interconnecting interstate and intrastate pipelines the transportation of natural gas from one location to another within the United States has become a relatively seamless operation. While intrastate pipeline systems often transports natural gas from production areas directly to consumers in

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

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

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

  14. Work with Biological Materials

    Broader source: All U.S. Department of Energy (DOE) Office 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 process or may be completed as an independent document. In the ESS, identify each material (including all biological materials) with which you will be working. The regulatory oversight for biological work is very complicated and we need to understand the risk levels involved with the material you plan to use at the ALS,

  15. Work with Biological Materials

    Broader source: All U.S. Department of Energy (DOE) Office 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 process or may be completed as an independent document. In the ESS, identify each material (including all biological materials) with which you will be working. The regulatory oversight for biological work is very complicated and we need to understand the risk levels involved with the material you plan to use at the ALS,

  16. Work with Biological Materials

    Broader source: All U.S. Department of Energy (DOE) Office 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 process or may be completed as an independent document. In the ESS, identify each material (including all biological materials) with which you will be working. The regulatory oversight for biological work is very complicated and we need to understand the risk levels involved with the material you plan to use at the ALS,

  17. AlumniLink: January 2015

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

    Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit IN THIS ISSUE New Science 100 supercomputers later Explosives performance key to stockpile stewardship Software speeds detection of diseases and cancer-treatment targets Alumni spotlight Ni Ni: University of California - Los Angeles Francesco Grilli: Karlsruhe Institute of Technology Funding opportunities Potential partnerships and funding from a variety of sources

  18. AlumniLink: May 2015

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

    Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit IN THIS ISSUE New Science Using magnetic fields to understand high-temperature superconductivity Los Alamos creates bioinformatics tool for metagenome analysis Multi-institutional project to study climate change's effect on tropical forests Where former employees are now Alumni: Claire White, Princeton University Alumni: Chih-Chun Chien, University of California Merced

  19. AlumniLink: September 2015

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

    Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit IN THIS ISSUE New science and news Young, Jupiter-like planet discovered Four Los Alamos projects selected as R&D 100 Award finalists Seven federally protected Mexican spotted owl chicks hatch on Lab property Where former employees are now Alumni: Duane Hatch, Belmont University Alumni: Alexia Schulz, MIT Lincoln Laboratory Funding opportunities Potential

  20. Topics: Uncovering the physics of magnetic self-organization and links to

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

    astrophysics - MST - UW Plasma Physics Uncovering the physics of magnetic self-organization and links to astrophysics UW Madison Madison Symmetric Torus Topics: Uncovering the physics of magnetic self-organization and links to astrophysics MST HomeGraduate Student InformationLinksTourControl and Auxiliary SystemsPhysics TopicsDeviceResearch MissionMST People mst logo CPLA Home Directory Publications Links Internal University of Wisconsin Physics Department Research funding includes support

  1. Join our highlighted LinkedIn discussion

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

    Join our highlighted LinkedIn discussion Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit Join our highlighted LinkedIn discussion What experiences have alumni had in software releases and deployments at different institutions? March 1, 2015 Robert Jilek Robert Jilek Contact Linda Anderman Email alumni LinkedIn Join us for a variety of discussions on the Lab's LinkedIn Alumni page What experiences have alumni had in

  2. Join our highlighted LinkedIn discussion

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

    Join our highlighted LinkedIn discussion Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit Join our highlighted LinkedIn discussion Congratulations to LANL's Claudia Mora for being selected president elect of the Geological Society of America! July 1, 2015 Claudia Mora Claudia Mora Contact Linda Anderman Email alumni LinkedIn Join us for a variety of discussions on the Lab's LinkedIn Alumni page Congratulations to

  3. SciTech Connect: Website Policies / Important Links

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

    Website Policies / Important Links Website Policies / Important Links Javascript Not Enabled OSTI Security Website Policies and Important Links

  4. SciTech Connect: Website Policies / Important Links

    Office of Scientific and Technical Information (OSTI)

    Website Policies / Important Links Website Policies / Important Links Javascript Not Enabled OSTI Security Website Policies and Important Links

  5. Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen

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

    Production | Department of Energy Boundary Analysis of Biological Pathways to Hydrogen Production Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen Production Report documenting the biological and engineering characteristics of five algal and bacterial hydrogen production systems selected by DOE and NREL for evaluation. Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen Production (3.63 MB) More Documents & Publications Techno-Economic Boundary Analysis

  6. 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

  7. Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen Production

    Fuel Cell Technologies Publication and Product Library (EERE)

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

  8. Technoeconomic Boundary Analysis of Biological Pathways to Hydrogen Production

    SciTech Connect (OSTI)

    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.

  9. 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) ...

  10. Micro/nanofabricated environments for synthetic biology

    SciTech Connect (OSTI)

    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.