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Sample records for folds grabens horst

  1. Horst and Graben | Open Energy Information

    Open Energy Info (EERE)

    W 49,500,000,000 mW 0.0495 GW 4.95e-5 TW 470.15 K197 C 386.6 F 846.27 R Brady Hot Springs Geothermal Area Northwest Basin and Range Geothermal Region Extensional...

  2. John Horst | Department of Energy

    Office of Environmental Management (EM)

    Horst About Us John Horst - Public Affairs Specialist with the Office of Energy Efficiency and Renewable Energy John Horst is a Public Affairs Specialist with the Office of Energy Efficiency and Renewable Energy. Most Recent Super Bowl City Leads on Energy Efficient Forefront February 2 Ultra Energy Efficient Data Center Saves NREL $200,000 November 14

  3. Anastomosing grabens, low-angle faults, and Tertiary thrust( ) faults, western Markagunt Plateau, southwestern Utah

    SciTech Connect (OSTI)

    Maldonado, F.; Sable, E.G. )

    1993-04-01

    A structurally complex terrane composed of grabens and horsts, low-angle faults, Tertiary thrust( ) faults, gravity-slide blocks, and debris deposits has been mapped along the western Markagunt Plateau, east of Parowan and Summit, southwestern Utah. This terrane, structurally situated within the transition between the Basin and Range and Colorado Plateau provinces, contains Tertiary volcanic and sedimentary and Cretaceous sedimentary rocks. The structures are mostly Miocene to Oligocene but some are Pleistocene. The oldest structure is the Red Hills low-angle shear zone, interpreted as a shallow structure that decoupled an upper plate composed of a Miocene-Oligocene volcanic ash-flow tuff and volcaniclastic succession from a lower plate of Tertiary sedimentary rocks. The period of deformation on the shear zone is bracketed from field relationships between 22.5 and 20 Ma. The graben-horst system trends northeast and formed after about 20 Ma (and probably much later) based on displacement of dated dikes and a laccolith. The central part of the system contains many grabens that merge toward its southerly end to become a single graben. Within these grabens, (1) older structures are preserved, (2) debris eroded from horst walls forms lobe-shaped deposits, (3) Pleistocene basaltic cinder cones have localized along graben-bounding faults, and (4) rock units are locally folded suggesting some component of lateral translation along graben-bounding faults. Megabreccia deposits and landslide debris are common. Megabreccia deposits are interpreted as gravity-slide blocks of Miocene-Oligocene( ) age resulting from formation of the Red Hills shear zone, although some may be related to volcanism, and still others to later deformation. The debris deposits are landslides of Pleistocene-Pliocene( ) age possibly caused by continued uplift of the Markagunt Plateau.

  4. Property:TopoFeatures | Open Energy Information

    Open Energy Info (EERE)

    Geothermal Area + Horst and Graben + Blue Mountain Geothermal Area + Horst and Graben + Brady Hot Springs Geothermal Area + Horst and Graben + C Coso Geothermal Area + Horst and...

  5. Interpretation of recent seismic data from a frontier hydrocarbon province: western Rough Creek graben, southern Illinois and western Kentucky

    SciTech Connect (OSTI)

    Bertagne, A.J.; Pisasale, E.T.; Leising, T.C.

    1986-05-01

    The northern basement fault of the Rough Creek graben is seismically discernible and has surface expression in the Rough Creek fault zone. The southern basement fault is not clearly defined seismically, but can be inferred from shallow faulting and gravity data. This fault is roughly coincident with the Pennyrile fault zone. Extensional faults that formed the rift boundaries were the sites of late-stage compressional and extensional tectonics. Flower structures observed along the graben boundaries probably indicate post-Pennsylvanian wrench faulting. The basement within the graben plunges north-northwest, with the lowest point occurring south of the Rough Creek fault zone. Pre-Knox sediments thicken to approximately 12,000 in this area. The Knox Megagroup thickens toward the Mississippi Embayment, ranging from 4800 ft (southeastern graben area) to more than 7000 ft (west end of graben). Upper Ordovician to Devonian units also display westward thickening. The top of the Meramecian, New Albany, Maquoketa, and the base of the Knox generate continuous, high-amplitude seismic reflections due to large impedance contrasts between clastic and carbonate units. Shallow oil and gas production (Mississippian and Pennsylvanian) is present in this area. However, deep horizons (Knox, Lower Cambrian) remain relatively untested. Potential hydrocarbon traps in the pre-Knox sequence observed on seismic include fault blocks and updip pinch-outs.

  6. Folded waveguide coupler

    DOE Patents [OSTI]

    Owens, Thomas L. (Kingston, TN)

    1988-03-01

    A resonant cavity waveguide coupler for ICRH of a magnetically confined plasma. The coupler consists of a series of inter-leaved metallic vanes disposed withn an enclosure analogous to a very wide, simple rectangular waveguide that has been "folded" several times. At the mouth of the coupler, a polarizing plate is provided which has coupling apertures aligned with selected folds of the waveguide through which rf waves are launched with magnetic fields of the waves aligned in parallel with the magnetic fields confining the plasma being heated to provide coupling to the fast magnetosonic wave within the plasma in the frequency usage of from about 50-200 mHz. A shorting plate terminates the back of the cavity at a distance approximately equal to one-half the guide wavelength from the mouth of the coupler to ensure that the electric field of the waves launched through the polarizing plate apertures are small while the magnetic field is near a maximum. Power is fed into the coupler folded cavity by means of an input coaxial line feed arrangement at a point which provides an impedance match between the cavity and the coaxial input line.

  7. Protein folding in the ER.

    SciTech Connect (OSTI)

    Stevens, F. J.; Argon, Y.; Biosciences Division; Univ. of Chicago

    1999-10-01

    The endoplasmic reticulum (ER) is a major protein folding compartment for secreted, plasma membrane and organelle proteins. Each of these newly-synthesized polypeptides folds in a deterministic process, affected by the unique conditions that exist in the ER. An understanding of protein folding in the ER is a fundamental biomolecular challenge at two levels. The first level addresses how the amino acid sequence programs that polypeptide to efficiently arrive at a particular fold out of a multitude of alternatives, and how different sequences obtain similar folds. At the second level are the issues introduced by folding not in the cytosol, but in the ER, including the risk of aggregation in a molecularly crowded environment, accommodation of post-translational modifications and the compatibility with subsequent intracellular trafficking. This review discusses both the physicochemical and cell biological constraints of folding, which are the challenges that the ER molecular chaperones help overcome.

  8. Graphene folding on flat substrates

    SciTech Connect (OSTI)

    Chen, Xiaoming; Zhao, Yadong; Ke, Changhong; Zhang, Liuyang; Wang, Xianqiao

    2014-10-28

    We present a combined experimental-theoretical study of graphene folding on flat substrates. The structure and deformation of the folded graphene sheet are experimentally characterized by atomic force microscopy. The local graphene folding behaviors are interpreted based on nonlinear continuum mechanics modeling and molecular dynamics simulations. Our study on self-folding of a trilayer graphene sheet reports a bending stiffness of about 6.57?eV, which is about four times the reported values for monolayer graphene. Our results reveal that an intriguing free sliding phenomenon occurs at the interlayer van der Waals interfaces during the graphene folding process. This work demonstrates that it is a plausible venue to quantify the bending stiffness of graphene based on its self-folding conformation on flat substrates. The findings reported in this work are useful to a better understanding of the mechanical properties of graphene and in the pursuit of its applications.

  9. Compact intermediates in RNA folding

    SciTech Connect (OSTI)

    Woodson, S.A. (JHU)

    2011-12-14

    Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

  10. Fast events in protein folding

    SciTech Connect (OSTI)

    Woodruff, W.; Callender, R.; Causgrove, T.; Dyer, R.; Williams, S.

    1996-04-01

    The primary objective of this work was to develop a molecular understanding of how proteins achieve their native three-dimensional (folded) structures. This requires the identification and characterization of intermediates in the protein folding process on all relevant timescales, from picoseconds to seconds. The short timescale events in protein folding have been entirely unknown. Prior to this work, state-of-the-art experimental approaches were limited to milliseconds or longer, when much of the folding process is already over. The gap between theory and experiment is enormous: current theoretical and computational methods cannot realistically model folding processes with lifetimes longer than one nanosecond. This unique approach to employ laser pump-probe techniques that combine novel methods of laser flash photolysis with time-resolved vibrational spectroscopic probes of protein transients. In this scheme, a short (picosecond to nanosecond) laser photolysis pulse was used to produce an instantaneous pH or temperature jump, thereby initiating a protein folding or unfolding reaction. Structure-specific, time-resolved vibrational probes were then used to identify and characterize protein folding intermediates.

  11. Controlling Structures | Open Energy Information

    Open Energy Info (EERE)

    fault terminations or tip-lines with multiple closely-spaced faults that enhance permeability. Mountainous, Horst and Graben Extensional Tectonics, Rift Zone Stepover or Relay...

  12. Mountainous | Open Energy Information

    Open Energy Info (EERE)

    Horst and Graben Shield Volcano Flat Lava Dome Stratovolcano Cinder Cone Caldera Depression Resurgent Dome Complex The interior of Iceland holds a vast expanse of mountainous...

  13. Lava Dome | Open Energy Information

    Open Energy Info (EERE)

    Horst and Graben Shield Volcano Flat Lava Dome Stratovolcano Cinder Cone Caldera Depression Resurgent Dome Complex "Volcanic or lava domes are formed by relatively small,...

  14. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01

    The three-dimensional structure of a protein is encoded in its linear sequence of amino acids. Studies of protein folding are aimed at understanding the nature of this code which translates one-dimensional information to three-dimensions. It is now well-established that protein folding intermediates exist and can be populated significantly under some conditions. A method to characterize kinetic folding intermediates is described. The method takes advantage of the decrease in exchange rates between amide protons (i.e., peptide backbone NH) and solvent water protons, when the amide proton is involved in structure. The feasibility of using amide proton exchange to pulse-label proteins during folding has been demonstrated using (/sup 3/H)-H/sub 2/O. The results with ribonuclease A (RNase A) support a framework model for folding, in which the secondary structure of a protein is formed before tertiary structure changes are complete. Extension of these studies using NMR should permit characterization of early secondary structure folding frameworks.

  15. SciTech Connect: "protein folding"

    Office of Scientific and Technical Information (OSTI)

    protein folding" Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: "protein folding" Semantic Semantic Term Title: Full Text: Bibliographic Data:...

  16. Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles, for Large-Scale Geologic Storage of CO₂

    SciTech Connect (OSTI)

    Bruno, Michael

    2014-12-08

    Geomechanics Technologies has completed a detailed characterization study of the Wilmington Graben offshore Southern California area for large-scale CO₂ storage. This effort has included: an evaluation of existing wells in both State and Federal waters, field acquisition of about 175 km (109 mi) of new seismic data, new well drilling, development of integrated 3D geologic, geomechanics, and fluid flow models for the area. The geologic analysis indicates that more than 796 MMt of storage capacity is available within the Pliocene and Miocene formations in the Graben for midrange geologic estimates (P50). Geomechanical analyses indicate that injection can be conducted without significant risk for surface deformation, induced stresses or fault activation. Numerical analysis of fluid migration indicates that injection into the Pliocene Formation at depths of 1525 m (5000 ft) would lead to undesirable vertical migration of the CO₂ plume. Recent well drilling however, indicates that deeper sand is present at depths exceeding 2135 m (7000 ft), which could be viable for large volume storage. For vertical containment, injection would need to be limited to about 250,000 metric tons per year per well, would need to be placed at depths greater than 7000ft, and would need to be placed in new wells located at least 1 mile from any existing offset wells. As a practical matter, this would likely limit storage operations in the Wilmington Graben to about 1 million tons per year or less. A quantitative risk analysis for the Wilmington Graben indicate that such large scale CO₂ storage in the area would represent higher risk than other similar size projects in the US and overseas.

  17. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect (OSTI)

    Zheng, Zhongzhou; Sosnick, Tobin R. (UC)

    2010-05-25

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu {yields} Glu{sup -}) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the {beta}5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  18. Cooperative Tertiary Interaction Network Guides RNA Folding

    SciTech Connect (OSTI)

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, R.M.; Woodson, Sarah A.

    2013-04-08

    Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

  19. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, R.R.; Cowan, T.E.

    1996-06-11

    Disclosed are fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate. 3 figs.

  20. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, Rajeev R. (Mountain View, CA); Cowan, Thomas E. (Livermore, CA)

    1996-01-01

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate.

  1. Mechanical Models of Fault-Related Folding

    SciTech Connect (OSTI)

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  2. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM); Cabantous, Stephanie (Los Alamos, NM)

    2008-06-24

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  3. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  4. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM); Cabantous, Stephanie (Los Alamos, NM)

    2011-06-14

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  5. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  6. Self-folding graphene-polymer bilayers

    SciTech Connect (OSTI)

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-05-18

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  7. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

    Carangelo, R.M.; Wright, D.D.

    1995-08-08

    A folded-path gas cell employs an elliptical concave mirror in confronting relationship to two substantially spherical concave mirrors. At least one of the spherical mirrors, and usually both, are formed with an added cylindrical component to increase orthogonal foci coincidence and thereby to increase the radiation energy throughput characteristic of the cell. 10 figs.

  8. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

    Ben-Naim, A. (Hebrew Univ., Jerusalem (Israel))

    1990-08-23

    The solvent-induced forces between various groups on the protein are examined. It is found that the intramolecular hydrophilic forces are likely to be the strongest forces mediated through the solvent. It is argued that these are probably the most important solvent-induced driving forces in the process of protein folding.

  9. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

    Carangelo, Robert M. (Glastonbury, CT); Wright, David D. (Vershire, VT)

    1995-01-01

    A folded-path gas cell employs an elliptical concave mirror in confronting relationship to two substantially spherical concave mirrors. At least one of the spherical mirrors, and usually both, are formed with an added cylindrical component to increase orthogonal focii coincidence and thereby to increase the radiation energy throughput characteristic of the cell.

  10. Simplified Protein Models: Predicting Folding Pathways and Structure...

    Office of Scientific and Technical Information (OSTI)

    Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences Title: Simplified Protein Models: Predicting Folding Pathways and Structure Using ...

  11. Geometry of Cenozoic extensional faulting: Dixie Valley, Nevada...

    Open Energy Info (EERE)

    was also 15 km instead of the previously reported 40 km. Local microearthquakes cluster around 10-15 km. The geometrical block models indicate that crustal horst-graben...

  12. Category:Topographic Features | Open Energy Information

    Open Energy Info (EERE)

    Features" The following 9 pages are in this category, out of 9 total. C Caldera Depression Cinder Cone F Flat H Horst and Graben L Lava Dome M Mountainous R Resurgent Dome...

  13. Microsoft Word - RNA_folding_Herschlag.doc

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

    March 2003 Exploring the Folding Landscape of a Structured RNA by SAXS Rick Russell, Ian S. Millett, Sebastian Doniach and Daniel Herschlag Stanford University One goal of genome projects is to systematically identify genes (1,2). The best current knowledge indicates that humans carry approximately 35000 genes. This number is an estimate that varies from expert to expert and range up to 100,000 (3-5). To anyone who has taken an elementary biology class, this ambiguity must seem strange. How hard

  14. Folding and association of a homotetrameric protein complex in...

    Office of Scientific and Technical Information (OSTI)

    Folding and association of a homotetrameric protein complex in an all-atom Go model Title: Folding and association of a homotetrameric protein complex in an all-atom Go model ...

  15. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding New Crystal Structures Lift Fog around Protein Folding Print Wednesday, 25 July 2012 00:00 Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a

  16. Manipulating and Visualizing Proteins Simon, Horst D. 59 BASIC...

    Office of Scientific and Technical Information (OSTI)

    ACIDS; CALIFORNIA; CHAINS; CHEMISTRY; DISEASES; FIBROSIS; FORECASTING; GENETICS; OPTIMIZATION; PROTEIN STRUCTURE; PROTEINS; QUEUES; SHAPE; SIMULATION PROTEIN STRUCTURE...

  17. Microsoft PowerPoint - Horst Simon.BitstoBuidings2

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

    ... on metrics http:www.thegreengrid.orgggcontent Energy Star Program http:... From Peter Kogge, DARPA gg , Exascale Study ... and the power costs will still be ...

  18. Accordian-folded boot shield for flexible swivel connection

    DOE Patents [OSTI]

    Hoh, Joseph C. (Naperville, IL)

    1986-01-01

    A flexible swivel boot connector for connecting a first boot shield section to a second boot shield section, both first and second boot sections having openings therethrough, the second boot section having at least two adjacent accordian folds at the end having the opening, the second boot section being positioned through the opening of the first boot section such that a first of the accordian folds is within the first boot section and a second of the accordian folds is outside of the first boot, includes first and second annular discs, the first disc being positioned within and across the first accordian fold, the second disc being positioned within and across the second accordian fold, such that the first boot section is moveably and rigidly connected between the first and second accordian folds of the second boot section.

  19. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  20. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  1. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  2. Microsecond Microfluidic Mixing for Investigation of Protein Folding

    Office of Scientific and Technical Information (OSTI)

    Kinetics (Conference) | SciTech Connect Conference: Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics Citation Details In-Document Search Title: Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics We have developed and characterized a mixer to study the reaction kinetics of protein folding on a microsecond timescale. The mixer uses hydrodynamic focusing of pressure-driven flow in a microfluidic channel to reduce diffusion times as first

  3. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these biomolecular nanomachines must first be folded into a dazzling variety of shapes and forms before they can perform the multitude of functions fundamental to life. However, the mechanisms behind the protein-folding process have remained a foggy mystery. Now the fog is lifting: a team of researchers from Berkeley Lab,

  4. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Kane, A; Hertzog, D; Baumgartel, P; Lengefeld, J; Horsley,...

  5. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding Print Nature's proteins set a high bar for nanotechnology. Macromolecules forged from peptide chains of amino acids, these...

  6. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Citation Details In-Document Search Title: MICROFLUIDIC MIXERS FOR THE...

  7. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, R.R.; Cowan, T.E.

    1994-12-27

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate. 3 figures.

  8. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

    Rohatgi, Rajeev R. (Mountain View, CA); Cowan, Thomas E. (Livermore, CA)

    1994-01-01

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate.

  9. Folding associated with extensional faulting: Sheep Range detachment, southern Nevada

    SciTech Connect (OSTI)

    Guth, P.L.

    1985-01-01

    The Sheep Range detachment is a major Miocene extensional fault system of the Great Basin. Its major faults have a scoop shape, with straight, N-S traces extending 15-30 km and then abruptly turning to strike E-W. Tertiary deformation involved simultaneous normal faulting, sedimentation, landsliding, and strike-slip faulting. Folds occur in two settings: landslide blocks and drag along major faults. Folds occur in landslide blocks and beneath them. Most folds within landslide blocks are tight anticlines, with limbs dipping 40-60 degrees. Brecciation of the folds and landslide blocks suggests brittle deformation. Near Quijinump Canyon in the Sheep Range, at least three landslide blocks (up to 500 by 1500 m) slid into a small Tertiary basin. Tertiary limestone beneath the Paleozoic blocks was isoclinally folded. Westward dips reveal drag folds along major normal faults, as regional dips are consistently to the east. The Chowderhead anticline is the largest drag fold, along an extensional fault that offsets Ordovician units 8 km. East-dipping Ordovician and Silurian rocks in the Desert Range form the hanging wall. East-dipping Cambrian and Ordovician units in the East Desert Range form the foot wall and east limb of the anticline. Caught along the fault plane, the anticline's west-dipping west limb contains mostly Cambrian units.

  10. Water dynamics clue to key residues in protein folding

    SciTech Connect (OSTI)

    Gao, Meng [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Zhu, Huaiqiu, E-mail: hqzhu@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Yao, Xin-Qiu [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China) [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China); Department of Biophysics, Kyoto University, Sakyo Kyoto 606-8502 (Japan); She, Zhen-Su, E-mail: she@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)] [State Key Laboratory for Turbulence and Complex Systems, and Department of Biomedical Engineering, and Center for Theoretical Biology, and Center for Protein Science, Peking University, Beijing 100871 (China)

    2010-01-29

    A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

  11. Office of Small and Disadvantaged Business Utilization Tri-Fold |

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

    Department of Energy Office of Small and Disadvantaged Business Utilization Tri-Fold Office of Small and Disadvantaged Business Utilization Tri-Fold OSDBU has created a downloadable, print-on-demand tri-fold PDF that introduces the office, its role in the Department of Energy and its goals for supporting small business nationwide. This document includes information on "rules of engagement," the Department of Energy's business model, the Mentor-Protégé program, the DOE Annual

  12. UFO (UnFold Operator) computer program abstract

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F.

    1982-11-01

    UFO (UnFold Operator) is an interactive user-oriented computer program designed to solve a wide range of problems commonly encountered in physical measurements. This document provides a summary of the capabilities of version 3A of UFO.

  13. Determining the role of hydration forces in protein folding

    SciTech Connect (OSTI)

    Sorenson, J.M. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry] [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Hura, G. [Univ. of California, Berkeley, CA (United States)] [Univ. of California, Berkeley, CA (United States); [Lawrence Berkeley National Lab., CA (United States). Life Sciences Div.; Soper, A.K. [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility] [Rutherford Appleton Lab., Didcot (United Kingdom). ISIS Facility; Pertsemlidis, A. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry] [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; Head-Gordon, T. [Lawrence Berkeley National Lab., CA (United States)] [Lawrence Berkeley National Lab., CA (United States)

    1999-07-01

    One of the primary issues in protein folding is determining what forces drive folding and eventually stabilize the native state. A delicate balance exists between electrostatic forces such as hydrogen bonding and salt bridges, and the hydrophobic effect, which are present for both intramolecular protein interactions and intermolecular contributions with the surrounding aqueous environment. This article describes a combined experimental, theoretical, and computational effort to show how the complexity of aqueous hydration can influence the structure, folding and aggregation, and stability of model protein systems. The unification of the theoretical and experimental work is the development or discovery of effective amino acid interactions that implicitly include the effects of aqueous solvent. The authors show that consideration of the full range of complexity of aqueous hydration forces such as many-body effects, long-ranged character of aqueous solvation, and the assumptions made about the degree of protein hydrophobicity can directly impact the observed structure, folding, and stability of model protein systems.

  14. Nonlinear vs. linear biasing in Trp-cage folding simulations

    SciTech Connect (OSTI)

    Spiwok, Vojt?ch Oborsk, Pavel; Krlov, Blanka; Pazrikov, Jana

    2015-03-21

    Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200?ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.

  15. Simplified Protein Models: Predicting Folding Pathways and Structure Using

    Office of Scientific and Technical Information (OSTI)

    Amino Acid Sequences (Journal Article) | DOE PAGES Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences Title: Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences Authors: Adhikari, Aashish N. ; Freed, Karl F. ; Sosnick, Tobin R. Publication Date: 2013-07-11 OSTI Identifier: 1103786 Type: Publisher's Accepted Manuscript Journal Name: Physical Review Letters Additional Journal Information: Journal Volume:

  16. Energy Landscapes: From Protein Folding to Molecular Assembly

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

    36th Annual Conference Energy Landscapes: From Protein Folding to Molecular Assembly WHEN: May 09, 2016 8:00 AM - May 12, 2016 5:00 PM WHERE: Hilton Santa Fe Historic Plaza Santa Fe, NM CONTACT: Angel Garcia (505) 665-3883 CATEGORY: Community Science TYPE: Conference INTERNAL: Calendar Login Event Description Nanoscale molecular assembly is very common in biology and in nanotechnology. Simple examples of self-assembly are the folding of proteins from a disorder polymer, the assembly of lipid

  17. Structural proteomics of minimal organisms: conservation ofprotein fold

    Office of Scientific and Technical Information (OSTI)

    usage and evolutionary implications (Journal Article) | SciTech Connect Structural proteomics of minimal organisms: conservation ofprotein fold usage and evolutionary implications Citation Details In-Document Search Title: Structural proteomics of minimal organisms: conservation ofprotein fold usage and evolutionary implications Background: Determining the complete repertoire of proteinstructures for all soluble, globular proteins in a single organism hasbeen one of the major goals of

  18. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING

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

    SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY (Conference) | SciTech Connect MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY Citation Details In-Document Search Title: MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY The purpose of this study is to design, fabricate and optimize microfluidic mixers to investigate the kinetics of protein

  19. Intermediates and the folding of proteins L and G

    SciTech Connect (OSTI)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

  20. Collective aspects of protein folding illustrated by a toy model

    SciTech Connect (OSTI)

    Stillinger, F.H. [AT& T Bell Laboratories, Murray Hill, New Jersey 07974 (United States)] [AT& T Bell Laboratories, Murray Hill, New Jersey 07974 (United States); Head-Gordon, T. [Life Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)] [Life Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)

    1995-09-01

    A simple toy model for polypeptides serves as a testbed to illuminate some nonlocal, or collective, aspects of protein folding phenomena. The model is two dimensional and has only two amino acids, but involves a continuous range of backbone bend angles. Global potential energy minima and their folding structures have been determined for leading members of two special and contrasting polypeptide sequences, center doped and Fibonacci, named descriptively for their primary structures. The results display the presence of spontaneous symmetry breaking, elastic strain, and substantial conformational variation for specific embedded amino acid strings. We conclude that collective variables generated by the primary amino acid structure may be required for fully effective protein folding predictors, including those based on neural networks.

  1. Heteropolymer freezing and design: Towards physical models of protein folding

    SciTech Connect (OSTI)

    Pande, Vijay S. [Chemistry Department, Stanford University, Stanford, California 94305-5080 (United States)] [Chemistry Department, Stanford University, Stanford, California 94305-5080 (United States); Grosberg, Alexander Yu. [Department of Physics, University of Minnesota, Minneapolis, Minnesota 55455 (United States)] [Department of Physics, University of Minnesota, Minneapolis, Minnesota 55455 (United States); Tanaka, Toyoichi [Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)] [Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    2000-01-01

    Protein folding has become one of the most actively studied problems in modern molecular biophysics. Approaches to the problem combine ideas from the physics of disordered systems, polymer physics, and molecular biology. Much can be learned from the statistical properties of model heteropolymers, the chain molecules having different monomers in irregular sequences. Even in highly evolved proteins, there is a strong random element in the sequences, which gives rise to a statistical ensemble of sequences for a given folded shape. Simple analytic models give rise to phase transitions between random, glassy, and folded states, depending on the temperature T and the design temperature T{sup des} of the ensemble of sequences. Besides considering the analytic results obtainable in a random-energy model and in the Flory mean-field model of polymers, the article reports on confirming numerical simulations. (c) 2000 The American Physical Society.

  2. Folding model description of reactions with exotic nuclei

    SciTech Connect (OSTI)

    Ibraheem, Awad A.; Hassanain, M. A.; Mokhtar, S. R.; Zaki, M. A.; Mahmoud, Zakaria M. M.; Farid, M. El-Azab

    2012-08-15

    Microscopic folding calculations based upon the effective M3Y nucleon-nucleon interaction and the nuclearmatter densities of the interacting nuclei have been carried out to explain recently measured experimental data of the {sup 6}He+{sup 120}Sn elastic scattering cross section at four different laboratory energies near the Coulomb barrier. The extracted reaction cross sections are also considered.

  3. Discovering The Folding Rules That Proteins Obey FY08 LDRD Final...

    Office of Scientific and Technical Information (OSTI)

    Technical Report: Discovering The Folding Rules That Proteins Obey FY08 LDRD Final Report Citation Details In-Document Search Title: Discovering The Folding Rules That Proteins ...

  4. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    SciTech Connect (OSTI)

    HART,WILLIAM E.; ISTRAIL,SORIN

    2000-06-01

    Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist invariants across lattices related to fundamental properties of the protein folding process. This paper considers whether performance-guaranteed approximability is such an invariant for HP lattice models. The authors define a master approximation algorithm that has provable performance guarantees provided that a specific sublattice exists within a given lattice. They describe a broad class of crystal lattices that are approximable, which further suggests that approximability is a general property of HP lattice models.

  5. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    SciTech Connect (OSTI)

    Hart, W.E.; Istrail, S.

    1995-12-11

    Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist ``invariants`` across lattices that define fundamental properties of protein folding process; an invariant defines a property that transcends particular lattice formulations. This paper identifies two classes of invariants, defined in terms of sublattices that are related to the design of algorithms for the structure prediction problem. The first class of invariants is, used to define a master approximation algorithm for which provable performance guarantees exist. This algorithm can be applied to generalizations of the hydrophobic-hydrophilic model that have lattices other than the cubic lattice, including most of the crystal lattices commonly used in protein folding lattice models. The second class of invariants applies to a related lattice model. Using these invariants, we show that for this model the structure prediction problem is intractable across a variety of three-dimensional lattices. It`` turns out that these two classes of invariants are respectively sublattices of the two- and three-dimensional square lattice. As the square lattices are the standard lattices used in empirical protein folding` studies, our results provide a rigorous confirmation of the ability of these lattices to provide insight into biological phenomenon. Our results are the first in the literature that identify algorithmic paradigms for the protein structure prediction problem which transcend particular lattice formulations.

  6. Combined approach to the inverse protein folding problem. Final report

    SciTech Connect (OSTI)

    Ruben A. Abagyan

    2000-06-01

    The main scientific contribution of the project ''Combined approach to the inverse protein folding problem'' submitted in 1996 and funded by the Department of Energy in 1997 is the formulation and development of the idea of the multilink recognition method for identification of functional and structural homologues of newly discovered genes. This idea became very popular after they first announced it and used it in prediction of the threading targets for the CASP2 competition (Critical Assessment of Structure Prediction).

  7. Modified Microbes Tolerate 50-Fold More Organic Acid - Energy Innovation

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

    Portal Modified Microbes Tolerate 50-Fold More Organic Acid Great Lakes Bioenergy Research Center Contact GLBRC About This Technology Technology Marketing Summary Production of industrial chemicals has long relied on petroleum-based starting material. As reserves of fossil carbon dwindle, a new approach is looking to microorganisms and their ability to convert renewable sources into valuable chemicals. The U.S. Department of Energy (DOE) recently targeted several 'building block' chemicals

  8. Directed evolution methods for improving polypeptide folding and solubility and superfolder fluorescent proteins generated thereby

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM)

    2007-09-18

    The current invention provides methods of improving folding of polypeptides using a poorly folding domain as a component of a fusion protein comprising the poorly folding domain and a polypeptide of interest to be improved. The invention also provides novel green fluorescent proteins (GFPs) and red fluorescent proteins that have enhanced folding properties.

  9. Protein-Folding Landscapes in Multi-Chain Systems (Journal Article) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Protein-Folding Landscapes in Multi-Chain Systems Citation Details In-Document Search Title: Protein-Folding Landscapes in Multi-Chain Systems Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the

  10. Protein-Folding Landscapes in Multi-Chain Systems (Journal Article) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Protein-Folding Landscapes in Multi-Chain Systems Citation Details In-Document Search Title: Protein-Folding Landscapes in Multi-Chain Systems Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the

  11. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect (OSTI)

    Hertzog, D E; Santiago, J G; Bakajin, O

    2005-02-10

    We have developed and characterized a mixer to study the reaction kinetics of protein folding on a microsecond timescale. The mixer uses hydrodynamic focusing of pressure-driven flow in a microfluidic channel to reduce diffusion times as first demonstrated by Knight et al.[1]. Features of the mixer include 1 {micro}s mixing times, sample consumptions of order 1 nl/s, loading sample volumes on the order of microliters, and the ability to manufacture in fused silica for compatibility with most spectroscopic methods.

  12. Chemical relationship between discharging fluids in the Siena-Radicofani Graben and the deep fluids produced by the geothermal fields of Mt Amiata, torre Afina and Latera (Central Italy)

    SciTech Connect (OSTI)

    Duchi, V.; Paolieri, M.; Prati, F ); Minissale, A. Centro di Studio per Mineralogia e la Geochimica dei Sedimenti, Via La Pira 4, 50121 Firenze ); Valori, A )

    1992-06-01

    This paper reports that the thermal springs discharging in the Siena-Radicofani basin and the deep fluids within the geothermal systems of Piancastagnaio (Mt Amiata), Torre Alfina and Latera (Vulsini Mts) have a common origin. The chemical composition and evolution towards the low enthalpy of the springs as compared to the high enthalpy of the geothermal fluids are affected by both the structural setting of the region and the deep hydraulic conditions. Recharge of both the shallow thermal aquifer and the deep geothermal systems takes place in the outcrop areas of Mesozoic carbonate rocks, which constitute the main potential geothermal reservoir in central Italy. The waters of meteoric origin are heated at depth, as a consequence of anomalous heat flow in the region; these waters acquire a CO[sub 2]-rich rising gas phase, equilibrate with the reservoir rocks and, finally, assume their Ca--HCO[sub 3]--SO[sub 4] composition. If these waters discharge rapidly from the border fault systems of the Siena-Radicofani basin they maintain their original composition. If, instead, they emerge from the inner faults of the graben, their temperature and dissolved solids increase so that they become Na--Cl with a high content of NH[sub 4], and H[sub 3]BO[sub 3].

  13. Folding and Function of Proteorhodopsins in Photoenergy Transducing Membranes

    SciTech Connect (OSTI)

    Spudich, John L

    2012-08-10

    The overall research objectives are to develop proteorhodopsin (PR) proteins as a model system for {alpha}?-helical membrane protein insertion and folding, and to advance understanding of the diversity and mechanisms of PRs, a large family of photoenergy transducers (~4000 identified) abundant in the worlds oceans. Specific aims are: (1) To develop a highefficiency genetic selection procedure for light-driven proton-pumping in E. coli cells. Such a procedure would provide a positive selection method for proper folding and function of PRs in the E. coli membrane. (2) Characterize flash-induced absorption changes and photocurrents in PR variants in organisms from various environments, and their expression level and function when expressed in E. coli. Subaims are to: (a) elucidate the relationship of the transport mechanism to mechanisms of other microbial rhodopsins, some of which like PRs function as ion transporters and some of which use light energy to activate signaling pathways (sensory rhodopsins); and (b) identify important residues and chemical events in light-driven proton transport by PRs. In addition to their importance to the energy of the biosphere PRs have attracted interest for their potential for use in making photoenergy-transducing membranes for bioengineering applications.

  14. A vault ribonucleoprotein particle exhibiting 39-fold dihedral symmetry

    SciTech Connect (OSTI)

    Kato, Koji; Tanaka, Hideaki; Sumizawa, Tomoyuki; Yoshimura, Masato; Yamashita, Eiki; Iwasaki, Kenji; Tsukihara, Tomitake

    2008-05-01

    A vault from rat liver was crystallized in space group C2. Rotational symmetry searches indicated that the particle has 39-fold dihedral symmetry. Vault is a 12.9 MDa ribonucleoprotein particle with a barrel-like shape, two protruding caps and an invaginated waist structure that is highly conserved in a wide variety of eukaryotes. Multimerization of the major vault protein (MVP) is sufficient to assemble the entire exterior shell of the barrel-shaped vault particle. Multiple copies of two additional proteins, vault poly(ADP-ribose) polymerase (VPARP) and telomerase-associated protein 1 (TEP1), as well as a small vault RNA (vRNA), are also associated with vault. Here, the crystallization of vault particles is reported. The crystals belong to space group C2, with unit-cell parameters a = 708.0, b = 385.0, c = 602.9 Å, β = 124.8°. Rotational symmetry searches based on the R factor and correlation coefficient from noncrystallographic symmetry (NCS) averaging indicated that the particle has 39-fold dihedral symmetry.

  15. Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding

    SciTech Connect (OSTI)

    Garde, S.; Hummer, G.; Garcia, A.E.; Paulaitis, M.E.; Pratt, L.R. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); [Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716 (United States); [Department of Chemical Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

    1996-12-01

    An information theory model of hydrophobic effects is used to construct a molecular explanation why hydrophobic solvation entropies of protein unfolding measured by high sensitivity calorimetry converge to zero at a common convergence temperature. The entropy convergence follows directly from the weak temperature dependence of occupancy fluctuations {l_angle}{delta}{ital n}{sup 2}{r_angle} for molecular-scale volumes in water. The macroscopic expression of the contrasting entropic behavior of water relative to common organic solvents is the {ital relative} temperature insensitivity of the water isothermal compressibility compared to hydrocarbon liquids. The information theory model used provides a quantitative description of small molecule hydration and, in addition, predicts that the value of the entropy at convergence is slightly {ital negative}. Interpretations of entropic contributions to protein folding should account for this result. {copyright} {ital 1996 The American Physical Society.}

  16. Development of a Fast Microfluidic Mixer for Studies of Protein Folding

    Office of Scientific and Technical Information (OSTI)

    KineticsFinal Report Cover Page (Technical Report) | SciTech Connect Development of a Fast Microfluidic Mixer for Studies of Protein Folding KineticsFinal Report Cover Page Citation Details In-Document Search Title: Development of a Fast Microfluidic Mixer for Studies of Protein Folding KineticsFinal Report Cover Page We designed and fabricated mixing devices that will help us elucidate the mechanisms of protein folding through measurements of folding reaction rates. These devices can be

  17. Development of a Fast Microfluidic Mixer for Studies of Protein Folding

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

    KineticsFinal Report Cover Page (Technical Report) | SciTech Connect Technical Report: Development of a Fast Microfluidic Mixer for Studies of Protein Folding KineticsFinal Report Cover Page Citation Details In-Document Search Title: Development of a Fast Microfluidic Mixer for Studies of Protein Folding KineticsFinal Report Cover Page We designed and fabricated mixing devices that will help us elucidate the mechanisms of protein folding through measurements of folding reaction rates. These

  18. Protein-Folding Landscapes in Multi-Chain Systems Cellmer, Troy...

    Office of Scientific and Technical Information (OSTI)

    37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; FREE ENERGY; MELTING; PROTEINS; THERMODYNAMICS; TOPOLOGY protein folding protein...

  19. Contact order revisited: Influence of protein size on the folding rate

    SciTech Connect (OSTI)

    Ivankov, Dmitry N.; Garbuzynskiy, Sergiy O.; Alm, Eric; Plaxco, Kevin W.; Baker, David; Finkelstein, Alexei V.

    2003-05-28

    Guided by the recent success of empirical model predicting the folding rates of small two-state folding proteins from the relative contact order (CO) of their native structures, by a theoretical model of protein folding that predicts that logarithm of the folding rate decreases with the protein chain length L as L2/3, and by the finding that the folding rates of multistate folding proteins strongly correlate with their sizes and have very bad correlation with CO, we reexamined the dependence of folding rate on CO and L in attempt to find a structural parameter that determines folding rates for the totality of proteins. We show that the Abs{sub CO} = CO x L, is able to predict rather accurately folding rates for both two-state and multistate folding proteins, as well as short peptides, and that this Abs{sub CO} scales with the protein chain length as L0.70 {+-} 0.07 for the totality of studied single-domain proteins and peptides.

  20. Energy barriers, cooperativity, and hidden intermediates in the folding of small proteins

    SciTech Connect (OSTI)

    Bai Yawen [Laboratory of Biochemistry, National Cancer Institute, NIH, Building 37, Room 6114E, Bethesda, MD 20892 (United States)]. E-mail: yawen@helix.nih.gov

    2006-02-17

    Current theoretical views of the folding process of small proteins (<{approx}100 amino acids) postulate that the landscape of potential mean force (PMF) for the formation of the native state has a funnel shape and that the free energy barrier to folding arises from the chain configurational entropy only. However, recent theoretical studies on the formation of hydrophobic clusters with explicit water suggest that a barrier should exist on the PMF of folding, consistent with the fact that protein folding generally involves a large positive activation enthalpy at room temperature. In addition, high-resolution structural studies of the hidden partially unfolded intermediates have revealed the existence of non-native interactions, suggesting that the correction of the non-native interactions during folding should also lead to barriers on PMF. To explore the effect of a PMF barrier on the folding behavior of proteins, we modified Zwanzig's model for protein folding with an uphill landscape of PMF for the formation of transition states. We found that the modified model for short peptide segments can satisfy the thermodynamic and kinetic criteria for an apparently two-state folding. Since the Levinthal paradox can be solved by a stepwise folding of short peptide segments, a landscape of PMF with a locally uphill search for the transition state and cooperative stabilization of folding intermediates/native state is able to explain the available experimental results for small proteins. We speculate that the existence of cooperative hidden folding intermediates in small proteins could be the consequence of the highly specific structures of the native state, which are selected by evolution to perform specific functions and fold in a biologically meaningful time scale.

  1. Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein

    SciTech Connect (OSTI)

    Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G.; Kevrekidis, Ioannis G.

    2015-02-28

    Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories in a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.

  2. MitoNEET is a Uniquely Folded Outer Mitochondrial Membrane Protein...

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

    MitoNEET is a Uniquely Folded Outer Mitochondrial Membrane Protein Stabilized by Diabetes Drugs The rise in obesity in the United States parallels a dramatic increase in...

  3. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model

    SciTech Connect (OSTI)

    Agarwala, R. [National Institutes of Health, Bethesda, MD (United States); Batzoglou, S. [MIT, Cambridge, MA (United States); Dancik, V. [Univ. of Southern California, Los Angeles, CA (United States)] [and others

    1997-06-01

    We consider the problem of determining the three-dimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill, which models protein as a chain of amino acid residues that are either hydrophobic or polar, and hydrophobic interactions are the dominant initial driving force for the protein folding. Hart and Istrail gave approximation algorithms for folding proteins on the cubic lattice under HP model. In this paper, we examine the choice of a lattice by considering its algorithmic and geometric implications and argue that triangular lattice is a more reasonable choice. We present a set of folding rules for a triangular lattice and analyze the approximation ratio which they achieve. In addition, we introduce a generalization of the HP model to account for residues having different levels of hydrophobicity. After describing the biological foundation for this generalization, we show that in the new model we are able to achieve similar constant factor approximation guarantees on the triangular lattice as were achieved in the standard HP model. While the structures derived from our folding rules are probably still far from biological reality, we hope that having a set of folding rules with different properties will yield more interesting folds when combined.

  4. Side chain and backbone contributions of Phe508 to CFTR folding

    SciTech Connect (OSTI)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  5. A Survey of lamba Repressor Fragments from Two-State to to Downhill Folding

    SciTech Connect (OSTI)

    Liu, F.; Gao, Y; Gruebele, M

    2010-01-01

    We survey the two-state to downhill folding transition by examining 20 {lambda}{sub 6-85}* mutants that cover a wide range of stabilities and folding rates. We investigated four new {lambda}{sub 6-85}* mutants designed to fold especially rapidly. Two were engineered using the core remodeling of Lim and Sauer, and two were engineered using Ferreiro et al.'s frustratometer. These proteins have probe-dependent melting temperatures as high as 80 C and exhibit a fast molecular phase with the characteristic temperature dependence of the amplitude expected for downhill folding. The survey reveals a correlation between melting temperature and downhill folding previously observed for the {beta}-sheet protein WW domain. A simple model explains this correlation and predicts the melting temperature at which downhill folding becomes possible. An X-ray crystal structure with a 1.64-{angstrom} resolution of a fast-folding mutant fragment shows regions of enhanced rigidity compared to the full wild-type protein.

  6. Time Resolved Collapse of a Folding Protein Observed with Small Angle X-Ray Scattering

    SciTech Connect (OSTI)

    Pollack, L.; Tate, M. W.; Finnefrock, A. C.; Kalidas, C.; Trotter, S.; Darnton, N. C.; Lurio, L.; Austin, R. H.; Batt, C. A.; Gruner, S. M. (and others)

    2001-05-21

    High-intensity, ''pink'' beam from an undulator was used in conjunction with microfabricated rapid-fluid mixing devices to monitor the early events in protein folding with time resolved small angle x-ray scattering. This Letter describes recent work on the protein bovine {beta} -lactoglobulin where collapse from an expanded to a compact set of states was directly observed on the millisecond time scale. The role of chain collapse, one of the initial stages of protein folding, is not currently understood. The characterization of transient, compact states is vital in assessing the validity of theories and models of the folding process.

  7. A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples

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

    A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Authors: Zhao, Z., Yan, H., and Liu, Y. Title: A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Source: Angewandte Chemie International Edition Year: 2010 Volume: 49 Pages: 1414-1417 ABSTRACT: A new strategy is presented to scale up DNA origami using multi-helical DNA tiles as folding staples. Atomic force microscopy images (see picture) demonstrate the two-dimensional structures formed by using this strategy.

  8. Crystallographic Structure of SurA, a Molecular Chaperone that Facilitates Folding of Outer Membrane Porins

    SciTech Connect (OSTI)

    Bitto, E.

    2002-01-01

    The SurA protein facilitates correct folding of outer membrane proteins in gram-negative bacteria. The sequence of Escherichia coli SurA presents four segments, two of which are peptidyl-prolyl isomerases (PPIases); the crystal structure reveals an asymmetric dumbbell, in which the amino-terminal, carboxy-terminal, and first PPIase segments of the sequence form a core structural module, and the second PPIase segment is a satellite domain tethered approximately 30 A from this module. The core module, which is implicated in membrane protein folding, has a novel fold that includes an extended crevice. Crystal contacts show that peptides bind within the crevice, suggesting a model for chaperone activity whereby segments of polypeptide may be repetitively sequestered and released during the membrane protein-folding process.

  9. Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits...

    Office of Scientific and Technical Information (OSTI)

    Title: Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits of the BLM Complex Mutations in BLM, a RecQ-like helicase, are linked to the autosomal recessive cancer-...

  10. Analyses of Candida Cdc13 Orthologues Revealed a Novel OB Fold Dimer

    Office of Scientific and Technical Information (OSTI)

    Arrangement, Dimerization-Assisted DNA Binding, and Substantial Structural Differences between Cdc13 and RPA70 (Journal Article) | SciTech Connect Analyses of Candida Cdc13 Orthologues Revealed a Novel OB Fold Dimer Arrangement, Dimerization-Assisted DNA Binding, and Substantial Structural Differences between Cdc13 and RPA70 Citation Details In-Document Search Title: Analyses of Candida Cdc13 Orthologues Revealed a Novel OB Fold Dimer Arrangement, Dimerization-Assisted DNA Binding, and

  11. Discovering The Folding Rules That Proteins Obey FY08 LDRD Final Report

    Office of Scientific and Technical Information (OSTI)

    (Technical Report) | SciTech Connect Technical Report: Discovering The Folding Rules That Proteins Obey FY08 LDRD Final Report Citation Details In-Document Search Title: Discovering The Folding Rules That Proteins Obey FY08 LDRD Final Report Authors: Bakajin, O Publication Date: 2009-02-26 OSTI Identifier: 1126773 Report Number(s): LLNL-TR-410921 DOE Contract Number: W-7405-ENG-48 Resource Type: Technical Report Research Org: Lawrence Livermore National Laboratory (LLNL), Livermore, CA

  12. Folding and association of a homotetrameric protein complex in an all-atom

    Office of Scientific and Technical Information (OSTI)

    Go model (Journal Article) | DOE PAGES Folding and association of a homotetrameric protein complex in an all-atom Go model Title: Folding and association of a homotetrameric protein complex in an all-atom Go model Authors: Berhanu, W. M. ; Jiang, P. ; Hansmann, U. H. E. Publication Date: 2013-01-11 OSTI Identifier: 1101879 Type: Publisher's Accepted Manuscript Journal Name: Physical Review E Additional Journal Information: Journal Volume: 87; Journal Issue: 1; Journal ID: ISSN 1539-3755

  13. New N-Acetyltransferase Fold in the Structure and Mechanism of the

    Office of Scientific and Technical Information (OSTI)

    Phosphonate Biosynthetic Enzyme FrbF (Journal Article) | SciTech Connect New N-Acetyltransferase Fold in the Structure and Mechanism of the Phosphonate Biosynthetic Enzyme FrbF Citation Details In-Document Search Title: New N-Acetyltransferase Fold in the Structure and Mechanism of the Phosphonate Biosynthetic Enzyme FrbF The enzyme FrbF from Streptomyces rubellomurinus has attracted significant attention due to its role in the biosynthesis of the antimalarial phosphonate FR-900098. The

  14. RNA Folding

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

    3 Rick Russell, Ian S. Millett, Sebastian Doniach and Daniel Herschlag Stanford University One goal of genome projects is to systematically identify genes (1,2). The best current knowledge indicates that humans carry approximately 35000 genes. This number is an estimate that varies from expert to expert and range up to 100,000 (3-5). To anyone who has taken an elementary biology class, this ambiguity must seem strange. How hard can it be to count genes? After all, don't cells translate genes

  15. Folding chair

    DOE Patents [OSTI]

    Cornell, Howell N. (Miami, FL)

    1985-08-20

    A foldable chair of the lawn chair type has ground-engaging front and rear legs, attached to and carrying a back frame and seat frame, the back frame and seat frame being pivotally attached to a spreader rod which extends beyond the back and seat frames to bear against one of the leg members when the chair is unfolded. A contact pad mounted on the extending portion of the spreader rod is formed as an externally-contoured bushing fit over the spreader rod and adapted to engage the leg member to restrict side-to-side movement of the spreader rod, with respect to the leg member, when the chair is unfolded.

  16. Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

    SciTech Connect (OSTI)

    Hsu, P. J.; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw [Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320 Taiwan (China); Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan (China); Cheong, S. A. [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)

    2014-05-28

    Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with ? helix and ? hairpin, but also the important role played by weaker correlations in such protein folding dynamics.

  17. Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein

    SciTech Connect (OSTI)

    Wu, Ying; Kondrashkina, Elena; Kayatekin, Can; Matthews, C. Robert; Bilsel, Osman (NWU); (UMASS, Amherst)

    2008-09-29

    The earliest kinetic folding events for ({beta}{alpha}){sub 8} barrels reflect the appearance of off-pathway intermediates. Continuous-flow microchannel mixing methods interfaced to small-angle x-ray scattering (SAXS), circular dichroism (CD), time-resolved Foerster resonant energy transfer (trFRET), and time-resolved fluorescence anisotropy (trFLAN) have been used to directly monitor global and specific dimensional properties of the partially folded state in the microsecond time range for a representative ({beta}{alpha}){sub 8} barrel protein. Within 150 {micro}s, the {alpha}-subunit of Trp synthase ({alpha}TS) experiences a global collapse and the partial formation of secondary structure. The time resolution of the folding reaction was enhanced with trFRET and trFLAN to show that, within 30 {micro}s, a distinct and autonomous partially collapsed structure has already formed in the N-terminal and central regions but not in the C-terminal region. A distance distribution analysis of the trFRET data confirmed the presence of a heterogeneous ensemble that persists for several hundreds of microseconds. Ready access to locally folded, stable substructures may be a hallmark of repeat-module proteins and the source of early kinetic traps in these very common motifs. Their folding free-energy landscapes should be elaborated to capture this source of frustration.

  18. Characterization of fold defects in AZ91D and AE42 magnesium alloy permanent mold castings

    SciTech Connect (OSTI)

    Bichler, L. [Centre for Near-net-shape Processing of Materials, Ryerson University, 101 Gerrard St. E., Toronto, M5B 2K3 (Canada); Ravindran, C., E-mail: rravindr@ryerson.ca [Centre for Near-net-shape Processing of Materials, Ryerson University, 101 Gerrard St. E., Toronto, M5B 2K3 (Canada)

    2010-03-15

    Casting premium-quality magnesium alloy components for aerospace and automotive applications poses unique challenges. Magnesium alloys are known to freeze rapidly prior to filling a casting cavity, resulting in misruns and cold shuts. In addition, melt oxidation, solute segregation and turbulent metal flow during casting contribute to the formation of fold defects. In this research, formation of fold defects in AZ91D and AE42 magnesium alloys cast via the permanent mold casting process was investigated. Computer simulations of the casting process predicted the development of a turbulent metal flow in a critical casting region with abrupt geometrical transitions. SEM and light optical microscopy examinations revealed the presence of folds in this region for both alloys. However, each alloy exhibited a unique mechanism responsible for fold formation. In the AZ91D alloy, melt oxidation and velocity gradients in the critical casting region prevented fusion of merging metal front streams. In the AE42 alloy, limited solubility of rare-earth intermetallic compounds in the {alpha}-Mg phase resulted in segregation of Al{sub 2}RE particles at the leading edge of a metal front and created microstructural inhomogeneity across the fold.

  19. Parallel continuation-based global optimization for molecular conformation and protein folding

    SciTech Connect (OSTI)

    Coleman, T.F.; Wu, Z. [Cornell Univ., Ithaca, NY (United States)

    1994-12-31

    This paper presents the authors` recent work on developing parallel algorithms and software for solving the global minimization problem for molecular conformation, especially protein folding. Global minimization problems are difficult to solve when the objective functions have many local minimizers, such as the energy functions for protein folding. In their approach, to avoid directly minimizing a ``difficult`` function, a special integral transformation is introduced to transform the function into a class of gradually deformed, but ``smoother`` or ``easier`` functions. An optimization procedure is then applied to the new functions successively, to trace their solutions back to the original function. The method can be applied to a large class of nonlinear partially separable functions including energy functions for molecular conformation and protein folding. Mathematical theory for the method, as a special continuation approach to global optimization, is established. Algorithms with different solution tracing strategies are developed. Different levels of parallelism are exploited for the implementation of the algorithms on massively parallel architectures.

  20. Femtosecond spectroscopy probes the folding quality of antibody fragments expressed as GFP fusions in the cytoplasm

    SciTech Connect (OSTI)

    Didier, P. [Faculte de Pharmacie, UMR 7175, 74, route du Rhin, 67412 Illkirch (France); Weiss, E.; Sibler, A.-P. [Ecole Superieure de Biotechnologie de Strasbourg, UMR 7175, Boulevard Sebastien Brant, F-67412 Illkirch (France); Philibert, P.; Martineau, P. [Centre de recherche en cancerologie de Montpellier, UMR 5160, Val d'Aurelle-Paul Lamarque, 34298 Montpellier cedex 5 (France); Bigot, J.-Y. [Institut de Physique et Chimie des Materiaux de Strasbourg, UMR 7504, 23, rue du Loess, F-67037 Strasbourg (France); Guidoni, L. [Institut de Physique et Chimie des Materiaux de Strasbourg, UMR 7504, 23, rue du Loess, F-67037 Strasbourg (France); Laboratoire Materiaux et Phenomenes Quantiques, UMR 7162, Batiment Condorcet, 10 rue Alice Domon et Leonie Duquet, 75205 Paris cedex 13 (France)], E-mail: luca.guidoni@univ-paris-diderot.fr

    2008-02-22

    Time-resolved femtosecond spectroscopy can improve the application of green fluorescent proteins (GFPs) as protein-folding reporters. The study of ultrafast excited-state dynamics (ESD) of GFP fused to single chain variable fragment (scFv) antibody fragments, allowed us to define and measure an empirical parameter that only depends on the folding quality (FQ) of the fusion. This method has been applied to the analysis of genetic fusions expressed in the bacterial cytoplasm and allowed us to distinguish folded and thus functional antibody fragments (high FQ) with respect to misfolded antibody fragments. Moreover, these findings were strongly correlated to the behavior of the same scFvs expressed in animal cells. This method is based on the sensitivity of the ESD to the modifications in the tertiary structure of the GFP induced by the aggregation state of the fusion partner. This approach may be applicable to the study of the FQ of polypeptides over-expressed under reducing conditions.

  1. Geometry of wrapped M5-branes in Calabi-Yau 2-folds

    SciTech Connect (OSTI)

    Fayyazuddin, Ansar; Husain, Tasneem Zehra; Pappa, Ioanna

    2006-06-15

    We study the geometry of M5-branes wrapping a 2-cycle which is special Lagrangian with respect to a specific complex structure in a Calabi-Yau 2-fold. Using methods recently applied to the 3-fold case, we are again able to find a characterization of the geometry, in terms of a nonintegrable almost complex structure and a (2,0) form. This time, however, due to the hyper-Kaehler nature of the underlying 2-fold, we also have the freedom of choosing a different almost complex structure with respect to which the wrapped 2-cycle is holomorphic. We show that this latter almost complex structure is integrable. We then relate our geometry to previously found geometries of M5-branes wrapping holomorphic cycles and go further to prove some previously unknown results for M5-branes on holomorphic cycles.

  2. The earliest events in protein folding: Helix dynamics in proteins and model peptides

    SciTech Connect (OSTI)

    Dyer, R.B.; Williams, S.; Woodruff, W.H. [Los Alamos National Lab., NM (United States)] [and others

    1996-12-31

    The earliest events in protein folding are critically important in determining the folding pathway, but have proved difficult to study by conventional approaches. We have developed new rapid initiation methods and structure-specific probes to interrogate the earliest events of protein folding. Our focus is the pathways. Folding or unfolding reactions are initiated on a fast timescale (10 ns) using a laser induced temperature jump (15 C) and probed with time-resolved infrared spectroscopy. We obtained the kinetics of the helix-coil transition for a model 21-residue peptide. The observed rate constant k{sub obs} = k{sub f} + k{sub u} for reversible kinetics; from the observed rate (6 x 10{sup 6} s{sup -1}) and the equilibrium constant favoring folding of 7.5 at 27 C, we calculate a folding lifetime of 180 ns and an unfolding lifetime of 1.4 {mu}s. The {open_quotes}molten globule{close_quotes} form of apomyoglobin (horse, pH*3, 0.15M NaCl) shows similar kinetics for helix that is unconstrained by tertiary structure (helix with an unusually low Amide I frequency, near 1633 cm{sup -1}). In {open_quotes}native{close_quotes} apomyoglobin (horse, pH*5.3, 10 mM NaCl) two very different rates (45 ns and 70 {mu}s) are observed and we infer that a third occurs on a timescales inaccessible to our experiment (> 1 ms). We suggest that the slower processes are due to helix formation that is rate-limited by the formation of tertiary structure.

  3. Protein-folding via divide-and-conquer optimization (Conference) | SciTech

    Office of Scientific and Technical Information (OSTI)

    Connect Protein-folding via divide-and-conquer optimization Citation Details In-Document Search Title: Protein-folding via divide-and-conquer optimization Authors: Oliva, Ricardo ; Crivelli, Silvia ; Meza, Juan Publication Date: 2004-07-11 OSTI Identifier: 882903 Report Number(s): LBNL--55869 R&D Project: 365969; BnR: YN0100000 DOE Contract Number: DE-AC02-05CH11231 Resource Type: Conference Resource Relation: Conference: SIAM Conference on the Life Sciences, Portland,OR, July 11-14,

  4. Deducing the Energetic Cost of Protein Folding in Zinc Finger Proteins Using Designed Metallopeptides

    SciTech Connect (OSTI)

    Reddi,A.; Guzman, T.; Breece, r.; Tierney, D.; Gibney, B.

    2007-01-01

    Zinc finger transcription factors represent the largest single class of metalloproteins in the human genome. Binding of Zn(II) to their canonical Cys4, Cys3His1, or Cys2His2 sites results in metal-induced protein folding events required to achieve their proper structure for biological activity. The thermodynamic contribution of Zn(II) in each of these coordination spheres toward protein folding is poorly understood because of the coupled nature of the metal-ligand and protein-protein interactions. Using an unstructured peptide scaffold, GGG, we have employed fluorimetry, potentiometry, and calorimetry to determine the thermodynamics of Zn(II) binding to the Cys4, Cys3His1, and Cys2His2 ligand sets with minimal interference from protein folding effects. The data show that Zn(II) complexation is entropy driven and modulated by proton release. The formation constants for Zn(II)-GGG with a Cys4, Cys3His1, or Cys2His2 site are 5.6 x 1016, 1.5 x 1015, or 2.5 x 1013 M-1, respectively. Thus, the Zn(II)-Cys4, Zn(II)-Cys3His1, and Zn(II)-Cys2His2 interactions can provide up to 22.8, 20.7, and 18.3 kcal/mol, respectively, in driving force for protein stabilization, folding, and/or assembly at pH values above the ligand pKa values. While the contributions from the three coordination motifs differ by 4.5 kcal/mol in Zn(II) affinity at pH 9.0, they are equivalent at physiological pH, ?G = -16.8 kcal/mol or a Ka = 2.0 x 1012 M-1. Calorimetric data show that this is due to proton-based enthalpy-entropy compensation between the favorable entropic term from proton release and the unfavorable enthalpic term due to thiol deprotonation. Since protein folding effects have been minimized in the GGG scaffold, these peptides possess nearly the tightest Zn(II) affinities possible for their coordination motifs. The Zn(II) affinities in each coordination motif are compared between the GGG scaffold and natural zinc finger proteins to determine the free energy required to fold the latter. Several proteins have identical Zn(II) affinities to GGG. That is, little, if any, of their Zn(II) binding energy is required to fold the protein, whereas some have affinities weakened by up to 5.7 kcal/mol; i.e., the Zn(II) binding energy is being used to fold the protein.

  5. Protein-folding via divide-and-conquer optimization (Conference) | SciTech

    Office of Scientific and Technical Information (OSTI)

    Connect Protein-folding via divide-and-conquer optimization Citation Details In-Document Search Title: Protein-folding via divide-and-conquer optimization Authors: Oliva, Ricardo ; Crivelli, Silvia ; Meza, Juan Publication Date: 2004-07-11 OSTI Identifier: 882903 Report Number(s): LBNL--55869 R&D Project: 365969; BnR: YN0100000 DOE Contract Number: DE-AC02-05CH11231 Resource Type: Conference Resource Relation: Conference: SIAM Conference on the Life Sciences, Portland,OR, July 11-14,

  6. Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits of the

    Office of Scientific and Technical Information (OSTI)

    BLM Complex (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits of the BLM Complex Citation Details In-Document Search Title: Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits of the BLM Complex Mutations in BLM, a RecQ-like helicase, are linked to the autosomal recessive cancer-prone disorder Bloom's syndrome. BLM associates with topoisomerase (Topo) III{alpha}, RMI1, and

  7. Microscopic Description of the Exotic Nuclei Reactions by Using Folding model Potentials

    SciTech Connect (OSTI)

    Ibraheem, Awad A.; Hassanain, M. A.; Mokhtar, S. R.; El-Azab Farid, M.; Zaki, M. A.; Mahmoud, Zakaria M. M.

    2011-10-27

    A microscopic folding approach based upon the effective M3Y nucleon-nucleon interaction and the nuclear matter densities of the interacting nuclei has been carried out to explain recently measured experimental data of the {sup 6}He+{sup 120}Sn elastic scattering reaction at four different laboratory energies near the Coulomb barrier. The corresponding reaction cross sections are also considered.

  8. Long range correlations and folding angle with applications to ?-helical proteins

    SciTech Connect (OSTI)

    Krokhotin, Andrey, E-mail: Andrei.Krokhotine@cern.ch [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden)] [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Nicolis, Stam, E-mail: Stam.Nicolis@lmpt.univ-tours.fr [Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours (France)] [Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours (France); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours (France); Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

    2014-03-07

    The conformational complexity of chain-like macromolecules such as proteins and other linear polymers is much larger than that of point-like atoms and molecules. Unlike particles, chains can bend, twist, and even become knotted. Thus chains might also display a much richer phase structure. Unfortunately, it is not very easy to characterize the phase of a long chain. Essentially, the only known attribute is the radius of gyration. The way how it changes when the degree of polymerization becomes different, and how it evolves when the ambient temperature and solvent properties change, is commonly used to disclose the phase. But in any finite length chain there are corrections to scaling that complicate the detailed analysis of the phase structure. Here we introduce a quantity that we call the folding angle to identify and scrutinize the phase structure, as a complement to the radius of gyration. We argue for a mean-field level relationship between the folding angle and the scaling exponent in the radius of gyration. We then estimate the value of the folding angle in the case of crystallographic ?-helical protein structures in the Protein Data Bank. We also show how the experimental value of the folding angle can be obtained computationally, using a semiclassical Born-Oppenheimer description of ?-helical chiral chains.

  9. Isolation, folding and structural investigations of the amino acid transporter OEP16

    SciTech Connect (OSTI)

    Ni, Da Qun; Zook, James; Klewer, Douglas A.; Nieman, Ronald A.; Soll, J.; Fromme, Petra

    2011-12-01

    Membrane proteins compose more than 30% of all proteins in the living cell. However, many membrane proteins have low abundance in the cell and cannot be isolated from natural sources in concentrations suitable for structure analysis. The overexpression, reconstitution, and stabilization of membrane proteins are complex and remain a formidable challenge in membrane protein characterization. Here we describe a novel, in vitro folding procedure for a cation-selective channel protein, the outer envelope membrane protein 16 (OEP16) of pea chloroplast, overexpressed in Escherichia coli in the form of inclusion bodies. The protein is purified and then folded with detergent on a Ni-NTA affinity column. Final concentrations of reconstituted OEP16 of up to 24 mg/ml have been achieved, which provides samples that are sufficient for structural studies by NMR and crystallography. Reconstitution of OEP16 in detergent micelles was monitored by circular dichroism, fluorescence, and NMR spectroscopy. Tryptophan fluorescence spectra of heterologous expressed OEP16 in micelles are similar to spectra of functionally active OEP16 in liposomes, which indicates folding of the membrane protein in detergent micelles. CD spectroscopy studies demonstrate a folded protein consisting primarily of a-helices. 15N-HSQC NMR spectra also provide evidence for a folded protein. We present here a convenient, effective and quantitative method to screen large numbers of conditions for optimal protein stability by using microdialysis chambers in combination with fluorescence spectroscopy. Recent collection of multidimensional NMR data at 500, 600 and 800 MHz demonstrated that the protein is suitable for structure determination by NMR and stable for weeks during data collection.

  10. Protein folding and protein metallocluster studies using synchrotron small angler X-ray scattering

    SciTech Connect (OSTI)

    Eliezer, D.

    1994-06-01

    Proteins, biological macromolecules composed of amino-acid building blocks, possess unique three dimensional shapes or conformations which are intimately related to their biological function. All of the information necessary to determine this conformation is stored in a protein`s amino acid sequence. The problem of understanding the process by which nature maps protein amino-acid sequences to three-dimensional conformations is known as the protein folding problem, and is one of the central unsolved problems in biophysics today. The possible applications of a solution are broad, ranging from the elucidation of thousands of protein structures to the rational modification and design of protein-based drugs. The scattering of X-rays by matter has long been useful as a tool for the characterization of physical properties of materials, including biological samples. The high photon flux available at synchrotron X-ray sources allows for the measurement of scattering cross-sections of dilute and/or disordered samples. Such measurements do not yield the detailed geometrical information available from crystalline samples, but do allow for lower resolution studies of dynamical processes not observable in the crystalline state. The main focus of the work described here has been the study of the protein folding process using time-resolved small-angle x-ray scattering measurements. The original intention was to observe the decrease in overall size which must accompany the folding of a protein from an extended conformation to its compact native state. Although this process proved too fast for the current time-resolution of the technique, upper bounds were set on the probable compaction times of several small proteins. In addition, an interesting and unexpected process was detected, in which the folding protein passes through an intermediate state which shows a tendency to associate. This state is proposed to be a kinetic molten globule folding intermediate.

  11. High-resolution structure of a retroviral protease folded as a monomer

    SciTech Connect (OSTI)

    Gilski, Miroslaw [A. Mickiewicz University, 60-780 Poznan (Poland); Polish Academy of Sciences, 61-704 Poznan (Poland); Kazmierczyk, Maciej; Krzywda, Szymon [A. Mickiewicz University, 60-780 Poznan (Poland); Zbransk, Helena [Academy of Sciences of the Czech Republic, 166 10 Prague (Czech Republic); Cooper, Seth; Popovi?, Zoran [University of Washington, Box 352350, Seattle, WA 98195 (United States); Khatib, Firas; DiMaio, Frank; Thompson, James; Baker, David [University of Washington, Box 357350, Seattle, WA 98195 (United States); Pichov, Iva [Academy of Sciences of the Czech Republic, 166 10 Prague (Czech Republic); Jaskolski, Mariusz, E-mail: mariuszj@amu.edu.pl [A. Mickiewicz University, 60-780 Poznan (Poland); Polish Academy of Sciences, 61-704 Poznan (Poland)

    2011-11-01

    The crystal structure of MasonPfizer monkey virus protease folded as a monomer has been solved by molecular replacement using a model generated by players of the online game Foldit. The structure shows at high resolution the details of a retroviral protease folded as a monomer which can guide rational design of protease dimerization inhibitors as retroviral drugs. MasonPfizer monkey virus (M-PMV), a D-type retrovirus assembling in the cytoplasm, causes simian acquired immunodeficiency syndrome (SAIDS) in rhesus monkeys. Its pepsin-like aspartic protease (retropepsin) is an integral part of the expressed retroviral polyproteins. As in all retroviral life cycles, release and dimerization of the protease (PR) is strictly required for polyprotein processing and virion maturation. Biophysical and NMR studies have indicated that in the absence of substrates or inhibitors M-PMV PR should fold into a stable monomer, but the crystal structure of this protein could not be solved by molecular replacement despite countless attempts. Ultimately, a solution was obtained in mr-rosetta using a model constructed by players of the online protein-folding game Foldit. The structure indeed shows a monomeric protein, with the N- and C-termini completely disordered. On the other hand, the flap loop, which normally gates access to the active site of homodimeric retropepsins, is clearly traceable in the electron density. The flap has an unusual curled shape and a different orientation from both the open and closed states known from dimeric retropepsins. The overall fold of the protein follows the retropepsin canon, but the C{sup ?} deviations are large and the active-site DTG loop (here NTG) deviates up to 2.7 from the standard conformation. This structure of a monomeric retropepsin determined at high resolution (1.6 ) provides important extra information for the design of dimerization inhibitors that might be developed as drugs for the treatment of retroviral infections, including AIDS.

  12. Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition

    SciTech Connect (OSTI)

    Wang, Jin; Lu, Qiang N.; Lu, H PETER.

    2006-07-01

    The study of associations between two biomolecules is the key to understand molecular recognition and function. Molecular function is often thought to be determined by the underlying structures. Here, combining single molecule study of protein binding with an energy landscape inspired microscopic model, we found strong evidences that bio-molecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse grained molecular dynamics performed on the residue level with the energy function biased towards the native binding structure (Go model). With our model, the underlying free energy landscape of the binding can be explored. Two distinct conformational states as free energy minimum, one with partially folding of CBD and significant binding of CBD to CDC42, and another with native folding of CBD and native binding of CBD to CDC42, are clearly seen. This shows the binding process proceeds with significant interface binding of CBD with CDC42 first without complete folding of CBD. Finally binding and folding are coupled with each other cooperatively to reach the native binding state. The single molecule experimental finding of the dynamic fluctuations between the loosely bound and closely bound conformational states can be identified with theoretically calculated free energy minimum and quantitatively explained in our model as a result of binding associated with large conformational changes. Theoretical predictions have identified certain key residues for binding which are consistent with mutational experiments. The combined study provides a test ground for fundamental mechanisms as well as insights into design and further explorations on biomolecular recognition with large conformational changes.

  13. Protein-Folding Landscapes in Multi-Chain Systems Major Classification: Biological Sciences

    Office of Scientific and Technical Information (OSTI)

    Protein-Folding Landscapes in Multi-Chain Systems Major Classification: Biological Sciences Minor Classification: Biophysics Authors: Troy Cellmer 1 , Dusan Bratko 1,2 , John M. Prausnitz 1,3 , and Harvey Blanch 1,* 1 Department of Chemical Engineering, University of California, Berkeley, CA 94720 2 Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284 3 Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 * corresponding author Tel:

  14. In the OSTI Collections: Determining How Proteins Fold | OSTI, US Dept of

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

    Energy, Office of Scientific and Technical Information Determining How Proteins Fold Article Acknowledgement: Dr. William N. Watson, Physicist DOE Office of Scientific and Technical Information Investigations Focused on Direct Experiments Investigations Focused on Computation References Research Organizations Reports available through OSTI's SciTech Connect Additional References Proteins are the materials in living cells whose primary structures are specified by the cell's DNA. These primary

  15. Hundred-Fold Improvement in Temperature Mapping Reveals the Stresses Inside

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

    Tiny Transistors | U.S. DOE Office of Science (SC) Hundred-Fold Improvement in Temperature Mapping Reveals the Stresses Inside Tiny Transistors Basic Energy Sciences (BES) BES Home About Research Facilities Science Highlights Benefits of BES Funding Opportunities Basic Energy Sciences Advisory Committee (BESAC) Community Resources Contact Information Basic Energy Sciences U.S. Department of Energy SC-22/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-3081 F:

  16. Wang-Landau sampling of the interplay between surface adsorption and folding of HP lattice proteins

    SciTech Connect (OSTI)

    Li, Ying Wai [ORNL] [ORNL; Wuest, Thomas [Swiss Federal Research Institute, Switzerland] [Swiss Federal Research Institute, Switzerland; Landau, David P [University of Georgia, Athens, GA] [University of Georgia, Athens, GA

    2014-01-01

    Generic features associated with the adsorption of proteins on solid surfaces are reviewed within the framework of the hydrophobic-polar (HP) lattice protein model. The thermodynamic behavior and structural properties of various HP protein sequences interacting with attractive surfaces have been studied using extensive Wang-Landau sampling with different types of surfaces, each of which attracts either: all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. Consequently, different types of folding behavior occur for varied surface strengths. Analysis of the combined patterns of various structural observables, e.g., the derivatives of the numbers of interaction contacts, together with the specific heat, leads to the identification of fundamental categories of folding and transition hierarchies. We also inferred a connection between the transition categories and the relative surface strengths, i.e., the ratios of the surface attractive strengths to the intra-chain attraction among H monomers. We thus believe that the folding hierarchies and identification scheme are generic for different HP sequences interacting with attractive surfaces, regardless of the chain length, sequence, or surface attraction.

  17. Structural Analysis of Protein Folding by the Long-Chain Archaeal Chaperone FKBP26

    SciTech Connect (OSTI)

    E Martinez-Hackert; W Hendrickson

    2011-12-31

    In the cell, protein folding is mediated by folding catalysts and chaperones. The two functions are often linked, especially when the catalytic module forms part of a multidomain protein, as in Methanococcus jannaschii peptidyl-prolyl cis/trans isomerase FKBP26. Here, we show that FKBP26 chaperone activity requires both a 50-residue insertion in the catalytic FKBP domain, also called 'Insert-in-Flap' or IF domain, and an 80-residue C-terminal domain. We determined FKBP26 structures from four crystal forms and analyzed chaperone domains in light of their ability to mediate protein-protein interactions. FKBP26 is a crescent-shaped homodimer. We reason that folding proteins are bound inside the large crescent cleft, thus enabling their access to inward-facing peptidyl-prolyl cis/trans isomerase catalytic sites and ipsilateral chaperone domain surfaces. As these chaperone surfaces participate extensively in crystal lattice contacts, we speculate that the observed lattice contacts reflect a proclivity for protein associations and represent substrate interactions by FKBP26 chaperone domains. Finally, we find that FKBP26 is an exceptionally flexible molecule, suggesting a mechanism for nonspecific substrate recognition.

  18. Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding

    SciTech Connect (OSTI)

    Huang, David M.; Chandler, David

    2000-04-01

    The Lum-Chandler-Weeks theory of hydrophobicity [J. Phys. Chem. 103, 4570 (1999)] is applied to treat the temperature dependence of hydrophobic solvation in water. The application illustrates how the temperature dependence for hydrophobic surfaces extending less than 1nm differs significantly from that for surfaces extending more than 1nm. The latter is the result of water depletion, a collective effect, that appears at length scales of 1nm and larger. Due to the contrasting behaviors at small and large length scales, hydrophobicity by itself can explain the variable behavior of protein folding.

  19. Protein folding and non-conventional drug design: a primer for nuclear structure physicists

    SciTech Connect (OSTI)

    Broglia, R.A. [Dipartimento di Fisica, Universita di Milano, Via Celoria 16, I-20133 Milan (Italy); INFN, Sezione di Milano, Via Celoria 16, I-20133 Milan (Italy); Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen (Denmark); Tiana, G.; Provasi, D. [Dipartimento di Fisica, Universita di Milano, Via Celoria 16, I-20133 Milan (Italy); INFN, Sezione di Milano, Via Celoria 16, I-20133 Milan (Italy)

    2004-02-27

    Some of the paradigms emerging from the study of the phenomena of phase transitions in finite many-body systems, like e.g. the atomic nucleus can be used at profit to solve the protein folding problem within the framework of simple (although not oversimplified) models. From this solution a paradigm emerges for the design of non-conventional drugs, which inhibit enzymatic action without inducing resistance (mutations). The application of these concepts to the design of an inhibitor to the HIV-protease central in the life cycle of the HIV virus is discussed.

  20. Trigger loop folding determines transcription rate of Escherichia colis RNA polymerase

    SciTech Connect (OSTI)

    Mejia, Yara X.; Nudler, Evgeny; Bustamante, Carlos

    2014-12-31

    Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAPs pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kinetic model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. The model suggests a finely tuned mechanism that balances transcription speed and fidelity.

  1. Trigger loop folding determines transcription rate of Escherichia coli’s RNA polymerase

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

    Mejia, Yara X.; Nudler, Evgeny; Bustamante, Carlos

    2014-12-31

    Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAP’s pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kineticmore » model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. The model suggests a finely tuned mechanism that balances transcription speed and fidelity.« less

  2. Protein Folding Dynamics Detected By Time-Resolved Synchrotron X-ray Small-Angle Scattering Technique

    SciTech Connect (OSTI)

    Fujisawa, Tetsuro; Takahashi, Satoshi [RIKEN Harima Institute, SPring-8 Center, Laboratory for Biometal Science, Hyogo 679-5148 (Japan); Institute for Protein Research, Osaka University Suita Osaka 565-0871/CREST, JST (Japan)

    2007-03-30

    The polypeptide collapse is an essential dynamics in protein folding. To understand the mechanism of the collapse, in situ observation of folding by various probes is necessary. The changes in secondary and tertiary structures in the folding process of globular proteins, whose chain lengths are less than 300 polypeptides, were observed by circular dichrosim and intrinsic fluorescence spectroscopies, respectively. On the other hand, those in protein compactness could be only detected by using time-resolved synchrotron x-ray small-angle scattering technique. The observed dynamics for several proteins with different topologies suggested a common folding mechanism termed 'collapse and search' dynamics, in which the polypeptide collapse precedes the formation of the native contact formation. In 'collapse and search' dynamics, the most outstanding feature lied in the compactness of the initial intermediates. The collapsed intermediates demonstrated the scaling relationship between radius of gyration (Rg) and chain length with a scaling exponent of 0.35 {+-} 0.11, which is close to the value (1/3) predicted by mechano-statistical theory for the collapsed globules of polymers in poor solvent. Thus, it was suggested that the initial collapse is caused by the coil-globule transition of polymers. Since the collapse is essential to the folding of larger proteins, further investigations on the collapse likely lead to an important insight into the protein folding phenomena.

  3. Improvements in Mixing Time and Mixing Uniformity in Devices Designed for Studies of Protein Folding Kinetics

    SciTech Connect (OSTI)

    Yao, Shuhuai [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bakajin, Olgica [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2007-08-01

    Using a microfluidic laminar flow mixer designed for studies of protein folding kinetics, we demonstrate a mixing time of 1 +/- 1 micros with sample consumption on the order of femtomoles. We recognize two limitations of previously proposed designs: (1) size and shape of the mixing region, which limits mixing uniformity and (2) the formation of Dean vortices at high flow rates, which limits the mixing time. We address these limitations by using a narrow shape-optimized nozzle and by reducing the bend of the side channel streamlines. The final design, which combines both of these features, achieves the best performance. We quantified the mixing performance of the different designs by numerical simulation of coupled Navier-Stokes and convection-diffusion equations and experiments using fluorescence resonance energy-transfer (FRET)-labeled DNA.

  4. Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-08-01

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

  5. Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-06-01

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

  6. Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone

    SciTech Connect (OSTI)

    Martinez-Hackert, E.; Hendrickson, W

    2009-01-01

    Trigger factor (TF) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. Thereby, we obtained an atomic-level picture of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding, and suggests a role for TF in the biogenesis of protein complexes.

  7. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model

    SciTech Connect (OSTI)

    Agarwala, R. [National Institutes of Health, Bethesda, MD (United States); Batzoglou, S. [MIT Lab. for Computer Science, Cambridge, MA (United States); Dancik, V. [Univ. of Southern California, Los Angeles, CA (United States)] [and others

    1997-12-01

    A long standing problem in molecular biology is to determine the three-dimensional structure of a protein, given its amino acid sequence. A variety of simplifying models have been proposed abstracting only the {open_quotes}essential physical properties{close_quotes} of real proteins. In these models, the three dimensional space is often represented by a lattice. Residues which are adjacent in the primary sequence (i.e. covalently linked) must be placed at adjacent points in the lattice. A conformation of a protein is simply a self-avoiding walk along the lattice. The protein folding problem STRING-FOLD is that of finding a conformation of the protein sequence on the lattice such that the overall energy is minimized, for some reasonable definition of energy. This formulation leaves open the choices of a lattice and an energy function. Once these choices are made, one may then address the algorithmic complexity of optimizing the energy function for the lattice. For a variety of such simple models, this minimization problem is in fact NP-hard. In this paper, we consider the Hydrophobic-Polar (HP) Model introduced by Dill. The HP model abstracts the problem by grouping the 20 amino acids into two classes: hydrophobic (or non-polar) residues and hydrophilic (or polar) residues. For concreteness, we will take our input to be a string from (H,P){sup +}, where P represents polar residues, and H represents hydrophobic residues. Dill et.al. survey the literature analyzing this model. 8 refs., 2 figs., 1 tab.

  8. The Influence of fold and fracture development on reservoir behavior of the Lisburne Group of northern Alaska

    SciTech Connect (OSTI)

    Wesley K. Wallace; Catherine L. Hanks; Jerry Jensen: Michael T. Whalen; Paul Atkinson; Joseph Brinton; Thang Bui; Margarete Jadamec; Alexandre Karpov; John Lorenz; Michelle M. McGee; T.M. Parris; Ryan Shackleton

    2004-07-01

    The Carboniferous Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is folded and thrust faulted where it is exposed throughout the Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study were to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of folds and their truncation by thrust faults. (2) The influence of folding on fracture patterns. (3) The influence of deformation on fluid flow. (4) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics. Symmetrical detachment folds characterize the Lisburne in the northeastern Brooks Range. In contrast, Lisburne in the main axis of the Brooks Range is deformed into imbricate thrust sheets with asymmetrical hangingwall anticlines and footwall synclines. The Continental Divide thrust front separates these different structural styles in the Lisburne and also marks the southern boundary of the northeastern Brooks Range. Field studies were conducted for this project during 1999 to 2001 in various locations in the northeastern Brooks Range and in the vicinity of Porcupine Lake, immediately south of the Continental Divide thrust front. Results are summarized below for the four main subject areas of the study.

  9. The role of hydrogen bonds in protein folding and protein association

    SciTech Connect (OSTI)

    Ben-Naim, A. (National Inst. of Health, Bethesda, MD (USA))

    1991-02-07

    The contribution of a pair of functional groups that can form either intermolecular or intramolecular hydrogen bonds to the total standard free energy of the process of protein folding or protein association is examined. It is found that this contribution can be quite large, either positive or negative, depending on the particular process and on the solvent density. This is in contrast to the common belief that the hydrogen-bond energies tend to be compensated in these processes. For the binding process, in which the two functional groups are completely removed from the aqueous environment, the contribution of such a pair of functional groups to {Delta}G can be as high as +6.4 kcal/mol. This is the main reason why hydrophobic rather than hydrophilic surfaces tend to attach to each other. In contrast, when the two functional groups are only partially removed from the aqueous environment, as in the case of the formation of {alpha}-helix, their contribution to {Delta}G can be negative and of the order of about 1 kcal/mol.

  10. Discriminating trpzip2 and trpzip4 peptides folding landscape using the two-dimensional infrared spectroscopy: A simulation study

    SciTech Connect (OSTI)

    Wu, Tianmin; Zhang, Ruiting; Li, Huanhuan; Zhuang, Wei, E-mail: wzhuang@dicp.ac.cn, E-mail: lijiangy@pku.edu.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning (China)] [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning (China); Yang, Lijiang, E-mail: wzhuang@dicp.ac.cn, E-mail: lijiangy@pku.edu.cn [College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871 (China)] [College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871 (China)

    2014-02-07

    We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two ?-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB{sup OBC} implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors.

  11. Energy and Mass Dependences of the Parameters of the Semimicroscopic Folding Model for Alpha Particles at Low and Intermediate Energies

    SciTech Connect (OSTI)

    Kuterbekov, K.A.; Zholdybayev, T.K.; Kukhtina, I.N.; Penionzhkevich, Yu.E.

    2005-06-01

    The energy and mass dependences of the parameters of the semimicroscopic alpha-particle potential are investigated for the first time in the region of low and intermediate energies. Within the semimicroscopic folding model, both elastic and inelastic differential and total cross sections for reactions on various nuclei are well described by using global parameters obtained in this study.

  12. Pattern of extensional faulting in pelagic carbonates of the Unbria-Marche Apennines of central Italy

    SciTech Connect (OSTI)

    Alvarez, W. )

    1990-05-01

    The Umbria-Marche Apennines provide a new region in which the nature passive-margin extensional faulting can be studied in outcrop. In these dominantly pelagic carbonate rocks of Jurassic and Cretaceous age, horsts acted as shallow, nonvolcani seamounts, while tilted half grabens formed deeper basins. One well-exposed seamount-basin transition agrees in general with the model of listric normal faulting and tilted half grabens, but shows interesting and significant divergences when studied in detail. A small sedimentary wedge at the faulted margin of a horst-block seamount thickens unexpectedly toward the adjacent basin. This wedge developed because of local convex-upward curvature of the shallowest part of a fault which at depth must have concave-up, listric geometry. The local sedimentary wedge resulted from deposition on the hanging wall as it tilted, followed by differential compaction of younger limestones that lapped onto the gentle slope leading from the horst-block seamount toward the basin. The map pattern of listric normal faulting in the Umbria-Marche Apennines suggests that both principal strain axes were extensional, in contrast to the usual pattern of listric faults crossed by transfer faults.

  13. The crystal structure of a partial mouse Notch-1 ankyrin domain: Repeats 4 through 7 preserve an ankyrin fold

    SciTech Connect (OSTI)

    Lubman, Olga Y.; Kopan, Raphael; Waksman, Gabriel; Korolev, Sergey (Birbeck); (St. Louis-MED); (WU-MED)

    2010-07-20

    Folding and stability of proteins containing ankyrin repeats (ARs) is of great interest because they mediate numerous protein-protein interactions involved in a wide range of regulatory cellular processes. Notch, an ankyrin domain containing protein, signals by converting a transcriptional repression complex into an activation complex. The Notch ANK domain is essential for Notch function and contains seven ARs. Here, we present the 2.2 {angstrom} crystal structure of ARs 4-7 from mouse Notch 1 (m1ANK). These C-terminal repeats were resistant to degradation during crystallization, and their secondary and tertiary structures are maintained in the absence of repeats 1-3. The crystallized fragment adopts a typical ankyrin fold including the poorly conserved seventh AR, as seen in the Drosophila Notch ANK domain (dANK). The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation.

  14. A Summary of Information on the Behavior of the Yakima Fold Belt as a Structural Entity -- Topical Report

    SciTech Connect (OSTI)

    Last, George V.; Winsor, Kelsey; Unwin, Stephen D.

    2012-08-01

    This document is one in a series of topical reports compiled by the Pacific Northwest National Laboratory to summarize technical information on selected topics important to the performance of a probabilistic seismic hazard analysis (PSHA) of the Hanford Site. The purpose of this report is to summarize available data and analyses relevant to the Yakima Fold Belt (YFB) that may bear on the question of whether or not the YFB behaves as a single seismotectonic province in which activity along one fold structure is representative of behavior along all other fold structures. This topic has met with a fairly high level of contention in the expert community and has the potential to result in significant impacts on an evaluation of seismic hazard at the Hanford Site. This report defines the relevant alternative conceptual models relevant to this technical issue and the arguments and data that support those models. It provides a brief description of the technical issue and principal uncertainties; a general overview on the nature of the technical issue, along with alternative conceptual models, supporting arguments and information, and uncertainties; and finally, it suggests some possible approaches for reducing uncertainties regarding this issue.

  15. Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal

    SciTech Connect (OSTI)

    Hart, W.E.; Istrail, S. [Sandia National Labs., Albuquerque, NM (United States). Algorithms and Discrete Mathematics Dept.

    1996-08-09

    This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains.

  16. Assessment of substrate-stabilizing factors for DnaK on the folding of aggregation-prone proteins

    SciTech Connect (OSTI)

    Ryu, Kisun; Kim, Chul Woo; Kim, Byung Hee [Department of Biotechnology, College of Engineering, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Han, Kyoung Sim [Protheon Incorporated, Yonsei Engineering Research Center B120E, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Kim, Kyun-Hwan [Department of Pharmacology, School of Medicine, and Center for Diagnostic Medicine, Institute of Biomedical Science and Technology, Konkuk University, Seoul 143-701 (Korea, Republic of); Choi, Seong Il [Department of Biotechnology, College of Engineering, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Institute of Life Science and Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of)], E-mail: seongilchoi@daum.net; Seong, Baik L. [Department of Biotechnology, College of Engineering, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Protheon Incorporated, Yonsei Engineering Research Center B120E, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of); Institute of Life Science and Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea, Republic of)], E-mail: blseong@yonsei.ac.kr

    2008-08-15

    Hydrophobic interactions between molecular chaperones and their nonnative substrates have been believed to be mainly responsible for both substrate recognition and stabilization against aggregation. However, the hydrophobic contact area between DnaK and its substrate proteins is very limited and other factors of DnaK for the substrate stabilization could not be excluded. Here, we covalently fused DnaK to the N-termini of aggregation-prone proteins in vivo. In the context of a fusion protein, DnaK has the ability to efficiently solubilize its linked proteins. The point mutation of the residue of DnaK critical for the substrate recognition and the deletion of the C-terminal substrate-binding domain did not have significant effect on the solubilizing ability of DnaK. The results imply that other factors of DnaK, distinct from the hydrophobic shielding of folding intermediates, also contributes to stabilization of its noncovalently bound substrates against aggregation. Elucidation of the nature of these factors would further enhance our understanding of the substrate stabilization of DnaK for expedited protein folding.

  17. Laser-induced temperature jump/time-resolved infrared study of the fast events in protein folding

    SciTech Connect (OSTI)

    Woodruff, W.H.; Dyer, R.B.; Williams, S. [Los Alamos National Laboratory, NM (United States); Callender, H.; Gilmanshin, R. [CUNY, NY (United States)

    1996-10-01

    Laser-induced temperature jump followed by time-resolved infrared probe of reaction dynamics are used to study the temporal evolution of polypeptide structure during protein folding and unfolding. Reactions are initiated in times of 50 ps or longer by T-jumps of 10`s of degrees, obtained by laser excitation of water overtone absorbances. Observation of the Amide I transient absorbances reveal melting lifetimes of helices unconstrained by tertiary structure to be ca. 160 ns in a model 21-peptide and ca. 30 ns in {open_quotes}molten globule{close_quotes} apomyoglobin. No other processes are observed in these systems over the timescale 50 ps to 2 ms. Equilibrium data suggest the corresponding helix formation lifetimes to be ca. 16 and 1 ns, respectively. In {open_quotes}native{close_quotes} apomyoglobin two helix melting lifetimes are observed and we infer that a third occurs on a timescale inaccessible to our experiment (> 1 ms). The shorter observed lifetime, as in the molten globule, is ca. 30 ns. The longer lifetime is ca. 70 {mu}s. We suggest that the slower process is helix melting that is rate-limited by the unfolding of tertiary structure. Equilibrium data suggest a lifetime of ca. 1 {mu}s for the development of these tertiary folds.

  18. Binding-induced folding of prokaryotic ubiquitin-like protein on the mycobacterium proteasomal ATPase targets substrates for degradation

    SciTech Connect (OSTI)

    Wang, T.; Li, H.; Darwin, K. H.

    2010-11-01

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

  19. Binding-induced Folding of Prokaryotic Ubiquitin-like Protein on the Mycobacterium Proteasomal ATPase Targets Substrates for Degradation

    SciTech Connect (OSTI)

    T Wang; K Heran Darwin; H Li

    2011-12-31

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

  20. A Summary of Coupled, Uncoupled, and Hybrid Tectonic Models for the Yakima Fold Belt--Topical Report

    SciTech Connect (OSTI)

    Chamness, Michele A.; Winsor, Kelsey; Unwin, Stephen D.

    2012-08-01

    This document is one in a series of topical reports compiled by the Pacific Northwest National Laboratory to summarize technical information on selected topics important to the performance of a probabilistic seismic hazard analysis of the Hanford Site. The purpose of this report is to summarize the range of opinions and supporting information expressed by the expert community regarding whether a coupled or uncoupled model, or a combination of both, best represents structures in the Yakima Fold Belt. This issue was assessed to have a high level of contention with up to moderate potential for impact on the hazard estimate. This report defines the alternative conceptual models relevant to this technical issue and the arguments and data that support those models. It provides a brief description of the technical issue and principal uncertainties; a general overview on the nature of the technical issue, along with alternative conceptual models, supporting arguments and information, and uncertainties; and finally, suggests some possible approaches for reducing uncertainties regarding this issue.

  1. Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b)

    SciTech Connect (OSTI)

    Singh, Priya; Sarkar, Subir K.; Bandyopadhyay, Pradipta

    2014-07-07

    We present the results of a high-statistics equilibrium study of the folding/unfolding transition for the 20-residue mini-protein Trp-cage (TC5b) in water. The ECEPP/3 force field is used and the interaction with water is treated by a solvent-accessible surface area method. A Wang-Landau type simulation is used to calculate the density of states and the conditional probabilities for the various values of the radius of gyration and the number of native contacts at fixed values of energyalong with a systematic check on their convergence. All thermodynamic quantities of interest are calculated from this information. The folding-unfolding transition corresponds to a peak in the temperature dependence of the computed specific heat. This is corroborated further by the structural signatures of folding in the distributions for radius of gyration and the number of native contacts as a function of temperature. The potentials of mean force are also calculated for these variables, both separately and jointly. A local free energy minimum, in addition to the global minimum, is found in a temperature range substantially below the folding temperature. The free energy at this second minimum is approximately 5?k{sub B}T higher than the value at the global minimum.

  2. 'Let the phage do the work': Using the phage P22 coat protein structures as a framework to understand its folding and assembly mutants

    SciTech Connect (OSTI)

    Teschke, Carolyn M., E-mail: Teschke@uconn.ed [Departments of Molecular and Cell Biology, and Chemistry, 91 N. Eagleville Rd., U-3125, University of Connecticut, Storrs, CT 06269-3125 (United States); Parent, Kristin N. [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA (United States)

    2010-06-05

    The amino acid sequence of viral capsid proteins contains information about their folding, structure and self-assembly processes. While some viruses assemble from small preformed oligomers of coat proteins, other viruses such as phage P22 and herpesvirus assemble from monomeric proteins (Fuller and King, 1980). The subunit assembly process is strictly controlled through protein:protein interactions such that icosahedral structures are formed with specific symmetries, rather than aberrant structures. dsDNA viruses commonly assemble by first forming a precursor capsid that serves as a DNA packaging machine. DNA packaging is accompanied by a conformational transition of the small precursor procapsid into a larger capsid for isometric viruses. Here we highlight the pseudo-atomic structures of phage P22 coat protein and rationalize several decades of data about P22 coat protein folding, assembly and maturation generated from a combination of genetics and biochemistry.

  3. Impact of the [delta]F508 Mutation in First Nucleotide-binding Domain of Human Cystic Fibrosis Transmembrane Conductance Regulator on Domain Folding and Structure

    SciTech Connect (OSTI)

    Lewis, Hal A.; Zhao, Xun; Wang, Chi; Sauder, J. Michael; Rooney, Isabelle; Noland, Brian W.; Lorimer, Don; Kearins, Margaret C.; Conners, Kris; Condon, Brad; Maloney, Peter C.; Guggino, William B.; Hunt, John F.; Emtage, Spencer (SG); (Columbia); (JHU)

    2010-07-19

    Cystic fibrosis is caused by defects in the cystic fibrosis transmembrane conductance regulator (CFTR), commonly the deletion of residue Phe-508 (DeltaF508) in the first nucleotide-binding domain (NBD1), which results in a severe reduction in the population of functional channels at the epithelial cell surface. Previous studies employing incomplete NBD1 domains have attributed this to aberrant folding of DeltaF508 NBD1. We report structural and biophysical studies on complete human NBD1 domains, which fail to demonstrate significant changes of in vitro stability or folding kinetics in the presence or absence of the DeltaF508 mutation. Crystal structures show minimal changes in protein conformation but substantial changes in local surface topography at the site of the mutation, which is located in the region of NBD1 believed to interact with the first membrane spanning domain of CFTR. These results raise the possibility that the primary effect of DeltaF508 is a disruption of proper interdomain interactions at this site in CFTR rather than interference with the folding of NBD1. Interestingly, increases in the stability of NBD1 constructs are observed upon introduction of second-site mutations that suppress the trafficking defect caused by the DeltaF508 mutation, suggesting that these suppressors might function indirectly by improving the folding efficiency of NBD1 in the context of the full-length protein. The human NBD1 structures also solidify the understanding of CFTR regulation by showing that its two protein segments that can be phosphorylated both adopt multiple conformations that modulate access to the ATPase active site and functional interdomain interfaces.

  4. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect (OSTI)

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variantwhile the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  5. Context-dependent protein folding of a virulence peptide in the bacterial and host environments: structure of an SycHYopH chaperoneeffector complex

    SciTech Connect (OSTI)

    Vujanac, Milos; Stebbins, C. Erec, E-mail: stebbins@rockefeller.edu [The Rockefeller University, New York, NY 10065 (United States)

    2013-04-01

    The structure of a SycHYopH chaperoneeffector complex from Yersinia reveals the bacterial state of a protein that adopts different folds in the host and pathogen environments. Yersinia pestis injects numerous bacterial proteins into host cells through an organic nanomachine called the type 3 secretion system. One such substrate is the tyrosine phosphatase YopH, which requires an interaction with a cognate chaperone in order to be effectively injected. Here, the first crystal structure of a SycHYopH complex is reported, determined to 1.9 resolution. The structure reveals the presence of (i) a nonglobular polypeptide in YopH, (ii) a so-called ?-motif in YopH and (iii) a conserved hydrophobic patch in SycH that recognizes the ?-motif. Biochemical studies establish that the ?-motif is critical to the stability of this complex. Finally, since previous work has shown that the N-terminal portion of YopH adopts a globular fold that is functional in the host cell, aspects of how this polypeptide adopts radically different folds in the host and in the bacterial environments are analysed.

  6. Investigation of the reaction {sup 208}Pb({sup 18}O, f): Folding angular distributions of fission fragments and gamma-ray multiplicity

    SciTech Connect (OSTI)

    Rusanov, A. Ya. Itkis, M. G.; Kondratiev, N. A.; Pokrovsky, I. V.; Salamatin, V. S.; Chubarian, G. G.

    2007-10-15

    Correlations between folding angular distributions of fission fragments and the gamma-ray multiplicity are studied for {sup 18}O + {sup 208}Pb interactions at energies of the beam of {sup 18}O ions in the range E{sub lab} = 78-198.5 MeV. The probabilities are determined for complete-and incomplete-fusion processes inevitably followed by the fission of nuclei formed in these processes. It is found that the probability of incomplete fusion followed by fission increases with increasing energy of bombarding ions. It is shown that, for the incomplete-fusion process, folding angular distributions of fission fragments have a two-component structure. The width of folding angular distributions (FWHM) for complete fusion grows linearly with increasing energy of {sup 18}O ions. The multiplicity of gamma rays from fission fragments as a function of the linear-momentum transfer behaves differently for different energies of projectile ions. This circumstance is explained here by the distinction between the average angular momenta of participant nuclei in the fusion and fission channels, which is due to the difference in the probabilities of fission in the cases where different numbers of nucleons are captured by the target nucleus.

  7. Geometry and evolution of the frontal part of the Magallanes foreland thrust and fold belt (Vicuna Area), Tierra del Fuego, southern Chile

    SciTech Connect (OSTI)

    Alvarez-Marron, J.; McClay, K.R. ); Harambour, S.; Rojas, L.; Skarmeta, J. )

    1993-11-01

    The Magallanes foreland thrust and fold belt is a thin-skinned foreland thrust and fold belt of Paleocene to Oligocene age that deforms Upper Jurassic through Tertiary volcanic, volcaniclastic, and siliciclastic strata of the Magallanes basin, southern Andean Cordillera, Chile. This paper is a detailed description and analysis of the geology and structural evolution of the thrust front (Vicuna area of southern Tierra del Fuego). Reflection seismic and well data, together with 1:50,000 scale geological mapping, have been used in the analysis. In the southern part of the Vicuna area, two different thrust systems have been found: an upper imbricate fan that deforms Upper Jurassic and Cretaceous strata, and a younger, lower duplex composed of Cretaceous and probably Upper Jurassic rocks. The imbricate fan is characterized by fault-propagation folding in which listric thrust faults merge downward into a sole thrust that probably is located within the Upper Jurassic stratigraphy. The sole thrust of the upper imbricates forms the roof thrust of the underlying duplex. In the northern part of the Vicuna area, the syntectonic sedimentary wedge of the foredeep consists of Late Cretaceous through Tertiary siliciclastics that have been deformed and uplifted by passive back thrusting at the triangle zone. The structural style in the foreland region shows three main subhorizontal detachment levels located within the sedimentary wedge as a result of the progressive transfer of slip from the thrust belt to the foreland. Minor blind thrusts produce stacked [open quotes]pop up[close quotes] and triangle structures that result in complex geometries in the cores of anticlines. A forward-breaking sequence of thrusting is interpreted. During deformation, the active foredeep wedge migrated at least 10 km northward. Balanced geological cross sections indicate approximately 60% (-30 km) shortening for this part of the Magallanes thrust belt.

  8. A two-fold interpenetrating 3D metal-organic framework material constructed from helical chains linked via 4,4'-H{sub 2}bpz fragments

    SciTech Connect (OSTI)

    Xie Yiming; Zhao Zhenguo; Wu Xiaoyuan; Zhang Qisheng; Chen Lijuan; Wang Fei; Chen Shanci; Lu Canzhong

    2008-12-15

    A 3-connected dia-f-type metal-organic framework compound {l_brace}[Ag(L){sub 3/2}H{sub 2}PO{sub 4}]{r_brace}{sub n} (1) has been synthesized by self-assembly of 4,4'-H{sub 2}bpz (L=4,4'-H{sub 2}bpz=3,3',5,5'-tetramethyl-4,4'-bipyrazole) and Ag{sub 4}P{sub 2}O{sub 7} under hydrothermal conditions. It crystallizes in the tetragonal space group I4{sub 1}/acd with a=21.406(4) A, b=21.406(4) A, c=36.298(8) A, Z=32. X-ray single-crystal diffraction reveals that 1 has a three-dimensional framework with an unprecedented alternate left- and right-handed helices structure, featuring a non-uniform two-fold interpenetrated (4.14{sup 2}) net. Photoluminescent investigation reveals that the title compound displays interesting emissions in a wide region, which shows that the title compound may be a good potential candidate as a photoelectric material. - Graphical abstract: A 3-connected dia-f-type metal-organic framework compound [Ag(4,4'-bpz){sub 3/2}H{sub 2}PO{sub 4}] shows unprecedented alternating left- and right-handed helices structure, featuring a non-uniform two-fold interpenetrated (4.14{sup 2}) net.

  9. Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

    SciTech Connect (OSTI)

    Oshima, Hiraku; Kinoshita, Masahiro

    2015-04-14

    In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model water, were employed in theoretical methods wherein the entropic effect was treated as an essential factor. However, there were similarities and differences in the results obtained from the two solvent models. In the present work, to unveil the physical origins of the similarities and differences, we simultaneously consider structural transition, cold denaturation, and pressure denaturation for the same protein by employing the two solvent models and considering three different thermodynamic states for each solvent model. The solvent-entropy change upon protein folding/unfolding is decomposed into the protein-solvent pair (PA) and many-body (MB) correlation components using the integral equation theories. Each component is further decomposed into the excluded-volume (EV) and solvent-accessible surface (SAS) terms by applying the morphometric approach. The four physically insightful constituents, (PA, EV), (PA, SAS), (MB, EV), and (MB, SAS), are thus obtained. Moreover, (MB, SAS) is discussed by dividing it into two factors. This all-inclusive investigation leads to the following results: (1) the protein-water many-body correlation always plays critical roles in a variety of folding/unfolding processes; (2) the hard-sphere solvent model fails when it does not correctly reproduce the protein-water many-body correlation; (3) the hard-sphere solvent model becomes problematic when the dependence of the many-body correlation on the solvent number density and temperature is essential: it is not quite suited to studies on cold and pressure denaturating of a protein; (4) when the temperature and solvent number density are limited to the ambient values, the hard-sphere solvent model is usually successful; and (5) even at the ambient values, however, the many-body correlation plays significant roles in the β-sheet formation and argument of relative stabilities of very similar structures of a protein. These results are argued in detail with respect to the four physically insightful constituents and the two factors mentioned above. The relevance to the absence or presence of hydrogen-bonding properties in the solvent is also discussed in detail.

  10. Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability

    SciTech Connect (OSTI)

    Lu, Jun; Wu, Ruiying; Adkins, Joshua N.; Joachimiak, Andrzej; Glover, Mark

    2014-09-16

    In the F-family of conjugative plasmids, TraJ is an essential transcriptional activator of the tra operon that encodes most of the proteins required for conjugation. Here we report for the first time the X-ray crystal structures of the TraJ N-terminal regions from the prototypic F plasmid (TraJF11-130) and from the Salmonella virulence plasmid pSLT (TraJpSLT 1-128). Both proteins form similar homodimeric Per-ARNT-Sim (PAS) fold structures. Mutational analysis reveals that the observed dimeric interface is critical for TraJF transcriptional activation, indicating that dimerization of TraJ is required for its in vivo function. An artificial ligand (oxidized dithiothreitol) occupies a cavity in the TraJF dimer interface, while a smaller cavity in corresponding region of the TraJpSLT structure lacks a ligand. Gas chromatography/mass spectrometry-electron ionization analysis of dithiothreitol-free TraJF suggests indole may be the natural TraJ ligand; however, disruption of the indole biosynthetic pathway does not affect TraJF function. Heterologous PAS domains from pSLT and R100 TraJ can functionally replace the TraJF PAS domain, suggesting that TraJ allelic specificity is mediated by the region C-terminal to the PAS domain.

  11. Exploration of multi-fold symmetry element-loaded superconducting radio frequency structure for reliable acceleration of low- & medium-beta ion species

    SciTech Connect (OSTI)

    Huang, Shichun; Geng, Rongli

    2015-09-01

    Reliable acceleration of low- to medium-beta proton or heavy ion species is needed for future high current superconducting radio frequency (SRF) accelerators. Due to the high-Q nature of an SRF resonator, it is sensitive to many factors such as electron loading (from either the accelerated beam or from parasitic field emitted electrons), mechanical vibration, and liquid helium bath pressure fluctuation etc. To increase the stability against those factors, a mechanically strong and stable RF structure is desirable. Guided by this consideration, multi-fold symmetry element-loaded SRF structures (MFSEL), cylindrical tanks with multiple (n>=3) rod-shaped radial elements, are being explored. The top goal of its optimization is to improve mechanical stability. A natural consequence of this structure is a lowered ratio of the peak surface electromagnetic field to the acceleration gradient as compared to the traditional spoke cavity. A disadvantage of this new structure is an increased size for a fixed resonant frequency and optimal beta. This paper describes the optimization of the electro-magnetic (EM) design and preliminary mechanical analysis for such structures.

  12. Exploiting parameter space in MOFs: a 20-fold enhancement of phosphate-ester hydrolysis with UiO-66-NH 2

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

    Katz, Michael J.; Moon, Su-Young; Mondloch, Joseph E.; Beyzavi, M. Hassan; Stephenson, Casey J.; Hupp, Joseph T.; Farha, Omar K.

    2015-02-24

    The hydrolysis of nerve agents is of primary concern due to the severe toxicity of these agents. Using a MOF-based catalyst (UiO-66), we have previously demonstrated that the hydrolysis can occur with relatively fast half-lives of 50 minutes. However, these rates are still prohibitively slow to be efficiently utilized for some practical applications (e.g., decontamination wipes used to clean exposed clothing/skin/vehicles). We thus turned our attention to derivatives of UiO-66 in order to probe the importance of functional groups on the hydrolysis rate. Three UiO-66 derivatives were explored; UiO-66-NO2 and UiO-66-(OH)2 showed little to no change in hydrolysis rate. However,more » UiO-66-NH2 showed a 20 fold increase in hydrolysis rate over the parent UiO-66 MOF. Half-lives of 1 minute were observed with this MOF. In order to probe the role of the amino moiety, we turned our attention to UiO-67, UiO-67-NMe2 and UiO-67-NH2. In these MOFs, the amino moiety is in close proximity to the zirconium node. We observed that UiO-67-NH2 is a faster catalyst than UiO-67 and UiO-67-NMe2. We conclude that the role of the amino moiety is to act as a proton-transfer agent during the catalytic cycle and not to hydrogen bond or to form a phosphorane intermediate.« less

  13. About the Deputy Director: Short Scientific Biography

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

    Lab Deputy Director Horst Simon Horst Simon is an internationally recognized expert in computer science and applied mathematics and the Deputy Director of Lawrence Berkeley...

  14. UFO (UnFold Operator) user guide

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F. ); Marking, T.R. )

    1991-06-01

    UFO is a collection of interactive utility programs for estimating unknown functions of one variable using a wide-ranging class of information as input, for miscellaneous data-analysis applications, for performing feasibility studies, and for supplementing our other software. Inverse problems, which include spectral unfolds, inverse heat-transfer problems, time-domain deconvolution, and unusual or difficult curve-fit problems, are classes of applications for which UFO is well suited. Extensive use of B-splines and (X,Y)-datasets is made to represent functions. The (X,Y)-dataset representation is unique in that it is not restricted to equally-spaced data. This feature is used, for example, in a table-generating algorithm that evaluates a function to a user-specified interpolation accuracy while minimizing the number of points stored in the corresponding dataset. UFO offers a variety of miscellaneous data-analysis options such as plotting, comparing, transforming, scaling, integrating; and adding, subtracting, multiplying, and dividing functions together. These options are often needed as intermediate steps in analyzing and solving difficult inverse problems, but they also find frequent use in other applications. Statistical options are available to calculate goodness-of-fit to measurements, specify error bands on solutions, give confidence limits on calculated quantities, and to point out the statistical consequences of operations such as smoothing. UFO is designed to do feasibility studies on a variety of engineering measurements. It is also tailored to supplement our Test Analysis and Design codes, SRAD Test-Data Archive software, and Digital Signal Analysis routines.

  15. Geology of the lower Yellow Creek Area, Northwestern Colorado

    SciTech Connect (OSTI)

    Hail, W.J.

    1990-01-01

    The lower Yellow Creek area is located in Rio Blanco and Moffat Counties of northwestern Colorado, about midway between the towns of Rangely and Meeker. The study area is in the northwestern part of the Piceance Creek basin, a very deep structural and sedimentary basin that formed during the Laramide orogeny. Potentially important resources in the area are oil shale and related minerals, oil and gas, coal, and uranium. Topics discussed in the report include: Stratigraphy (Subsurface rocks, Cretaceous rocks, Tertiary rocks, and Quaternary deposits); Structure (Midland anticline, graben at Pinyon Ridge, and Crooked Wash syncline, Folds and faults in the vicinity of the White River, Red Wash syncline and central graben zone, Yellow Creek anticlinal nose); Economic geology (Oil shale and associated minerals, Coal, Oil and gas, Uranium, Gravel).

  16. New Crystal Structures Lift Fog around Protein Folding

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

    genetic code embodied by the nucleotide sequences in DNA and collected in the form of genes is well known. Biological macromolecules like proteins comprise strings of amino acids...

  17. UFO (UnFold Operator) default data format

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F. ); Marking, T.R. )

    1991-05-01

    The default format for the storage of x,y data for use with the UFO code is described. The format assumes that the data stored in a file is a matrix of values; two columns of this matrix are selected to define a function of the form y = f(x). This format is specifically designed to allow for easy importation of data obtained from other sources, or easy entry of data using a text editor, with a minimum of reformatting. This format is flexible and extensible through the use of inline directives stored in the optional header of the file. A special extension of the format implements encoded data which significantly reduces the storage required as compared wth the unencoded form. UFO supports several extensions to the file specification that implement execute-time operations, such as, transformation of the x and/or y values, selection of specific columns of the matrix for association with the x and y values, input of data directly from other formats (e.g., DAMP and PFF), and a simple type of library-structured file format. Several examples of the use of the format are given.

  18. New Crystal Structures Lift Fog around Protein Folding

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

    incorrect or "misfolding" of proteins has been linked to many diseases, including Alzheimer's, Parkinson's, and some forms of cancer. So far, however, a complete...

  19. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING...

    Office of Scientific and Technical Information (OSTI)

    ; Baumgartel, P ; Lengefeld, J ; Horsley, D ; Schuler, B ; Bakajin, O Publication Date: 2006-03-20 OSTI Identifier: 928522 Report Number(s): UCRL-PROC-220084 TRN: US0803280 DOE...

  20. Heavy metal ions are potent inhibitors of protein folding

    SciTech Connect (OSTI)

    Sharma, Sandeep K. [Biochemisches Institut, Universitaet Zuerich, CH-8057 Zuerich (Switzerland); Departement de Biologie Moleculaire Vegetale, Universite de Lausanne, CH-1015 Lausanne (Switzerland); Goloubinoff, Pierre [Departement de Biologie Moleculaire Vegetale, Universite de Lausanne, CH-1015 Lausanne (Switzerland); Christen, Philipp [Biochemisches Institut, Universitaet Zuerich, CH-8057 Zuerich (Switzerland)], E-mail: christen@bioc.uzh.ch

    2008-07-25

    Environmental and occupational exposure to heavy metals such as cadmium, mercury and lead results in severe health hazards including prenatal and developmental defects. The deleterious effects of heavy metal ions have hitherto been attributed to their interactions with specific, particularly susceptible native proteins. Here, we report an as yet undescribed mode of heavy metal toxicity. Cd{sup 2+}, Hg{sup 2+} and Pb{sup 2+} proved to inhibit very efficiently the spontaneous refolding of chemically denatured proteins by forming high-affinity multidentate complexes with thiol and other functional groups (IC{sub 50} in the nanomolar range). With similar efficacy, the heavy metal ions inhibited the chaperone-assisted refolding of chemically denatured and heat-denatured proteins. Thus, the toxic effects of heavy metal ions may result as well from their interaction with the more readily accessible functional groups of proteins in nascent and other non-native form. The toxic scope of heavy metals seems to be substantially larger than assumed so far.

  1. Simplified Protein Models: Predicting Folding Pathways and Structure...

    Office of Scientific and Technical Information (OSTI)

    None USDOE United States 2013-07-01 English Journal Article Journal Name: Physical Review Letters; Journal Volume: 111; Journal Issue: 2 Medium: X OSTI ID: 1103786, Legacy ID:...

  2. Method of identifying hairpin DNA probes by partial fold analysis

    DOE Patents [OSTI]

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2008-10-28

    Methods of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  3. Method of identifying hairpin DNA probes by partial fold analysis

    DOE Patents [OSTI]

    Miller, Benjamin L. (Penfield, NY); Strohsahl, Christopher M. (Saugerties, NY)

    2009-10-06

    Method of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  4. Tank 19F Folding Crawler Final Evaluation, Rev. 0

    SciTech Connect (OSTI)

    Nance, T.

    2000-10-25

    The Department of Energy (DOE) is committed to removing millions of gallons of high-level radioactive waste from 51 underground waste storage tanks at the Savannah River Site (SRS). The primary radioactive waste constituents are strontium, plutonium,and cesium. It is recognized that the continued storage of this waste is a risk to the public, workers, and the environment. SRS was the first site in the DOE complex to have emptied and operationally closed a high-level radioactive waste tank. The task of emptying and closing the rest of the tanks will be completed by FY28.

  5. DOE Science Showcase - Protein Folding | OSTI, US Dept of Energy...

    Office of Scientific and Technical Information (OSTI)

    are believed to cause some neurodegenerative diseases such as alzheimer's disease, cystic fibrosis, amyotrophic lateral sclerosis, huntington's and parkinson's diseases and cancer. ...

  6. VERIFI code optimization yields three-fold increase in engine...

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

    Greg Cunningham at (630) 252-8232 or media@anl.gov. Connect Find an Argonne expert by subject. Follow Argonne on Twitter, Facebook, Google+ and LinkedIn. For inquiries on...

  7. Brochure (8 1/2 x 11, landscape, 2-fold)

    National Nuclear Security Administration (NNSA)

    kind found. You should also determine whether any administrative or disciplinary action needs to be taken against the individuals who created HWE/ harassment. In doing so, you should consult the Department's Table of Penalties, your EEO Manager or OHCM EMRB. What if the inquiry indicates that there is no harassment or hostile work environment. Do I still need to do anything? You should reaffirm your commitment to nondiscrimination and harassment in the workplace with your employees. You should

  8. Simplified Protein Models: Predicting Folding Pathways and Structure...

    Office of Scientific and Technical Information (OSTI)

    Publisher: American Physical Society Sponsoring Org: USDOE Country of Publication: United States Language: English Word Cloud More Like This Free Publicly Accessible Full Text ...

  9. Folding and association of a homotetrameric protein complex in...

    Office of Scientific and Technical Information (OSTI)

    Publisher: American Physical Society Sponsoring Org: USDOE Country of Publication: United States Language: English Word Cloud More Like This Free Publicly Accessible Full Text ...

  10. New Crystal Structures Lift Fog around Protein Folding

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

    lid. A Molecular Origami Machine The genetic code embodied by the nucleotide sequences in DNA and collected in the form of genes is well known. Biological macromolecules like...

  11. Brochure (8 1/2 x 11, landscape, 2-fold)

    National Nuclear Security Administration (NNSA)

    of Civil Rights, NA-1.2 PO Box 5400 Albuquerque, NM 87185 Phone: (505) 845-5517 Toll Free: (800) 825-5256 (enter 845-5517 at voice prompt) TTY: (866) 872-1011 Fax: (505)...

  12. Rift Zone | Open Energy Information

    Open Energy Info (EERE)

    - increased volcanic activity and the formation of graben structures (reference: science-art.com) Rift valleys occur at divergent plate boundaries, resulting in large graben...

  13. Deputy-Director

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

    Deputy-Director Director Deputy Director Leadership Team Advisory Board Directorate Staff Org Chart ⇒ Navigate Section Director Deputy Director Leadership Team Advisory Board Directorate Staff Org Chart Berkeley Lab Deputy Director Horst Simon horst-simon Horst Simon is an internationally recognized expert in computer science and applied mathematics and the Deputy Director of Lawrence Berkeley National Laboratory (Berkeley Lab). Simon joined Berkeley Lab in early 1996 as director of the newly

  14. Notes and Action Items

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

    Rick Kendall, Tom Kitchens, Horst Simon SubCommittee on Visualization and Graphics Software Responsibility: JN Leboeuf, Judy Giarrusso, Steve Jardin, and Steve Lau Actions:...

  15. NREL: Sustainable NREL - Media Contacts for the Research Support...

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

    viable. With this building, DOE leads by example and hopes to spur innovation and replication throughout government and the commercial building sector. John Horst U.S....

  16. Berkeley Lab Joins DOE's New HPC4Manufacturing Program

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

    At the 2015 ACME summit: From left, Horst Simon (LBNL), Trish Damkroger (LLNL), John Turner (ORNL), Peg Folta (LLNL), David Skinner (LBNL), Dona Crawford (LLNL), Jeff Roberts...

  17. Presentations

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

    Horst Simon | Scheduled for Monday, November 18, 2002 at the Marriot Inner Harbor Hotel West Ballroom, in Baltimore, Maryland. The meeting will coincide with SC2002, the...

  18. Structure of Mesita del Buey at TA-54, Los Alamos National Laboratory, New Mexico

    SciTech Connect (OSTI)

    Reneau, S.L.; Broxton, D.E.; Carney, J.S.; LaDelfe, C.

    1998-04-23

    The geological structure of Mesita del Buey at Technical Area 54 (TA-54) was examined using precise surveying of the contact between units 1v and 2 of the Tshirege Member of the Bandelier Tuff at 3.5 km along the north wall of Pajarito Canyon and 0.6 km along the north wall of a tributary to Canada del Buey. Estimated structure contours on this contact indicate typical strikes of N40E to N70E along this part of Mesita del Buey, although the apparent strike of the tuff is E-W at the western part of the survey. Typical dips are 1.0{degree} to 2.0{degree} to the east or southeast, with an estimated maximum dip of 3.2{degree} near the west end of Material Disposal Area G. Thirty seven faults with vertical displacements of 5 to 65 cm were observed in outcrop along the Pajarito Canyon traverse, and, due to the incomplete exposure of the unit 1v-unit 2 contact, many more faults of this magnitude undoubtedly exist. The faults have a wide range in strike and have either down-to-the-west and down-to-the-east components of offset, although about 65% of the observed displacement is down-to-the-west or northwest. These faults are not clearly associated with major fault zones, indicated by the general absence of larger-scale offsets or inflections along the unit 1v-unit 2 contact in areas where the small-scale faults were observed; they may instead record distributed secondary deformation across the Pajarito Plateau associated with large earthquakes on the main Pajarito fault zone 8--11 km to the west, or perhaps other faults in the region. The survey data also suggest that a 150--250 m wide zone of greater magnitude faulting is present near the west end of the traverse associated with a horst-and-graben structure displaying about 1.5--3.5 m of offset on individual faults, although the total amount of offset across this structure and its orientation are not known.

  19. How to Achieve a Four-Fold Productivity Increase at Fenton Hill...

    Open Energy Info (EERE)

    rate of 340 gpm and at a production temperature of 204C (400F). Author Donald W. Brown Conference GRC Annual Meeting; Salt Lake City, Utah; 19941002 Published Geothermal...

  20. Analyses of Candida Cdc13 Orthologues Revealed a Novel OB Fold...

    Office of Scientific and Technical Information (OSTI)

    OSTI Identifier: 1186936 Resource Type: Journal Article Resource Relation: Journal Name: Molecular and Cellular Biology; Journal Volume: 32; Journal Issue: (1) ; 01, 2012 Research ...

  1. New N-Acetyltransferase Fold in the Structure and Mechanism of...

    Office of Scientific and Technical Information (OSTI)

    FrbF The enzyme FrbF from Streptomyces rubellomurinus has attracted significant attention due to its role in the biosynthesis of the antimalarial phosphonate FR-900098. The ...

  2. Protein folding of the H0P model: A parallel Wang-Landau study

    SciTech Connect (OSTI)

    Shi, Guangjie; Wuest, Thomas; Li, Ying Wai; Landau, David P

    2015-01-01

    We propose a simple modication to the hydrophobic-polar (HP) protein model, by introducing a new type of monomer, "0", with intermediate hydrophobicity of some amino acids between H and P. With the replica-exchange Wang-Landau sampling method, we investigate some widely studied HP sequences as well as their H0P counterparts and observe that the H0P sequences exhibit dramatically reduced ground state degeneracy and more signicant transition signals at low temperature for some thermodynamic properties, such as the specific heat.

  3. Kinks, loops, and protein folding, with protein A as an example

    SciTech Connect (OSTI)

    Krokhotin, Andrey, E-mail: Andrei.Krokhotine@cern.ch [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden)] [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Liwo, Adam, E-mail: adam@chem.univ.gda.pl [Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk (Poland)] [Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk (Poland); Maisuradze, Gia G., E-mail: gm56@cornell.edu; Scheraga, Harold A., E-mail: has5@cornell.edu [Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301 (United States); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fdration Denis Poisson, Universit de Tours, Parc de Grandmont, F37200 Tours, France and Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

    2014-01-14

    The dynamics and energetics of formation of loops in the 46-residue N-terminal fragment of the B-domain of staphylococcal protein A has been studied. Numerical simulations have been performed using coarse-grained molecular dynamics with the united-residue (UNRES) force field. The results have been analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrdinger (DNLS) equation. In the case of proteins, the DNLS equation arises from a C{sup ?}-trace-based energy function. Three individual kink profiles were identified in the experimental three-?-helix structure of protein A, in the range of the Glu16-Asn29, Leu20-Asn29, and Gln33-Asn44 residues, respectively; these correspond to two loops in the native structure. UNRES simulations were started from the full right-handed ?-helix to obtain a clear picture of kink formation, which would otherwise be blurred by helix formation. All three kinks emerged during coarse-grained simulations. It was found that the formation of each is accompanied by a local free energy increase; this is expressed as the change of UNRES energy which has the physical sense of the potential of mean force of a polypeptide chain. The increase is about 7 kcal/mol. This value can thus be considered as the free energy barrier to kink formation in full ?-helical segments of polypeptide chains. During the simulations, the kinks emerge, disappear, propagate, and annihilate each other many times. It was found that the formation of a kink is initiated by an abrupt change in the orientation of a pair of consecutive side chains in the loop region. This resembles the formation of a Bloch wall along a spin chain, where the C{sup ?} backbone corresponds to the chain, and the amino acid side chains are interpreted as the spin variables. This observation suggests that nearest-neighbor side chainside chain interactions are responsible for initiation of loop formation. It was also found that the individual kinks are reflected as clear peaks in the principal modes of the analyzed trajectory of protein A, the shapes of which resemble the directional derivatives of the kinks along the chain. These observations suggest that the kinks of the DNLS equation determine the functionally important motions of proteins.

  4. VERIFI code optimization yields three-fold increase in engine simulation

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

    speed | Argonne National Laboratory Using high-performance computer-generated models, VERIFI researchers demonstrated that in gasoline compression ignition, varying the start of injection (SOI) timing produces significant differences in the reactivity of the the fuel mixture, delaying ignition. Such high-resolution modeling was made possible by optimizing the CONVERGE for parallel read/write processes. (Click image to view larger.) Using high-performance computer-generated models, VERIFI

  5. Discovering The Folding Rules That Proteins Obey FY08 LDRD Final...

    Office of Scientific and Technical Information (OSTI)

    Bakajin, O Publication Date: 2009-02-26 OSTI Identifier: 1126773 Report Number(s): LLNL-TR-410921 DOE Contract Number: W-7405-ENG-48 Resource Type: Technical Report Research Org:...

  6. Tri-fold- Agencies Assisting with EEOICPA and the Former worker Program

    Broader source: Energy.gov [DOE]

    Agencies Assisting with EEOICPA and the Former Worker Program The Joint Outreach Task Group (JOTG) includes representatives from DOE, Department of Labor (DOL), the National Institute for Occupational Safety and Health (NIOSH), the Offices of the Ombudsman for DOL and NIOSH, and the DOE-funded FWP projects. The JOTG was established in 2009 under the premise that agencies/programs with common goals can work together by combining resources and coordinating outreach efforts. Each involved agency has a different mission, but the missions are complementary. By working together, the agencies are better able to serve the DOE workforce. The JOTG focuses on educating the former workers on the programs and resources available to them.

  7. New structural limits on magma chamber locations at the Valley of Ten Thousand Smokes, Katmai National Park, Alaska

    SciTech Connect (OSTI)

    Wallmann, P.C.; Pollard, D.D. ); Hildreth, W. ); Eichelberger, J.C. )

    1990-12-01

    New structural data from the Novarupta basin, Katmai National Park, Alaska, site of the largest volcanic eruption of this century (1912), provide limits for the location of magma chambers associated with this eruption. To investigate the subsurface structure of the 1912 vents, and to support an interdisciplinary study of this young volcanic system, a project of geologic mapping of surficial and bedrock structures in the vent region of the 1912 eruption has been undertaken. Landslide scarps, arcuate grabens, a monoclinal fold, and truncated ridges circumscribe the Novarupta basin, marking the inferred outer rim of the vent. A set of radial fissures crosses the southern margin of the basin, striking {approximately}140{degree}, subparallel to the dominant bedrock joint set. These fissures and joints, along with the local plate-motion vector and the inferred regional stress orientation, are consistent with a feeder dike propagating from a reservoir beneath Trident volcano to the eruptive vent.

  8. Berkeley Lab Transportation and Parking Demand Management Committee

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

    510-486-6647 JMDahlgard@lbl.gov Mat Vail Facilities 510-495-2849 MEVail@lbl.gov Doug Goodman OCFO 510-486-7632 DGoodman@lbl.gov Blair Horst Facilities 510-486-4902...

  9. NUG 2003

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

    9:15 Opening Remarks Horst Simon 9:30 Performance Evaluation Activites at NERSC Adrian Wong 10:00 Seaborg Code Scalability Project Richard Gerber 10:30 Green's function Monte...

  10. Distribution of Quaternary Rhyolite Dome of the Coso Range California...

    Open Energy Info (EERE)

    rhyolite of similar major element chemical composition were erupted over the past 1 m.y. from vents arranged in a crudely S-shaped array atop a granitic horst in the Coso...

  11. Distribution of quaternary rhyolite dome of the Coso Range, California...

    Open Energy Info (EERE)

    rhyolite of similar major element chemical composition were erupted over the past 1 m.y. from vents arranged in a crudely S-shaped array atop a granitic horst in the Coso...

  12. Attendee List

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

    OSF Sep 17 Yes Richard Saykally Department of Chemistry, UC Berkeley OSF Sep 17-20 No John Shalf LBNL OSF Sep 17 No Horst Simon LBNL OSF Sep 17 Yes David Skinner LBLNERSC OSF...

  13. NREL'S Carlisle Earns Solar Service Award

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

    Carlisle Earns Solar Service Award Media may contact: John Horst, 303-275-4709 email: John Horst Golden, Colo., July 27, 2000 - Nancy Carlisle recently received the American Solar Energy Society's (ASES) prestigious Rebecca Vories Award, named after the solar energy pioneer who dedicated her personal and professional life to promoting solar energy applications. The award recognizes those who have helped the society meet its mission. Carlisle is a senior project leader for solar energy and

  14. Microsoft Word - Document1

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

    of NERSC Address Horst Simon Director, NERSC Division Bill Kramer Director, High Performance Computing Department NERSC Accomplishments in 1996 Horst Simon - 1/28/97 http://www.nersc.gov/research/whitepaper/whitepaper.html NERSC Mission Statement Provide reliable, high quality, state of the art computing resources and client support in a timely manner-- independent of client location--while wisely advancing the state of computational and computer science. Major Milestones Feb 96 Four NERSC

  15. Germencik Geothermal Area | Open Energy Information

    Open Energy Info (EERE)

    graben, Turkey. Geothermics. 32(1):669-678. Benjamin Matek. Geo-energy Internet. Geothermal Energy Association. updated 20150428;cited 20150428. Available from:...

  16. Gumuskoy Geothermal Area | Open Energy Information

    Open Energy Info (EERE)

    graben, Turkey. Geothermics. 32(1):669-678. Benjamin Matek. Geo-energy Internet. Geothermal Energy Association. updated 20150428;cited 20150428. Available from:...

  17. Hydrogeological And Isotopic Survey Of Geothermal Fields In The...

    Open Energy Info (EERE)

    Hydrogeological And Isotopic Survey Of Geothermal Fields In The Buyuk Menderes Graben, Turkey Jump to: navigation, search OpenEI Reference LibraryAdd to library Journal Article:...

  18. Integrated Geophysical Exploration of a Known Geothermal Resource...

    Open Energy Info (EERE)

    a half-graben basin. This basin-bounding fault serves as the primary conduit for deep water circulation. Potential field, electrical, and seismic data characterize this major...

  19. Stratigraphic Record Of The Yellowstone Hotspot Track, Neogene...

    Open Energy Info (EERE)

    grabens diverted the Middle Miocene drainage patterns in southwest Montana. Authors James W. Sears, Marc S. Hendrix, Robert C. Thomas and William J. Fritz Published Journal...

  20. File:GM-79 A-Aprime.pdf | Open Energy Information

    Open Energy Info (EERE)

    section through the Valles Caldera. The section transects the Valles and Toledo ring fracture zones, the Redondo Creek Graben, and the Sulphur Springs hydrothermal system at core...

  1. Agenda

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

    Agenda Agenda Energy Research Scientific Computing Users Group (ERSUG) Schedule April 6, 1998 Monday April 6, 1998 Berkeley Lab - Perseverance Hall Time Scheduled Event Speaker / Session Leader 08:00 Continental Breakfast 08:30 Welcome Ricky Kendall 08:35 View From Washington Tom Kitchens 08:55 New NERSC Staff Introductions Horst Simon 09:00 NERSC Research Efforts (Leverage to the NERSC Program) Horst Simon 09:30 Strategic Computing Initiative Bill McCurdy 10:00 ERCAP Changes Tom Kitchens 10:20

  2. Running Greener: E-Mobility at SAP

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

    Running Greener: E-Mobility at SAP 5.000 Electric Vehicles in 2020 Ashok R, Horst Terhalle, Marcus Wagner November 14th 2014 © 2014 SAP SE or an SAP affiliate company. All rights reserved. 2 Public Running Greener: E-Mobility at SAP AGENDA Why is e-Mobility important Marcus Wagner Our strategy "20% e-cars by 2020" Marcus Wagner Regional highlights Ashok R. E-Mobility Service Provider Solution Horst Terhalle FAQ all © 2014 SAP SE or an SAP affiliate company. All rights reserved. 3

  3. INNOVATIVE METHODOLOGY FOR DETECTION OF FRACTURE-CONTROLLED SWEET SPOTS IN THE NORTHERN APPALACHIAN BASIN

    SciTech Connect (OSTI)

    Robert Jacobi; John Fountain

    2001-06-30

    In the structure task, the authors completed reducing the data they had collected from a N-S transect on the east side of Seneca Lake. They have calculated the fracture frequency for all the fracture sets at each site, and constructed modified rose diagrams that summarize the fracture attributes at each site. These data indicate a N-striking fault near the southeastern shore of Seneca Lake, and also indicate NE and ENE-trending FIDs and faults north of Valois. The orientation and existence of the ENE-striking FIDs and faults are thought to be guided by faults in the Precambrian basement. These basement faults apparently were sufficiently reactivated to cause faulting in the Paleozoic section. Other faults are thrust ramps above the Silurian salt section that were controlled by a far-field Alleghanian stress field. Structure contour maps and isopach maps have been revised based on additional well log analyses. Except for the Glodes Corners Field, the well spacing generally is insufficient to definitely identify faults. However, relatively sharp elevational changes east of Keuka Lake support the contention that faults occur along the east side of Keuka Lake. Outcrop stratigraphy along the east side of Seneca Lake indicates that faults and gentle folds can be inferred from some exposures along Seneca Lake, but the lensing nature of the individual sandstones can preclude long-distance definite correlations and structure identification. Soil gas data collected during the 2000 field season was reduced and displayed in the previous semiannual report. The seismic data that Quest licensed has been reprocessed. Several grabens observed in the Trenton reflector are consistent with surface structure, soil gas, and aeromagnetic anomalies. In this report they display an interpreted seismic line that crosses the Glodes Corners and Muck Farms fields. The final report from the subcontractor concerning the completed aeromagnetic survey is included. Prominent magnetic anomalies suggest that faults in the Precambrian basement are located beneath regions where grabens in the Trenton are located. The trend and location of these faults based on aeromagnetics agrees with the location based on FIDs. These data indicate that integration of aeromagnetic and topographic lineaments, surface structure, soil gas with seismic and well logs allows them to extrapolate Trenton-Black River trends away from confirmatory seismic lines.

  4. INNOVATIVE METHODOLOGY FOR DETECTION OF FRACTURE-CONTROLLED SWEET SPOTS IN THE NORTHERN APPALACHIAN BASIN

    SciTech Connect (OSTI)

    Robert Jacobi; John Fountain

    2002-01-30

    In the structure task, we completed reducing the data we had collected from a N-S transect on the east of Seneca Lake. We have calculated the fracture frequency for all the fracture sets at each site, and constructed modified rose diagrams that summarize the fracture attributes at each site. These data indicate a N-striking fault near the southeastern shore of Seneca Lake, and also indicate NE and ENE-trending FIDs and faults north of Valois. The orientation and existence of the ENE-striking FIDs and faults are thought to be guided by faults in the Precambrian basement; these basement faults apparently were sufficiently reactivated to cause faulting in the Paleozoic section. Other faults are thrust ramps above the Silurian salt section that were controlled by a far-field Alleghanian stress field. Structure contour maps and isopach maps have been revised based on additional well log analyses. Except for the Glodes Corners Field, the well spacing generally is insufficient to definitively identify faults. However, relatively sharp elevational changes east of Keuka Lake support the contention that faults occur along the east side of Keuka Lake. Outcrop stratigraphy along the east side of Seneca Lake indicates that faults and gentle folds can be inferred from the some exposures along Seneca Lake, but the lensing nature of the individual sandstones can preclude long-distance definitive correlations and structure identification. Soil gas data collected during the 2000 field season was reduced and displayed in the previous semiannual report. The seismic data that Quest licensed has been reprocessed. Several grabens observed in the Trenton reflector are consistent with surface structure, soil gas, and aeromagnetic anomalies. In this report we display an interpreted seismic line that crosses the Glodes Corners and Muck Farm fields. The final report from the subcontractor concerning the completed aeromagnetic survey is included. Prominent magnetic anomalies suggest that faults in the Precambrian basement are located beneath regions where grabens in the Trenton are located. The trend and location of these faults based on aeromagnetics agrees with the location based on FIDs. These data indicate that integration of aeromagnetic and topographic lineaments, surface structure, soil gas with seismic and well logs allows us to extrapolate Trenton-Black River trends away from confirmatory seismic lines.

  5. Attendee List

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

    Samtaney PPPL, Princeton University OSF Oct. 2-3 Yes Yukiko Sekine DOE OSF Oct. 2-3 No John Shalf NERSC OSF Oct. 2-3 No Horst Simon LBNL OSF Oct. 2-3 Yes David Skinner NERSC OSF...

  6. Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-Monophosphate

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

    Tian, Yuanyuan; Cui, Wenjun; Huang, Manna; Robinson, Howard; Wan, Yiqian; Wang, Yousheng; Ke, Hengming

    2014-08-05

    Cyclic nucleotide phosphodiesterases (PDEs) decompose second messengers cAMP and cGMP that play critical roles in many physiological processes. PDE1 of Saccharomyces cerevisiae has been subcloned and expressed in Escherichia coli. Recombinant yPDE1 has a KM of 110 μM and a kcat of 16.9 s⁻¹ for cAMP and a KM of 105 μM and a kcat of 11.8 s₅⁻¹ for cGMP. Thus, the specificity constant (kcat/KMcAMP)/(kcat/KMcGMP) of 1.4 indicates a dual specificity of yPDE1 for hydrolysis of both cAMP and cGMP. The crystal structures of unliganded yPDE1 and its complex with GMP at 1.31 Å resolution reveal a new structural foldingmore » that is different from those of human PDEs but is partially similar to that of some other metalloenzymes such as metallo-β-lactamase. In spite of their different structures and divalent metals, yPDE1 and human PDEs may share a common mechanism for hydrolysis of cAMP and cGMP.« less

  7. CX-012265: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles… CX(s) Applied: B3.1 Date: 06/26/2014 Location(s): California, California, California Offices(s): National Energy Technology Laboratory

  8. CX-010451: Categorical Exclusion Determination

    Office of Energy Efficiency and Renewable Energy (EERE)

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles CX(s) Applied: B3.16 Date: 06/17/2013 Location(s): California Offices(s): National Energy Technology Laboratory

  9. CX-012266: Categorical Exclusion Determination

    Office of Energy Efficiency and Renewable Energy (EERE)

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles CX(s) Applied: A9 Date: 06/26/2014 Location(s): California Offices(s): National Energy Technology Laboratory

  10. Southern Basin and Range Geothermal Region | Open Energy Information

    Open Energy Info (EERE)

    faults form the western edge of the Sierra Madre Occidental plateau in northeastern Sonora. These faults and associated half-grabens extend over a distance of more than 300 km...

  11. Regional Gravity Survey of the Northern Great Salt Lake Desert...

    Open Energy Info (EERE)

    of about -196 mgal over the alluvium-covered graben areas. The gravity high over the Raft River Mountains apparently corresponds with the Raft River Mountains anticline. A belt...

  12. NERSC Celebrates 40 Years at the Forefront

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

    NERSC Celebrates 40 Years of Supercomputing NERSC Celebrates 40 Years at the Forefront DOE supercomputing facility has been supporting broad-based scientific research since 1974 January 29, 2014 Contact: Kathy Kincade, KKincade@lbl.gov, +1 510 495 2124 horstsimon2013 Horst Simon This year, the Department of Energy's (DOE) National Energy Research Scientific Computing Center (NERSC) is celebrating yet another milestone: its 40th anniversary. Since its founding in 1974, NERSC has become the

  13. NUG 1998

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

    NUG 1998 Dates April 8 & 9, 1998 Location Lawrence Berkeley National Lab NERSC's Web Site Presentations Agenda Energy Research Scientific Computing Users Group (ERSUG) Schedule April 6, 1998 Monday April 6, 1998 Berkeley Lab - Perseverance Hall Time Scheduled Event Speaker / Session Leader 08:00 Continental Breakfast 08:30 Welcome Ricky Kendall 08:35 View From Washington Tom Kitchens 08:55 New NERSC Staff Introductions Horst Simon 09:00 NERSC Research Efforts (Leverage to the NERSC Program)

  14. ALSNews Vol. 325

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

    5 Print 2011 ALS User Meeting Draws Record Numbers Siegfried S. Hecker regales the audience with stories from his visits to North Korea, working with plutonium. A record 461 people registered for the 2011 ALS User Meeting, packing the plenary sessions, workshops, and meals. Berkeley Lab Deputy Director Horst Simon welcomed guests to the meeting, touching on the ominous challenge of data storage and processing. ALS Director Roger Falcone gave an in-depth overview of ALS progress and prospects,

  15. ALSNews Vol. 325

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

    ALSNews Vol. 325 Print 2011 ALS User Meeting Draws Record Numbers Siegfried S. Hecker regales the audience with stories from his visits to North Korea, working with plutonium. A record 461 people registered for the 2011 ALS User Meeting, packing the plenary sessions, workshops, and meals. Berkeley Lab Deputy Director Horst Simon welcomed guests to the meeting, touching on the ominous challenge of data storage and processing. ALS Director Roger Falcone gave an in-depth overview of ALS progress

  16. ALSNews Vol. 325

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

    ALSNews Vol. 325 Print 2011 ALS User Meeting Draws Record Numbers Siegfried S. Hecker regales the audience with stories from his visits to North Korea, working with plutonium. A record 461 people registered for the 2011 ALS User Meeting, packing the plenary sessions, workshops, and meals. Berkeley Lab Deputy Director Horst Simon welcomed guests to the meeting, touching on the ominous challenge of data storage and processing. ALS Director Roger Falcone gave an in-depth overview of ALS progress

  17. Lessons Learned Quarterly Report, March 2016 | Department of Energy

    Energy Savers [EERE]

    6 Lessons Learned Quarterly Report, March 2016 Welcome to the 86th quarterly report on lessons learned in the NEPA process. This issue highlights practices to improve NEPA implementation for environmental justice and public access to references; these practices remind us of NEPA's emphasis on meaningful public involvement. The articles include: Promising Practices Report on EJ in NEPA Reviews DOE Annual Cooperating Agencies Report to CEQ Horst Greczmiel Retires from CEQ Insights from Mr.

  18. Robert B. Laughlin and the Fractional Quantum Hall Effect

    Office of Scientific and Technical Information (OSTI)

    Robert B. Laughlin and the Fractional Quantum Hall Effect Resources with Additional Information Robert B. Laughlin Photo Courtesy of LLNL Robert B. Laughlin shared the 1998 Nobel Prize in Physics with Horst L. Störmer and Daniel C. Tsui for 'their discovery of a new form of quantum fluid with fractionally charged excitations'. ' ... [I]n 1982 ... Störmer and Tsui discovered the effect. In 1983, Laughlin, then at the Lawrence Livermore National Laboratory, provided the theoretical explanation

  19. Previous Members | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Previous ASCAC Members Advanced Scientific Computing Advisory Committee (ASCAC) ASCAC Home Meetings Members ASCAC Members Bio Previous ASCAC Members Charges/Reports ASCAC Charter 2015 - signed .pdf file (134KB) ASCR Committees of Visitors Federal Advisory Committees ASCR Home Members Previous ASCAC Members Print Text Size: A A A FeedbackShare Page Dr. F. Ronald Bailey Computer Sciences Corp. 591 Branciforte Ridge Santa Cruz, CA 95065 Dr. Horst D. Simon Director, Computational Research Division

  20. Microsoft PowerPoint - FNC NEPA GHG Climate Slides -- 16Jan2015 updated 23Jan2015.pptx [Read-Only]

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

    OVERVIEW OF THE COUNCIL ON ENVIRONMENTAL QUALITY'S REVISED DRAFT GUIDANCE ON CONSIDERATION OF GREENHOUSE GAS EMISSIONS AND THE EFFECTS OF CLIMATE CHANGE IN NATIONAL ENVIRONMENTAL POLICY ACT REVIEWS HORST G GRECZMIEL ASSOCIATE DIRECTOR FOR NEPA OVERSIGHT FEDERAL NEPA CONTACTS MEETING 16 JANUARY 2015 UPDATED 23 JANUARY 2015 2 WHERE Revised Draft Guidance for Federal Departments and Agencies on Consideration of Greenhouse Gas Emissions and the Effects of Climate Change in NEPA Reviews  NEPA.GOV

  1. DOE Announces First 'HPC for Manufacturing' Industry Partnerships

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

    DOE Announces First 'HPC for Manufacturing' Industry Partnerships DOE Announces First 'HPC for Manufacturing' Industry Partnerships February 17, 2016 HPC4mfgevent On February 17, DOE announced the first 10 new HPC4Mfg projects during an event at Berkeley Lab that included representatives from EERE, LLNL, Berkeley Lab and ORNL. From left to right are Robin Miles, LLNL; Horst Simon, LBNL; Peter Nugent, LBNL; Trish Damkroger, LLNL; Dona Crawford, LLNL; Mark Johnson, DOE EERE; Kathy Yelick, LBNL;

  2. Microsoft PowerPoint - salishan_v2 [Read-Only]

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

    Petascale Computing for Science Horst Simon Lenny Oliker, David Skinner, and Erich Strohmaier Lawrence Berkeley National Laboratory The Salishan Conference on High-Speed Computing April 19, 2005 Outline * Science Driven Architecture * Performance on today's (2004 - 2005) platforms * Challenges with scaling to the Petaflop/s level * Two tools that can help: IPM and APEX/MAP Scientific Applications and Underlying Algorithms Drive Architectural Design * 50 Tflop/s - 100 Tflop/s sustained

  3. Assessment of Geothermal Resource Potential at a High-Priority Area on the Utah Testing and Training RangeSouth (UTTRS)

    SciTech Connect (OSTI)

    Richard P. Smith, PhD., PG; Robert P. Breckenridge, PhD.; Thomas R. Wood, PhD.

    2012-04-01

    Field investigations conducted during 2011 support and expand the conclusion of the original Preliminary Report that discovery of a viable geothermal system is possible in the northwestern part of the Utah Testing and Training Range-South (UTTR-S), referred to henceforth as Focus Area 1. The investigations defined the southward extent of the Wendover graben into and near Focus Area 1, enhanced the understanding of subsurface conditions, and focused further geothermal exploration efforts towards the northwestern-most part of Focus Area 1. Specifically, the detailed gravity survey shows that the Wendover graben, first defined by Cook et al. (1964) for areas north of Interstate Highway 80, extends and deepens southwest-ward to the northwest corner of Focus Area 1. At its deepest point, the intersection with a northwest-trending graben there is favorable for enhanced permeability associated with intersecting faults. Processing and modeling of the gravity data collected during 2011 provide a good understanding of graben depth and distribution of faults bounding the graben and has focused the interest area of the study. Down-hole logging of temperatures in wells made available near the Intrepid, Inc., evaporation ponds, just north of Focus Area 1, provide a good understanding of the variability of thermal gradients in that area and corroborate the more extensive temperature data reported by Turk (1973) for the depth range of 300-500 m. Moderate temperature gradients in the northern part of the Intrepid area increase to much higher gradients and bottom-hole temperatures southeastward, towards graben-bounding faults, suggesting upwelling geothermal waters along those faults. Water sampling, analysis, and temperature measurements of Blue Lakes and Mosquito Willey's springs, on the western boundary of Focus Area 1, also show elevated temperatures along the graben-bounding fault system. In addition, water chemistry suggests origin of those waters in limestone rocks beneath the graben in areas with temperatures as high as 140 C (284 F). In conclusion, all of the field data collected during 2011 and documented in the Appendices of this report indicate that there is reasonable potential for a viable geothermal resource along faults that bound the Wendover graben. Prospects for a system capable of binary electrical generation are especially good, and the possibility of a flash steam system is also within reason. The next steps should focus on securing the necessary funding for detailed geophysical surveys and for drilling a set of temperature gradient wells to further evaluate the resource, and to focus deep exploration efforts in the most promising areas.

  4. A new geophysical contribution to the study of the Campidano Geothermal area (Sardinia, Italy)

    SciTech Connect (OSTI)

    Balia, R. )

    1991-01-01

    This paper reports that in order to achieve a better definition of the geothermal potential in the area of the Campidano graben (Sardinia, Italy), where there are some thermal springs, a multi-methodological geophysical survey has been combined with recent surface and subsurface geological information. New gravity and magnetic stations, distributed over the northern part of the area (Campidano of Oristano), have been measured to complement already published data for the central-southern part of the graben. Deep dipole-dipole geoelectrical soundings have also been performed along two profiles perpendicular to the strike of the graben. The geological interpretation of the geophysical data allows us to conclude that no shallow, exploitable, geothermal reservoir exists in the survey area.

  5. CX-000752: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Characterization of Pilocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles for Large Scale Geologic Storage of Carbon Dioxide (Pier F Drilling)CX(s) Applied: A9, B3.1Date: 01/29/2010Location(s): Long Beach, CaliforniaOffice(s): Fossil Energy, National Energy Technology Laboratory

  6. CX-000753: Categorical Exclusion Determination

    Office of Energy Efficiency and Renewable Energy (EERE)

    Characterization of Pilocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles for Large Scale Geologic Storage of Carbon Dioxide (Literature and Computer Review)CX(s) Applied: B3.1Date: 01/29/2010Location(s): Arcadia, CaliforniaOffice(s): Fossil Energy, National Energy Technology Laboratory

  7. CX-003827: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles for Large Scale Geologic Storage of Carbon DioxideCX(s) Applied: A9, B3.1Date: 09/09/2010Location(s): San Pedro, CaliforniaOffice(s): Fossil Energy, National Energy Technology Laboratory

  8. CX-000750: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Characterization of Pilocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles for Large Scale Geologic Storage of Carbon Dioxide (Terminal Island Drilling)CX(s) Applied: A9, B3.1Date: 01/29/2010Location(s): San Pedro, CaliforniaOffice(s): Fossil Energy, National Energy Technology Laboratory

  9. CX-003829: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles for Large Scale Geologic Storage of Carbon DioxideCX(s) Applied: A9, B3.1Date: 09/09/2010Location(s): San Pedro, CaliforniaOffice(s): Fossil Energy, National Energy Technology Laboratory

  10. CX-003825: Categorical Exclusion Determination

    Office of Energy Efficiency and Renewable Energy (EERE)

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles for Large Scale Geologic Storage of Carbon DioxideCX(s) Applied: A9, B3.1Date: 09/09/2010Location(s): Long Beach, CaliforniaOffice(s): Fossil Energy, National Energy Technology Laboratory

  11. CX-003818: Categorical Exclusion Determination

    Office of Energy Efficiency and Renewable Energy (EERE)

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles for Large Scale Geologic Storage of Carbon DioxideCX(s) Applied: A9, B3.1Date: 09/09/2010Location(s): Long Beach, CaliforniaOffice(s): Fossil Energy, National Energy Technology Laboratory

  12. CX-003814: Categorical Exclusion Determination

    Office of Energy Efficiency and Renewable Energy (EERE)

    Characterization of Pliocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles for Large Scale Geologic Storage of Carbon DioxideCX(s) Applied: A9Date: 09/09/2010Location(s): Arcadia, CaliforniaOffice(s): Fossil Energy, National Energy Technology Laboratory

  13. CX-000751: Categorical Exclusion Determination

    Office of Energy Efficiency and Renewable Energy (EERE)

    Characterization of Pilocene and Miocene Formations in the Wilmington Graben, Offshore Los Angeles for Large Scale Geologic Storage of Carbon Dioxide (Seismic)CX(s) Applied: A9, B3.1Date: 01/29/2010Location(s): Long Beach, CaliforniaOffice(s): Fossil Energy, National Energy Technology Laboratory

  14. NERSC Scientists Contribute to SC14 Technical Program

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

    NERSC Scientists Contribute to SC14 Technical Program NERSC Scientists Contribute to SC14 Technical Program November 17, 2014 SC14logo3 Here's a look at the various talks, presentations, tutorials and demos that NERSC and other Berkeley Lab staff will be participating in during SC14: Invited Speaker Usable Exascale and Beyond Moore's Law, Horst Simon, Lab Directorate. 3:30-4:15 p.m. Tuesday, Nov. 18, New Orleans Theater. Papers A Computation- And Communication-Optimal Parallel Direct 3-Body

  15. Geologic map of the Ojo Caliente Quadrangle, Rio Arriba and Taos Counties, New Mexico

    SciTech Connect (OSTI)

    Stix, J.

    1986-11-01

    The Ojo Caliente area forms part of the western limb of the Espanola basin within the Rio Grande rift of northern New Mexico (Manley, 1979; May, 1979). The geology consists of Miocene basin-fill sedimentary rocks that rest unconformably on, or are faulted against, Proterozoic crystalline metamorphic rocks. The Miocene rocks dip gently to the southeast, except where the attitudes are controlled by faulting or by the underlying basement topography. The Precambrian and Miocene rocks are unconformably overlain by Quaternary pediment and river gravels, loess, travertine, landslide debris, and alluvium. The Precambrian rocks are faulted into horsts in several areas by north - northeast - trending normal faults.

  16. Presentations

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

    Report on Vectorization Application Review January 27, 1997 | Author(s): S.C. Jardin | Download File: Report-on-Vectorization-Application-Review.pdf | pdf | 93 KB State of NERSC address January 28, 1997 | Author(s): Horst SImon | Download File: State-of-NERSC-Address.pdf | pdf | 176 KB Report on Users' Questions about NERSC 1997 January 28, 1997 | Author(s): Ricky Kendall | Download File: Questions-for-the-ERSUG-Meeting.pdf | pdf | 80 KB Report on Graphics Packages January 28, 1997 | Author(s):

  17. Presentations

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

    State of NERSC address January 28, 1997 | Author(s): Horst SImon | Download File: State-of-NERSC-Address.pdf | pdf | 176 KB Report on Users' Questions about NERSC 1997 January 28, 1997 | Author(s): Ricky Kendall | Download File: Questions-for-the-ERSUG-Meeting.pdf | pdf | 80 KB Report on Graphics Packages January 28, 1997 | Author(s): Stephen Lau, Nancy Johnston, Terry Ligocki | Download File: NERSC1.pdf | pdf | 85 KB The Scientific Computing Group January 28, 1997 | Author(s): Tammy Welcome |

  18. Featured Announcements

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

    January 2014 NERSC's 40th Anniversary Kicks Off with a Special User Group Meeting January 15, 2014 by Francesca Verdier Registration is now open for NUG 2014, the annual meeting of the NERSC Users' Group, Feb. 3-6, 2014. This year's NUG meeting is special, it kicks off NERSC's 40th anniversary celebration. The highlight of NUG 2014 is a two-day "Celebration of Science and Technology" featuring talks by Berkeley Lab's Horst Simon and Kathy Yelick, NERSC Director Sudip Dosanjh, prominent

  19. Agenda

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

    Agenda Agenda ERSUG Business Meeting Special Special Pre-ERSUG-meeting Training Day: Monday, January 27, 1997 ERSUG Meeting (Day 1) January 28th Tuesday, Perseverance Hall Time Topic Speaker 8:30 Pickup from Hotel 9:00 Welcome Klaus Berkner - Associate Laboratory Director, Berkeley Lab 9:10 Agenda Review Ricky Kendall 9:15 View from Washington Tom Kitchens 9:40 NERSC Accomplishments in 1996 Overview of NERSC at LBNL Horst Simon Bill Kramer 10:30 Break 10:40 Chair's Session a) review of action

  20. Agenda

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

    Agenda Agenda November 18, 2002 in Baltimore Note: all times are Eastern Time. Time Speaker Topic 8:00- 8:30 Continental Breakfast 8:30- 8:45 Rob Ryne Welcome / Introductions 8:45- 9:30 Horst Simon Overview: NERSC status report and plans for FY03, NERSC-3 status, user survey, mass storage, big splash, budget issues 9:30-10:00 Cary Whitney NERSC-3 in production 10:00-10:30 Break 10:30-11:00 Walt Polansky Report from Washington DC 11:00-11:30 Brent Gorda NERSC 4 procurement and decision for NERSC

  1. Agenda

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

    Agenda Agenda May 29: NUG Business Meeting Agenda All times are Central Time (subtract 2 hours for Pacific Time; add 1 hour for Eastern Time). 9:00 Welcome, Introductions Doug Rotman 9:15 Opening Remarks Horst Simon 9:30 Performance Evaluation Activites at NERSC Adrian Wong 10:00 Seaborg Code Scalability Project Richard Gerber 10:30 Green's function Monte Carlo Calculations of Light Nuclei Steven Pieper 10:45 Lattice QCD in Extreme Environments Don Sinclair 11:00 Break 11:15 Global Climate

  2. NERSC's 40th Anniversary Kicks Off with a Special User Group Meeting

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

    40th Anniversary Kicks Off with a Special User Group Meeting NERSC's 40th Anniversary Kicks Off with a Special User Group Meeting January 15, 2014 by Francesca Verdier Registration is now open for NUG 2014, the annual meeting of the NERSC Users' Group, Feb. 3-6, 2014. This year's NUG meeting is special, it kicks off NERSC's 40th anniversary celebration. The highlight of NUG 2014 is a two-day "Celebration of Science and Technology" featuring talks by Berkeley Lab's Horst Simon and Kathy

  3. BACA Project: geothermal demonstration power plant. Final report

    SciTech Connect (OSTI)

    Not Available

    1982-12-01

    The various activities that have been conducted by Union in the Redondo Creek area while attempting to develop the resource for a 50 MW power plant are described. The results of the geologic work, drilling activities and reservoir studies are summarized. In addition, sections discussing the historical costs for Union's involvement with the project, production engineering (for anticipated surface equipment), and environmental work are included. Nineteen geothermal wells have been drilled in the Redondo Creek area of the Valles Caldera: a prominent geologic feature of the Jemez mountains consisting of Pliocene and Pleistocene age volcanics. The Redondo Creek area is within a complex longitudinal graben on the northwest flank of the resurgent structural dome of Redondo Peak and Redondo Border. The major graben faults, with associated fracturing, are geologically plausible candidates for permeable and productive zones in the reservoir. The distribution of such permeable zones is too erratic and the locations too imprecisely known to offer an attractive drilling target. Log analysis indicates there is a preferred mean fracture strike of N31W in the upper portion of Redondo Creek wells. This is approximately perpendicular to the major structure in the area, the northeast-striking Redondo Creek graben. The geothermal fluid found in the Redondo Creek reservoir is relatively benign with low brine concentrations and moderate H/sub 2/S concentrations. Geothermometer calculations indicate that the reservoir temperature generally lies between 500/sup 0/F and 600/sup 0/F, with near wellbore flashing occurring during the majority of the wells' production.

  4. Development of a Fast Microfluidic Mixer for Studies of Protein...

    Office of Scientific and Technical Information (OSTI)

    Studies of Protein Folding KineticsFinal Report Cover Page Citation Details In-Document Search Title: Development of a Fast Microfluidic Mixer for Studies of Protein Folding ...

  5. The crystal structure of choline kinase reveals a eukaryotic...

    Office of Scientific and Technical Information (OSTI)

    reveals a eukaryotic protein kinase fold Citation Details In-Document Search Title: The crystal structure of choline kinase reveals a eukaryotic protein kinase fold Choline ...

  6. Microsecond Microfluidic Mixing for Investigation of Protein...

    Office of Scientific and Technical Information (OSTI)

    for Investigation of Protein Folding Kinetics Citation Details In-Document Search Title: Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics We have ...

  7. ALS Capabilities Reveal Multiple Functions of Ebola Virus

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

    Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function....

  8. Bend me, shape me, any way you want me: Scientists curve nanoparticle...

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

    VIDEO Hexagonal Ordering of Nanoparticles This highly magnified image of a folded gold nanoparticle scroll shows that even though researchers can fold the membrane, the internal...

  9. Engineering and Characterization of a Superfolder Green Fluorescent Protein

    SciTech Connect (OSTI)

    Pedelacq,J.; Cabantous, S.; Tran, T.; Terwilliger, T.; Waldo, G.

    2006-01-01

    Existing variants of green fluorescent protein (GFP) often misfold when expressed as fusions with other proteins. We have generated a robustly folded version of GFP, called 'superfolder' GFP, that folds well even when fused to poorly folded polypeptides. Compared to 'folding reporter' GFP, a folding-enhanced GFP containing the 'cycle-3' mutations and the 'enhanced GFP' mutations F64L and S65T, superfolder GFP shows improved tolerance of circular permutation, greater resistance to chemical denaturants and improved folding kinetics. The fluorescence of Escherichia coli cells expressing each of eighteen proteins from Pyrobaculum aerophilum as fusions with superfolder GFP was proportional to total protein expression. In contrast, fluorescence of folding reporter GFP fusion proteins was strongly correlated with the productive folding yield of the passenger protein. X-ray crystallographic structural analyses helped explain the enhanced folding of superfolder GFP relative to folding reporter GFP.

  10. Sedimentation and reservoir distribution related to a tilted block system in the Sardinia Oligocene-Miocene rift (Italy)

    SciTech Connect (OSTI)

    Tremolieres, P.; Cherchi, A.; Eschard, R.; De Graciansky, P.C.; Montadert, L.

    1988-08-01

    In the western Mediterranean basin lies a rift system about 250 km long and 50 km wide and its infilling outcrop (central Sardinia). Seismic reflection surveys show its offshore extension. Block tilting started during the late Oligocene and lasted during Aquitanian-early Burdigalian time. Two main fault trends, with synthetic and antithetic throws, define the more-or-less collapsed blocks. This morphology guided the transit and trapping of sediments. The sedimentation started in a continental environment then, since the Chattian, in marine conditions. In the central part, the series can reach a thickness of 2,000 m. The basement composition and the volcanics products related to the main fault motion controlled the nature of the synrift deposits. According to their location in the rift context, the tilted blocks trap either continental deposits or marine siliciclastic or carbonate deposits. In the deeper part of the graben, sands were redeposited by gravity flows into the basinal marls. The younger prerift deposits are from Eocene to early Oligocene age and locally comprise thick coal layers. Postrift deposits, mainly marls, sealed the blocks and synrift sedimentary bodies. In middle and late Miocene time some faults were reactivated during compressional events. Then, a quaternary extensional phase created the Campidano graben, filled with about 1,000 m of sediments superimposed on the Oligocene-Miocene rift.

  11. Development of Improved Caprock Integrity and Risk Assessment Techniques

    SciTech Connect (OSTI)

    Bruno, Michael

    2014-09-30

    GeoMechanics Technologies has completed a geomechanical caprock integrity analysis and risk assessment study funded through the US Department of Energy. The project included: a detailed review of historical caprock integrity problems experienced in the natural gas storage industry; a theoretical description and documentation of caprock integrity issues; advanced coupled transport flow modelling and geomechanical simulation of three large-scale potential geologic sequestration sites to estimate geomechanical effects from CO₂ injection; development of a quantitative risk and decision analysis tool to assess caprock integrity risks; and, ultimately the development of recommendations and guidelines for caprock characterization and CO₂ injection operating practices. Historical data from gas storage operations and CO₂ sequestration projects suggest that leakage and containment incident risks are on the order of 10-1 to 10-2, which is higher risk than some previous studies have suggested for CO₂. Geomechanical analysis, as described herein, can be applied to quantify risks and to provide operating guidelines to reduce risks. The risk assessment tool developed for this project has been applied to five areas: The Wilmington Graben offshore Southern California, Kevin Dome in Montana, the Louden Field in Illinois, the Sleipner CO₂ sequestration operation in the North Sea, and the In Salah CO₂ sequestration operation in North Africa. Of these five, the Wilmington Graben area represents the highest relative risk while the Kevin Dome area represents the lowest relative risk.

  12. Area balance and strain in an extensional fault system: Strategies for improved oil recovery in fractured chalk, Gilbertown Field, southwestern Alabama. Annual report, March 1996--March 1997

    SciTech Connect (OSTI)

    Pashin, J.C.; Raymond, D.E.; Rindsberg, A.K.; Alabi, G.G.; Groshong, R.H.

    1997-08-01

    Gilbertown Field is the oldest oil field in Alabama and produces oil from chalk of the Upper Cretaceous Selma Group and from sandstone of the Eutaw Formation along the southern margin of the Gilbertown fault system. Most of the field has been in primary recovery since establishment, but production has declined to marginally economic levels. This investigation applies advanced geologic concepts designed to aid implementation of improved recovery programs. The Gilbertown fault system is detached at the base of Jurassic salt. The fault system began forming as a half graben and evolved in to a full graben by the Late Cretaceous. Conventional trapping mechanisms are effective in Eutaw sandstone, whereas oil in Selma chalk is trapped in faults and fault-related fractures. Burial modeling establishes that the subsidence history of the Gilbertown area is typical of extensional basins and includes a major component of sediment loading and compaction. Surface mapping and fracture analysis indicate that faults offset strata as young as Miocene and that joints may be related to regional uplift postdating fault movement. Preliminary balanced structural models of the Gilbertown fault system indicate that synsedimentary growth factors need to be incorporated into the basic equations of area balance to model strain and predict fractures in Selma and Eutaw reservoirs.

  13. Sediment infill within rift basins: Facies distribution and effects of deformation: Examples from the Kenya and Tanganyika Rifts, East Africa

    SciTech Connect (OSTI)

    Tiercelin, J.J.; Lezzar, K.E. ); Richert, J.P. )

    1994-07-01

    Oil is known from lacustrine basins of the east African rift. The geology of such basins is complex and different depending on location in the eastern and western branches. The western branch has little volcanism, leading to long-lived basins, such as Lake Tanganyika, whereas a large quantity of volcanics results in the eastern branch characterized by ephemeral basins, as the Baringo-Bogoria basin in Kenya. The Baringo-Bogoria basin is a north-south half graben formed in the middle Pleistocene and presently occupied by the hypersaline Lake Bogoria and the freshwater Lake Baringo. Lake Bogoria is fed by hot springs and ephemeral streams controlled by grid faults bounding the basin to the west. The sedimentary fill is formed by cycles of organic oozes having a good petroleum potential and evaporites. On the other hand, and as a consequence of the grid faults, Lake Baringo is fed by permanent streams bringing into the basin large quantities of terrigenous sediments. Lake Tanganyika is a meromictic lake 1470 m deep and 700 km long, of middle Miocene age. It is subdivided into seven asymmetric half grabens separated by transverse ridges. The sedimentary fill is thick and formed by organic oozes having a very good petroleum potential. In contrast to Bogoria, the lateral distribution of organic matter is characterized by considerable heterogeneity due to the existence of structural blocks or to redepositional processes.

  14. Potiguar basin: geologic model and habitat of oil of a Brazilian equatorial basin

    SciTech Connect (OSTI)

    Falkenhein, F.U.; Barros, R.M.; Da Costa, I.G.; Cainelli, C.

    1984-04-01

    The Potiguar basin integrates the eastern part of the Brazilian equatorial Atlantic-type margin. The rifting stage of this basin occurred during the Neocomian and Aptian. The drifting stage and sea-floor spreading began in the Late Albian. The rifting stage clearly was intracratonic during the Neocomian and is recognized as a mosaic of half-grabens trending mostly northeast-southwest and filled with syntectonic lacustrine siliciclastics. The half-graben pattern exhibits rotation of beds into the major fault zone, and the preserved uplifted margins display either paleostructures of paleogeomorphic features with hydrocarbons. A regional pre-Aptian unconformity preceded the Aptian proto-oceanic rifting stage which was characterized by syntectonic fluvio-deltaic sediments. The Aptian tectonics were represented by reactivation of former lineaments superimposed by predominant east-west normal faulting. Structural highs during this stage are so far the most prolific oil accumulations. The most important source beds and reservoir rocks are both Neocomian and Aptian sediments. Geochemistry and hydrodynamics have shown that hydrocarbon migration was driven through fracture or fault zones in both Aptian or Albian plays. Lithofacies maps support this interpretation because pools occur whenever adjacent downthrown blocks present a high shale content.

  15. INNOVATIVE METHODOLOGY FOR DETECTION OF FRACTURE-CONTROLLED SWEET SPOTS IN THE NORTHERN APPALACHIAN BASIN

    SciTech Connect (OSTI)

    Robert Jacobi; John Fountain

    2001-02-28

    In the structure task, we completed a N-S transect east of Seneca Lake that indicated a N-striking fault near the southeastern shore of Seneca Lake, and also indicated NE and ENE-trending FIDs and faults north of Valois. The orientation and existence of the NE-striking FIDs and faults are thought to be controlled by basement faults, rather than thrust ramps above the Salina salt controlled only by a far-field Alleghanian stress field. Structure contour maps based on well log analyses have been constructed but not interpreted. Soil gas data displayed a number of ethane-charged soil gas ''spikes'' on a N-S transect from Ovid south to near Valois. The soil gas team found a larger number of spikes in the northern half of the survey, suggesting more open fractures (and faults) in the northern half of the survey. Seismic data has been purchased and reprocessed. Several grabens observed in the Trenton reflector are consistent with surface structure, soil gas, and aeromagnetic anomalies. The aeromagnetic survey is completed and the data is processed. Prominent magnetic anomalies suggest that faults in the Precambrian basement are located beneath regions where grabens in the Trenton are located.

  16. INNOVATAIVE METHODOLOGY FOR DETECTION OF FRACTURE-CONTROLLED SWEET SPOTS IN THE NORTHERN APPALACHIAN BASIN

    SciTech Connect (OSTI)

    Robert Jacobi; John Fountain

    2002-06-30

    In the structure task, for this reporting period, the authors also edited and revised the map that displays the modified rose diagrams for the data they collected and reduced along the east side of Seneca Lake. They also revised the N-S transect that displays the frequency of ENE-striking fractures, and constructed a new N-S transect that shows the frequency of E-striking fractures. This transect compliments the earlier transect they constructed for fracture frequency of ENE-striking fractures. Significantly, the fracture frequency transect for E-W fractures shows a spike in fracture frequency in the region of the E-striking Firtree anticline that is observed on seismic reflection sections. The ENE fracture set does not exhibit an unusually high fracture frequency in this area. In contrast, the fracture frequency of the ENE-striking set is anomalously high in the region of the Trenton/Black River grabens. They have nearly completed reducing the data they collected from a NNW-SSE transect on the west side of Cayuga Lake and they have constructed modified rose diagrams for most sites. Structure contour maps and isopach maps have been revised based on additional well log analyses. Except for the Glodes Corners Field, the well spacing generally remains insufficient to identify faults or their precise locations. However, relatively sharp elevational changes east of Keuka Lake support the contention that faults occur along the east side of Keuka Lake. Similarly, a single well east of Seneca Lake shows that the Trenton there is low compared to distant wells, based on an assumed regional slope. This same area is where one of the Trenton grabens occurs. They have completed the interpretation of the reprocessed data that Quest licensed and had reprocessed. Several grabens observed in the Trenton and Black River reflectors are consistent with surface structure, soil gas, and aeromagnetic anomalies. In this report they display all four interpreted seismic lines. These data indicate that integration of aeromagnetic and topographic lineaments, surface structure, soil gas with seismic and well logs allows them to extrapolate Trenton-Black River trends away from confirmatory seismic lines.

  17. ALS Capabilities Reveal Multiple Functions of Ebola Virus

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

    Functions of Ebola Virus Print Friday, 13 June 2014 10:25 A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function....

  18. Influence of Transcontinental arch on Cretaceous listric-normal faulting, west flank, Denver basin

    SciTech Connect (OSTI)

    Davis, T.L.

    1983-08-01

    Seismic studies along the west flank of the Denver basin near Boulder and Greeley, Colorado illustrate the interrelationship between shallow listric-normal faulting in the Cretaceous and deeper basement-controlled faulting. Deeper fault systems, primarily associated with the Transcontinental arch, control the styles and causative mechanisms of listric-normal faulting that developed in the Cretaceous. Three major stratigraphic levels of listric-normal faulting occur in the Boulder-Greeley area. These tectonic sensitive intervals are present in the following Cretaceous formations: Laramie-Fox Hills-upper Pierre, middle Pierre Hygiene zone, and the Niobrara-Carlile-Greenhorn. Documentation of the listric-normal fault style reveals a Wattenberg high, a horst block or positive feature of the greater Transcontinental arch, was active in the east Boulder-Greeley area during Cretaceous time. Paleotectonic events associated with the Wattenberg high are traced through analysis of the listric-normal fault systems that occur in the area. These styles are important to recognize because of their stratigraphic and structural influence on Cretaceous petroleum reservoir systems in the Denver basin. Similar styles of listric-normal faulting occur in the Cretaceous in many Rocky Mountain foreland basins.

  19. Brochure, Understanding UCNI- August 2014

    Broader source: Energy.gov [DOE]

    Tri-fold brochure outlining what UCNI is and the guidelines on identifying, marking and protecting UCNI.

  20. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    Harvey INORGANIC ORGANIC PHYSICAL AND ANALYTICAL CHEMISTRY BASIC BIOLOGICAL SCIENCES FREE ENERGY MELTING PROTEINS THERMODYNAMICS TOPOLOGY protein folding protein aggregation...

  1. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; FREE ENERGY; MELTING; PROTEINS; THERMODYNAMICS; TOPOLOGY protein folding protein...

  2. Paleogeographic and structural setting of Miocene strata in central western Nevada

    SciTech Connect (OSTI)

    Stewart, J.H. )

    1993-04-01

    Late Cenozoic sedimentary rocks as old as 19 Ma are widely distributed in central western Nevada. They are greatly more abundant than older Cenozoic strata and are commonly interpreted to have formed in fault-bounded basins that mark the onset of widespread extension in the Basin and Range Province. Miocene strata are largely coeval with a magmatic arc that extended south southeast near the boundary of the Basin and Range and Sierra Nevada Provinces. This arc produced voluminous andesitic flows and lahars that locally interfinger with the Miocene strata. Miocene depositional basins apparently varied greatly in size. The largest that can be defined clearly is the Esmeralda Basin that was at least 65 km long and 45 km wide. Other basins may have been larger but are difficult to reconstruct; still other basins may be small and isolated, particularly within the magmatic arc. Lacustrine deposits and minor interfingering deltaic and distal fluvial units predominate; near-source, coarse alluvial-fan and megabreccia landslide deposits are locally conspicuous. coarse near-source deposits, particularly landslide deposits, are interpreted to be adjacent to basin-bounding normal faults. The Esmeralda, Coal Valley, and Gabbs Valley-Stewart Valley-Tonopah Basins are interpreted to be related to large-scale Miocene extension. Other basins may be (1) pull-apart structures related to strike-slip faults, (2) downdropped blocks in areas of cross-cutting normal and/or strike-slip faults related to changes in the extension direction or (3) grabens or half-grabens related to uniform extension. Younger Cenozoic basins, including present-day basins, overprint and cut across the Miocene basins.

  3. Petroleum possibilities in continental margin off central Chile

    SciTech Connect (OSTI)

    Gonzalez, E.

    1986-07-01

    The continental margin off central Chile, from Valparaiso to Valdivia, encompassing an area of 100,000 km/sup 2/, has been the target of exploratory activity by Empresa Nacional del Petroleo since 1970. Exploratory drilling began in 1972. By August 1984, total exploratory efforts had resulted in drilling 14 offshore wells and acquiring 12,130 km of seismic reflection lines. A biogenic gas accumulation was discovered in the F well. Because these attempts to find oil were unsuccessful and because drilling costs have escalated, exploratory activities have been curtailed. Forearc basins off central Chile are characterized by low geothermal gradient and a sedimentary filling of Cretaceous and Tertiary strata. Tertiary sequences are characterized by low organic carbon content, immature humic-type organic matter, and a biogenic gas potential. Cretaceous sequences are characterized by higher organic carbon content, good reservoir rocks, and fair to good source rocks. The organic matter is sapropelic, with vitrinite and liptinites, and is favorable for oil and gas generation. Seismic and well data suggest that Mesozoic and Cenozoic sedimentary rock sequences filling the basins (more than 4000 m thick at the shelf edge) extend 40-70 km beyond the present shelf edge. Mesozoic rocks deposited on the slope may generate petroleum and gas that could migrate upslope and accumulate in traps associated with the faulted basement highs and graben-type depressions existing at the shelf edge. This geologic setting favors the development of large petroleum accumulations along the shelf edge and graben on the sedimentary basins off central Chile.

  4. Structural framework, stratigraphy, and evolution of Brazilian marginal basins

    SciTech Connect (OSTI)

    Ojeda, H.A.O.

    1982-06-01

    The structural framework of the Brazilian continental margin is basically composed of eight structural types: antithetic tilted step-fault blocks, synthetic untilted step-fault blocks, structural inversion axes, hinges with compensation grabens, homoclinal structures, growth faults with rollovers, diapirs, and igneous structures. The antithetic tilted and synthetic untilted step-fault blocks are considered as synchronous, complementary structural systems, separated by an inversion axis. Two evaporitic cycles (Paripueira and Ibura) were differentiated in the Sergipe-Alagoas type basin and tentatively correlated to the evaporitic section of other Brazilian marginal basis. Four phases are considered in the evolution of the Brazilian marginal basins: pre-rift, rift, transitional, and drift. During the pre-rift phase (Late Jurassic-Early Cretaceous), continental sediments were deposited in peripheral intracratonic basins. In the rift phase (Early Cretaceous), the breakup of the continental crust of the Gondwana continent gave rise to a central graben and rift valleys where lacustrine sediments were deposited. The transitional phase (Aptian) developed under relative tectonic stability, when evaporitic and clastic lacustrine sequences were being deposited. In the drift phase (Albian to Holocene), a regionl homoclinal structure developed, consisting of two distinct sedimentary sequences, a lower clastic-carbonate and an upper clastic. From the Albian to the Holocene Epoch, structures associated to plastic displacement of salt or shale developed in many Brazilian marginal basins. Two phases of major igneous activity occurred: one in the Early Cretaceous associated with the rift phase of the Gondwana continent, and the other in the Tertiary during the migration phase of the South American and African plates.

  5. Cenozoic stratigraphic evolution, North Sea and Labrador Sea

    SciTech Connect (OSTI)

    Gradstein, F.M.; Grant, A.C.; Mudford, B.S. ); Berggren, W.A. ); Kaminski, M.A. ); D'Lorio, M.A. ); Cloetingh, S. ); Griffiths, C.M. )

    1990-05-01

    The authors are studying Cenozoic correlation patterns, burial trends, and subsidence history of the Central North Sea, Labrador, and Orphan basins. The authors objectives are (1) to detail intraregional mid-high latitude biozonations using noise filtering and probabilistic zonation techniques; (2) to detail paleobathymetric trends from basin margins to centers; (3) to apply this knowledge to model basin evolution, in the perspective of the evolving North Atlantic Ocean; (4) to evaluate causes for the occurrence of major hiatuses and rapid changes of subsidence; and (5) to relate rapid changes in sedimentation in the last few millions of years to model observed undercompaction trends. Cenozoic microfossil assemblages in these basins are similar, related to similarities in sedimentary and paleoeceanographic conditions. In more basinal wells, flysch-type agglutinated foraminiferal assemblages occur, also known from Carpathians, Trinidad, and Moroccan foredeeps. Over 90% of agglutinated taxa are common between these basins, although local stratigraphic ranges vary sufficiently to rely on the concept of average ranges, rather than total ones for correlations. Cenozoic stratigraphic resolution in the North Sea and Labrador basins generally is in 3-5-Ma units. and paleobathymetric zonations define a minimum of five niches, from inner shelf to middle slope regimes. Significant hiatuses occurred in the late Eocene through the Miocene, particularly in northern Labrador and northern North Sea. Subsidence in the Labrador/Grand Banks passive margin half grabens was strongly influenced by Labrador Sea opening between anomalies 34 (Campanian) and 13 (early Oligocene), when subsidence exceeded sedimentation and bathyal conditions prevailed along the margin. Thermally induced subsidence in the central North Sea grabens was considerable in the late Paleocene, when the Norwegian Sea started to open.

  6. The Preston Geothermal Resources; Renewed Interest in a Known Geothermal Resource Area

    SciTech Connect (OSTI)

    Wood, Thomas R.; Worthing, Wade; Cannon, Cody; Palmer, Carl; Neupane, Ghanashyam; McLing, Travis L; Mattson, Earl; Dobson, Patric; Conrad, Mark

    2015-01-01

    The Preston Geothermal prospect is located in northern Cache Valley approximately 8 kilometers north of the city of Preston, in southeast Idaho. The Cache Valley is a structural graben of the northern portion of the Basin and Range Province, just south of the border with the Eastern Snake River Plain (ESRP). This is a known geothermal resource area (KGRA) that was evaluated in the 1970's by the State of Idaho Department of Water Resources (IDWR) and by exploratory wells drilled by Sunedco Energy Development. The resource is poorly defined but current interpretations suggest that it is associated with the Cache Valley structural graben. Thermal waters moving upward along steeply dipping northwest trending basin and range faults emanate in numerous hot springs in the area. Springs reach temperatures as hot as 84 C. Traditional geothermometry models estimated reservoir temperatures of approximately 125 C in the 1970s study. In January of 2014, interest was renewed in the areas when a water well drilled to 79 m (260 ft) yielded a bottom hole temperature of 104 C (217 F). The well was sampled in June of 2014 to investigate the chemical composition of the water for modeling geothermometry reservoir temperature. Traditional magnesium corrected Na-K-Ca geothermometry estimates this new well to be tapping water from a thermal reservoir of 227 C (440 F). Even without the application of improved predictive methods, the results indicate much higher temperatures present at much shallower depths than previously thought. This new data provides strong support for further investigation and sampling of wells and springs in the Northern Cache Valley, proposed for the summer of 2015. The results of the water will be analyzed utilizing a new multicomponent equilibrium geothermometry (MEG) tool called Reservoir Temperature Estimate (RTEst) to obtain an improved estimate of the reservoir temperature. The new data suggest that other KGRAs and overlooked areas may need to be investigated using improved geothermal exploration methods.

  7. Regional geology of Georges Bank basin - OCS Sale 42 drilling results

    SciTech Connect (OSTI)

    High, L.R. Jr.

    1985-02-01

    Industry bid aggressively in OCS Sale 42, spending $816 million. Eight wildcats were drilled in 1981-82 to test 5 major plays. All wells were dry; no potential reservoir or source rocks were found. The tectonic-stratigraphic framework of the Georges Bank basin is that of an Atlantic-type plate margin. Two major unconformities divide the section into prerift, synrift, and postrift sequences. The prerift sequence consists of Paleozoic metasediments in basement fault blocks. Synrift sediments consist of Newark Group equivalents: the Argo Salt and the Iroquoi Formation. The postrift sequence consists of Mohican red beds overlain by progradational wedges, with the carbonate Abenaki Formation at the base. The objective in 4 of the 8 wildcats was the Iroquois Formation. Mobil 312-1 and Shell 357-1 were drilled into a seismic anomaly interpreted to be a reef. This structure was found to be a complex carbonate mound. Exxon 975-1 was drilled on a seismic amplitude anomaly variously interpreted to be the result of salt, coal, or porous carbonates. This anomaly proved to be caused by a salt bed. The objective in Shell 410-1R was carbonate banks over a basement horst block. No significant zones of porosity were found. The remaining 4 wildcats were drilled on Abenaki prospects. Mobil 273-1, Tenneco 187-1d, and Conoco 145-1 were drilled for possible carbonate banks over a salt structure. Only thin oolitic grainstone intervals were found. Exxon 133-1 was based on a seismic anomaly interpreted to be a patch reef. This feature was found to be a volcanic cone.

  8. Flexible swivel connection

    DOE Patents [OSTI]

    Hoh, J.C.

    1985-02-19

    A flexible swivel boot connector for connecting a first boot shield section to a second boot shield section, both first and second boot sections having openings therethrough, the second boot section having at least two adjacent accordian folds at the end having the opening, the second boot section being positioned through the opening of the first boot section such that a first of the accordian folds is within the first boot section and a second of the accordian folds is outside of the first boot, includes first and second annular discs, the first disc being positioned within and across the first accordian fold, the second disc being positioned within and across the second accordian fold, such that the first boot section is moveably and rigidly connected between the first and second accordian folds of the second boot section.

  9. Bend me, shape me, any way you want me: Scientists curve nanoparticle

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

    sheets into complex forms | Argonne National Laboratory VIDEO Hexagonal Ordering of Nanoparticles This highly magnified image of a folded gold nanoparticle scroll shows that even though researchers can fold the membrane, the internal structure remains intact. Image credit: Xiao-Min Lin et. al, taken using a scanning electron microscope at the University of Chicago. (Click image to view larger.) This highly magnified image of a folded gold nanoparticle scroll shows that even though

  10. Essential roles of protein-solvent many-body correlation in solvent-entropy

    Office of Scientific and Technical Information (OSTI)

    effect on protein folding and denaturation: Comparison between hard-sphere solvent and water (Journal Article) | SciTech Connect Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water Citation Details In-Document Search Title: Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere

  11. The enterococcal cytolysin synthetase has an unanticipated lipid kinase

    Office of Scientific and Technical Information (OSTI)

    fold (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: The enterococcal cytolysin synthetase has an unanticipated lipid kinase fold Citation Details In-Document Search Title: The enterococcal cytolysin synthetase has an unanticipated lipid kinase fold Authors: Dong, Shi-Hui ; Tang, Weixin ; Lukk, Tiit ; Yu, Yi ; Nair, Satish K. ; van der Donk, Wilfred A. [1] ; UIUC) [2] + Show Author Affiliations Cornell ( Publication Date: 2016-02-05 OSTI Identifier:

  12. The crystal structure of choline kinase reveals a eukaryotic protein kinase

    Office of Scientific and Technical Information (OSTI)

    fold (Journal Article) | SciTech Connect The crystal structure of choline kinase reveals a eukaryotic protein kinase fold Citation Details In-Document Search Title: The crystal structure of choline kinase reveals a eukaryotic protein kinase fold Choline kinase catalyzes the ATP-dependent phosphorylation of choline, the first committed step in the CDP-choline pathway for the biosynthesis of phosphatidylcholine. The 2.0 {angstrom} crystal structure of a choline kinase from C. elegans (CKA-2)

  13. The non-detergent sulfobetaine-201 acts as a pharmacological chaperone to

    Office of Scientific and Technical Information (OSTI)

    promote folding and crystallization of the type II TGF-[beta] receptor extracellular domain (Journal Article) | SciTech Connect The non-detergent sulfobetaine-201 acts as a pharmacological chaperone to promote folding and crystallization of the type II TGF-[beta] receptor extracellular domain Citation Details In-Document Search Title: The non-detergent sulfobetaine-201 acts as a pharmacological chaperone to promote folding and crystallization of the type II TGF-[beta] receptor extracellular

  14. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    Folding KineticsFinal Report Cover Page Bakajin O BASIC BIOLOGICAL SCIENCES ENGINEERING CONSUMPTION RATES DEAD TIME DETECTION DIFFUSION DNA ENERGY TRANSFER FABRICATION...

  15. Securing America's Clean Energy Future (Brochure)

    SciTech Connect (OSTI)

    Not Available

    2011-08-01

    This letter-fold brochure provides an overview of the activities and programs in DOE's Office of Energy Efficiency and Renewable Energy.

  16. SSRL HEADLINES March 2003

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

    Contents of This Issue: Science Highlight - Exploring the Folding Landscape of a Structured RNA by SAXS SPEAR2 Ends a Remarkable 30 Years on March 31 More on...

  17. PNA-peptide Assembly in a 3D DNA Nanocage at Room Temperature

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

    Proteins and peptides fold into dynamic structures that access a broad functional landscape, however, designing artificial polypeptide systems is still a great challenge....

  18. PowerPoint Presentation

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

    answer) * Inexpensive: 50-200 fold reduction in required reagent volumes * Minimally-invasive: <20L whole blood input (finger puncture) * Simplerobust: Based on...

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

    SciTech Connect (OSTI)

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

    1995-07-01

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

  20. News Item

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

    lens aberrations due to 2- and 3- fold astigmatism, coma, and spherical aberration. Holography Electron holography can produce high-resolution images by recording images...

  1. Building America Partner Program: A Program of the Home Builders Association of Central New Mexico

    SciTech Connect (OSTI)

    Not Available

    2001-11-01

    This tri-fold brochure introduces the Building America Partner Program in central New Mexico and encourages home builders and home owners to participate.

  2. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION ... mixers to investigate the kinetics of protein secondary structure formation with ...

  3. Structural investigations at the Coso geothermal area using remote...

    Open Energy Info (EERE)

    During SevierLaramide orogeny, the Sierra Nevada Mountains were thrust eastward over Rose Valleylndian Wells Valley. Relatively thin graniticmetamorphic plates were folded to...

  4. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    Protein folding via divide and conquer optimization Oliva Ricardo Crivelli Silvia Meza Juan APPLIED LIFE SCIENCES Ernest Orlando Lawrence Berkeley NationalLaboratory Berkeley CA US...

  5. Crivelli, Silvia; Meza, Juan 60 APPLIED LIFE SCIENCES Ernest...

    Office of Scientific and Technical Information (OSTI)

    folding via divide-and-conquer optimization Oliva, Ricardo; Crivelli, Silvia; Meza, Juan 60 APPLIED LIFE SCIENCES Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA...

  6. Symmetry Breaking of H2 Dissociation by a Single Photon

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

    six-fold rotational symmetry, abound but are only approximately true because the objects of our macroscopic world are highly complex. Once we reduce their size and...

  7. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    Simplified Protein Models Predicting Folding Pathways and Structure Using Amino Acid Sequences Adhikari Aashish N Freed Karl F Sosnick Tobin R Not Available American Physical...

  8. LANL >> GFP Website >> Home

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

    of a protein are soluble Evaluate how a protein interacts with other proteins (protein-protein interaction) Reveal the effect of a small molecule on the protein's folding...

  9. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    solution of mass radius conformations assembly and shape changes associated with protein folding and functions SAXS can efficiently reveal the spatial organization of protein...

  10. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    RESIDUES; SENSITIVITY; SPECIFICITY",,"In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for...

  11. Protein Structure Recognition: From Eigenvector Analysis to Structural

    Office of Scientific and Technical Information (OSTI)

    RESIDUES; SENSITIVITY; SPECIFICITY In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for...

  12. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    PROTEINS RESIDUES SENSITIVITY SPECIFICITY In this work they try to understand the protein folding problem using pair wise hydrophobic interaction as the dominant interaction for...

  13. Structural analysis of flexible proteins in solution by SmallAngle...

    Office of Scientific and Technical Information (OSTI)

    of mass, radius, conformations, assembly, and shape changes associated with protein folding and functions. SAXS can efficiently reveal the spatial organization of protein...

  14. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    of mass, radius, conformations, assembly, and shape changes associated with protein folding and functions. SAXS can efficiently reveal the spatial organization of protein...

  15. Slide 1

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

    membrane. CESA has not yet been crystallized but new ab initio computational protein folding reveals the approximate 3D CESA structure, which in turn clarifies how it...

  16. Slide 1

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

    proteins; - Increased yield of functional, BcsAB cellulose synthase 10-fold over E. coli - based system; - Demonstrated expression of functional forms of challenging membrane...

  17. Natural Gas Weekly Update

    Gasoline and Diesel Fuel Update (EIA)

    Indicate Increases in ENERGY STAR qualified Homes in the United States. The number of ENERGY STAR qualified homes built in the United States has increased nearly 20-fold...

  18. Natural Gas Weekly Update, Printer-Friendly Version

    Annual Energy Outlook [U.S. Energy Information Administration (EIA)]

    Indicate Increases in ENERGY STAR qualified Homes in the United States. The number of ENERGY STAR qualified homes built in the United States has increased nearly 20-fold...

  19. Studies reveal a unified approach to combating several bacterial...

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

    (Click image to enlarge.) The Corynebacterium diphtheria MdbA enzyme's thiol-disulfide oxidoreductase fold is shown as arrows and two flanking helices in the lower...

  20. Structural mapping of the ClpB ATPases of Plasmodium falciparum...

    Office of Scientific and Technical Information (OSTI)

    Structural mapping of the ClpB ATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design Citation Details In-Document Search Title:...

  1. Structure Illuminates Mechanism of Fungal Polyketide Cyclization

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

    specific cyclization pattern exclusive to fungi, an amazing feat of origami. In contrast, bacteria fold the linear chain into a completely different pattern, as promoted by an...

  2. Manufacturing Advanced Engineered Components Using Lost Foam Casting Technology

    SciTech Connect (OSTI)

    None

    2004-11-01

    The project will further reduce porosity and fold defects in lost foam casting to improve production efficiency, mechanical properties, and marketability of castings.

  3. Symmetry Breaking of H2 Dissociation by a Single Photon

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

    breaking the molecular symmetry. A Molecular Paradox Symmetries in nature, such as the human body's bilateral symmetry and the snowflake's six-fold rotational symmetry, abound but...

  4. The non-detergent sulfobetaine-201 acts as a pharmacological...

    Office of Scientific and Technical Information (OSTI)

    The non-detergent sulfobetaine-201 acts as a pharmacological chaperone to promote folding and crystallization of the type II TGF-beta receptor extracellular domain Citation ...

  5. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Previous bioinformatics analysis revealed a putative oligonucleotideoligosaccharide-binding (OB) fold at the N terminus of Stn1 (Stn1N) that shows limited sequence similarity to ...

  6. Early Lessons Learned

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

    since 1990 * 10-fold increase every 47 months, on average More large scientific instruments coming on line * Large Hadron Collider in CERN, telescopes, advance light sources, etc. ...

  7. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Structural proteomics of minimal organisms: conservation ofprotein fold usage and ... Results: We report that this goal has nearly been reachedfor several "minimal ...

  8. Structural proteomics of minimal organisms: conservation ofprotein...

    Office of Scientific and Technical Information (OSTI)

    of minimal organisms: conservation ofprotein fold usage and evolutionary implications Citation Details In-Document Search Title: Structural proteomics of minimal organisms: ...

  9. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... The strategy incurs minimal overhead and is scalable. March 2004 , IEEE Protein-folding via divide-and-conquer optimization Oliva, Ricardo ; Crivelli, Silvia ; Meza, Juan Full Text ...

  10. Structural Genomics: Expectations and Reality

    Office of Scientific and Technical Information (OSTI)

    proteomics of minimal organisms: Conservation of protein fold usage and evolutionary ... Results: We report that this goal has nearly been reached for several "minimal ...

  11. Protein kinesis: The dynamics of protein trafficking and stability

    SciTech Connect (OSTI)

    NONE

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  12. PROTEIN QUALITY CONTROL IN BACTERIAL CELLS: INTEGRATED NETWORKS OF CHAPERONES AND ATP-DEPENDENT PROTEASES.

    SciTech Connect (OSTI)

    FLANAGAN,J.M.; BEWLEY,M.C.

    2001-12-03

    It is generally accepted that the information necessary to specify the native, functional, three-dimensional structure of a protein is encoded entirely within its amino acid sequence; however, efficient reversible folding and unfolding is observed only with a subset of small single-domain proteins. Refolding experiments often lead to the formation of kinetically-trapped, misfolded species that aggregate, even in dilute solution. In the cellular environment, the barriers to efficient protein folding and maintenance of native structure are even larger due to the nature of this process. First, nascent polypeptides must fold in an extremely crowded environment where the concentration of macromolecules approaches 300-400 mg/mL and on average, each ribosome is within its own diameter of another ribosome (1-3). These conditions of severe molecular crowding, coupled with high concentrations of nascent polypeptide chains, favor nonspecific aggregation over productive folding (3). Second, folding of newly-translated polypeptides occurs in the context of their vehtorial synthesis process. Amino acids are added to a growing nascent chain at the rate of -5 residues per set, which means that for a 300 residue protein its N-terminus will be exposed to the cytosol {approx}1 min before its C-terminus and be free to begin the folding process. However, because protein folding is highly cooperative, the nascent polypeptide cannot reach its native state until a complete folding domain (50-250 residues) has emerged from the ribosome. Thus, for a single-domain protein, the final steps in folding are only completed post-translationally since {approx}40 residues of a nascent chain are sequestered within the exit channel of the ribosome and are not available for folding (4). A direct consequence of this limitation in cellular folding is that during translation incomplete domains will exist in partially-folded states that tend to expose hydrophobic residues that are prone to aggregation and/or misfolding. Thus it is not surprising that, in cells, the protein folding process is error prone and organisms have evolved ''editing'' or quality control (QC) systems to assist in the folding, maintenance and, when necessary, selective removal of damaged proteins. In fact, there is growing evidence that failure of these QC-systems contributes to a number of disease states (5-8). This chapter describes our current understanding of the nature and mechanisms of the protein quality control systems in the cytosol of bacteria. Parallel systems are exploited in the cytosol and mitochondria of eukaryotes to prevent the accumulation of misfolded proteins.

  13. Apacheta, a new geothermal prospect in Northern Chile

    SciTech Connect (OSTI)

    Urzua, Luis; Powell, Tom; Cumming, William B.; Dobson, Patrick

    2002-05-24

    The discovery of two high-temperature fumaroles, with gas geochemistry compatible with an economic geothermal system, established Apacheta as one of the most attractive geothermal exploration prospects in northern Chile. These remote fumaroles at 5,150 m elevation were first sampled in 1999 by ENAP and its partners, following up on the reports of a CODELCO water exploration well that flowed small amounts of dry steam at 4,540 m elevation in the valley 4.5 km east of the fumaroles. The prospect is associated with a Plio-Pleistocene volcanic complex located within a NW-trending graben along the axis of the high Andes. The regional water table is 4,200 masl. There are no hot springs, just the 88 degrees C steam well and the 109 degrees and 118 degrees C fumaroles with gas compositions that indicate reservoir temperatures of greater than or equal to 250 degrees C, using a variety of gas geothermometers. An MT-TDEM survey was completed in 2001-2002 by Geotermica del Norte (SDN), an ENAP-C ODELCO partnership, to explore the Apacheta geothermal concession. The survey results indicated that base of the low resistivity clay cap has a structural apex just west of the fumaroles, a pattern typically associated with shallow permeability within a high temperature geothermal resource. SGN plans to drill at least one exploration well in 2002-03 to characterize a possible economic resource at Apacheta.

  14. Regional seismic evaluation of basement control on paleozoic sedimentation in Ohio and West Virginia

    SciTech Connect (OSTI)

    Jovita, D.B.; Wilson, T.H. [West Virginia Univ., Morgantown, WV (United States)

    1995-09-01

    Paleozoic sediments of the central Appalachian lie upon a complexly deformed basement that continued to deform during the Paleozoic. In West Virginia basement is cut by an aulocogen known as the Rome trough. Seismic data reveal that the Rome Trough is an asymmetrical graben with a faulted eastern margin, and generally rotational western margin. Differential subsidence across the western margin decreases exponentially following the early Cambrian inception of the Trough. Displacement of the East Margin fault appears coupled to west-flank rotation. Minor inversion of Trough structure is also observed following the initial phase of rapid subsidence. Inversion influences local sedimentation patterns and results in minor structures that may influence hydrocarbon distribution. Regional seismic evaluation has been extended further west into Ohio to define regional scale subsidence history and local structural reactivation. Three seismic lines have been analyzed in Ohio that extend northwest from West Virginia to the Ohio COCORP line. Seismic expressions of the basement is marked by a relatively coherent reflection event. The basement faults in the distal part have similar offsets and therefore less influence on the sedimentary features. This analysis evaluates the structural affects of Coshocton zone, Cambridge Arch and Burning Spring anticline on the depositional history of Paleozoic sedimentation in Ohio.

  15. Structure of Precambrian crust in the U. S. from COCORP deep seismic profiling

    SciTech Connect (OSTI)

    Brown, L.D. (Cornell Univ., Ithaca, NY (United States))

    1992-01-01

    COCORP and industry seismic reflection profiles probing beneath the thin veneer of Paleozoic sedimentary rocks of the US mid-continent are mapping a complex, largely unknown three dimensional mosaic of major fault zones and sutures, a highly variable Moho, and extensive sequences of unexplored volcanic and/or sedimentary strata. Key features of the Precambrian suggested by COCORP and other deep profiling include: Pervasive, distributed reflectivity, often diffractive, dominating the middle and lower crust. Moho that is rarely reflective, usually evident as a downward transition of distributed crustal reflectivity into mantle transparency. Volcano-clastic filled graben of the late Proterozoic Keweenawan rift buried beneath Paleozoic strata in Kansas and Michigan. Extensive, subhorizontal Precambrian stratification in the upper crust beneath the east- central US and the Texas-Oklahoma border region, argued to be either an extensive volcano-clastic basin, a voluminous felsic volcanic outpouring or a major intrusive sill complex. Crustal penetrating, dipping reflection zones that mark known (Grenville front) or inferred (Cashocton zone, Trans-Hudson orogen) shear zones. Non-reflective ( ) basement beneath the Appalachian foreland suggesting transparent massifs'' that serve as collisional buttresses during terrane accretion. Deep structure is sometimes at odds with simple extrapolations of surface geology. Clearly deep seismic profiling has only begun to reveal the buried craton in the US. It is time for an integrated program for the systematic exploration of this special scientific frontier.

  16. PROTEIN QUALITY CONTROL IN BACTERIAL CELLS: INTEGRATED NETWORKS OF CHAPERONES AND ATP-DEPENDENT PROTEASES.

    SciTech Connect (OSTI)

    FLANAGAN,J.M.BEWLEY,M.C.

    2002-10-01

    It is generally accepted that the information necessary to specify the native, functional, three-dimensional structure of a protein is encoded entirely within its amino acid sequence; however, efficient reversible folding and unfolding is observed only with a subset of small single-domain proteins. Refolding experiments often lead to the formation of kinetically-trapped, misfolded species that aggregate, even in dilute solution. In the cellular environment, the barriers to efficient protein folding and maintenance of native structure are even larger due to the nature of this process. First, nascent polypeptides must fold in an extremely crowded environment where the concentration of macromolecules approaches 300-400 mg/mL and on average, each ribosome is within its own diameter of another ribosome (1-3). These conditions of severe molecular crowding, coupled with high concentrations of nascent polypeptide chains, favor nonspecific aggregation over productive folding (3). Second, folding of newly-translated polypeptides occurs in the context of their vehtorial synthesis process. Amino acids are added to a growing nascent chain at the rate of {approx}5 residues per set, which means that for a 300 residue protein its N-terminus will be exposed to the cytosol {approx}1 min before its C-terminus and be free to begin the folding process. However, because protein folding is highly cooperative, the nascent polypeptide cannot reach its native state until a complete folding domain (50-250 residues) has emerged from the ribosome. Thus, for a single-domain protein, the final steps in ffolding are only completed post-translationally since {approx}40 residues of a nascent chain are sequestered within the exit channel of the ribosome and are not available for folding (4). A direct consequence of this limitation in cellular folding is that during translation incomplete domains will exist in partially-folded states that tend to expose hydrophobic residues that are prone to aggregation and/or mislfolding. Thus it is not surprising that, in cells, the protein folding process is error prone and organisms have evolved ''editing'' or quality control (QC) systems to assist in the folding, maintenance and, when necessary, selective removal of damaged proteins. In fact, there is growing evidence that failure of these QC-systems contributes to a number of disease states (5-8). This chapter describes our current understanding of the nature and mechanisms of the protein quality control systems in the cytosol of bacteria. Parallel systems are exploited in the cytosol and mitochondria of eukaryotes to prevent the accumulation of misfolded proteins.

  17. Peppytides: Interactive Models of Polypeptide Chains

    ScienceCinema (OSTI)

    Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

    2014-10-28

    Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

  18. Flexible fuel cell gas manifold system

    DOE Patents [OSTI]

    Cramer, Michael; Shah, Jagdish; Hayes, Richard P.; Kelley, Dana A.

    2005-05-03

    A fuel cell stack manifold system in which a flexible manifold body includes a pan having a central area, sidewall extending outward from the periphery of the central area, and at least one compound fold comprising a central area fold connecting adjacent portions of the central area and extending between opposite sides of the central area, and a sidewall fold connecting adjacent portions of the sidewall. The manifold system further includes a rail assembly for attachment to the manifold body and adapted to receive pins by which dielectric insulators are joined to the manifold assembly.

  19. Peppytides: Interactive Models of Polypeptide Chains

    SciTech Connect (OSTI)

    Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

    2014-01-21

    Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

  20. Essential roles of protein-solvent many-body correlation in solvent...

    Office of Scientific and Technical Information (OSTI)

    Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water Citation ...

  1. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water Oshima, ...

  2. Tianjin Coslight Electric Bicycle Co Ltd | Open Energy Information

    Open Energy Info (EERE)

    Bicycle Co., Ltd. Place: China Product: China-based company making folding bikes and lithium-ion powered e-bikes. References: Tianjin Coslight Electric Bicycle Co., Ltd.1 This...

  3. Discovery of Pulsations from the Pulsar J0205 6449 in SNR 3C...

    Office of Scientific and Technical Information (OSTI)

    the radio rotational ephemeris used to fold gamma-rays was obtained using both the Green Bank Telescope and the Lovell telescope at Jodrell Bank. The light curve consists of...

  4. Unique Auxin Regulation Mechanism Discovered

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

    of life, auxin fulfills its role well. In addition, it does something that most other hormones of its type do not. Instead of changing shape (folding), auxin acts as a molecular...

  5. Secretary Ernest J. Moniz's Written Testimony on Climate Change...

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

    ... Since 2009, the number of super-efficient LED lights in the United States has grown 50-fold. And since 2008, the price of electric vehicle batteries has dropped by an estimated ...

  6. Energy Independence . . . It's up to us. Hawaii Clean Energy Initiative (HCEI) (Brochure)

    SciTech Connect (OSTI)

    Not Available

    2009-11-01

    This tri-fold brochure provides an overview of how the State of Hawaii will work toward a goal of 70% clean energy by 2030 and the importance of meeting this goal.

  7. Project Profile: Deployable Commercial Rooftop Solar Electric System

    Broader source: Energy.gov [DOE]

    Individual PV modules are mechanically interconnected using flexible hinges that allow a string of modules to be folded for transportation and storage into a compact form and then unfolded for...

  8. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences","Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.","2013-07-01T04:00:00Z",11...

  9. Structurally efficient inflatable protective device

    DOE Patents [OSTI]

    Nelsen, J.M.; Whinery, L.D.; Gwinn, K.W.; McBride, D.D.; Luna, D.A.; Holder, J.P.; Bliton, R.J.

    1997-03-04

    An apparatus and method are disclosed for making a low cost, self-venting, inflatable protective cushion of simple and structurally efficient design with a shape and construction that optimizes the cushion`s ability to withstand inflation pressures and impact when deployed which includes a sheet defined by at least one fold line and a plurality of flap portions, each flap portion having a base edge corresponding to a fold line and at least two side edges each extending outwardly from a base edge and ultimately converging to meet each other, the flap portions being folded at the fold line(s) and being joined at corresponding side edges to define an inflatable chamber. The inflatable protective cushion and method for making same may further include a lightweight, low permeability, fabric that optimizes the cushion`s ability to withstand inflation pressures and impact when deployed and minimizes the packed volume of the cushion when stored. 22 figs.

  10. Structurally efficient inflatable protective device

    DOE Patents [OSTI]

    Nelsen, J.M.; Whinery, L.D.; Gwinn, K.W.; McBride, D.D.; Luna, D.A.; Holder, J.P.; Bliton, R.J.

    1996-01-09

    An apparatus and method are disclosed for making a low cost, self-venting, inflatable protective cushion of simple and structurally efficient design with a shape and construction that optimizes the cushion`s ability to withstand inflation pressures and impact when deployed which includes a sheet defined by at least one fold line and a plurality of flap portions, each flap portion having a base edge corresponding to a fold line and at least two side edges each extending outwardly from a base edge and ultimately converging to meet each other, the flap portions being folded at the fold line(s) and being joined at corresponding side edges to define an inflatable chamber. The inflatable protective cushion and method for making same may further include a lightweight, low permeability, fabric that optimizes the cushion`s ability to withstand inflation pressures and impact when deployed and minimizes the packed volume of the cushion when stored. 22 figs.

  11. Geek-Up[6.17.2011]: Metallic Glass and 3D Plasmon Rulers

    Broader source: Energy.gov [DOE]

    How did scientists find a hidden property of gas? And a new ruler could help provide scientists with unprecedented details into a variety of biological events, including the interaction between DNA and enzymes, protein folding and cell membrane vibrations.

  12. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25

    A modified gene encoding a modified DNA polymerase is disclosed. The modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase. 6 figs.

  13. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles

    1997-01-01

    Modified gene encoding a modified DNA polymerase wherein the modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase.

  14. News Item

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

    Protein Folding Funnels Apply to Self-Assembly; Should Benefit Biomimicry and Nanosynthesis Jim DeYorero and Carolyn Bertozzi led a team of researchers at the Molecular Foundry...

  15. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    Development of a Fast Microfluidic Mixer for Studies of Protein Folding KineticsFinal Report Cover Page","Bakajin, O","2005-02-10T05:00:00Z",917494,"10.2172917494","UCRL-TR-209715...

  16. On the computational complexity of sequence design problems

    SciTech Connect (OSTI)

    Hart, W.E. [Sandia National Labs., Albuquerque, NM (United States)

    1997-12-01

    Inverse protein folding concerns the identification of an amino acid sequence that folds to a given structure. Sequence design problems attempt to avoid the apparant difficulty of inverse protein folding by defining an energy that can be minimized to find protein-like sequences. We evaluate the practical relevance of two sequence design problems by analyzing their computational complexity. We show that the canonical method of sequence design is intractable and describe approximation algorithms for this problem. We also describe an efficient algorithm that exactly solves the grand canonical method. Our analysis shows how sequence design problems can fail to reduce the difficulty of the inverse protein folding problem and highlights the need to analyze these problems to evaluate their practical relevance. 10 refs., 8 figs.

  17. On the computational complexity of sequence design problems

    SciTech Connect (OSTI)

    Hart, W.E. [Sandia National Labs., Albuquerque, NM (United States). Algorithms and Discrete Mathematics Dept.

    1996-12-31

    Inverse protein folding concerns the identification of an amino acid sequence that folds to a given structure. Sequence design problems attempt to avoid the apparent difficulty of inverse protein folding by defining an energy that can be minimized to find protein-like sequences. The authors evaluate the practical relevance of two sequence design problems by analyzing their computation complexity. They show that the canonical method of sequence design is intractable, and describe approximation algorithms for this problem. The authors also describe an efficient algorithm that exactly solves the grand canonical method. The analysis shows how sequence design problems can fail to reduce the difficulty of the inverse protein folding problem, and highlights the need to analyze these problems to evaluate their practical relevance.

  18. Statement of Dr. Ernest J. Moniz

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

    and we are working to make them even cheaper. Since 2009, the number of super-efficient LED lights in the United States has grown 50-fold. And since 2008, the price of electric...

  19. Current Collection Through The Ends Of A Spirally Wound Electrochemical Cell

    DOE Patents [OSTI]

    Oweis, Salah (Ellicott City, MD); Chagnon, Guy (Columbia, MD); Alunans, Peter (Baltimore, MD); Romero, Antonio (Parkton, MD)

    1999-10-26

    An electrochemical cell, including a jelly-roll type electrode stack, and a method for making such cell. The electrochemical cell includes folded electrode portions which form a plane recessed from the end of the electrode stack. The folded electrode portions are preferably formed by making pairs of slits in the electrode end and bending over the electrode portions between each pair of slits. The recessed plane forms a large area to which a current collection tab is subsequently connected. A coating may be applied to the folded portions of the electrode to further increase the contact area with the current collection tab by eliminating the slight variations in the recessed plane which are due to the overlap of the folded electrode portions.

  20. Increasing Importance of Natural Gas Imports on the U.S. Marketplace

    Reports and Publications (EIA)

    2000-01-01

    The growing importance of imported natural gas supplies in the U.S. marketplace, especially the northeast, is reflected in the two-fold increase in Canadian and overall net imports since 1990.

  1. Solar Energy Careers | Department of Energy

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

    The solar energy industry is booming. Since 2008, the amount of solar energy connected to the grid has increased 20 fold, reaching 22.7 GW today. This expansion has resulted in the ...

  2. Structurally efficient inflatable protective device

    DOE Patents [OSTI]

    Nelsen, James M.; Whinery, Larry D.; Gwinn, Kenneth W.; McBride, Donald D.; Luna, Daniel A.; Holder, Joseph P.; Bliton, Richard J.

    1996-01-01

    An apparatus and method for making a low cost, self-venting, inflatable protective cushion of simple and structurally efficient design with a shape and construction that optimizes the cushion's ability to withstand inflation pressures and impact when deployed which includes a sheet defined by at least one fold line and a plurality of flap portions, each flap portion having a base edge corresponding to a fold line and at least two side edges each extending outwardly from a base edge and ultimately converging to meet each other, the flap portions being folded at the fold line(s) and being Joined at corresponding side edges to define an inflatable chamber. The inflatable protective cushion and method for making same may further include a lightweight, low permeability, fabric that optimizes the cushion's ability to withstand inflation pressures and impact when deployed and minimizes the packed volume of the cushion when stored.

  3. Structurally efficient inflatable protective device

    DOE Patents [OSTI]

    Nelsen, James M.; Whinery, Larry D.; Gwinn, Kenneth W.; McBride, Donald D.; Luna, Daniel A.; Holder, Joseph P.; Bliton, Richard J.

    1996-01-01

    An apparatus and method for making a low cost, self-venting, inflatable protective cushion of simple and structurally efficient design with a shape and construction that optimizes the cushion's ability to withstand inflation pressures and impact when deployed which includes a sheet defined by at least one fold line and a plurality of flap portions, each flap portion having a base edge corresponding to a fold line and at least two side edges each extending outwardly from a base edge and ultimately converging to meet each other, the flap portions being folded at the fold line(s) and being joined at corresponding side edges to define an inflatable chamber. The inflatable protective cushion and method for making same may further include a lightweight, low permeability, fabric that optimizes the cushion's ability to withstand inflation pressures and impact when deployed and minimizes the packed volume of the cushion when stored.

  4. Structurally efficient inflatable protective device

    DOE Patents [OSTI]

    Nelsen, James M.; Whinery, Larry D.; Gwinn, Kenneth W.; McBride, Donald D.; Luna, Daniel A.; Holder, Joseph P.; Bliton, Richard J.

    1997-01-01

    An apparatus and method for making a low cost, self-venting, inflatable protective cushion of simple and structurally efficient design with a shape and construction that optimizes the cushion's ability to withstand inflation pressures and impact when deployed which includes a sheet defined by at least one fold line and a plurality of flap portions, each flap portion having a base edge corresponding to a fold line and at least two side edges each extending outwardly from a base edge and ultimately converging to meet each other, the flap portions being folded at the fold line(s) and being joined at corresponding side edges to define an inflatable chamber. The inflatable protective cushion and method for making same may further include a lightweight, low permeability, fabric that optimizes the cushion's ability to withstand inflation pressures and impact when deployed and minimizes the packed volume of the cushion when stored.

  5. Operating Experience Level 3, Laboratory Tests Indicate Conditions that Could Potentially Impact Certain Type of HEPA Filter Performance

    Broader source: Energy.gov [DOE]

    OE-3: 2013-02 This Operating Experience Summary provides new information on a potential performance issue associated with certain axial flow high efficiency particulate air (HEPA) filters that do not contain separators in the folded media (separatorless).

  6. Microsoft Word - Mitoneet.doc

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

    2007 MitoNEET is a Uniquely Folded Outer Mitochondrial Membrane Protein Stabilized by Diabetes Drugs The rise in obesity in the United States parallels a dramatic increase in...

  7. Novera Energy UK Ltd | Open Energy Information

    Open Energy Info (EERE)

    UK Ltd Place: Warrington, United Kingdom Zip: WA4 6HL Product: Novera was a landfill gas-to-power business in the UK acquired by Primergy in 2002 and folded into Novera...

  8. SAND2007-1643

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

    Hydrophobic effects,12 for example, are one of the dominant driving forces for protein folding13, 14 and other self-assembly processes such as formation of micelles and lipid...

  9. From Flapping Birds to Space Telescopes: The Modern Science of Origami (BNL Women in Science Lecture)

    SciTech Connect (OSTI)

    Lang, Robert J

    2010-06-24

    During the 1990s, the development and application of mathematical techniques to origami revolutionized this centuries-old Japanese art of paper folding. In his talk, Lang will describe how geometric concepts led to the solution of a broad class of origami-folding problems. Conversely, algorithms and theorems of origami design have shed light on long-standing mathematical questions and have solved practical engineering problems. Lang will discuss how origami has led to huge space telescopes, safer airbags, and more.

  10. Al{sub 70}Pd{sub 21.5}Mn{sub 8.5}: A quasicrystal showing the de haas-van Alphen effect

    SciTech Connect (OSTI)

    Haanappel, E.G. [National High Magnetic Field Laboratory, Los Alamos, NM (United States). Pulsed Field Facility; Kycia, S.W.; Harmon, B.N.; Canfield, P.C.; Goldman, A.I. [Iowa State Univ., Ames, IA (United States). Ames Lab.; Rabson, D.A.; Thompson, J.D.; Mueller, F.M. [Los Alamos National Lab., NM (United States)

    1995-07-01

    We have measured the de Haas-van Alphen effect in the icosahedral quasicrystal Al{sub 70}Pd{sub 21.5}Mn{sub 8.5}. We have found two well-defined frequencies with the magnetic field parallel to a five-fold axis, and two different ones with the field parallel to a two-fold axis. On increasing the temperature, the amplitude of the oscillations substantially decreased, suggesting that the carriers have large masses.

  11. ALS Capabilities Reveal Multiple Functions of Ebola Virus

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

    ALS Capabilities Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the protein. Recently, researchers used beamline capabilities at the ALS to demonstrate that a

  12. ALS Capabilities Reveal Multiple Functions of Ebola Virus

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

    ALS Capabilities Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the protein. Recently, researchers used beamline capabilities at the ALS to demonstrate that a

  13. ALS Capabilities Reveal Multiple Functions of Ebola Virus

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

    ALS Capabilities Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the protein. Recently, researchers used beamline capabilities at the ALS to demonstrate that a

  14. ALS Capabilities Reveal Multiple Functions of Ebola Virus

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

    ALS Capabilities Reveal Multiple Functions of Ebola Virus ALS Capabilities Reveal Multiple Functions of Ebola Virus Print Friday, 13 June 2014 10:25 A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the

  15. Protein Structure Recognition: From Eigenvector Analysis to Structural

    Office of Scientific and Technical Information (OSTI)

    Threading Method (Thesis/Dissertation) | SciTech Connect SciTech Connect Search Results Thesis/Dissertation: Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method Citation Details In-Document Search Title: Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process.

  16. Protein Structure Recognition: From Eigenvector Analysis to Structural

    Office of Scientific and Technical Information (OSTI)

    Threading Method (Thesis/Dissertation) | SciTech Connect Thesis/Dissertation: Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method Citation Details In-Document Search Title: Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation

  17. Ricardo Oliva

    Office of Scientific and Technical Information (OSTI)

    Protein folding via divide-and-conquer optimization Ricardo Oliva collaborators Silvia Crivelli, Juan Meza Computational Sciences Division Lawrence Berkeley National Laboratory This premise brings the protein-folding problem into the realm of numerical optimization algorithms (e.g. LBFGS) Compute an X * that minimizes E(X), where X is the vector of atom coordinates, and E is a potential energy function (e.g. Amber). This is a challenging problem: * Potential function E is only a model. *

  18. Few-Layer Graphene as a Dry Lubricant | Argonne National Laboratory

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

    Few-Layer Graphene as a Dry Lubricant Technology available for licensing: Graphene layers act as a two-dimensional nanomaterial and form a conformal protective coating on sliding contact interfaces. These factors facilitate shear and slow down oxidation (tribo-corrosion), thus drastically reduce wear. Functions as a dry lubricant, reducing wear four-fold and friction six-fold Cost-competitive with oil-based lubricants; may replace oil-based lubricants in some applications PDF icon

  19. ALS Capabilities Reveal Multiple Functions of Ebola Virus

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

    ALS Capabilities Reveal Multiple Functions of Ebola Virus Print A central dogma of molecular biology is that a protein's sequence dictates its fold, and the fold dictates its function. Scientists typically expect that a protein has a singular structure (with some conformational variation), and that when an experimental structure is solved, it can used to understand the known biological function(s) of the protein. Recently, researchers used beamline capabilities at the ALS to demonstrate that a

  20. Recuperator assembly and procedures

    DOE Patents [OSTI]

    Kang, Yungmo; McKeirnan, Jr., Robert D.

    2006-06-27

    A construction of recuperator core segments is provided which insures proper assembly of the components of the recuperator core segment, and of a plurality of recuperator core segments. Each recuperator core segment must be constructed so as to prevent nesting of fin folds of the adjacent heat exchanger foils of the recuperator core segment. A plurality of recuperator core segments must be assembled together so as to prevent nesting of adjacent fin folds of adjacent recuperator core segments.

  1. Recuperator assembly and procedures

    DOE Patents [OSTI]

    Kang, Yungmo (La Canada Flintridge, CA); McKeirnan, Jr., Robert D. (Westlake Village, CA)

    2008-08-26

    A construction of recuperator core segments is provided which insures proper assembly of the components of the recuperator core segment, and of a plurality of recuperator core segments. Each recuperator core segment must be constructed so as to prevent nesting of fin folds of the adjacent heat exchanger foils of the recuperator core segment. A plurality of recuperator core segments must be assembled together so as to prevent nesting of adjacent fin folds of adjacent recuperator core segments.

  2. Actinide/beryllium neutron sources with reduced dispersion characteristics

    DOE Patents [OSTI]

    Schulte, Louis D.

    2012-08-14

    Neutron source comprising a composite, said composite comprising crystals comprising BeO and AmBe.sub.13, and an excess of beryllium, wherein the crystals have an average size of less than 2 microns; the size distribution of the crystals is less than 2 microns; and the beryllium is present in a 7-fold to a 75-fold excess by weight of the amount of AmBe.sub.13; and methods of making thereof.

  3. Thermionic gas switch

    DOE Patents [OSTI]

    Hatch, G.L.; Brummond, W.A.; Barrus, D.M.

    1984-04-05

    The present invention is directed to an improved temperature responsive thermionic gas switch utilizing a hollow cathode and a folded emitter surface area. The folded emitter surface area of the thermionic switch substantially increases the on/off ratio by changing the conduction surface area involved in the two modes thereof. The improved switch of this invention provides an on/off ratio of 450:1 compared to the 10:1 ratio of the prior known thermionic switch, while providing for adjusting the on current. In the improved switch of this invention the conduction area is made small in the off mode, while in the on mode the conduction area is made large. This is achieved by utilizing a folded hollow cathode configuration and utilizing a folded emitter surface area, and by making the dimensions of the folds small enough so that a space charge will develop in the convolutions of the folds and suppress unignited current, thus limiting the current carrying surface in the off mode.

  4. Petroleum geology of Kate Spring field, Railroad Valley, Nye County, Nevada

    SciTech Connect (OSTI)

    French, D.E.

    1991-06-01

    Kate Spring field was opened by Marathon Oil Company at the 1 Kate Spring well in December 1985. Because of poor market conditions and production problems, the well was not produced and the field was not confirmed until the Evans 1 Taylor well was completed in October 1987. As of August 1990, five wells have produced over 575,000 bbl of oil and have the capacity to flow at rates of several hundred to several thousand barrels per day. The oil is 10-12{degrees} API and is saturated with gas. The oil is used for road asphalt which limits its marketability. Production is from landslide blocks of Paleozoic and lower Tertiary strata that were emplaced in Miocene-Pliocene time, during the structural development of the Railroad Valley basin. The slide blocks are overlain by valley fill and probably correspond to similar blocks encountered within the valley fill at Eagle Springs field, adjacent to the north. The pay is at a depth of 4,500 ft. Kate Spring is a part of the fault-block bench that contains Eagle Springs field and is situated on the east flank of the Railroad Valley graben. There is east-west closure on the structure of the field, but the north end of the field has not been defined. The accumulation is sealed by the unconformity at the slide block-valley fill contact. The nature of the reservoir implies that the production is controlled by fractures and precludes useful extrapolation of any measurable matrix porosity. Based on volumetric calculations, the field will probably produce 2-3 million bbl of oil.

  5. Oil and gas resources of the Fergana basin (Uzbekistan, Tadzhikistan, and Kyrgyzstan). Advance summary

    SciTech Connect (OSTI)

    Not Available

    1993-12-07

    The Energy Information Administration (EIA), in cooperation with the US Geological Survey (USGS), has assessed 13 major petroleum producing regions outside of the United States. This series of assessments has been performed under EIA`s Foreign Energy Supply Assessment Program (FESAP). The basic approach used in these assessments was to combine historical drilling, discovery, and production data with EIA reserve estimates and USGS undiscovered resource estimates. Field-level data for discovered oil were used for these previous assessments. In FESAP, supply projections through depletion were typically formulated for the country or major producing region. Until now, EIA has not prepared an assessment of oil and gas provinces in the former Soviet Union (FSU). Before breakup of the Soviet Union in 1991, the Fergana basin was selected for a trial assessment of its discovered and undiscovered oil and gas. The object was to see if enough data could be collected and estimated to perform reasonable field-level estimates of oil and gas in this basin. If so, then assessments of other basins in the FSU could be considered. The objective was met and assessments of other basins can be considered. Collected data for this assessment cover discoveries through 1987. Compared to most other oil and gas provinces in the FSU, the Fergana basin is relatively small in geographic size, and in number and size of most of its oil and gas fields. However, with recent emphasis given to the central graben as a result of the relatively large Mingbulak field, the basin`s oil and gas potential has significantly increased. At least 7 additional fields to the 53 fields analyzed are known and are assumed to have been discovered after 1987.

  6. Geothermal potential for commercial and industrial direct heat applications in Salida, Colorado. Final report

    SciTech Connect (OSTI)

    Coe, B.A.; Dick, J.D.; Galloway, M.J.; Gross, J.T.; Meyer, R.T.; Raskin, R.; Zocholl, J.R.

    1982-10-01

    The Salida Geothermal Prospect (Poncha Hot Springs) was evaluated for industrial and commercial direct heat applications at Salida, Colorado, which is located approximately five miles east of Poncha Hot Springs. Chaffee Geothermal, Ltd., holds the geothermal leases on the prospect and the right-of-way for the main pipeline to Salida. The Poncha Hot Springs are located at the intersection of two major structural trends, immediately between the Upper Arkansas graben and the Sangre de Cristo uplift. Prominent east-west faulting occurs at the actual location of the hot springs. Preliminary exploration indicates that 1600 gpm of geothermal fluid as hot as 250/sup 0/F is likely to be found at around 1500 feet in depth. The prospective existing endusers were estimated to require 5.02 x 10/sup 10/ Btu per year, but the total annual amount of geothermal energy available for existing and future endusers is 28.14 x 10/sup 10/ Btu. The engineering design for the study assumed that the 1600 gpm would be fully utilized. Some users would be cascaded and the spent fluid would be cooled and discharged to nearby rivers. The economic analysis assumes that two separate businesses, the energy producer and the energy distributor, are participants in the geothermal project. The producer would be an existing limited partnership, with Chaffee Geothermal, Ltd. as one of the partners; the distributor would be a new Colorado corporation without additional income sources. Economic evaluations were performed in full for four cases: the Base Case and three alternate scenarios. Alternate 1 assumes a three-year delay in realizing full production relative to the Base Case; Alternate 2 assumes that the geothermal reservoir is of a higher quality than is assumed for the Base Case; and Alternate 3 assumes a lower quality reservoir. 11 refs., 34 figs., 40 tabs.

  7. Facies distributions within contrasting structural components of a rift lake: Lake Tanganyika, Africa

    SciTech Connect (OSTI)

    Soreghan, M.J.; Cohen, A.S. )

    1991-03-01

    Lake Tanganyika is the most widely cited modern analog for interpreting ancient rift lakes; thus, understanding controls on its facies distribution is critical for refining stratigraphic models for rifts. Four recurrent margin types occur along the alternating half-graben structure of the lake: rift axes, platforms, escarpments, and accommodation zones. Data from study sites in the northern part of the lake suggest that predictable facies differences exist between these structural margin types. The rift axis site comprises a low-gradient, clastic (wave/current)-dominated deltaic system, with strong facies asymmetry and minor carbonate accumulations on raised benches. The platform margin site comprises a series of structurally controlled benches over which long, continuous facies tracts occur. Carbonate sands, muds, and shell gravel dominate; clastics are limited to moderate-sized silty deltas and long, narrow shoreface sands. The escarpment margin site is a steep-gradient system along which small ({lt}1 km{sup 2}) fan deltas alternate with cemented talus. The accommodation zone margin sites are also dominated by rugged structural relief, generally small fan deltas, and semicontinuous shoreface sand belts ({gt}5 km) onshore and poorly sorted silts offshore. TOC from fine-grained samples reflects the contrast in margin types. TOC values for the platform and rift axis range from 0.4 - 2.1 wt. % (avg. 1.3%), whereas accommodation zone and escarpment margin values range from 0.5-5.5% (avg. 3.0%). Acid insoluble sulfur shows a similar trend. Although all data are significantly correlated with depth, the relative area of the lake margin above and below the oxicline is directly controlled by the structural style of the lake margin.

  8. Salt tectonics and structural styles in the deep-water province of the Cabo Frio Region, Rio de Janeiro, Brazil

    SciTech Connect (OSTI)

    Mohriak, W.U.; Macedo, J.M.; Castellani, R.T.

    1996-12-31

    The Cabo Frio region, offshore Rio de Janeiro, lies between two of the most prolific Brazilian oil provinces, the Campos and Santos basins. Major geologic features have been identified using a multidisciplinary approach integrating seismic, gravity, petrographic, and borehole data. The Cabo Frio frontier region is characterized by marked changes in stratigraphy and structural style and is unique among the Brazilian marginal basins. Major geologic features include the deflection of the coastline and pre-Aptian hings line from northeast to east; a large east-striking offshore graben related to salt tectonics; a northwest-trending lineament extending from oceanic crust to the continent; basement-involved landward-dipping (antithetic) normal faults in shallow water; a stable platform in the southern Campos Basin; a thick sequence of postbreakup intrusive and extrusive rocks; and, near the Santos Basin, a mobilized sequence of deep-water postrift strata affected by landward-dipping listric normal faults. These faults are unusual in salt-related passive margins in that they dip landward, apparently detach on the Aptian salt, and show large late Tertiary offsets. Locally, the older sequences do not show substantial growth in the downthrown blocks. South of the Rio de Janeiro coast, a phenomenal landward-dipping fault system detaches blocks of the Albian platform to the north and, to the south, coincides with the depositional limit of the Albian platform. Two end-member processes of salt tectonics in the Cabo Frio region result in either synthetic or antithetic basal shear along the fault weld under the overburden: (1) thin-skinned processes, in which the listric faults were caused by salt flow in response to gravity forces related to massive clastic progradation from the continent; and (2) thick-skinned processes, in which faulting was indirectly triggered by diastrophic causes or disequilibrium in the basement topography.

  9. 2012 Groundwater Monitoring Report Central Nevada Test Area, Subsurface Corrective Action Unit 443

    SciTech Connect (OSTI)

    2013-04-01

    The Central Nevada Test Area was the site of a 0.2- to 1-megaton underground nuclear test in 1968. The surface of the site has been closed, but the subsurface is still in the corrective action process. The corrective action alternative selected for the site was monitoring with institutional controls. Annual sampling and hydraulic head monitoring are conducted as part of the subsurface corrective action strategy. The site is currently in the fourth year of the 5-year proof-of-concept period that is intended to validate the compliance boundary. Analytical results from the 2012 monitoring are consistent with those of previous years. Tritium remains at levels below the laboratory minimum detectable concentration in all wells in the monitoring network. Samples collected from reentry well UC-1-P-2SR, which is not in the monitoring network but was sampled as part of supplemental activities conducted during the 2012 monitoring, indicate concentrations of tritium that are consistent with previous sampling results. This well was drilled into the chimney shortly after the detonation, and water levels continue to rise, demonstrating the very low permeability of the volcanic rocks. Water level data from new wells MV-4 and MV-5 and recompleted well HTH-1RC indicate that hydraulic heads are still recovering from installation and testing. Data from wells MV-4 and MV-5 also indicate that head levels have not yet recovered from the 2011 sampling event during which several thousand gallons of water were purged. It has been recommended that a low-flow sampling method be adopted for these wells to allow head levels to recover to steady-state conditions. Despite the lack of steady-state groundwater conditions, hydraulic head data collected from alluvial wells installed in 2009 continue to support the conceptual model that the southeast-bounding graben fault acts as a barrier to groundwater flow at the site.

  10. Geology and geothermal resources of the Santiam Pass area of the Oregon Cascade Range, Deschutes, Jefferson and Linn Counties, Oregon. Final report

    SciTech Connect (OSTI)

    Hill, B.E.

    1992-10-01

    This open-file report presents the results of the Santiam Pass drilling program. The first phase of this program was to compile all available geological, geophysical and geothermal data for the Santiam Pass area and select a drill site on the basis of these data (see Priest and others, 1987a), A summary of the drilling operations and costs associated with the project are presented in chapter 1 by Hill and Benoit. An Overview of the geology of the Santiam Pass area is presented by Hill and Priest in chapter 2. Geologic mapping and isotopic age determinations in the Santiam Pass-Mount Jefferson area completed since 1987 are summarized in chapter 2. One of the more important conclusions reached in chapter 2 is that a minimum of 2 km vertical displacement has occurred in the High Cascade graben in the Santiam Pass area. The petrology of the Santiam Pass drill core is presented by Hill in chapter 3. Most of the major volcanic units in the core have been analyzed for major, minor, and trace element abundances and have been studied petrographically. Three K-Ar ages are interpreted in conjunction with the magnetostratigraphy of the core to show that the oldest rocks in the core are approximately 1.8 Ma. Geothermal and geophysical data collected from the Santiam Pass well are presented by Blackwell in chapter 4. The Santiam Pass well failed to penetrate beneath the zone of lateral groundwater flow associated with highly permeable Quaternary volcanic rocks. Calculated geothermal gradients range from about 50{degree}C/km at depth 700-900 m, to roughly 110{degree}C/km from 900 m to the bottom of the well at 929 m. Heat-flow values for the bottom part of the hole bracket the regional average for the High Cascades. Blackwell concludes that heat flow along the High Cascades axis is equal to or higher than along the western edge of the High Cascades.

  11. ADVANCED CHARACTERIZATION OF FRACTURED RESERVOIRS IN CARBONATE ROCKS: THE MICHIGAN BASIN

    SciTech Connect (OSTI)

    James R. Wood; William B. Harrison

    2000-04-01

    Progress in year 2 of this project is highlighted by the completing of the writing and testing of the project database, ''Atlas'', and populating it with all the project data gathered to date. This includes digitization of 17,000+ original Scout Tickets for the Michigan Basin. Work continues on the Driller's Reports, where they have scanned about 50,000 pages out of an estimated 300,000 pages. All of the scanned images have been attached to ''Atlas'', the visual database viewer developed for this project. A complete set of the 1/24,000 USGS DEM (Digital Elevation Models) for the State of Michigan has been downloaded from the USGS Web sites, decompressed and converted to ArcView Grid files. A large-scale map (48 inches x 84 inches) has been constructed by mosaicking of the high-resolution files. This map shows excellent ground surface detail and has drawn much comment and requests for copies at the venues where it has been displayed. Although it was generated for mapping of surface lineations the map has other uses, particularly analysis of the glacial drift in Michigan. It presents unusual problems due to its size and they are working with vendors on compression and display algorithms (e.g. MrSID{copyright}) in an attempt to make it available over the Internet, both for viewing and download. A set of aeromagnetic data for the Michigan Basin has been acquired and is being incorporated into the study. As reported previously, the general fracture picture in the Michigan Basin is a dominant NW-SE trend with a conjugate NE-SW trend. Subsurface, DEM and gravity data support the interpretation of a graben-type deep basement structural trend coincident with the Michigan Basin Gravity High. They plan to incorporate the aeromagnetic data into this interpretation as well.

  12. Deep structure of the Texas Gulf passive margin and its Ouachita-Precambrian basement: Results of the COCORP San Marcos arch survey

    SciTech Connect (OSTI)

    Culotta, R.; Latham, T.; Oliver, J.; Brown, L.; Kaufman, S. (Cornell Univ., Ithaca, NY (United States)); Sydow, M. (Pennzoil, Houston, TX (United States))

    1992-02-01

    This COCORP deep seismic survey provides a comprehensive image of the southeast-Texas part of the Gulf passive margin and its accreted Ouachita arc foundation. Beneath the updip limit of the Cenozoic sediment wedge, a prominent antiformal structure is imaged within the interior zone of the buried late Paleozoic Ouachita orogen. The structure appears to involve Precambrian Grenville basement. The crest of the antiform is coincident with the Cretaceous-Tertiary Luling-Mexia-Talco fault zone. Some of these faults dip to the northwest, counter to the general regional pattern of down-to-the-basin faulting, and appear to sole into the top of the antiform, suggesting that the Ouachita structure has been reactivated as a hingeline to the subsiding passive margin. The antiform may be tied via this fault system and the Ouachita gravity gradient to the similar Devils River, Waco, and Benton uplifts, interpreted as Precambrian basement-cored massifs. Above the Paleozoic sequence, a possible rift-related graben is imaged near the updip limit of Jurassic salt. Paleoshelf edges of the major Tertiary depositional sequences are marked by expanded sections disrupted by growth faults and shale diapirs. Within the Wilcox Formation, the transect crosses the mouth of the 900-m-deep Yoakum Canyon, a principal pathway of sediment delivery from the Laramide belt to the Gulf. Beneath the Wilcox, the Comanchean (Lower Cretaceous) shelf edge, capped by the Stuart City reef, is imaged as a pronounced topographic break onlapped by several moundy sediment packages. Because this segment of the line parallels strike, the topographic break may be interpreted as a 2,000-m-deep embayment in the Cretaceous shelf-edge, and possibly a major submarine canyon older and deeper than the Yoakum Canyon.

  13. Geology and geothermal resources of the Santiam Pass area of the Oregon Cascade Range, Deschutes, Jefferson and Linn Counties, Oregon

    SciTech Connect (OSTI)

    Hill, B.E. (ed.)

    1992-10-01

    This open-file report presents the results of the Santiam Pass drilling program. The first phase of this program was to compile all available geological, geophysical and geothermal data for the Santiam Pass area and select a drill site on the basis of these data (see Priest and others, 1987a), A summary of the drilling operations and costs associated with the project are presented in chapter 1 by Hill and Benoit. An Overview of the geology of the Santiam Pass area is presented by Hill and Priest in chapter 2. Geologic mapping and isotopic age determinations in the Santiam Pass-Mount Jefferson area completed since 1987 are summarized in chapter 2. One of the more important conclusions reached in chapter 2 is that a minimum of 2 km vertical displacement has occurred in the High Cascade graben in the Santiam Pass area. The petrology of the Santiam Pass drill core is presented by Hill in chapter 3. Most of the major volcanic units in the core have been analyzed for major, minor, and trace element abundances and have been studied petrographically. Three K-Ar ages are interpreted in conjunction with the magnetostratigraphy of the core to show that the oldest rocks in the core are approximately 1.8 Ma. Geothermal and geophysical data collected from the Santiam Pass well are presented by Blackwell in chapter 4. The Santiam Pass well failed to penetrate beneath the zone of lateral groundwater flow associated with highly permeable Quaternary volcanic rocks. Calculated geothermal gradients range from about 50[degree]C/km at depth 700-900 m, to roughly 110[degree]C/km from 900 m to the bottom of the well at 929 m. Heat-flow values for the bottom part of the hole bracket the regional average for the High Cascades. Blackwell concludes that heat flow along the High Cascades axis is equal to or higher than along the western edge of the High Cascades.

  14. Experimental Support for the Evolution of Symmetric Protein Architecture from a Simple Peptide Motif

    SciTech Connect (OSTI)

    J Lee; M Blaber

    2011-12-31

    The majority of protein architectures exhibit elements of structural symmetry, and 'gene duplication and fusion' is the evolutionary mechanism generally hypothesized to be responsible for their emergence from simple peptide motifs. Despite the central importance of the gene duplication and fusion hypothesis, experimental support for a plausible evolutionary pathway for a specific protein architecture has yet to be effectively demonstrated. To address this question, a unique 'top-down symmetric deconstruction' strategy was utilized to successfully identify a simple peptide motif capable of recapitulating, via gene duplication and fusion processes, a symmetric protein architecture (the threefold symmetric {beta}-trefoil fold). The folding properties of intermediary forms in this deconstruction agree precisely with a previously proposed 'conserved architecture' model for symmetric protein evolution. Furthermore, a route through foldable sequence-space between the simple peptide motif and extant protein fold is demonstrated. These results provide compelling experimental support for a plausible evolutionary pathway of symmetric protein architecture via gene duplication and fusion processes.

  15. Oxidation of aqueous pollutants using ultrasound: Salt-induced enhancement

    SciTech Connect (OSTI)

    Seymour, J.D.; Gupta, R.B.

    1997-09-01

    Ultrasound can be used to oxidize aqueous pollutants; however, due to economic reasons, higher oxidation/destruction rates are needed. This study reports enhancements of reaction rates by the addition of sodium chloride salt. Using 20 kHz ultrasound, large salt-induced enhancements are observed--6-fold for chlorobenzene, 7-fold for p-ethylphenol, and 3-fold for phenol oxidation. The reaction rate enhancements are proportional to the diethyl ether--water partitioning coefficient of the pollutants. It appears that the majority of oxidation reactions occur in the bubble-bulk interface region. The addition of salt increases the ionic strength of the aqueous phase which drives the organic pollutants toward the bubble-bulk interface. A first order reaction rate equation is proposed which can represent the observed enhancement with a good accuracy. A new sonochemical-waste-oxidation process is proposed utilizing the salt-induced enhancement.

  16. Sprague-Dawley rats display sex-linked differences in the pharmacokinetics of 3,4-methylenedioxymethamphetamine (MDMA) and its metabolite 3,4-methylenedioxyamphetamine (MDA)

    SciTech Connect (OSTI)

    Fonsart, Julien, E-mail: julien.fonsart@lrb.aphp.f [Universite Paris Descartes, Faculte de Pharmacie, Paris F-75006 (France); CNRS, UMR 7157, Paris F-75006 (France); INSERM, U705, Paris F-75006 (France); Assistance Publique-Hopitaux de Paris, Laboratoire de Toxicologie Biologique, Hopital Lariboisiere, Paris F-75010 (France); Menet, Marie-Claude [Universite Paris Descartes, Faculte de Pharmacie, Paris F-75006 (France); Universite Paris Descartes, Faculte de Pharmacie, Plateau Spectrometrie de Masse (IFR 71), Service de Chimie Analytique, Paris F-75006 (France); Debray, Marcel; Hirt, Deborah; Noble, Florence; Scherrmann, Jean-Michel; Decleves, Xavier [Universite Paris Descartes, Faculte de Pharmacie, Paris F-75006 (France); CNRS, UMR 7157, Paris F-75006 (France); INSERM, U705, Paris F-75006 (France)

    2009-12-15

    The use of 3,4-methylenedioxymethamphetamine (MDMA, ecstasy) has increased in recent years; it can lead to life-threatening hyperthermia and serotonin syndrome. Human and rodent males appear to be more sensitive to acute toxicity than are females. MDMA is metabolized to five main metabolites by the enzymes CYP1A2, CYP2D and COMT. Little is presently known about sex-dependent differences in the pharmacokinetics of MDMA and its metabolites. We therefore analyzed MDMA disposition in male and female rats by measuring the plasma and urine concentrations of MDMA and its metabolites using a validated LC-MS method. MDA AUC{sub last} and C{sub max} were 1.6- to 1.7-fold higher in males than in females given MDMA (5 mg/kg sc), while HMMA C{sub max} and AUC{sub last} were 3.2- and 3.5-fold higher, respectively. MDMA renal clearance was 1.26-fold higher in males, and that of MDA was 2.2-fold higher. MDMA AUC{sub last} and t{sub 1/2} were 50% higher in females given MDMA (1 mg/kg iv). MDA C{sub max} and AUC{sub last} were 75-82% higher in males, with a 2.8-fold higher metabolic index. Finally, the AUC{sub last} of MDA was 0.73-fold lower in males given 1 mg/kg iv MDA. The volumes of distribution of MDMA and MDA at steady-state were similar in the two sexes. These data strongly suggest that differences in the N-demethylation of MDMA to MDA are major influences on the MDMA and MDA pharmacokinetics in male and female rats. Hence, males are exposed to significantly more toxic MDA, which could explain previously reported sexual dysmorphism in the acute effects and toxicity of MDMA in rats.

  17. The use of bulk states to accelerate the band edge state calculation of a semiconductor quantum dot

    SciTech Connect (OSTI)

    Voemel, Christof . E-mail: voemel@eecs.berkeley.edu; Tomov, Stanimire Z. . E-mail: tomov@cs.utk.edu; Wang, Lin-Wang . E-mail: LWWang@lbl.gov; Marques, Osni A. . E-mail: OAMarques@lbl.gov; Dongarra, Jack J. . E-mail: dongarra@cs.utk.edu

    2007-05-01

    We present a new technique to accelerate the convergence of the folded spectrum method in empirical pseudopotential band edge state calculations for colloidal quantum dots. We use bulk band states of the materials constituent of the quantum dot to construct initial vectors and a preconditioner. We apply these to accelerate the convergence of the folded spectrum method for the interior states at the top of the valence and the bottom of the conduction band. For large CdSe quantum dots, the number of iteration steps until convergence decreases by about a factor of 4 compared to previous calculations.

  18. The use of bulk states to accelerate the band edge statecalculation of a semiconductor quantum dot

    SciTech Connect (OSTI)

    Vomel, Christof; Tomov, Stanimire Z.; Wang, Lin-Wang; Marques,Osni A.; Dongarra, Jack J.

    2006-05-10

    We present a new technique to accelerate the convergence of the folded spectrum method in empirical pseudopotential band edge state calculations for colloidal quantum dots. We use bulk band states of the materials constituent of the quantum dot to construct initial vectors and a preconditioner. We apply these to accelerate the convergence of the folded spectrum method for the interior states at the top of the valence and the bottom of the conduction band. For large CdSe quantum dots, the number of iteration steps until convergence decreases by about a factor of 4 compared to previous calculations.

  19. How much better are InGaN/GaN nanodisks than quantum wellsOscillator strength enhancement and changes in optical properties

    SciTech Connect (OSTI)

    Zhang, Lei; Hill, Tyler A.; Deng, Hui E-mail: peicheng@umich.edu; Lee, Leung-Kway; Teng, Chu-Hsiang; Ku, Pei-Cheng E-mail: peicheng@umich.edu

    2014-02-03

    We show over 100-fold enhancement of the exciton oscillator strength as the diameter of an InGaN nanodisk in a GaN nanopillar is reduced from a few micrometers to less than 40?nm, corresponding to the quantum dot limit. The enhancement results from significant strain relaxation in nanodisks less than 100?nm in diameter. Meanwhile, the radiative decay rate is only improved by 10 folds due to strong reduction of the local density of photon states in small nanodisks. Further increase in the radiative decay rate can be achieved by engineering the local density of photon states, such as adding a dielectric coating.

  20. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    SciTech Connect (OSTI)

    Xia, Kelin [Department of Mathematics, Michigan State University, Michigan 48824 (United States)] [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Mathematics, Michigan State University, Michigan 48824 (United States) [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States)

    2014-03-15

    This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction.

  1. Measurement of sin(2beta) in Tree-dominated B^0-Decays and Ambiguity Removal

    SciTech Connect (OSTI)

    Lacker, Heiko

    2007-03-05

    The most recent results from the B-factories on the time-dependent CP asymmetries measured in B{sup 0}-decays mediated by b {yields} c{bar c}s quark-transitions are reviewed. The Standard Model interpretation of the results in terms of the parameter sin 2{beta} leads to a four-fold ambiguity on the unitarity triangle {beta} which can be reduced to a two-fold ambiguity by measuring the sign of the parameter cos 2{beta}. The results on cos 2{beta} obtained so far are reviewed.

  2. Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres (Journal Article) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres Citation Details In-Document Search Title: Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres In budding yeast, Cdc13, Stn1, and Ten1 form a heterotrimeric complex (CST) that is essential for telomere protection and maintenance. Previous bioinformatics analysis revealed a putative oligonucleotide/oligosaccharide-binding (OB) fold at the N terminus of Stn1 (Stn1N) that shows limited sequence similarity to the OB fold of

  3. Origami-enabled deformable silicon solar cells

    SciTech Connect (OSTI)

    Tang, Rui; Huang, Hai; Liang, Hanshuang; Liang, Mengbing; Tu, Hongen; Xu, Yong; Song, Zeming; Jiang, Hanqing; Yu, Hongyu

    2014-02-24

    Deformable electronics have found various applications and elastomeric materials have been widely used to reach flexibility and stretchability. In this Letter, we report an alternative approach to enable deformability through origami. In this approach, the deformability is achieved through folding and unfolding at the creases while the functional devices do not experience strain. We have demonstrated an example of origami-enabled silicon solar cells and showed that this solar cell can reach up to 644% areal compactness while maintaining reasonable good performance upon cyclic folding/unfolding. This approach opens an alternative direction of producing flexible, stretchable, and deformable electronics.

  4. Workers Complete Retrieval of 11th Single-Shell Tank at EM's Hanford Site

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

    | Department of Energy composite image comprised of dozens of photos taken inside C-110 provides a rare panoramic view of the tank interior. Portions of the tank floor and the FoldTrack waste-retrieval system are clearly visible. A composite image comprised of dozens of photos taken inside C-110 provides a rare panoramic view of the tank interior. Portions of the tank floor and the FoldTrack waste-retrieval system are clearly visible. Operators use multiple technologies to remove waste from

  5. Chemical Profiles of Microalgae with Emphasis on Lipids: Final Report

    SciTech Connect (OSTI)

    Benemann, J. R.; Tillett, D. M.; Suen, Y.; Hubbard, J.; Tornabene, T. G.

    1986-02-01

    This final report details progress during the third year of this subcontract. The overall objective of this subcontract was two fold: to provide the analytical capability required for selecting microalgae strains with high energy contents and to develop fundamental knowledge required for optimizing the energy yield from microalgae cultures. The progress made towards these objectives during this year is detailed in this report.

  6. The Wallula fault and tectonic framework of south-central Washington, as interpreted from magnetic and gravity anomalies

    SciTech Connect (OSTI)

    Blakely, Richard J.; Sherrod, Brian; Weaver, Craig; Wells, Ray E.; Rohay, Alan C.

    2014-06-11

    Magnetic and gravity data, collected in south-central Washington near the Yakima Fold and Thrust Belt (YFTB) are used to model upper crustal structure, the extent of the late Columbia River Basalt flow named the Ice Harbor member, the vertical conduits (dikes) that the Ice Harbor erupted from, and whether the dikes are offset or affected by faulting on the Wallula Fault zone.

  7. Geologic Map and GIS Data for the Wabuska Geothermal Area

    SciTech Connect (OSTI)

    Hinz, Nick

    2013-09-30

    WabuskaESRI geodatabase (ArcGeology v1.3): - Contains all the geologic map data, including faults, contacts, folds, veins, dikes, unit polygons, and attitudes of strata. - List of stratigraphic units and stratigraphic correlation diagram. - One cross?section.

  8. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    Protein-folding via divide-and-conquer optimization","Oliva, Ricardo; Crivelli, Silvia; Meza, Juan","2004-07-11T04:00:00Z",882903,,"LBNL--55869","DE-AC02-05CH11231","R&D Project:...

  9. Photoluminescence Enhancement in CdSe/ZnSDNA linkedAu Nanoparticle Heterodimers Probed by Single Molecule Spectroscopy

    SciTech Connect (OSTI)

    Cotlet, M.; Maye, M.M.; Gang, O.

    2010-07-26

    Photoluminescence enhancement of up to 20 fold is demonstrated at the single molecule level for heterodimers composed of a core/shell CdSe/ZnS semiconductive quantum dot and a gold nanoparticle of 60 nm size separated by a 32 nm-long dsDNA linker when employing optical excitation at wavelengths near the surface plasmon resonance of the gold nanoparticle.

  10. Identifying low-coverage surface species on noble metal nanoparticles by DNP-NMR

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

    Johnson, Robert L.; Perras, Frdric A.; Kobayashi, Takeshi; Schwartz, Thomas J.; Dumesic, James A.; Shanks, Brent H.; Pruski, Marek

    2015-11-20

    DNP-NMR spectroscopy has been applied to enhance the signal for organic molecules adsorbed on ?-Al2O3-supported Pd nanoparticles. In addition, by offering >2500-fold time savings, the technique enabled the observation of 13C-13C cross-peaks for low coverage species, which were assigned to products from oxidative degradation of methionine adsorbed on the nanoparticle surface.

  11. Evidence for small-molecule-mediated loop stabilization in the structure of the isolated Pin1 WW domain

    SciTech Connect (OSTI)

    Mortenson, David E.; Kreitler, Dale F.; Yun, Hyun Gi; Gellman, Samuel H., E-mail: gellman@chem.wisc.edu; Forest, Katrina T., E-mail: gellman@chem.wisc.edu [University of Wisconsin-Madison, Madison, WI 53706 (United States)

    2013-12-01

    Two structures of a small protein with a defined tertiary fold, the isolated Pin1 WW domain, have been determined via racemic crystallization with small-molecule additives. These additives, which are either racemic or achiral, appear to stabilize a dynamic loop region of the structure. The human Pin1 WW domain is a small autonomously folding protein that has been useful as a model system for biophysical studies of ?-sheet folding. This domain has resisted previous attempts at crystallization for X-ray diffraction studies, perhaps because of intrinsic conformational flexibility that interferes with the formation of a crystal lattice. Here, the crystal structure of the human Pin1 WW domain has been obtained via racemic crystallization in the presence of small-molecule additives. Both enantiomers of a 36-residue variant of the Pin1 WW domain were synthesized chemically, and the l- and d-polypeptides were combined to afford diffracting crystals. The structural data revealed packing interactions of small carboxylic acids, either achiral citrate or a d,l mixture of malic acid, with a mobile loop region of the WW-domain fold. These interactions with solution additives may explain our success in crystallization of this protein racemate. Molecular-dynamics simulations starting from the structure of the Pin1 WW domain suggest that the crystal structure closely resembles the conformation of this domain in solution. The structural data presented here should provide a basis for further studies of this important model system.

  12. Preliminary X-ray crystallographic studies of mouse UPR responsive protein P58(IPK) TPR fragment

    SciTech Connect (OSTI)

    Tao, Jiahui; Wu, Yunkun [Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294 (United States); Ron, David [Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016 (United States); Sha, Bingdong, E-mail: bdsha@uab.edu [Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294 (United States)

    2008-02-01

    To investigate the mechanism by which P58(IPK) functions to promote protein folding within the ER, a P58(IPK) TPR fragment without the C-terminal J-domain has been crystallized. Endoplasmic reticulum (ER) stress induces the unfolded protein response (UPR), which can promote protein folding and misfolded protein degradation and attenuate protein translation and protein translocation into the ER. P58(IPK) has been proposed to function as a molecular chaperone to maintain protein-folding homeostasis in the ER under normal and stressed conditions. P58(IPK) contains nine TPR motifs and a C-terminal J-domain within its primary sequence. To investigate the mechanism by which P58(IPK) functions to promote protein folding within the ER, a P58(IPK) TPR fragment without the C-terminal J-domain was crystallized. The crystals diffract to 2.5 resolution using a synchrotron X-ray source. The crystals belong to space group P2{sub 1}, with unit-cell parameters a = 83.53, b = 92.75, c = 84.32 , ? = 90.00, ? = 119.36, ? = 90.00. There are two P58(IPK) molecules in the asymmetric unit, which corresponds to a solvent content of approximately 60%. Structure determination by MAD methods is under way.

  13. Exploring the structural dynamics of the E. coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states

    SciTech Connect (OSTI)

    Chaudhry, Charu; Horwich, Arthur L.; Brunger, Axel T.; Adams, Paul D.

    2004-08-12

    Large rigid-body domain movements are critical to GroEL-mediated protein folding, especially apical domain elevation and twist associated with the formation of a folding chamber upon binding ATP and co-chaperonin GroES. Here, we have modeled the anisotropic displacements of GroEL domains from various crystallized states, unliganded GroEL, ATP?S-bound, ADP-AlFx/GroES-bound, and ADP/GroES bound, using translation-libration-screw (TLS) analysis. Remarkably, the TLS results show that the inherent motions of unliganded GroEL, a polypeptide-accepting state, are biased along the transition pathway that leads to the folding-active state. In the ADP-AlFx/GroES-bound folding-active state the dynamic modes of the apical domains become reoriented and coupled to the motions of bound GroES. The ADP/GroES complex exhibits these same motions, but they are increased in magnitude, potentially reflecting the decreased stability of the complex after nucleotide hydrolysis. Our results have allowed the visualization of the anisotropic molecular motions that link the static conformations previously observed by X-ray crystallography. Application of the same analyses to other macromolecules where rigid body motions occur may give insight into the large scale dynamics critical for function and thus has the potential to extend our fundamental understanding of molecular machines.

  14. Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains

    SciTech Connect (OSTI)

    Daidone, Isabella [University of Heidelberg; Neuweiler, H [University of Heidelberg; Doose, S [University of Heidelberg; Sauer, M [University of Heidelberg; Smith, Jeremy C [ORNL

    2010-12-01

    Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20-100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient beta-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events.

  15. Finding the needle in the haystack: Algorithms for conformational optimization

    SciTech Connect (OSTI)

    Andricioaei, I.; Straub, J.E.

    1996-09-01

    Algorithms are given for comformational optimization of proteins. The protein folding problems is regarded as a problem of global energy mimimization. Since proteins have hundreds of atoms, finding the lowest-energy conformation in a many-dimensional configuration space becomes a computationally demanding problem.{copyright} {ital American Institute of Physics.}

  16. Wide angle x-ray scattering of proteins : effect of beam exposure on protein integrity.

    SciTech Connect (OSTI)

    Fischetti, R. F.; Rodi, D. J.; Mirza, A.; Makowski, L.; Illinois Inst. of Tech.

    2003-01-01

    Wide-angle X-ray scattering patterns from proteins in solution contain information relevant to the determination of protein fold. At relevant scattering angles, however, these data are weak, and the degree to which they might be used to categorize the fold of a protein is unknown. Preliminary work has been performed at the BioCAT insertion-device beamline at the Advanced Photon Source which demonstrates that one can collect X-ray scattering data from proteins in solution to spacings of at least 2.2 {angstrom} (q = 2.8 {angstrom}-1). These data are sensitive to protein conformational states, and are in good agreement with the scattering predicted by the program CRYSOL using the known three-dimensional atomic coordinates of the protein. An important issue in the exploitation of this technique as a tool for structural genomics is the extent to which the high intensity of X-rays available at third-generation synchrotron sources chemically or structurally damage proteins. Various data-collection protocols have been investigated demonstrating conditions under which structural degradation of even sensitive proteins can be minimized, making this technique a viable tool for protein fold categorization, the study of protein folding, unfolding, protein-ligand interactions and domain movement.

  17. Deposition and Characterization of Improved Hydrogen Getter Materials - Report on FY 14-15 Activities

    SciTech Connect (OSTI)

    Hubbard, Kevin Mark; Sandoval, Cynthia Wathen

    2015-10-15

    The goals of this work have been two-fold. First, to perform an initial, quantitative, optimization of getter performance, with the primary variables being DEB/Pd ratio and UV power. Second, to simplify the deposition process to make it more compatible with the DOE production environment.

  18. Biocatalytic conversion of ethylene to ethylene oxide using an engineered toluene monooxygenase

    SciTech Connect (OSTI)

    Carlin, DA; Bertolani, SJ; Siegel, JB

    2015-01-01

    Mutants of toluene o-xylene monooxygenase are demonstrated to oxidize ethylene to ethylene oxide in vivo at yields of >99%. The best mutant increases ethylene oxidation activity by >5500-fold relative to the native enzyme. This is the first report of a recombinant enzyme capable of carrying out this industrially significant chemical conversion.

  19. Reduced Call-Backs with High Performance Production Builders- Building America Top Innovation

    Broader source: Energy.gov [DOE]

    This Building America Innovations profile describes ways Building America teams have helped builders cut call backs. Harvard University study found builders who worked with Building America had a 50% drop in callbacks. One builder reported a 50-fold reduction in the incidence of pipe freezing, a 50% reduction in drywall cracking, and a 60% decline in call-backs.

  20. Geologic Map and GID Data for the Salt Wells Geothermal Area

    SciTech Connect (OSTI)

    Hinz, Nick

    2011-10-31

    Salt WellsESRI Geodatabase (ArcGeology v1.3): - Contains all the geologic map data, including faults, contacts, folds, dikes, unit polygons, and attitudes of strata and faults. - List of stratigraphic units and stratigraphic correlation diagram. - Locations of 40Ar/39Ar samples.

  1. Geologic Map and GIS Data for the Patua Geothermal Area

    SciTech Connect (OSTI)

    Faulds, James E.

    2011-10-31

    PatuaESRI Geodatabase (ArcGeology v1.3): - Contains all the geologic map data, including faults, contacts, folds, veins, dikes, unit polygons, and attitudes of strata and faults. - List of stratigraphic units. - Locations of geothermal wells. - Locations of 40Ar/39Ar and tephra samples.

  2. Plasmids containing the gene for DNA polymerase I from Streptococcus pneumoniae

    DOE Patents [OSTI]

    Lacks, S.A.; Martinez, S.; Lopez, P.; Espinosa, M.

    1987-08-28

    A method is disclosed for cloning the gene which encodes a DNA polymerase-exonuclease of /und Streptococcus/ /und pneumoniae/. Plasmid pSM22, the vector containing the pneumococcal polA gene, facilitates the expression of 50-fold greater amounts of the PolI enzyme. 1 fig., 1 tab.

  3. Plasmids containing the gene for DNA polymerase I from Streptococcus pneumoniae

    DOE Patents [OSTI]

    Lacks, S.A.; Martinez, S.; Lopez, P.; Espinosa, M.

    1991-03-26

    A method is disclosed for cloning the gene which encodes a DNA polymerase-exonuclease of Streptococcus pneumoniae. Plasmid pSM22, the vector containing the pneumocccal polA gene, facilitates the expression of 50-fold greater amounts of the PolI enzyme. 1 figure.

  4. Brochure, Understanding UCNI - July 2010 | Department of Energy

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

    UCNI - July 2010 Brochure, Understanding UCNI - July 2010 July 2010 Tri-fold brochure outlining what UCNI is and the guidelines on identifying, marking and protecting UCNI. PDF icon Brochure, Understanding UCNI - July 2010 More Documents & Publications Briefing, For Persons With Access to UCNI - June 2014 Summary, UCNI Document Markings - November 2011 Unclassified Controlled Nuclear Information General Guideline

  5. Affinity and selectivity of beta-adrenoceptor antagonists in vitro

    SciTech Connect (OSTI)

    Wellstein, A.; Palm, D.; Belz, G.G.

    1986-01-01

    The potency order of the catecholamines (-)-isoprenaline (Iso), (-)-noradrenaline (NA), and (-)-adrenaline (Adr) in competition for radiolabelled sites is used for their pharmacological classification. It is shown that the radioligand /sup 3/H-CGP 12177 exclusively labels beta 1-adrenoceptors in rat salivary gland membranes (Iso greater than NA greater than Adr), and beta 2-adrenoceptors in rat reticulocytes (Iso greater than Adr greater than or equal to NA). These models are then used to derive the subtype-selectivity of the classical beta-adrenoceptor antagonists (+/-)-propranolol (prop; twofold beta 2-selective) and (+/-)-atenolol (aten; 35-fold beta 1-selective), as well as of the newer antagonists (+/-)-betaxolol and (+/-)-bisoprolol (betax and biso; 35-fold and 75-fold beta 1-selective, respectively). The ligand with the highest selectivity is ICI 118,551 (ICI), with a 300-fold beta 2-subtype selectivity. For comparison with antagonistic effects in humans at given plasma concentrations, the equilibrium dissociation constants of the ligands are measured in the presence of native human plasma and yield values for the relative selectively labelled subtype in the mean (Ki-values in nmol/l): prop: 20, aten: 250, biso: 24, betax: 23, and ICI: 2.5.

  6. Plasimids containing the gene for DNA polymerase I from Streptococcus pneumoniae

    DOE Patents [OSTI]

    Lacks, Sanford A. (Brookhaven, NY); Martinez, Susana (Sound Beach, NY); Lopez, Paloma (Madrid, ES); Espinosa, Manuel (Madrid, ES)

    1991-01-01

    A method is disclosed for cloning the gene which encodes a DNA polymerase-exonuclease of Streptococcus pneumoniae. Plasmid pSM22, the vector containing the pneumocccal polA gene, facilitates the expression of 50-fold greater amounts of the PolI enzyme.

  7. Improved cathode materials for microbial electrosynthesis

    SciTech Connect (OSTI)

    Zhang, T; Nie, HR; Bain, TS; Lu, HY; Cui, MM; Snoeyenbos-West, OL; Franks, AE; Nevin, KP; Russell, TP; Lovley, DR

    2013-01-01

    Microbial electrosynthesis is a promising strategy for the microbial conversion of carbon dioxide to transportation fuels and other organic commodities, but optimization of this process is required for commercialization. Cathodes which enhance electrode-microbe electron transfer might improve rates of product formation. To evaluate this possibility, biofilms of Sporomusa ovata, which are effective in acetate electrosynthesis, were grown on a range of cathode materials and acetate production was monitored over time. Modifications of carbon cloth that resulted in a positive-charge enhanced microbial electrosynthesis. Functionalization with chitosan or cyanuric chloride increased acetate production rates 6-7 fold and modification with 3-aminopropyltriethoxysilane gave rates 3-fold higher than untreated controls. A 3-fold increase in electrosynthesis over untreated carbon cloth cathodes was also achieved with polyaniline cathodes. However, not all strategies to provide positively charged surfaces were successful, as treatment of carbon cloth with melamine or ammonia gas did not stimulate acetate electrosynthesis. Treating carbon cloth with metal, in particular gold, palladium, or nickel nanoparticles, also promoted electrosynthesis, yielding electrosynthesis rates that were 6-,4.7- or 4.5-fold faster than the untreated control, respectively. Cathodes comprised of cotton or polyester fabric treated with carbon nanotubes yielded cathodes that supported acetate electrosynthesis rates that were similar to 3-fold higher than carbon cloth controls. Recovery of electrons consumed in acetate was similar to 80% for all materials. The results demonstrate that one approach to increase rates of carbon dioxide reduction in microbial electrosynthesis is to modify cathode surfaces to improve microbe-electrode interactions.

  8. Innovative Methodology for Detection of Fracture-Controlled Sweet Spots in the Northern Appalachian Basin

    SciTech Connect (OSTI)

    Robert Jacobi; John Fountain; Stuart Loewenstein; Edward DeRidder; Bruce Hart

    2007-03-31

    For two consecutive years, 2004 and 2005, the largest natural gas well (in terms of gas flow/day) drilled onshore USA targeted the Ordovician Trenton/Black River (T/BR) play in the Appalachian Basin of New York State (NYS). Yet, little data were available concerning the characteristics of the play, or how to recognize and track T/BR prospects across the region. Traditional exploration techniques for entry into a hot play were of limited use here, since existing deep well logs and public domain seismic were almost non-existent. To help mitigate this problem, this research project was conceived with two objectives: (1) to demonstrate that integrative traditional and innovative techniques could be used as a cost-effective reconnaissance exploration methodology in this, and other, areas where existing data in targeted fracture-play horizons are almost non-existent, and (2) determine critical characteristics of the T/BR fields. The research region between Seneca and Cayuga lakes (in the Finger Lakes of NYS) is on strike and east of the discovery fields, and the southern boundary of the field area is about 8 km north of more recently discovered T/BR fields. Phase I, completed in 2004, consisted of integrating detailed outcrop fracture analyses with detailed soil gas analyses, lineaments, stratigraphy, seismic reflection data, well log data, and aeromagnetics. In the Seneca Lake region, Landsat lineaments (EarthSat, 1997) were coincident with fracture intensification domains (FIDs) and minor faults observed in outcrop and inferred from stratigraphy. Soil gas anomalies corresponded to ENE-trending lineaments and FIDs. N- and ENE-trending lineaments were parallel to aeromagnetic anomalies, whereas E-trending lineaments crossed aeromagnetic trends. 2-D seismic reflection data confirmed that the E-trending lineaments and FIDs occur where shallow level Alleghanian salt-cored thrust-faulted anticlines occur. In contrast, the ENE-trending FIDs and lineaments occur where Iapetan rift faults have been episodically reactivated, and a few of these faults extend through the entire stratigraphic section. The ENE-trending faults and N-striking transfer zones controlled the development of the T/BR grabens. In both the Seneca Lake and Cayuga Lake regions, we found more FIDs than Landsat lineaments, both in terms of individual FIDs and trends of FIDs. Our fused Landsat/ASTER image provided more lineaments, but the structural framework inferred from these lineaments is incomplete even for the fused image. Individual lineaments may not predict surface FIDs (within 500m). However, an individual lineament that has been groundtruthed by outcrop FIDs can be used as a proxy for the trend of intense fracturing. Aeromagnetics and seismic reflection data across the discovery fields west of Keuka Lake demonstrate that the fields terminate on the east against northerly-striking faults that extend from Precambrian basement to, in some cases, the surface; the fields terminate in the west at N- and NW-striking faults. Seismic and well log data show that the fields must be compartmentalized, since different parts of the same field show different histories of development. T/BR fields south of the research area also terminate (on the east) against northerly-trending lineaments which we suggest mark faults. Phase II, completed in 2006, consisted of collection and analysis of an oriented, horizontal core retrieved from one of the T/BR fields in a graben south of the field area. The field is located along ENE-trending EarthSat (1997) lineaments, similar to that hypothesized for the study area. The horizontal core shows much evidence for reactivation along the ENE-trending faults, with multiple events of vein development and both horizontal and vertical stylolite growth. Horizontal veins that post- and pre-date other vein sets indicate that at least two orogenic phases (separated by unloading) affected vein development. Many of the veins and releasing bend features (rhombochasms) are consistent with strike-slip motion (oblique) along ENE-striking faults as a result

  9. Sodium arsenite represses the expression of myogenin in C2C12 mouse myoblast cells through histone modifications and altered expression of Ezh2, Glp, and Igf-1

    SciTech Connect (OSTI)

    Hong, Gia-Ming; Present address: The University of Chicago, Section of Hematology Bain, Lisa J.

    2012-05-01

    Arsenic is a toxicant commonly found in water systems and chronic exposure can result in adverse developmental effects including increased neonatal death, stillbirths, and miscarriages, low birth weight, and altered locomotor activity. Previous studies indicate that 20 nM sodium arsenite exposure to C2C12 mouse myocyte cells delayed myoblast differentiation due to reduced myogenin expression, the transcription factor that differentiates myoblasts into myotubes. In this study, several mechanisms by which arsenic could alter myogenin expression were examined. Exposing differentiating C2C12 cells to 20 nM arsenic increased H3K9 dimethylation (H3K9me2) and H3K9 trimethylation (H3K9me3) by 3-fold near the transcription start site of myogenin, which is indicative of increased repressive marks, and reduced H3K9 acetylation (H3K9Ac) by 0.5-fold, indicative of reduced permissive marks. Protein expression of Glp or Ehmt1, a H3-K9 methyltransferase, was also increased by 1.6-fold in arsenic-exposed cells. In addition to the altered histone remodeling status on the myogenin promoter, protein and mRNA levels of Igf-1, a myogenic growth factor, were significantly repressed by arsenic exposure. Moreover, a 2-fold induction of Ezh2 expression, and an increased recruitment of Ezh2 (3.3-fold) and Dnmt3a (? 2-fold) to the myogenin promoter at the transcription start site (? 40 to + 42), were detected in the arsenic-treated cells. Together, we conclude that the repressed myogenin expression in arsenic-exposed C2C12 cells was likely due to a combination of reduced expression of Igf-1, enhanced nuclear expression and promoter recruitment of Ezh2, and altered histone remodeling status on myogenin promoter (? 40 to + 42). -- Highlights: ? Igf-1 expression is decreased in C2C12 cells after 20 nM arsenite exposure. ? Arsenic exposure alters histone remodeling on the myogenin promoter. ? Glp expression, a H3K9 methyltransferase, was increased in arsenic-exposed cells. ? Ezh2 and Dnmt3a localization to the myogenin promoter is induced by arsenic.

  10. Plastic Laminate Pulsed Power Development

    SciTech Connect (OSTI)

    ALEXANDER,JEFF A.; SHOPE,STEVEN L.; PATE,RONALD C.; RINEHART,LARRY F.; JOJOLA,JOHN M.; RUEBUSH,MITCHELL H.; CROWE,WAYNE; LUNDSTROM,J.; SMITH,T.; ZAGAR,D.; PRESTWICH,K.

    2000-09-01

    The desire to move high-energy Pulsed Power systems from the laboratory to practical field systems requires the development of compact lightweight drivers. This paper concerns an effort to develop such a system based on a plastic laminate strip Blumlein as the final pulseshaping stage for a 600 kV, 50ns, 5-ohm driver. A lifetime and breakdown study conducted with small-area samples identified Kapton sheet impregnated with Propylene Carbonate as the best material combination of those evaluated. The program has successfully demonstrated techniques for folding large area systems into compact geometry's and vacuum impregnating the laminate in the folded systems. The major operational challenges encountered revolve around edge grading and low inductance, low impedance switching. The design iterations and lessons learned are discussed. A multistage prototype testing program has demonstrated 600kV operation on a short 6ns line. Full-scale prototypes are currently undergoing development and testing.

  11. Fuel cell separator plate with bellows-type sealing flanges

    DOE Patents [OSTI]

    Louis, George A. (West Hartford, CT)

    1986-08-05

    A fuel cell separator includes a rectangular flat plate having two unitary upper sealing flanges respectively comprising opposite marginal edges of the plate folded upwardly and back on themselves and two lower sealing flanges respectively comprising the other two marginal edges of the plate folded downwardly and back on themselves. Each of the sealing flanges includes a flat wall spaced from the plate and substantially parallel thereto and two accordion-pleated side walls, one of which interconnects the flat wall with the plate and the other of which stops just short of the plate, these side walls affording resilient compressibility to the sealing flange in a directiongenerally normal to the plane of the plate. Four corner members close the ends of the sealing flanges. An additional resiliently compressible reinforcing member may be inserted in the passages formed by each of the sealing flanges with the plate.

  12. A Summary of Fault Recurrence and Strain Rates in the Vicinity of the Hanford Site--Topical Report

    SciTech Connect (OSTI)

    Bjornstad, Bruce N.; Winsor, Kelsey; Unwin, Stephen D.

    2012-08-01

    This document is one in a series of topical reports compiled by the Pacific Northwest National Laboratory to summarize technical information on selected topics important to the performance of a probabilistic seismic hazard analysis of the Hanford Site. The purpose of this report is to summarize available data and analyses relevant to fault recurrence and strain rates within the Yakima Fold Belt. Strain rates have met with contention in the expert community and may have a significant potential for impact on the seismic hazard estimate at the Hanford Site. This report identifies the alternative conceptual models relevant to this technical issue and the arguments and data that support those models. It provides a brief description of the technical issue and principal uncertainties; a general overview on the nature of the technical issue, along with alternative conceptual models, supporting arguments and information, and uncertainties; and finally, suggests some prospective approaches to reducing uncertainties about earthquake recurrence rates for the Yakima Fold Belt.

  13. Fast-growing willow shrub named `Tully Champion`

    DOE Patents [OSTI]

    Abrahamson, Lawrence P.; Kopp, Richard F.; Smart, Lawrence B.; Volk, Timothy A.

    2007-08-28

    A distinct female cultivar of Salix viminalis.times.S. miyabeana named `Tully Champion`, characterized by rapid stem growth producing greater than 25% more woody biomass than two current production clones (Salix dasyclados `SV1` and Salix miyabeana `SX64`), more than 2.5-fold greater biomass than one of its parents (Salix miyabeana `SX67`), and nearly 3-fold more biomass than another production clone (Salix sacchalinensis, `SX61`) when grown in the same field for the same length of time (two growing seasons after coppice) in Tully, N.Y. `Tully Champion` can be planted from dormant stem cuttings, produces multiple stems after coppice, and the stem biomass can be harvested when the plant is dormant. In the spring following harvest, the plant will re-sprout very vigorously, producing new stems that can be harvested repeatedly after two to four years of growth. `Tully Champion` displays a low incidence of rust disease and is not damaged by potato leafhoppers.

  14. Local structure underlying anomalous tetragonal distortions in BiFeO{sub 3}-PbTiO{sub 3} ferroelectrics

    SciTech Connect (OSTI)

    Levin, I.; Krayzman, V.; Woicik, J. C.; Tucker, M. G.

    2014-06-16

    The local structure of tetragonal BiFeO{sub 3}-PbTiO{sub 3} solid solutions featuring anomalous lattice distortions has been determined using simultaneous fitting of neutron total scattering and extended X-ray absorption fine structure data. On the local scale, the large tetragonal distortion, promoted by the displacements of the A-cations (Bi and Pb), is accommodated primarily by the [FeO{sub 6}] octahedra, even though both Fe and Ti acquire (5+1)-fold coordination. Bi cations exhibit considerably larger displacements than Pb. The combination of the A-cation displacements and the ability of M-cations to adopt 5-fold coordination is suggested as key for stabilizing the large tetragonality in BiMO{sub 3}-PbTiO{sub 3} systems.

  15. Heterologous protein production using the twin arginine translocation pathway

    DOE Patents [OSTI]

    Pohlschroder, Mechtild; Kissinger, Jessica C; Rose, R. Wesley; Brueser, Thomas; Dilks, Kieran

    2008-11-04

    Provided are means for evaluating and identifying putative substrates of the twin arginine translocation (Tat) secretory pathway in Streptomyces and other bacterial species. Also provided, therefore, are simple ways to express, secrete and purify correctly folded heterologous proteins on a large scale using host microorganisms, such as, Streptomyces and the Tat pathway therein. Many of the thus-produced proteins are of significant therapeutic value in the pharmaceutical and biochemical industries, particularly when they can be secreted from the host in fully-folded active form. Accordingly, there are further provided the heterologous proteins produced by the Tat secretion pathway using the foregoing methods, and the computer algorithm used to identify the Tat signal sequence and putative substrates.

  16. Quasicrystalline structures and uses thereof

    DOE Patents [OSTI]

    Steinhardt, Paul Joseph; Chaikin, Paul Michael; Man, Weining

    2013-08-13

    This invention relates generally to devices constructed from quasicrystalline heterostructures. In preferred embodiments, two or more dielectric materials are arranged in a two- or three-dimensional space in a lattice pattern having at least a five-fold symmetry axis and not a six-fold symmetry axis, such that the quasicrystalline heterostructure exhibits an energy band structure in the space, the band structure having corresponding symmetry, which symmetry is forbidden in crystals, and which band structure comprises a complete band gap. The constructed devices are adapted for manipulating, controlling, modulating, trapping, reflecting and otherwise directing waves including electromagnetic, sound, spin, and surface waves, for a pre-selected range of wavelengths propagating within or through the heterostructure in multiple directions.

  17. Determination of the Fe magnetic anisotropies and the CoO frozen spins in epitaxial CoO/Fe/Ag(001)

    SciTech Connect (OSTI)

    Meng, J. Li, Y.; Park, J. S.; Jenkins, C. A.; Arenholz, E.; Scholl, A.; Tan, A.; Son, H.; Zhao, H. W.; Hwang, Chanyong; Qiu, Z. Q.

    2011-04-28

    CoO/Fe/Ag(001) films were grown epitaxially and studied by X-ray Magnetic Circular Dichroism (XMCD) and X-ray Magnetic Linear Dichroism (XMLD). After field cooling along the Fe[100] axis to 80 K, exchange bias, uniaxial anisotropy, and 4-fold anisotropy of the films were determined by hysteresis loop and XMCD measurements by rotating the Fe magnetization within the film plane. The CoO frozen spins were determined by XMLD measurement as a function of CoO thickness.We find that among the exchange bias, uniaxial anisotropy, and 4-fold anisotropy, only the uniaxial magnetic anisotropy follows thickness dependence of the CoO frozen spins.

  18. Solimoes megashear: Intraplate tectonics in northwestern Brazil

    SciTech Connect (OSTI)

    Caputo, M.V. )

    1991-03-01

    A belt of deformation in the Solimoes basin of northwestern Brazil extends east-northeast from near the Peruvian border for about 1300 km. The belt is characterized by the en echelon arrangement of folds and faults interpreted as the result of right-slip displacements in a transpressive regime. The structures were formed during Late Jurassic time, probably due to collision of South America with allochthonous terranes as the opening of the South Atlantic Ocean began. The Iquitos arch near the western end of the megashear separates the Solimoes basin from Subandean basins. The development of the Iquitos arch is interpreted to be related to orogenic loading along western South America by the Andean mountain belt. In Brazil, folds and faults associated with the Solimoes megashear hold hydrocarbons within Paleozoic strata, and 15 gas and oil fields have so far been discovered.

  19. Library Resources for Bac End Sequencing. Final Technical Report

    SciTech Connect (OSTI)

    Pieter J. de Jong

    2000-10-01

    Studies directed towards the specific aims outlined for this research award are summarized. The RPCI II Human Bac Library has been expanded by the addition of 6.9-fold genomic coverage. This segment has been generated from a MBOI partial digest of the same anonymous donor DNA used for the rest of the library. A new cloning vector, pTARBAC1, has been constructed and used in the construction of RPCI-II segment 5. This new cloning vector provides a new strategy in identifying targeted genomic regions and will greatly facilitate a large-scale analysis for positional cloning. A new maleCS7BC/6J mouse BAC library has been constructed. RPCI-23 contain 576 plates (approx 210,000 clones) and represents approximately 11-fold coverage of the mouse genome.

  20. Structural Diversity in Free and Bound States of Intrinsically Disordered Protein Phosphatase 1 Regulators

    SciTech Connect (OSTI)

    Marsh, J.A.; Allaire, M.; Dancheck, B.; Ragusa, M.J.; Forman-Kay, J.D.; Peti, Wolfgang

    2010-09-08

    Complete folding is not a prerequisite for protein function, as disordered and partially folded states of proteins frequently perform essential biological functions. In order to understand their functions at the molecular level, we utilized diverse experimental measurements to calculate ensemble models of three nonhomologous, intrinsically disordered proteins: I-2, spinophilin, and DARPP-32, which bind to and regulate protein phosphatase 1 (PP1). The models demonstrate that these proteins have dissimilar propensities for secondary and tertiary structure in their unbound forms. Direct comparison of these ensemble models with recently determined PP1 complex structures suggests a significant role for transient, preformed structure in the interactions of these proteins with PP1. Finally, we generated an ensemble model of partially disordered I-2 bound to PP1 that provides insight into the relationship between flexibility and biological function in this dynamic complex.

  1. Fabrication method for cores of structural sandwich materials including star shaped core cells

    DOE Patents [OSTI]

    Christensen, R.M.

    1997-07-15

    A method for fabricating structural sandwich materials having a core pattern which utilizes star and non-star shaped cells is disclosed. The sheets of material are bonded together or a single folded sheet is used, and bonded or welded at specific locations, into a flat configuration, and are then mechanically pulled or expanded normal to the plane of the sheets which expand to form the cells. This method can be utilized to fabricate other geometric cell arrangements than the star/non-star shaped cells. Four sheets of material (either a pair of bonded sheets or a single folded sheet) are bonded so as to define an area therebetween, which forms the star shaped cell when expanded. 3 figs.

  2. Antenna structure with distributed strip

    DOE Patents [OSTI]

    Rodenbeck, Christopher T. (Albuquerque, NM)

    2008-03-18

    An antenna comprises electrical conductors arranged to form a radiating element including a folded line configuration and a distributed strip configuration, where the radiating element is in proximity to a ground conductor. The folded line and the distributed strip can be electrically interconnected and substantially coplanar. The ground conductor can be spaced from, and coplanar to, the radiating element, or can alternatively lie in a plane set at an angle to the radiating element. Embodiments of the antenna include conductor patterns formed on a printed wiring board, having a ground plane, spacedly adjacent to and coplanar with the radiating element. Other embodiments of the antenna comprise a ground plane and radiating element on opposed sides of a printed wiring board. Other embodiments of the antenna comprise conductors that can be arranged as free standing "foils". Other embodiments include antennas that are encapsulated into a package containing the antenna.

  3. Antenna structure with distributed strip

    DOE Patents [OSTI]

    Rodenbeck, Christopher T. (Albuquerque, NM)

    2008-10-21

    An antenna comprises electrical conductors arranged to form a radiating element including a folded line configuration and a distributed strip configuration, where the radiating element is in proximity to a ground conductor. The folded line and the distributed strip can be electrically interconnected and substantially coplanar. The ground conductor can be spaced from, and coplanar to, the radiating element, or can alternatively lie in a plane set at an angle to the radiating element. Embodiments of the antenna include conductor patterns formed on a printed wiring board, having a ground plane, spacedly adjacent to and coplanar with the radiating element. Other embodiments of the antenna comprise a ground plane and radiating element on opposed sides of a printed wiring board. Other embodiments of the antenna comprise conductors that can be arranged as free standing "foils". Other embodiments include antennas that are encapsulated into a package containing the antenna.

  4. Simulating Biomolecules on the Petascale Supercomputers

    SciTech Connect (OSTI)

    Alam, Sadaf R [ORNL; Agarwal, Pratul K [ORNL; Geist, Al [ORNL

    2007-11-01

    Computing continues to make a signicant impact on biology. A variety of computational techniques have allowed rapid developments in design of experiments as well as collection, storage and analysis of experimental data. These developments have and are leading to novel insights into a variety of biological processes. The strength of computing in biology, however, comes from the ability to investigate those aspects of biological processes that are either dicult or are beyond the reach of experimental techniques. Particularly in the last 3 decades, availability of increasing computing power has had a signicant impact on the fundamental understanding of the biomolecules at the molecular level. Molecular biochemists and biophysicists, through theoretical multi-scale modeling and computational simulations, have been able to obtain atomistic level understanding of biomolecular structure, dynamics, folding and function. The protein folding problem, in particular, has attracted considerable interest from a variety of researchers and simulation scientists.

  5. Mechanical unfolding of a beta-hairpin using molecular dynamics

    SciTech Connect (OSTI)

    Bryant, Zev; Pande, Vijay S.; Rokhsar, Daniel S.

    1999-10-16

    Single molecule mechanical unfolding experiments have the potential to provide insights into the details of protein folding pathways. To investigate the relationship between force-extension unfolding curves and microscopic events, we performed molecular dynamics simulations of the mechanical unfolding of the C-terminal hairpin of protein G. We have studied the dependence of the unfolding pathway on pulling speed, cantilever stiffness, and attachment points. Under conditions which generate low forces, the unfolding trajectory mimics the untethered, thermally accessible pathway previously proposed based on high temperature studies. In this stepwise pathway, complete breakdown of backbone hydrogen bonds precedes dissociation of the hydrophobic cluster. Under more extreme conditions, the cluster and hydrogen bonds break simultaneously. Transitions between folding intermediates can be identified in our simulations as features of the calculated force-extension curves.

  6. Effect of hexafluoroisopropanol on the thermodynamics of peptide secondary structure formation

    SciTech Connect (OSTI)

    Andersen, N.H.; Dyer, R.B.; Fesinmeyer, R.M.; Gai, F.; Liu, Z.; Neidigh, J.W.; Tong, H.

    1999-10-27

    This report provides additional evidence for the importance of hydrophobic interactions in peptide secondary structure formation. For the hydrophobically driven {beta} hairpin formation examined, the addition of HFIP to the 8% level increases hairpin formation and increases {Delta}C{sub p} by nearly a factor of 3. Surprisingly, {alpha} helices bearing a few non-interacting hydrophobic residues can display even larger {Delta}C{sub p} values. The initial phase of secondary structure induction during fluoroalcohol titrations of peptides appears to be largely the result of these effects rather than differential stabilization (or destabilization) of the folded versus coil conformation by alcohol/peptide binding interactions, as the latter would be reflected predominantly in the enthalpy term. The addition of limited quantities of fluoroalcohol may mimic the early hydrophobic collapse stage of protein folding.

  7. Purification of chaperonins.

    SciTech Connect (OSTI)

    Quaite-Randall, F.; Joachimiak, A.; Center for Mechanistic Biology and Biotechnology

    1999-01-01

    The availability of protein samples of sufficient quality and in sufficient quantity is a driving force in biology and biotechnology. Protein samples that are free of critical contaminants are required for specific assays. Large amounts of highly homogeneous and reproducible material are needed for crystallography and nuclear magnetic resonance studies of protein structure. Protein-based therapeutic factors used in human medicine must not contain any contaminants that might interfere with treatment. The roles played by molecular chaperones in protein folding and in many cellular processes make these proteins very attractive candidates as biochemical reagents, and the class of chaperones called chaperonins is one of the most important candidates. Methods for successfully purifying chaperonins are needed to advance the field of chaperonin-mediated protein folding. This article outlines the strategies and methods used to obtain pure chaperonin samples from different biological sources. The objective is to help new researchers obtain better quality samples of chaperonins from many new organisms.

  8. The effects of 5-fluorouracil and doxorubicin on expression of human immunodeficiency virus type 1 long terminal repeat

    SciTech Connect (OSTI)

    Panozzo, J.; Akan, E.; Griffiths, T.D.; Woloschak, G.E.

    1996-03-01

    Previous work by many groups has documented induction of the HIV-LTR following exposure of cells to ultraviolet light and other DNA damaging agents. Our experiments set out to determine the relative activation or repression of the HIV-LTR in response to two classes of chemotherapeutic agents: Doxorubicin is a DNA-damage inducing agent, and 5-fluorouracil has an antimetabolic mode of action. Using HeLa cells stably transfected with a construct in which HIV-LTR drives expression of the chloramphenicol acetyl transferase reporter gene, we demonstrated an up to 10-fold induction following doxorubicin treatment in 24 h post-treatment. This induction was repressed by treatment with salicylic acid, suggesting a role for prostaglandin/cyclo-oxygenase pathways and/or NFKB in the inductive response. Induction by 5-fluorouracil, in contrast, was more modest (two-fold at most) though it was consistently elevated over controls.

  9. Mode-mismatched confocal thermal-lens microscope with collimated probe beam

    SciTech Connect (OSTI)

    Cabrera, Humberto; Korte, Dorota; Franko, Mladen

    2015-05-15

    We report a thermal lens microscope (TLM) based on an optimized mode-mismatched configuration. It takes advantage of the coaxial counter propagating tightly focused excitation and collimated probe beams, instead of both focused at the sample, as it is in currently known TLM setups. A simple mathematical model that takes into account the main features of the instrument is presented. The confocal detection scheme and the introduction of highly collimated probe beam allow enhancing the versatility, limit of detection (LOD), and sensitivity of the instrument. The theory is experimentally verified measuring ethanols absorption coefficient at 532.8 nm. Additionally, the presented technique is applied for detection of ultra-trace amounts of Cr(III) in liquid solution. The achieved LOD is 1.3 ppb, which represents 20-fold enhancement compared to transmission mode spectrometric techniques and a 7.5-fold improvement compared to previously reported methods for Cr(III) based on thermal lens effect.

  10. Interaction of interleukin-5 with its receptors on murine leukemic BCL1 cells and its implication in biological activity

    SciTech Connect (OSTI)

    Tsuruoka, N.; Funakoshi, K.; Kodama, S.; Tsujimoto, M. (Suntory Institute for Biomedical Research, Mishima, Osaka (Japan))

    1990-02-01

    Interaction of interleukin (IL)-5 with its receptors on murine leukemic cell line, BCL1 cells was examined. {sup 125}I-labeled recombinant murine IL-5(rmIL-5) bound specifically to high-affinity receptors on BCL1 cells. rmIL-5, which was about 2500-fold more active than recombinant human IL-5(rhIL-5) in IgM-inducing activity on BCL1 cells, also showed about 5000-fold higher affinity to receptors. These results suggest that the bioactivity of IL-5 correlates with its receptor-binding activity. When disulfide bond formation was blocked, rmIL-5 dissociated into a monomer and lost its biological activity. This monomeric form of rmIL-5 also lost its ability to bind to cells, suggesting that dimer formation is essential for the biological activity of IL-5.

  11. Co-firing high sulfur coal with refuse derived fuels. Technical progress report No. 6, January--March 1996

    SciTech Connect (OSTI)

    Pan, W.P.; Riley, J.T.; Lloyd, W.G.

    1996-02-29

    The objectives for this quarter of study on the co-firing of high sulfur coals with refuse derived fuels were two-fold. First, the effects of different experimental parameters such as temperature, flow rates and reaction times on the formation of chlorinated organic compounds were studied using the tubular furnace as a reactor followed by GC/MS analysis. Secondly, the effect of fuel/air ratio on the flue gas composition and combustion efficiency were studied with the AFBC system.

  12. Deployable telescope having a thin-film mirror and metering structure

    DOE Patents [OSTI]

    Krumel, Leslie J. (Cedar Crest, NM); Martin, Jeffrey W. (Albuquerque, NM)

    2010-08-24

    A deployable thin-film mirror telescope comprises a base structure and a metering structure. The base structure houses a thin-film mirror, which can be rolled for stowage and unrolled for deployment. The metering structure is coupled to the base structure and can be folded for stowage and unfolded for deployment. In the deployed state, the unrolled thin-film mirror forms a primary minor for the telescope and the unfolded metering structure positions a secondary minor for the telescope.

  13. A detailed investigation on the impact of post-growth annealing on the materials and device characteristics of 35-layer In{sub 0.50}Ga{sub 0.50}As/GaAs quantum dot infrared photodetector with quaternary In{sub 0.21}Al{sub 0.21}Ga{sub 0.58}As capping

    SciTech Connect (OSTI)

    Adhikary, Sourav; Chakrabarti, Subhananda

    2012-11-15

    Highlights: ? We investigated the effect of ex situ annealing on InGaAs/GaAs QDIP with InAlGaAs layer. ? As-grown defect was removed by using post-growth annealing treatment. ? Increase in the compressive strain due to annealing is calculated from XRD curve. ? Three-fold enhancement in responsivity is observed in the QDIPs annealed at 650 C. ? Two-fold enhancement in D* is observed sample annealed at 650 C compared to as grown. -- Abstract: The effect of post-growth rapid thermal annealing on 35-layer In{sub 0.50}Ga{sub 0.50}As/GaAs quantum dot infrared photodetector (QDIP) with quaternary In{sub 0.21}Al{sub 0.21}Ga{sub 0.58}As capping has been investigated. Transmission electron microscopy showed some as-grown defects were removed by post growth annealing treatment. An increase in the compressive strain in the heterostructure due to annealing was identified from X-ray diffraction curve. A two-color photoresponse in the long-wave region (8.5 and 10.2 ?m) was observed in both as-grown device and those annealed at 650 C temperature. A three-fold enhancement in peak responsivity was observed in the QDIPs annealed at 650 C (1.19 A/W) compared to that in the as-grown (0.34 A/W). Detectivity also increased by two fold from as-grown to 650 C annealed device. The changes are attributed to the removal of as-grown defects and dislocations during epitaxial growth. These removals changed the confinement potential profile, which resulted in an improvement in the detectivity and responsivity of the annealed sample.

  14. Relic vector field and CMB large scale anomalies

    SciTech Connect (OSTI)

    Chen, Xingang; Wang, Yi E-mail: yw366@cam.ac.uk

    2014-10-01

    We study the most general effects of relic vector fields on the inflationary background and density perturbations. Such effects are observable if the number of inflationary e-folds is close to the minimum requirement to solve the horizon problem. We show that this can potentially explain two CMB large scale anomalies: the quadrupole-octopole alignment and the quadrupole power suppression. We discuss its effect on the parity anomaly. We also provide analytical template for more detailed data comparison.

  15. Plasma Wakefield Acceleration and FACET - Facilities for Accelerator Science and Experimental Test Beams at SLAC

    ScienceCinema (OSTI)

    Andrei Seryi

    2010-01-08

    Plasma wakefield acceleration is one of the most promising approaches to advancing accelerator technology. This approach offers a potential 1,000-fold or more increase in acceleration over a given distance, compared to existing accelerators.  FACET, enabled by the Recovery Act funds, will study plasma acceleration, using short, intense pulses of electrons and positrons. In this lecture, the physics of plasma acceleration and features of FACET will be presented.  

  16. SRNL Science and Innovation - National Security

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

    Forensics/Law Enforcement Science and Innovation National Security - Forensics/Law Enforcement In 2006, the Federal Bureau of Investigation (FBI) and SRNL announced the opening of a new laboratory and office suite for the forensic examination of radiological material and associated evidence, located at SRNL. In 2010, the FBI and SRNL celebrated the opening of a six-fold expansion of the facility. These laboratory facilities provide the FBI with a flexible radiological containment laboratory

  17. LANL Transfers Glowing Bio Technology to Sandia Biotech

    ScienceCinema (OSTI)

    Nakhla, Tony;

    2014-06-25

    Partnering with Los Alamos National Laboratory, an Albuquerque-based company is seeking to transform the way protein and peptide analysis is conducted around the world. Sandia Biotech is using a biological technology licensed from Los Alamos called split green fluorescent protein (sGFP), as a detecting and tracking tool for the protein and peptide industry, valuable in the fields of Alzheimer's research, drug development and other biotechnology fields using protein folding to understand protein expression and mechanisms of action.

  18. Hydrogen Education Curriculum Path at Michigan Technological University

    SciTech Connect (OSTI)

    Keith, Jason; Crowl, Daniel; Caspary, David; Naber, Jeff; Allen, Jeff; Mukerjee, Abhijit; Meng, Desheng; Lukowski, John; Solomon, Barry; Meldrum, Jay

    2012-01-03

    The objective of this project was four-fold. First, we developed new courses in alternative energy and hydrogen laboratory and update existing courses in fuel cells. Secondly, we developed hydrogen technology degree programs. Thirdly, we developed hydrogen technology related course material for core courses in chemical engineering, mechanical engineering, and electrical engineering. Finally, we developed fuel cell subject material to supplement the Felder & Rousseau and the Geankoplis chemical engineering undergraduate textbooks.

  19. Amino acid-sensing ion channels in plants

    SciTech Connect (OSTI)

    Spalding, Edgar P.

    2014-08-12

    The title of our project is “Amino acid-sensing ion channels in plants”. Its goals are two-fold: to determine the molecular functions of glutamate receptor-like (GLR) proteins, and to elucidate their biological roles (physiological or developmental) in plants. Here is our final technical report. We were highly successful in two of the three aims, modestly successful in the third.

  20. 1

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

    Los Alamos approach may be key to quantum dot solar cells with real gains in efficiency June 18, 2014 Nanoengineering boosts carrier multiplication in quantum dots LOS ALAMOS, N.M., June 18, 2014-Los Alamos researchers have demonstrated an almost four-fold boost of the carrier multiplication yield with nanoengineered quantum dots. Carrier multiplication is when a single photon can excite multiple electrons. Quantum dots are novel nanostructures that can become the basis of the next generation of

  1. ALSNews Vol. 333

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

    3 Print A Surprising Path for Proton Transfer Without Hydrogen Bonds proton transtfer Scientists working at the ALS have discovered a new route for proton movement from one molecule to another--a basic step in countless chemical and biological reactions--thereby opening new avenues for research in biology, environmental science, and green chemistry. Read more... Contact: Musa Ahmed New Crystal Structures Lift Fog around Protein Folding new crystal thumb At the ALS, researchers have deciphered

  2. ALSNews Vol. 333

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

    3 ALSNews Vol. 333 Print Tuesday, 24 July 2012 09:07 A Surprising Path for Proton Transfer Without Hydrogen Bonds proton transtfer Scientists working at the ALS have discovered a new route for proton movement from one molecule to another--a basic step in countless chemical and biological reactions--thereby opening new avenues for research in biology, environmental science, and green chemistry. Read more... Contact: Musa Ahmed New Crystal Structures Lift Fog around Protein Folding new crystal

  3. ALSNews Vol. 333

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

    3 Print A Surprising Path for Proton Transfer Without Hydrogen Bonds proton transtfer Scientists working at the ALS have discovered a new route for proton movement from one molecule to another--a basic step in countless chemical and biological reactions--thereby opening new avenues for research in biology, environmental science, and green chemistry. Read more... Contact: Musa Ahmed New Crystal Structures Lift Fog around Protein Folding new crystal thumb At the ALS, researchers have deciphered

  4. ALSNews Vol. 333

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

    ALSNews Vol. 333 Print A Surprising Path for Proton Transfer Without Hydrogen Bonds proton transtfer Scientists working at the ALS have discovered a new route for proton movement from one molecule to another--a basic step in countless chemical and biological reactions--thereby opening new avenues for research in biology, environmental science, and green chemistry. Read more... Contact: Musa Ahmed New Crystal Structures Lift Fog around Protein Folding new crystal thumb At the ALS, researchers

  5. Continuous-time quantum walks on star graphs

    SciTech Connect (OSTI)

    Salimi, S.

    2009-06-15

    In this paper, we investigate continuous-time quantum walk on star graphs. It is shown that quantum central limit theorem for a continuous-time quantum walk on star graphs for N-fold star power graph, which are invariant under the quantum component of adjacency matrix, converges to continuous-time quantum walk on K{sub 2} graphs (complete graph with two vertices) and the probability of observing walk tends to the uniform distribution.

  6. A Designed Supramolecular Protein Assembly with in-Vivo Enzymatic Activity

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

    | Stanford Synchrotron Radiation Lightsource A Designed Supramolecular Protein Assembly with in-Vivo Enzymatic Activity Thursday, April 30, 2015 A major goal in molecular design and engineering is the creation of new enzymes from scratch. However, the design of 3-dimensional protein architectures from first principles represents a formidable challenge, and as a result, the generation of new enzymatic activities has primarily relied on repurposing the interiors of pre-existing protein folds

  7. Protein Dynamics Hit the Big Screen

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

    Protein Dynamics Hit the Big Screen Protein Dynamics Hit the Big Screen Now playing at a supercomputer near you: proteins in action June 29, 2005 Contact: Dan Krotz, dakrotz@lbl.gov 06tyrosinekinasechanging.jpg This simulation of a tyrosine kinase reveals how the protein changes shape. Scientists from Berkeley Lab and UC Berkeley are using one the world's most powerful computers to simulate how protein molecules move, rotate, and fold as they carry out life's most fundamental tasks.Although they

  8. News Item

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

    Cooling Microprocessors with Carbon Nanotubes Researchers at the Molecular Foundry, through a User project with Intel, have developed a "process friendly" technique that would enable the cooling of microprocessor chips through carbon nanotubes. Using organic molecules to form strong covalent bonds between carbon nanotubes and metal surfaces, the team's new approach improved by six-fold the flow of heat from the metal to the carbon nanotubes, paving the way for faster, more efficient

  9. 2007 Fuel Cell Technologies Market Report

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

    FUEL CELL TECHNOLOGIES MARKET REPORT JULY 2009 Table of Contents Introduction 1 Worldwide Fuel Cell Shipments Increased 70% from 2006 to 2007 3 Percent Production Increase Highest in North America in 2007 4 North American Units Shipped Increased Three-Fold 6 Commercial Viability of Stationary Units Accompanied by Fewer Demonstrations 7 Large Stationary Units Continue to Increase in Size 8 Small Stationary Shipments Increase Led by Increases in PEM Units Manufactured in North America 9 Fuel

  10. Membrane binding mode of intrinsically disordered cytoplasmic domains of T cell receptor signaling subunits depends on lipid composition

    SciTech Connect (OSTI)

    Sigalov, Alexander B., E-mail: Alexander.sigalov@umassmed.edu [University of Massachusetts Medical School, Worcester, MA 01655 (United States); Hendricks, Gregory M. [University of Massachusetts Medical School, Worcester, MA 01655 (United States)] [University of Massachusetts Medical School, Worcester, MA 01655 (United States)

    2009-11-13

    Intrinsically disordered cytoplasmic domains of T cell receptor (TCR) signaling subunits including {zeta}{sub cyt} and CD3{epsilon}{sub cyt} all contain one or more copies of an immunoreceptor tyrosine-based activation motif (ITAM), tyrosine residues of which are phosphorylated upon receptor triggering. Membrane binding-induced helical folding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} ITAMs is thought to control TCR activation. However, the question whether or not lipid binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} is necessarily accompanied by a folding transition of ITAMs remains open. In this study, we investigate whether the membrane binding mechanisms of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depend on the membrane model used. Circular dichroic and fluorescence data indicate that binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} to detergent micelles and unstable vesicles is accompanied by a disorder-to-order transition, whereas upon binding to stable vesicles these proteins remain unfolded. Using electron microscopy and dynamic light scattering, we show that upon protein binding, unstable vesicles fuse and rupture. In contrast, stable vesicles remain intact under these conditions. This suggests different membrane binding modes for {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depending on the bilayer stability: (1) coupled binding and folding, and (2) binding without folding. These findings explain the long-standing puzzle in the literature and highlight the importance of the choice of an appropriate membrane model for protein-lipid interactions studies.

  11. Hanford_FinalReport_20140130

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

    209054 - Hanford PSHA Seismicity Analysis - Felix Waldhauser - Final Report - 1/31/14 3:37 PM 1 Final Report Project Name: Hanford Site-Wide Probabilistic Seismic Hazard Analysis (PSHA): High-Resolution Seismicity Analysis of the Yakima Fold and Thrust Belt Region, Washington Contract Number: Battelle - 209054 Prepared by: Dr. Felix Waldhauser 423 W 120 th Street, Apt 88 New York, NY 10027 Tel: 212 678 4804 Email: felixw@ldeo.columbia.edu Prepared for: Pacific Northwest National Laboratory

  12. ProteinShop: A tool for interactive protein manipulation and steering

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Journal Article: ProteinShop: A tool for interactive protein manipulation and steering Citation Details In-Document Search Title: ProteinShop: A tool for interactive protein manipulation and steering We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein

  13. Development of a fast position-sensitive laser beam detector

    SciTech Connect (OSTI)

    Chavez, Isaac; Huang Rongxin; Henderson, Kevin; Florin, Ernst-Ludwig; Raizen, Mark G. [Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States)

    2008-10-15

    We report the development of a fast position-sensitive laser beam detector. The detector uses a fiber-optic bundle that spatially splits the incident beam, followed by a fast balanced photodetector. The detector is applied to the study of Brownian motion of particles on fast time scales with 1 A spatial resolution. Future applications include the study of molecule motors, protein folding, as well as cellular processes.

  14. LANL Transfers Glowing Bio Technology to Sandia Biotech

    SciTech Connect (OSTI)

    Nakhla, Tony; ,

    2012-05-21

    Partnering with Los Alamos National Laboratory, an Albuquerque-based company is seeking to transform the way protein and peptide analysis is conducted around the world. Sandia Biotech is using a biological technology licensed from Los Alamos called split green fluorescent protein (sGFP), as a detecting and tracking tool for the protein and peptide industry, valuable in the fields of Alzheimer's research, drug development and other biotechnology fields using protein folding to understand protein expression and mechanisms of action.

  15. Fly-scan ptychography

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

    Huang, Xiaojing; Lauer, Kenneth; Clark, Jesse N.; Xu, Weihe; Nazaretski, Evgeny; Harder, Ross; Robinson, Ian K.; Chu, Yong S.

    2015-03-13

    We report an experimental ptychography measurement performed in fly-scan mode. With a visible-light laser source, we demonstrate a 5-fold reduction of data acquisition time. By including multiple mutually incoherent modes into the incident illumination, high quality images were successfully reconstructed from blurry diffraction patterns. This approach significantly increases the throughput of ptychography, especially for three-dimensional applications and the visualization of dynamic systems.

  16. INHOUSE | Department of Energy

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

    INHOUSE Solar Decathlon INHOUSE INhouse, the 2015 Solar Decathlon project from the California Polytechnic State University team, was designed to incorporate to the university's spectacular surroundings in San Luis Obispo near the Pacific Ocean. With a 15-foot glass wall in the living room that folds back accordion-style to double the living space, the open architecture also employs a variety of techniques to boost INhouse's sustainability. For example, the team installed a gutter system that

  17. IMPROVED MISCIBLE NITROGEN FLOOD PERFORMANCE UTILIZING ADVANCED RESERVOIR CHARACTERIZATION AND HORIZONTAL LATERALS IN A CLASS I RESERVOIR - EAST BINGER (MARCHAND) UNIT

    SciTech Connect (OSTI)

    Joe Sinner

    2002-03-26

    The objective of this project is two-fold. It will demonstrate use of nitrogen as a widely available, cost-effective and environmentally superior injectant for miscible floods. It will also demonstrate the effectiveness of horizontal wellbores in reducing gas breakthrough and cycling. It is expected that the demonstration will lead to implementation of nitrogen injection projects in areas without readily available carbon dioxide sources. Technology transfer will occur throughout the project.

  18. ProteinShop: A tool for interactive protein manipulation and steering

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect ProteinShop: A tool for interactive protein manipulation and steering Citation Details In-Document Search Title: ProteinShop: A tool for interactive protein manipulation and steering We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing

  19. Solar Energy - It's Growth, Development, and Use

    Office of Scientific and Technical Information (OSTI)

    Solar Energy Resources with Additional Information Solar Energy Courtesy of National Renewable Energy Laboratory Credit-Robb Williamson The Department of Energy has played a major role in solar energy development through previous research and ongoing activities. As a result of research and development, the "cost of solar energy has been reduced 100-fold over the past two decades." 1 Concentrating Solar Power (CSP) systems use reflective materials that concentrate the sun's heat energy

  20. Structure and Function of Microbial Metal-Reduction Proteins (Other) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Other: Structure and Function of Microbial Metal-Reduction Proteins Citation Details In-Document Search Title: Structure and Function of Microbial Metal-Reduction Proteins In this project, we proposed (i) identification of metal-reduction genes, (ii) development of new threading techniques and (iii) fold recognition and structure prediction of metal-reduction proteins. However, due to the reduction of the budget, we revised our plan to focus on two specific aims of (i)

  1. First principle thousand atom quantum dot calculations

    SciTech Connect (OSTI)

    Wang, Lin-Wang; Li, Jingbo

    2004-03-30

    A charge patching method and an idealized surface passivation are used to calculate the single electronic states of IV-IV, III-V, II-VI semiconductor quantum dots up to a thousand atoms. This approach scales linearly and has a 1000 fold speed-up compared to direct first principle methods with a cost of eigen energy error of about 20 meV. The calculated quantum dot band gaps are parametrized for future references.

  2. Other EEOICP Links and Previous Federal Register Notices | Department of

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

    Energy Other EEOICP Links and Previous Federal Register Notices Other EEOICP Links and Previous Federal Register Notices Other EEOICP Links MOU between DOL and DOE MOU between HSS and DOE Tri-fold: Agencies Assisting with EEOIPA and the Former Worker Program Deputy Secretary Memo Regarnding Energy Emplyees Occupational Illness Compensation Program Act Interviews of Current and Former Workers Department of Labor Division of Energy Employees Occupational Illness Compensation National Institute

  3. DOE ASSESSMENT SEAB Recommendations Related to High Performance Computing

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

    DOE ASSESSMENT SEAB Recommendations Related to High Performance Computing 1. Introduction The Department of Energy (DOE) is planning to develop and deliver capable exascale computing systems by 2023-24. These systems are expected to have a one-hundred to one-thousand-fold increase in sustained performance over today's computing capabilities, capabilities critical to enabling the next-generation computing for national security, science, engineering, and large- scale data analytics needed to

  4. De novo design of functional proteins: Toward artificial hydrogenases

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

    De novo design of functional proteins: Toward artificial hydrogenases Authors: Faiella, M., Roy, A., Sommer, D., Ghirlanda, G. Title: De novo design of functional proteins: Toward artificial hydrogenases Source: Biopolymers Year: 2013 Volume: 100 Pages: 558 - 571 ABSTRACT: Over the last 25 years, de novo design has proven to be a valid approach to generate novel, well-folded proteins, and most recently, functional proteins. In response to societal needs, this approach is been used increasingly

  5. Expanding the World's Largest Database of Elastic Properties

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

    Expanding the World's Largest Database of Elastic Properties Expanding the World's Largest Database of Elastic Properties NERSC, Materials Project Help Scientists Increase Available Data Almost Ten-Fold April 7, 2015 Contact: Julie Chao, jchao@lbl.gov, 510.486.6491 Scientists at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have published the world's largest set of data on the complete elastic properties of inorganic compounds, increasing by an order of

  6. Chemistry, Life, and Earth Sciences

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

    ADCLES Chemistry, Life, and Earth Sciences The CLES Directorate is home to world class capabilities in chemistry, bioscience, and earth and environmental sciences. Structural protein research Structural protein research A wide range of protein folding research Field Instrument Deployments and Operations (FIDO) Field Instrument Deployments and Operations (FIDO) Atmospheric science research Quantum Dots Quantum Dots Quantum dot research for energy and light Contact Us Associate Director Nan Sauer

  7. Microsoft Word - rare earth speech 3-18 6am

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

    REMARKS PREPARED FOR DELIVERY TECHNOLOGY AND RARE EARTH METALS CONFERENCE 2010 KEYNOTE ADDRESS DAVID SANDALOW ASSISTANT SECRETARY FOR POLICY & INTERNATIONAL AFFAIRS U.S. DEPARTMENT OF ENERGY WASHINGTON, D.C. MARCH 17, 2010 [Acknowledgements.] 1. INTRODUCTION Thank you for the invitation to speak at this important conference. At energy conferences today, no topic is hotter than shale gas. The story is striking: recoverable reserves of shale gas have increased six-fold in the past few years,

  8. Identifying low-coverage surface species on supported noble metal nanoparticle catalysts by DNP-NMR

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

    Johnson, Robert L.; Perras, Frédéric A.; Kobayashi, Takeshi; Schwartz, Thomas J.; Dumesic, James A.; Shanks, Brent H.; Pruski, Marek

    2015-11-20

    DNP-NMR spectroscopy has been applied to enhance the signal for organic molecules adsorbed on γ-Al2O3-supported Pd nanoparticles. In addition, by offering >2500-fold time savings, the technique enabled the observation of 13C-13C cross-peaks for low coverage species, which were assigned to products from oxidative degradation of methionine adsorbed on the nanoparticle surface.

  9. William Morris | Center for Gas SeparationsRelevant to Clean Energy

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

    Technologies | Blandine Jerome William Morris Previous Next List Morris William Morris Formerly: PhD Student, Department of Chemistry & Biochemistry University of California, Los Angeles Presently: Posdoctoral Fellow, Northwestern University MSc in Chemistry, Manchester University, UK EFRC research: Metal Organic Frameworks (MOFs) are porous crystalline materials, comprised of organic struts and metal oxide secondary building units. My research in the area of carbon capture is two fold.

  10. 2012 NISE Awards Summary Table

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

    Awards » 2012 NISE Summary Table 2012 NISE Awards Summary Table Investigator NERSC repo Hours awarded DOE Office Project Title Gilbert Compo, University of Colorado at Boulder m958 10,000,000 BER Climate Research Ocean-Atmosphere Reanalysis for Climate Applications (OARCA) 1850-2013 Silvia Crivelli, Lawrence Berkeley National Laboratory m1532 1,550,000 BER Biological Systems Science WeFold: A collaborative effort for protein structure prediction Thomas Hamill, National Oceanic & Atmospheric

  11. Sprague-Dawley rats display metabolism-mediated sex differences in the acute toxicity of 3,4-methylenedioxymethamphetamine (MDMA, ecstasy)

    SciTech Connect (OSTI)

    Fonsart, Julien [Universite Paris Descartes, Faculte de Pharmacie, Paris F-75006 (France)]|[CNRS, UMR 7157, Paris F-75006 (France)]|[INSERM, U705, Paris F-75006 (France); Menet, Marie-Claude [Universite Paris Descartes, Faculte de Pharmacie, Paris F-75006 (France)]|[Universite Paris Descartes, Faculte de Pharmacie, Plateau Spectrometrie de Masse (IFR 71), Service de Chimie Analytique, Paris F-75006 (France); Decleves, Xavier [Universite Paris Descartes, Faculte de Pharmacie, Paris F-75006 (France)]|[CNRS, UMR 7157, Paris F-75006 (France)]|[INSERM, U705, Paris F-75006 (France); Galons, Herve [Universite Paris Descartes, Faculte de Pharmacie, Paris F-75006 (France)]|[INSERM, U648, Paris F-75006 (France); Crete, Dominique; Debray, Marcel; Scherrmann, Jean-Michel [Universite Paris Descartes, Faculte de Pharmacie, Paris F-75006 (France)]|[CNRS, UMR 7157, Paris F-75006 (France)]|[INSERM, U705, Paris F-75006 (France); Noble, Florence [Universite Paris Descartes, Faculte de Pharmacie, Paris F-75006 (France)]|[CNRS, UMR 7157, Paris F-75006 (France)]|[INSERM, U705, Paris F-75006 (France)], E-mail: florence.noble@univ-paris5.fr

    2008-07-01

    The use of the amphetamine derivative 3,4-methylenedioxymethamphetamine (MDMA, ecstasy) has been associated with unexplained deaths. Male humans and rodents are more sensitive to acute toxicity than are females, including a potentially lethal hyperthermia. MDMA is highly metabolized to five main metabolites, by the enzymes CYP1A2 and CYP2D. The major metabolite in rats, 3,4-methylenedioxyamphetamine (MDA), also causes hyperthermia. We postulated that the reported sex difference in rats is due to a sexual dimorphism(s). We therefore determined (1) the LD50 of MDMA and MDA, (2) their hyperthermic effects, (3) the activities of liver CYP1A2 and CYP2D, (4) the liver microsomal metabolism of MDMA and MDA, (5) and the plasma concentrations of MDMA and its metabolites 3 h after giving male and female Sprague-Dawley (SD) rats MDMA (5 mg.kg{sup -1} sc). The LD50 of MDMA was 2.4-times lower in males than in females. MDMA induced greater hyperthermia (0.9 deg. C) in males. The plasma MDA concentration was 1.3-fold higher in males, as were CYP1A2 activity (twice) and N-demethylation to MDA (3.3-fold), but the plasma MDMA concentration (1.4-fold) and CYP2D activity (1.3-fold) were higher in females. These results suggest that male SD rats are more sensitive to MDMA acute toxicity than are females, probably because their CYP1A2 is more active, leading to higher N-demethylation and plasma MDA concentration. This metabolic pathway could be responsible for the lethality of MDMA, as the LD50 of MDA is the same in both sexes. These data strongly suggest that the toxicity of amphetamine-related drugs largely depends on metabolic differences.

  12. Resistance after firing protected electric match

    DOE Patents [OSTI]

    Montoya, Arsenio P. (Albuquerque, NM)

    1981-11-10

    An electric match having electrical leads embedded in flame-producing compound is protected against an accidental resistance across the leads after firing by a length of heat-shrinkable tubing encircling the match body and having a skirt portion extending beyond the leads. The heat of the burning match and an adjacent thermal battery causes the tubing to fold over the end of the match body, covering the ends of the leads and protecting them from molten pieces of the battery.

  13. Publication, Letterhead, and Business Card Templates | Department of Energy

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

    Templates » Publication, Letterhead, and Business Card Templates Publication, Letterhead, and Business Card Templates The Office of Energy Efficiency and Renewable Energy's (EERE's) official print templates for letterhead, business cards, and publications including fact sheets, tri-fold fact sheets, report covers, and Word documents. We encourage you to use these templates for your EERE products. These templates were designed to allow EERE staff and contractors to produce EERE-branded files

  14. Community Events

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

    Community Community Events Learn about our science, take classes, listen to lectures, meet peers and share ideas...have fun at the Bradbury Science Museum. May 16 Mon 8:00 AM Data Science and Optimal Learning for Material Discovery and Design Hilton Santa Fe Accelerating materials discovery has been an emerging theme in several Office of Science and other government reports and proposal calls. May 9 Mon 8:00 AM Energy Landscapes: From Protein Folding to Molecular Assembly Hilton Santa Fe

  15. Molecular Foundry

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

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

  16. Nanostructured Anodes for Lithium-Ion Batteries - Energy Innovation Portal

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

    Energy Storage Energy Storage Advanced Materials Advanced Materials Find More Like This Return to Search Nanostructured Anodes for Lithium-Ion Batteries New Anodes for Lithium-ion Batteries Increase Energy Density Four-Fold Savannah River National Laboratory Contact SRNL About This Technology Technology Marketing Summary Savannah River Nuclear Solutions (SRNS), managing contractor of the Savannah River Site (SRS) for the Department of Energy, has developed new anodes for lithium-ion batteries

  17. Resistance after firing protected electric match. [Patent application

    DOE Patents [OSTI]

    Montoya, A.P.

    1980-03-20

    An electric match having electrical leads embedded in flame-producing compound is protected against an accidental resistance across the leads after firing by a length of heat-shrinkable tubing encircling the match body and having a skirt portion extending beyond the leads. The heat of the burning match and an adjacent thermal battery causes the tubing to fold over the end of the match body, covering the ends of the leads and protecting them from molten pieces of the battery.

  18. Ultracold Neutrons at Los Alamos National Laboratory

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

    UCN Facility LANSCE is home to one of the most intense sources of some of the coldest subatomic particles: ultracold neutrons (UCNs). The LANSCE Ultracold Neutron (UCN) source is a unique facility that produces high energy spallation neutrons and uses solid deuterium to cool the neutrons by one million billion-fold. The resulting UCNs have some unique properties that allow them to be studied precisely: they move at speeds of only a few meters per second, and are completely confined by magnetic

  19. Geologic Map and GIS Data for the Tuscarora Geothermal Area

    SciTech Connect (OSTI)

    Faulds, James E.

    2013-12-31

    TuscaroraESRI Geodatabase (ArcGeology v1.3): - Contains all the geologic map data, including faults, contacts, folds, unit polygons, and attitudes of strata and faults. - List of stratigraphic units and stratigraphic correlation diagram. - Detailed unit descriptions of stratigraphic units. - Five cross?sections. - Locations of production, injection, and monitor wells. - 3D model constructed with EarthVision using geologic map data, cross?sections, drill?hole data, and geophysics (model not in the ESRI geodatabase).

  20. Disassembly of hot nuclear matter formed in Au-induced reactions near the Fermi energy

    SciTech Connect (OSTI)

    Delis, D.N.

    1993-09-01

    Complex fragment emission has been studied in the 60 MeV/A {sup 197}Au + {sup 12}C, {sup 27}Al, {sup 51}V, {sup nat}Cu, and {sup 197}Au reactions. Velocity spectra, angular distributions and cross sections have been constructed for each target from the inclusive data. Coincidence data including 2-, 3-, 4-, and 5-fold events have also been examined. Furthermore neutron multiplicity distributions have been obtained for the above reactions by utilizing a novel neutron calorimetric approach.

  1. Identifying low-coverage surface species on supported noble metal nanoparticle catalysts by DNP-NMR

    SciTech Connect (OSTI)

    Johnson, Robert L.; Perras, Frdric A.; Kobayashi, Takeshi; Schwartz, Thomas J.; Dumesic, James A.; Shanks, Brent H.; Pruski, Marek

    2015-11-20

    DNP-NMR spectroscopy has been applied to enhance the signal for organic molecules adsorbed on ?-Al2O3-supported Pd nanoparticles. In addition, by offering >2500-fold time savings, the technique enabled the observation of 13C-13C cross-peaks for low coverage species, which were assigned to products from oxidative degradation of methionine adsorbed on the nanoparticle surface.

  2. Microsoft Word - SyrB2.doc

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

    6 Figure 1. Crystal structure of the non-heme iron halogenase SyrB2. A. Overall structure showing cupin fold. B. Active site iron coordination. Iron (brown) is coordinated by two histidines, α- ketoglutarate (grey sticks), water (cyan), and chloride (green). Crystal Structure of Iron-dependent Halogenase Over 4000 natural products contain halide atoms such as chlorine, bromine, or iodine. 1 Halogenated natural products are medically valuable and include antibiotics (chlorotetracycline and

  3. Structure and Function of Microbial Metal-Reduction Proteins (Other) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Other: Structure and Function of Microbial Metal-Reduction Proteins Citation Details In-Document Search Title: Structure and Function of Microbial Metal-Reduction Proteins In this project, we proposed (i) identification of metal-reduction genes, (ii) development of new threading techniques and (iii) fold recognition and structure prediction of metal-reduction proteins. However, due to the reduction of the budget, we revised our plan to focus on two specific aims of (i)

  4. May Events

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

    May May 2016 Events May 2016 event highlights May 9 Mon 8:00 AM Energy Landscapes: From Protein Folding to Molecular Assembly Hilton Santa Fe Historic Plaza - Santa Fe, NM Nanoscale molecular assembly is very common in biology and in nanotechnology. May 16 Mon 8:00 AM Data Science and Optimal Learning for Material Discovery and Design Hilton Santa Fe Accelerating materials discovery has been an emerging theme in several Office of Science and other government reports and proposal calls

  5. Brochure, Understanding Official Use Only - June 2011 | Department of

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

    Energy Official Use Only - June 2011 Brochure, Understanding Official Use Only - June 2011 June 2011 Tri-fold brochure outlining what Official Use Only is and guidelines on determining if the document contains OUO, how the document must be marked and list of exemptions related to Freedom of Information Act. PDF icon Brochure, Understanding Official Use Only - June 2011 More Documents & Publications Briefing, DOE's Official Use Only Program - June 2014 Pamphlet, Understanding Official Use

  6. Workshop Proceedings: Communication and Control Systems for Distributed Energy Implementation and Testing; May 14-15, 2002

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

    Energetics, Incorporated i June 2002 Executive Summary This report presents the proceedings of a technical workshop on communication and control systems for the implementation and testing of distributed energy devices such as microturbines, fuel cells, and photovoltaic arrays. The purpose of the workshop was two- fold: To develop ideas for conducting large-scale demonstration projects of distributed energy devices in high levels of saturation on particular feeder lines or substations, and

  7. Audit Report: OAS-RA-11-05 | Department of Energy

    Energy Savers [EERE]

    5 Audit Report: OAS-RA-11-05 March 22, 2011 The Department of Energy's Geothermal Technologies Programunder the American Recovery and Reinvestment Act Under the American Recovery and Reinvestment Act of 2009 (Recovery Act), the Department of Energy's Geothermal Technologies Program received $400 million to promote the exploration and development of new geothermal fields and innovative research into advanced geothermal technologies. This funding represents an almost ten-fold increase over the $44

  8. Ultraviolet Resonant Raman Enhancements in the Detection of Explosives

    SciTech Connect (OSTI)

    Short, B J; Carter, J C; Gunter, D; Hovland, P; Jagode, H; Karavanic, K; Marin, G; Mellor-Crummey, J; Moore, S; Norris, B; Oliker, L; Olschanowsky, C; Roth, P C; Schulz, M; Shende, S; Snavely, A; Spear, W

    2009-06-03

    Raman-based spectroscopy is potentially militarily useful for standoff detection of high explosives. Normal (non-resonance) and resonance Raman spectroscopies are both light scattering techniques that use a laser to measure the vibrational spectrum of a sample. In resonance Raman, the laser is tuned to match the wavelength of a strong electronic absorbance in the molecule of interest, whereas, in normal Raman the laser is not tuned to any strong electronic absorbance bands. The selection of appropriate excitation wavelengths in resonance Raman can result in a dramatic increase in the Raman scattering efficiency of select band(s) associated with the electronic transition. Other than the excitation wavelength, however, resonance Raman is performed experimentally the same as normal Raman. In these studies, normal and resonance Raman spectral signatures of select solid high explosive (HE) samples and explosive precursors were collected at 785 nm, 244 nm and 229 nm. Solutions of PETN, TNT, and explosive precursors (DNT & PNT) in acetonitrile solvent as an internal Raman standard were quantitatively evaluated using ultraviolet resonance Raman (UVRR) microscopy and normal Raman spectroscopy as a function of power and select excitation wavelengths. Use of an internal standard allowed resonance enhancements to be estimated at 229 nm and 244 nm. Investigations demonstrated that UVRR provided {approx}2000-fold enhancement at 244 nm and {approx}800-fold improvement at 229 nm while PETN showed a maximum of {approx}25-fold at 244 nm and {approx}190-fold enhancement at 229 nm solely from resonance effects when compared to normal Raman measurements. In addition to the observed resonance enhancements, additional Raman signal enhancements are obtained with ultraviolet excitation (i.e., Raman scattering scales as !4 for measurements based on scattered photons). A model, based partly on the resonance Raman enhancement results for HE solutions, is presented for estimating Raman enhancements for solid HE samples.

  9. About Us | Department of Energy

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

    About Us About Us Learn more about our staff by reading their bios, below. View an organizational chart of our office. Download our office's informational tri-fold. Leadership John Hale III Director, Office of Small and Disadvantaged Business Utilization John Hale III is the Director of the Office of Small and Disadvantaged Business Utilization at the Department of Energy, reporting directly to the Office of the Secretary. In this role, Hale advocates for small businesses including small

  10. Education and Workforce Development | Department of Energy

    Office of Environmental Management (EM)

    and Workforce Development Education and Workforce Development bioenergizeHeader480.png Future leaders and innovators exploring America's bioenergy choices. OPERATION BioenergizeME is the Bioenergy Technologies Office's (BETO's) education and workforce development base camp for students and educators and anyone seeking to better understand the promises and challenges in developing a thriving bioeconomy. OPERATION BioenergizeME has a three-fold mission: Improve public accessibility to information

  11. Database Search

    National Nuclear Security Administration (NNSA)

    Frenchman Mountain fault (Class A) No. 1117 Brief Report ||Partial Report citation for this record: Anderson, R.Ernest, compiler, 1999, Fault number 1117, Frenchman Mountain fault, in Quaternary fault and fold database of the United States: U.S. Geological Survey website, http://earthquakes.usgs.gov/regional/qfaults, accessed 03/29/2010 03:57 PM. Synopsis The Frenchman Mountain fault strikes generally north, dips mostly west, is broadly arcuate (convex west), and forms the structural boundary

  12. Towards the Understanding of Resistance Mechanisms in Clinically Isolated Trimethoprim-resistant, Methicillin-resistant Staphylococcus aureus Dihydrofolate Reductase

    SciTech Connect (OSTI)

    Frey, K.; Lombardo, M; Wright, D; Anderson, A

    2010-01-01

    Resistance to therapeutics such as trimethoprim-sulfamethoxazole has become an increasing problem in strains of methicillin-resistant Staphylococcus aureus (MRSA). Clinically isolated trimethoprim-resistant strains reveal a double mutation, H30N/F98Y, in dihydrofolate reductase (DHFR). In order to develop novel and effective therapeutics against these resistant strains, we evaluated a series of propargyl-linked antifolate lead compounds for inhibition of the mutant enzyme. For the propargyl-linked antifolates, the F98Y mutation generates minimal (between 1.2- and 6-fold) losses of affinity and the H30N mutation generates greater losses (between 2.4- and 48-fold). Conversely, trimethoprim affinity is largely diminished by the F98Y mutation (36-fold) and is not affected by the H30N mutation. In order to elucidate a mechanism of resistance, we determined a crystal structure of a complex of this double mutant with a lead propargyl-linked antifolate. This structure suggests a resistance mechanism consistent both for the propargyl-linked class of antifolates and for trimethoprim that is based on the loss of a conserved water-mediated hydrogen bond.

  13. Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme

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

    Lee, Hui-Ting; Kilburn, D.; Behrouzi, R.; Briber, R. M.; Woodson, S. A.

    2014-12-05

    The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg2+ concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg2+more » concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.« less

  14. Quantifying the 'naturalness' of the curvaton model

    SciTech Connect (OSTI)

    Lerner, Rose N.; Melville, Scott E-mail: scott.melville@queens.ox.ac.uk

    2014-07-01

    We investigate the probability of obtaining an observable curvature perturbation, using as an example the minimal curvaton-higgs (MCH) model. We determine ''probably observable'' and ''probably excluded'' regions of parameter space assuming generic initial conditions and applying a stochastic approach for the curvaton's evolution during inflation. Inflation is assumed to last longer than the N{sub obs} ? 55 observable e-folds, and the total number of e-folds of inflation determines the particular ranges of parameters that are probable. For the MCH model, these ''probably observable'' regions always lie within the range 8 10{sup 4}GeV ? m{sub ?} ? 2 10{sup 7}GeV, where m{sub ?} is the curvaton mass, and the Hubble scale at horizon exit is chosen as H{sub *} = 10{sup 10}GeV. Because the ''probably observable'' region depends on the total duration of inflation, information on parameters in the Lagrangian from particle physics and from precision CMB observations can therefore provide information about the total duration of inflation, not just the last N{sub obs} e-folds. This method could also be applied to any model that contains additional scalar fields to determine the probability that these scalar fields contribute to the curvature perturbation.

  15. Export is the default pathway for soluble unfolded polypeptides that accumulate during expression in Escherichia coli

    SciTech Connect (OSTI)

    Scotto-Lavino, E.; Freimuth, P.; Bai, M.; Zhang, Y.-B.

    2011-09-01

    Several E. coli endogenous, cytoplasmic proteins that are known clients of the chaperonin GroEL were overexpressed to examine the fate of accumulated unfolded polypeptides. Substantial fractions of about half of the proteins formed insoluble aggregates, consistent with the hypothesis that these proteins were produced at rates or in amounts that exceeded the protein-folding capacity of GroEL. In addition, large fractions of three overexpressed GroEL client proteins were localized in an extra-cytoplasmic, osmotically-sensitive compartment, suggesting they had initially accumulated in the cytoplasm as soluble unfolded polypeptides and thus were able to access a protein export pathway. Consistent with this model, an intrinsically unfoldable, hydrophilic, non-secretory polypeptide was quantitatively exported from the E. coli cytoplasm into an osmotically-sensitive compartment. Our results support the conclusion that a soluble, unfolded conformation alone may be sufficient to direct non-secretory polypeptides into a protein export pathway for signal peptide-independent translocation across the inner membrane, and that export rather than degradation by cytoplasmic proteases is the preferred fate for newly-synthesized, soluble, unfolded polypeptides that accumulate in the cytoplasm. The stable folded conformation of exported GroEL client proteins further suggests that the requirement for GroEL may be conditional on protein folding in the molecularly-crowded environment of the cytoplasm.

  16. Crystal structure of P58(IPK) TPR fragment reveals the mechanism for its molecular chaperone activity in UPR

    SciTech Connect (OSTI)

    Tao, Jiahui; Petrova, Kseniya; Ron, David; Sha, Bingdong (UAB); (NYUSM)

    2010-05-25

    P58(IPK) might function as an endoplasmic reticulum molecular chaperone to maintain protein folding homeostasis during unfolded protein responses. P58(IPK) contains nine tetratricopeptide repeat (TPR) motifs and a C-terminal J-domain within its primary sequence. To investigate the mechanism by which P58(IPK) functions to promote protein folding within the endoplasmic reticulum, we have determined the crystal structure of P58(IPK) TPR fragment to 2.5 {angstrom} resolution by the SAD method. The crystal structure of P58(IPK) revealed three domains (I-III) with similar folds and each domain contains three TPR motifs. An ELISA assay indicated that P58(IPK) acts as a molecular chaperone by interacting with misfolded proteins such as luciferase and rhodanese. The P58(IPK) structure reveals a conserved hydrophobic patch located in domain I that might be involved in binding the misfolded polypeptides. Structure-based mutagenesis for the conserved hydrophobic residues located in domain I significantly reduced the molecular chaperone activity of P58(IPK).

  17. Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms

    SciTech Connect (OSTI)

    Pal, Somedatta; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302 (India)] [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302 (India)

    2013-12-21

    Identification of the intermediates along the folding-unfolding pathways and probing their interactions with surrounding solvent are two important but relatively unexplored issues in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to study the thermal unfolding of barstar in aqueous solution from its folded native form at two different temperatures (400 K and 450 K). The calculations at 400 K reveal partial unfolding of two ?-helices (helix-1 and helix-2) and their interconnecting loop. At 450 K, on the other hand, the entire protein attains an expanded flexible conformation due to disruption of a large fraction of tertiary contacts and breaking of almost all the secondary structures. These two disordered structures obtained at such high temperatures are then studied around room temperature to probe their influence on the properties of surrounding solvent. It is found that though the unfolding of the protein in general leads to increasingly hydrated interface, but new structural motifs with locally dehydrated interface may also form during the structural transition. Additionally, independent of the conformational state of the protein, its influence on surrounding solvent has been found to be restricted to the first hydration layer.

  18. Crystal Structure of Neurotropism-Associated Variable Surface Protein 1 (VSP1) of Borrelia Turicatae

    SciTech Connect (OSTI)

    Lawson,C.; Yung, B.; Barbour, A.; Zuckert, W.

    2006-01-01

    Vsp surface lipoproteins are serotype-defining antigens of relapsing fever spirochetes that undergo multiphasic antigenic variation to allow bacterial persistence in spite of an immune response. Two isogenic serotypes of Borrelia turicatae strain Oz1 differ in their Vsp sequences and in disease manifestations in infected mice: Vsp1 is associated with the selection of a neurological niche, while Vsp2 is associated with blood and skin infection. We report here crystal structures of the Vsp1 dimer at 2.7 and 2.2 Angstroms. The structures confirm that relapsing fever Vsp proteins share a common helical fold with OspCs of Lyme disease-causing Borrelia. The fold features an inner stem formed by highly conserved N and C termini and an outer 'dome' formed by the variable central residues. Both Vsp1 and OspC structures possess small water-filled cavities, or pockets, that are lined largely by variable residues and are thus highly variable in shape. These features appear to signify tolerance of the Vsp-OspC fold for imperfect packing of residues at its antigenic surface. Structural comparison of Vsp1 with a homology model for Vsp2 suggests that observed differences in disease manifestation may arise in part from distinct differences in electrostatic surface properties; additional predicted positively charged surface patches on Vsp2 compared to Vsp1 may be sufficient to explain the relative propensity of Vsp2 to bind to acidic glycosaminoglycans.

  19. Molecular cloning of amphioxus uncoupling protein and assessment of its uncoupling activity using a yeast heterologous expression system

    SciTech Connect (OSTI)

    Chen, Kun; Sun, Guoxun; Lv, Zhiyuan; Wang, Chen; Jiang, Xueyuan; Li, Donghai; Zhang, Chenyu

    2010-10-01

    Research highlights: {yields} Invertebrates, for example amphioxus, do express uncoupling proteins. {yields} Both the sequence and the uncoupling activity of amphioxus UCP resemble UCP2. {yields} UCP1 is the only UCP that can form dimer on yeast mitochondria. -- Abstract: The present study describes the molecular cloning of a novel cDNA fragment from amphioxus (Branchiostoma belcheri) encoding a 343-amino acid protein that is highly homologous to human uncoupling proteins (UCP), this protein is therefore named amphioxus UCP. This amphioxus UCP shares more homology with and is phylogenetically more related to mammalian UCP2 as compared with UCP1. To further assess the functional similarity of amphioxus UCP to mammalian UCP1 and -2, the amphioxus UCP, rat UCP1, and human UCP2 were separately expressed in Saccharomyces cerevisiae, and the recombinant yeast mitochondria were isolated and assayed for the state 4 respiration rate and proton leak, using pYES2 empty vector as the control. UCP1 increased the state 4 respiration rate by 2.8-fold, and the uncoupling activity was strongly inhibited by GDP, while UCP2 and amphioxus UCP only increased the state 4 respiration rate by 1.5-fold and 1.7-fold in a GDP-insensitive manner, moreover, the proton leak kinetics of amphioxus UCP was very similar to UCP2, but much different from UCP1. In conclusion, the amphioxus UCP has a mild, unregulated uncoupling activity in the yeast system, which resembles mammalian UCP2, but not UCP1.

  20. Petroleum systems of Jianghan Basin, Hubel Province, China

    SciTech Connect (OSTI)

    Cunningham, A.E.; Schaps, S.; McGregor, D.

    1996-12-31

    The Jianghan Basin is a Cretaceous-Tertiary nonmarine rift basin superimposed on a late Precambrian to Jurassic passive margin and foreland basin succession deformed by mid-Mesozoic folding and thrusting. Hence the basin has potential for superimposed petroleum systems. Oil production is established in a Tertiary petroleum system developed in two major depocenters, the Jiangling (west) and Qianjiang (east) Depressions. Lacustrine source beds in the early Eocene Xingouzhui and late Eocene Qianjiang Formations generated hydrocarbons during local maximum basin fill in the Oligocene to present. Very early, low temperature generation of petroleum occurs where Type 1S Qianjiang Formation kerogen is present. Tertiary fluvial and deltaic sandstones form reservoirs that trap oil in highs or rollover structures formed by normal faulting and salt movement. The pre-rift section contains large folds and good source-beds, but has high exploration risk. Factors limiting effectiveness of older petroleum systems are: (1) Uplift and erosion of thrust structures; (2) Overmaturation of pre-Permian source rocks prior to folding and thrusting; (3) Limited extent of secondary maturation of Late Paleozoic and Mesozoic source beds; and (4) Disruption of older traps and seals by widespread normal faulting. Production of hydrocarbons from Permian and Triassic rocks to the west of Hubei suggests that further seismic work and drilling are merited to evaluate pre-Tertiary potential in the Jianghan Basin.