Sample records for appalachian fold belt

  1. Implications of thermal events on thrust emplacement sequence in the Appalachian fold and thrust belt: Some new vitrinite reflectance data

    SciTech Connect (OSTI)

    Lewis, S.E.; Hower, J.C. (Montana Tech, Butte (USA))

    1990-11-01T23:59:59.000Z

    Interpretation of existing geothermometry data combined with new vitrinite reflectance data, within the framework of a detailed composite tectonic setting, elucidates the evolution of structural sequencing of thrust sheets during the Alleghanian event in the Valley and Ridge Province in Virginia. That the Pulaski thrust sheet preceded the Saltville thrust sheet in the emplacement sequence, and that both reached thermal maxima prior to, or during, respective emplacement may be inferred from vitrinite and other geothermometry data. In contrast, the Narrows and St. Clair thrust sheets probably each attained their thermal maximum after emplacement. New vitrinite reflectance data are consistent with CAI and other temperature-sensitive information heretofore ascertained in the Valley and Ridge Province and support previously established maximum temperatures of ca. 200C for strata of the Saltville thrust sheet as young as Mississippian. R{sub max} values from Mississippian coals in the Price Formation of the Saltville sheet, beneath but near the Pulaski thrust, range from 1.61% to 2.60%. At the structural front of the fold and thrust belt, a single Mississippian coal sample from the Bluefield Formation yields an R{sub max} value of 1.35%. Those coals showing highest R{sub max} values are more intensely fractured with secondary minerals filling the fractures. Warm fluids introduced during tectonic events may have played at least as important a role as that of combined stratigraphic and tectonic burial.

  2. The Role of Climate in the Deformation of a Fold and Thrust Belt

    E-Print Network [OSTI]

    Steen, Sean Kristian

    2012-02-14T23:59:59.000Z

    and uplifted in large folds. In order to test this and related ideas in a natural example, we have compared modeled rainfall to measured thrust sheet displacement, geometry, and internal deformation in the Appalachian fold and thrust belt. We use mean annual...

  3. abakaliki fold belt: Topics by E-print Network

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

    Cenozoic partitioning of oblique plate convergence in the Zagros fold-and-thrust belt (Iran) Physics Websites Summary: of oblique plate convergence in the Zagros fold-and-thrust...

  4. Structure and evolution of the active fold and thrust belt of southwestern Taiwan using GPS geodesy

    E-Print Network [OSTI]

    Hickman, John Bibb

    1999-01-01T23:59:59.000Z

    ) from north to south, a dramatic change in the width of the deformation front of the fold and thrust belt which is accentuated across the Michih fault, and 4) the Tulungwan fault, a bounding fault between the Western Foothills and the Slate Belt, appears...

  5. The evolution and hydrocarbon habitat of the Papuan fold belt, PNG

    SciTech Connect (OSTI)

    Dalton, D.G.; Smith, R.I.; Cawley, S.J. (BP Australia Ltd., Melbourne, Victoria (Australia))

    1990-05-01T23:59:59.000Z

    After over 70 years of hydrocarbon exploration in the Papuan fold belt of PNG (Papua New Guinea) there have been a number of hydrocarbon discoveries over recent years that have confirmed its potential as a significant producing province. The Papuan basin developed during the early Mesozoic as part of the northeast corner of the Australian passive margin. The basin's tertiary evolution and the development of the Papuan fold belt within the Papuan basin has evolved in response to oblique convergence between the northerly moving Australian plate and westerly moving Pacific plate. Restacking of the Mesozoic passive margin sequence within the Papuan Basin was initiated in the early miocene by southward abduction of the Solomon Sea plate and the subsequent collision, in the late Miocene, of the Melanesian Island arc along the northeastern margin of PNG. This later collision provided the driving mechanism for the development of the papuan thrust belt. To date, all the significant hydrocarbon discoveries made within the Papuan fold belt have been located within the frontal zone of the fold belt, which is characterized by relatively simple ramp anticlines and thick-skinned inversion structures. The primary proven reservoir fairway is the Jurassic Toro formation, which is a sequence of stacked submarine bars prograding out across a shallow-marine low-gradient shelf. Geochemical analysis of produced hydrocarbons and samples collected from the many surface seeps found in the fold belt indicate two main families of oil. A model explains the distribution of hydrocarbons discovered to date, which involves Jurassic and Cretaceous source intervals and a complex history of secondary migration and entrapment. The unique technical problems associated with exploration of the Papuan fold belt leave many elements of the proven play systems uncertain, but in so doing, they present many challenges and opportunities for the future.

  6. Mechanical characteristics of folds in Upper Cretaceous strata in the Disturbed Belt of northwestern Montana

    E-Print Network [OSTI]

    Gilbert, Pat Kader

    1974-01-01T23:59:59.000Z

    controlled cross section through a wave trai. n of these folds, The citations on these pages follow the style of the U. S. Geological Survey Bulletin. other field observations, laboratory analysis of collected samples, and theoretical considerations...MECHANICAL CHARACTERISTICS OF FOLDS IN UPPER CRETACEOUS STRATA IN THE DISTURBED BELT OF NORTHWESTERN MONTANA A Thesis by PAT KADER GILBERT Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirements...

  7. Timing of granite emplacement and cooling in the SongpanGarze^ Fold Belt (eastern Tibetan Plateau) with tectonic implications

    E-Print Network [OSTI]

    Timing of granite emplacement and cooling in the Songpan­Garze^ Fold Belt (eastern Tibetan Plateau Abstract New U­Pb and Rb­Sr geochronology on syn- and post-orogenic granites provide constraints on the timing of major tectonic events in the Songpan­Garze^ fold belt, west Sichuan, China. The Ma Nai granite

  8. Oak Ridge fault, Ventura fold belt, and the Sisar decollement, Ventura basin, California

    SciTech Connect (OSTI)

    Yeats, R.S.; Huftile, G.J.; Grigsby, F.B. (Oregon State Univ. Corvallis (USA))

    1988-12-01T23:59:59.000Z

    The rootless Ventura Avenue, San Miguelito, and Rincon anticlines (Ventura fold belt) in Pliocene -Pleistocene turbidites are fault-propagation folds related to south-dipping reverse faults rising from a decollement in Miocene shale. To the east, the Sulfur Mountain anticlinorium overlies and is cut by the Sisar, Big Canyon, and Lion south-dipping thrusts that merge downward into the Sisar decollement in lower Miocene shale. Shortening of the Miocene and younger sequence is {approximately} 3 km greater than that of underlying competent Paleogens strata in the Ventura fold belt and {approximately} 7 km greater farther east at Sulfur Mountain. Cross-section balancing requires that this difference be taken up by the Paleogene sequence at the Oak Ridge fault to the south. Convergence is northeast to north-northeast on the base of earthquake focal mechanisms, borehole breakouts, and piercing-point offest of the South Mountain seaknoll by the Oak Ridge fault. A northeast-trending line connecting the west end of Oak Ridge and the east end of Sisar fault separates an eastern domain where late Quaternary displacement is taken up entirely on the Oak Ridge fault and a western domain where displacement is transferred to the Sisar decollement and its overlying rootless folds. This implies that (1) the Oak Ridge fault near the coast presents as much seismic risk as it does farther east, despite negligible near-surface late Quaternary movement; (2) ground-rupture hazard is high for the Sisar fault set in the upper Ojai Valley; and (3) the decollement itself could produce an earthquake analogous to the 1987 Whittier Narrows event in Low Angeles.

  9. Mass movement-induced fold-and-thrust belt structures in unconsolidated sediments in Lake Lucerne (Switzerland)

    E-Print Network [OSTI]

    Gilli, Adrian

    Mass movement-induced fold-and-thrust belt structures in unconsolidated sediments in Lake Lucerne coring in Lake Lucerne, Switzerland, have revealed surprising deformation structures in flat in Lake Lucerne affecting four sections of the lake floor with areas ranging from 025 to 65 km2 in area

  10. Growth and erosion of fold-and-thrust belts with an application to the Aconcagua fold-and-thrust belt, Argentina

    E-Print Network [OSTI]

    Hilley, George

    -and-thrust belt, Argentina G. E. Hilley1 and M. R. Strecker Institut fu¨r Geowissenschaften, Universita¨t Potsdam, Potsdam, Germany V. A. Ramos Department de Geologia, Universidad de Buenos Aires, Buenos Aires, Argentina in the central Andes of Argentina where wedge development over time is well constrained. We solve

  11. Predicting stress distributions in fold-and-thrust belts and accretionary wedges by optimization

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    element method (EEM) provides the stress distribution in geometrical models of folds, relevant to fold for discontinuities. The example chosen to illustrate the potential of the EEM and to validate our implementation is the thrusting of a rectangular sheet over a flat and weak de´collement. The EEM reproduces the solution proposed

  12. 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.

    2012-08-01T23:59:59.000Z

    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.

  13. Mechanical characteristics of folds in Upper Cretaceous strata in the Disturbed Belt of northwestern Montana

    E-Print Network [OSTI]

    Gilbert, Pat Kader

    1974-01-01T23:59:59.000Z

    -shape. The trough in S3 (see unit 23, Plate 2) is hi. ghly fractured in the sandstone and shows considerable flowage in the shale. From the air, it is readily apparent that these folds of the upper Two Medicine are much smaller in lateral extent along strike than... Formation (mostly shale), the Virgelle Sandstone, and the Two Medi. cine Formation (mostly shale), Montana Group, Upper Cretaceous. The Virgelle Sand- stone, about 54 meters thick, lies between the shales and behaved as the most competent member...

  14. 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.

    2012-08-01T23:59:59.000Z

    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.

  15. The vertical separation of mainshock rupture and microseismicity at Qeshm island in the Zagros fold-and-thrust belt, Iran

    E-Print Network [OSTI]

    Elliott, John

    -and-thrust belt, Iran E. Nissen a, , F. Yamini-Fard b , M. Tatar b , A. Gholamzadeh b,1 , E. Bergman c , J Engineering and Seismology, PO Box 19395-3913, Tehran, Iran c Department of Physics, University of Colorado rights reserved. 1. Introduction The Zagros mountains in south-western Iran are one of the most rapidly

  16. Subsidence history of the Alabama promontory in response to Late Paleozoic Appalachian-Ouachita thrusting

    SciTech Connect (OSTI)

    Whitting, B.M.; Thomas, W.A. (Univ. of Kentucky, Lexington, KY (United States). Dept. of Geological Sciences)

    1994-03-01T23:59:59.000Z

    The Alabama promontory of North American continental crust was framed during late Precambrian-Cambrian rifting by the northeast-striking Blue Ridge rift and the northwest-striking alabama-Oklahoma transform fault. A passive margin persisted along the western side of the promontory from Cambrian to Mississippian time, but the eastern side was affected by the Taconic and Acadian orogenies. Prior to initiation of Ouachita and Appalachian (Alleghanian) thrusting, the outline of the rifted margin of continental crust on the Alabama promontory remained intact; and the late paleozoic thrust belt conformed to the shape of the promontory, defining northwest-striking Ouachita thrust faults along the southwest side of the promontory, north-striking Appalachian (Georgia-Tennessee) thrust faults on the east, and northeast-striking Appalachian (Alabama) thrust faults across the corner of the promontory. Subsidence profiles perpendicular to each of the strike domains of the thrust belt have been constructed by calculating total subsidence from decompacted thickness of the synorogenic sedimentary deposits. The profile perpendicular to the Ouachita thrust belt shows increasing subsidence rates through time and toward the thrust front, indicating the classic signature of an orogenic foreland basin. The profile perpendicular to the Georgia-Tennessee Appalachian thrust belt similarly shows increasing subsidence rates through time and toward the orogenic hinterland. These quantitative results support the conclusion that Black Warrior basin subsidence is tectonically rather than sedimentologically driven, and the timing of subsidence events reported here has implications for regional tectonic models.

  17. APPALACHIAN COLLEGES COMMUNITY ECONOMIC DEVELOPMENT PARTNERSHIP

    E-Print Network [OSTI]

    Engel, Jonathan

    customized community economic development engagement strategies. Provide on-site Partnership evaluation to undertake new economic development programs. Communication, Sustainability, and Evaluation--Years 1, 2 and 3APPALACHIAN COLLEGES COMMUNITY ECONOMIC DEVELOPMENT PARTNERSHIP The UNC-Chapel Hill Office

  18. Page 1 of 3 Appalachian State University

    E-Print Network [OSTI]

    Rose, Annkatrin

    with the department head and appropriate vice chancellor. Physical Plant New River Light & Power Food Service In the event of severe weather conditions, emergency situations, or serious public health threats, Appalachian

  19. The Appalachian Laboratory Graduate Student Handbook

    E-Print Network [OSTI]

    Boynton, Walter R.

    Biology/Biotechnology ....................... 11 Environmental Science. UNIVERSITY OF MARYLAND CENTER FOR ENVIRONMENTAL SCIENCE APPALACHIAN LABORATORY #12;2 Table of Contents for Environmental Science .........................................6 Highlights of some of the University

  20. Laterally bendable belt conveyor

    DOE Patents [OSTI]

    Peterson, William J. (Coraopolis, PA)

    1985-01-01T23:59:59.000Z

    An endless, laterally flexible and bendable belt conveyor particularly adapted for coal mining applications in facilitating the transport of the extracted coal up- or downslope and around corners in a continuous manner is disclosed. The conveying means includes a flat rubber belt reinforced along the middle portion thereof along which the major portion of the belt tension is directed so as to cause rotation of the tubular shaped belt when trammed around lateral turns thus preventing excessive belt bulging distortion between adjacent belt supports which would inhibit belt transport. Pretension induced into the fabric reinforced flat rubber belt by conventional belt take-up means supports the load conveyed when the belt conveyor is making lateral turns. The carrying and return portions of the belt are supported and formed into a tubular shape by a plurality of shapers positioned along its length. Each shaper is supported from above by a monorail and includes clusters of idler rollers which support the belt. Additional cluster rollers in each shaper permit the belt supporting roller clusters to rotate in response to the belt's operating tension imposed upon the cluster rollers by induced lateral belt friction forces. The freely rotating roller clusters thus permit the belt to twist on lateral curves without damage to itself while precluding escape of the conveyed material by effectively enclosing it in the tube-shaped, inner belt transport length.

  1. Atlas of major Appalachian basin gas plays

    SciTech Connect (OSTI)

    Aminian, K.; Avary, K.L.; Baranoski, M.T.; Flaherty, K.; Humphreys, M.; Smosna, R.A.

    1995-06-01T23:59:59.000Z

    This regional study of gas reservoirs in the Appalachian basin has four main objectives: to organize all of the -as reservoirs in the Appalachian basin into unique plays based on common age, lithology, trap type and other geologic similarities; to write, illustrate and publish an atlas of major gas plays; to prepare and submit a digital data base of geologic, engineering and reservoir parameters for each gas field; and technology transfer to the oil and gas industry during the preparation of the atlas and data base.

  2. Selecting major Appalachian basin gas plays

    SciTech Connect (OSTI)

    Patchen, D.G.; Nuttall, B.C.; Baranoski, M.T.; Harper, J.A.; Schwietering, J.F.; Van Tyne, A.; Aminian, K.; Smosna, R.A.

    1992-01-01T23:59:59.000Z

    Under a cooperative agreement with the Morgantown Energy Technology Center (METC) the Appalachian Oil and Natural Gas Research Consortium (AONGRC) is preparing a geologic atlas of the major gas plays in the Appalachian basin, and compiling a database for all fields in each geologic play. the first obligation under this agreement was to prepare a topical report that identifies the major gas plays, briefly describes each play, and explains how the plays were selected. Four main objectives have been defined for this initial task: assign each gas reservoir to a geologic play, based on age, trap type, degree of structural control, and depositional environment; organize all plays into geologically-similar groups based on the main criteria that defines each play; prepare a topical report for METC; and transfer this technology to industry through posters and talks at regional geological and engineering meetings including the Appalachian Petroleum Geology Symposium, Northeastern Section meeting of the Geological Society of America, the METC Gas Contractors Review meeting, the Kentucky Oil and Gas Association, and the Appalachian Energy Group.

  3. Selecting major Appalachian basin gas plays

    SciTech Connect (OSTI)

    Patchen, D.G.; Nuttall, B.C.; Baranoski, M.T.; Harper, J.A.; Schwietering, J.F.; Van Tyne, A.; Aminian, K.; Smosna, R.A.

    1992-06-01T23:59:59.000Z

    Under a cooperative agreement with the Morgantown Energy Technology Center (METC) the Appalachian Oil and Natural Gas Research Consortium (AONGRC) is preparing a geologic atlas of the major gas plays in the Appalachian basin, and compiling a database for all fields in each geologic play. the first obligation under this agreement was to prepare a topical report that identifies the major gas plays, briefly describes each play, and explains how the plays were selected. Four main objectives have been defined for this initial task: assign each gas reservoir to a geologic play, based on age, trap type, degree of structural control, and depositional environment; organize all plays into geologically-similar groups based on the main criteria that defines each play; prepare a topical report for METC; and transfer this technology to industry through posters and talks at regional geological and engineering meetings including the Appalachian Petroleum Geology Symposium, Northeastern Section meeting of the Geological Society of America, the METC Gas Contractors Review meeting, the Kentucky Oil and Gas Association, and the Appalachian Energy Group.

  4. AEP Appalachian Power- Commercial and Industrial Rebate Programs (West Virginia)

    Broader source: Energy.gov [DOE]

    Appalachian Power and Wheeling Power are offering prescriptive incentives under the APCo C&I Prescriptive program to facilitate the implementation of cost-effective energy efficiency...

  5. appalachian region: Topics by E-print Network

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

    Thaxton, Christopher S. 27 ECONOMIC IMPACT OF THE APPALACHIAN GATEWAY Fossil Fuels Websites Summary: , natural gas demand is forecast to increase through 2035. The...

  6. appalachian ohio region: Topics by E-print Network

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

    Thaxton, Christopher S. 34 ECONOMIC IMPACT OF THE APPALACHIAN GATEWAY Fossil Fuels Websites Summary: , natural gas demand is forecast to increase through 2035. The...

  7. Appalachian States Low-Level Radioactive Waste Compact (Maryland)

    Broader source: Energy.gov [DOE]

    This legislation authorizes Maryland's entrance into the Appalachian States Low-Level Radioactive Waste Compact, which seeks to promote interstate cooperation for the proper management and disposal...

  8. Alabama's Appalachian overthrust amid exploratory drilling resurgence

    SciTech Connect (OSTI)

    Taylor, J.D. (J.R. Holland and Associates, Northport, AL (US)); Epsman, M.L.

    1991-06-24T23:59:59.000Z

    Oil and gas exploration has been carried out sporadically in the Appalachian overthrust region of Alabama for years, but recently interest in the play has had a major resurgence. The Appalachian overthrust region of Alabama is best exposed in the valley and ridge physiographic province in the northeast part of the state. Resistant ridges of sandstone and chert and valleys of shales and carbonate have been thrust toward the northwest. Seismic data show that this structural style continues under the Cretaceous overlap. The surface and subsurface expression of the Alabama overthrust extends for more than 4,000 sq miles. Oil and gas have been produced for many years from Cambro-Ordovician, Ordovician, Mississippian, and Pennsylvanian rocks in the nearby Black Warrior basin in Alabama and Mississippi and the Cumberland plateau in Tennessee. The same zones are also potential producing horizons in the Alabama overthrust region.

  9. appalachian clean coal: Topics by E-print Network

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

    appalachian clean coal First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 1 INTRODUCTION Appalachian coal...

  10. Origin Basin Destination State STB EIA STB EIA Northern Appalachian...

    Annual Energy Outlook 2013 [U.S. Energy Information Administration (EIA)]

    20.69 19.60 -5.3% 74.23 26.4% 4,845 31.9% 97.7% Northern Appalachian Basin Michigan 13.74 16.13 17.4% 99.82 16.2% 840 32.1% 100.0% Northern Appalachian Basin New...

  11. Origin Basin Destination State STB EIA STB EIA Northern Appalachian...

    Gasoline and Diesel Fuel Update (EIA)

    19.73 19.64 -0.4% 81.15 24.2% 4,650 24.8% 99.3% Northern Appalachian Basin Michigan W 14.02 W 76.22 18.4% 713 W 100.0% Northern Appalachian Basin New Hampshire W...

  12. Salt-related structures in northern Appalachian basin

    SciTech Connect (OSTI)

    Towey, P.

    1988-08-01T23:59:59.000Z

    The Plateau province of the northern Appalachian basin is characterized by a series of sharp, detached, thrust-faulted anticlines roughly parallel with the Allegheny Front. In southwestern Pennsylvania and northern West Virginia, major thrusting of Alleghenian age is dominantly from the east, with numerous smaller thrusts from the west. Although the principal decollement is in the Silurian Salina Group, evidence of deeper detachment zones close to the front is abundant. In central and northern Pennsylvania, however, major thrusting is from the west. In those areas, thrusts from the east are rare to absent. Folds there are thin skinned above a decollement in the Salina Group, with no evidence of deeper detachment. Some recent workers have dismissed thrusting from the west as merely back thrusts of Alleghenian age, but seismic and well information indicate that the structural history of the Plateau province was dominated by a tectonic regime characterized by faults from the west and later overprinted near the structural front by the structures of the Alleghenian orogeny with its compression from the east. The basic idea is not new, but evidence in support of it has not been widely published.

  13. Appalachian Power Co | Open Energy Information

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page onYou are now leaving Energy.gov You are now leaving Energy.gov You are beingZealand Jump to:Ezfeedflag JumpID-fTriWildcatAntrim County, Michigan: EnergySalient ofApowerAppalachian Power

  14. AEP Appalachian Power- Non-Residential Custom Rebate Program

    Broader source: Energy.gov [DOE]

    The Appalachian Power Custom C&I program offers custom incentives for some of the more common energy efficiency measures. Program incentives are available under the Custom C&I program to ...

  15. CLIMATE-FIRE RELATIONSHIPS IN THE SOUTHERN APPALACHIAN MOUNTAINS

    E-Print Network [OSTI]

    Baker, Ralph C.

    2011-01-11T23:59:59.000Z

    This study is meant to explain the fire regime of the southern Appalachian Mountain Range of the southeastern United States by analyzing spatial statistics and climate-fire relationships. The spatial statistics were created by obtaining...

  16. Geologic Controls of Hydrocarbon Occurrence in the Appalachian Basin in Eastern Tennessee, Southwestern Virginia, Eastern Kentucky, and Southern West Virginia

    SciTech Connect (OSTI)

    Hatcher, Robert D

    2005-11-30T23:59:59.000Z

    This report summarizes the accomplishments of a three-year program to investigate the geologic controls of hydrocarbon occurrence in the southern Appalachian basin in eastern Tennessee, southwestern Virginia, eastern Kentucky, and southern West Virginia. The project: (1) employed the petroleum system approach to understand the geologic controls of hydrocarbons; (2) attempted to characterize the P-T parameters driving petroleum evolution; (3) attempted to obtain more quantitative definitions of reservoir architecture and identify new traps; (4) is worked with USGS and industry partners to develop new play concepts and geophysical log standards for subsurface correlation; and (5) geochemically characterized the hydrocarbons (cooperatively with USGS). Third-year results include: All project milestones have been met and addressed. We also have disseminated this research and related information through presentations at professional meetings, convening a major workshop in August 2003, and the publication of results. Our work in geophysical log correlation in the Middle Ordovician units is bearing fruit in recognition that the criteria developed locally in Tennessee and southern Kentucky are more extendible than anticipated earlier. We have identified a major 60 mi-long structure in the western part of the Valley and Ridge thrust belt that has been successfully tested by a local independent and is now producing commercial amounts of hydrocarbons. If this structure is productive along strike, it will be one of the largest producing structures in the Appalachians. We are completing a more quantitative structural reconstruction of the Valley and Ridge and Cumberland Plateau than has been made before. This should yield major dividends in future exploration in the southern Appalachian basin. Our work in mapping, retrodeformation, and modeling of the Sevier basin is a major component of the understanding of the Ordovician petroleum system in this region. Prior to our undertaking this project, this system was the least understood in the Appalachian basin. This project, in contrast to many if not most programs undertaken in DOE laboratories, has a major educational component wherein three Ph.D. students have been partially supported by this grant, one M.S. student partially supported, and another M.S. student fully supported by the project. These students will be well prepared for professional careers in the oil and gas industry.

  17. Study seeks to boost Appalachian gas recovery

    SciTech Connect (OSTI)

    Not Available

    1992-07-20T23:59:59.000Z

    Ashland Exploration Inc. and the Gas Research Institute (GRI) are trying to find ways to increase gas recovery in the Appalachian basin. They are working together to investigate Mississippian Berea sandstone and Devonian shale in a program designed to achieve better understanding and improved performance of tight natural gas formations in the area. This paper reports that three wells on Ashland Exploration acreage in Pike County, Ky., are involved in the research program. Findings from the first two wells will be used to optimize evaluation and completion of the third well. The first two wells have been drilled. Drilling of the third well was under way at last report. Ashland Exploration has been involved with GRI's Devonian shale research since 1988. GRI's initial focus was on well stimulation because Devonian shale wells it reviewed had much lower recoveries than could be expected, based on estimated gas in place. Research during the past few years was designed to improve the execution and quality control of well stimulation.

  18. SLH Timing Belt Powertrain

    SciTech Connect (OSTI)

    Schneider, Abe

    2014-04-09T23:59:59.000Z

    The main goal of this proposal was to develop and test a novel powertrain solution for the SLH hydroEngine?, a low-cost, efficient low-head hydropower technology. Nearly two-thirds of U.S. renewable electricity is produced by hydropower (EIA 2010). According to the U.S. Department of Energy; this amount could be increased by 50% with small hydropower plants, often using already-existing dams (Hall 2004). There are more than 80,000 existing dams, and of these, less than 4% generate power (Blankinship 2009). In addition, there are over 800 irrigation districts in the U.S., many with multiple, non-power, low-head drops. These existing, non-power dams and irrigation drops could be retrofitted to produce distributed, baseload, renewable energy with appropriate technology. The problem is that most existing dams are low-head, or less than 30 feet in height (Ragon 2009). Only about 2% of the available low-head hydropower resource in the U.S. has been developed, leaving more than 70 GW of annual mean potential low-head capacity untapped (Hall 2004). Natel Energy, Inc. is developing a low-head hydropower turbine that operates efficiently at heads less than 6 meters and is cost-effective for deployment across multiple low-head structures. Because of the unique racetrack-like path taken by the prime-movers in the SLH, a flexible powertrain is required. Historically, the only viable technological solution was roller chain. Despite the having the ability to easily attach blades, roller chain is characterized by significant drawbacks, including high cost, wear, and vibration from chordal action. Advanced carbon-#12;fiber-reinforced timing belts have been recently developed which, coupled with a novel belt attachment system developed by Natel Energy, result in a large reduction in moving parts, reduced mass and cost, and elimination of chordal action for increased fatigue life. The work done in this project affirmatively addressed each of the following 3 major uncertainties concerning a timing-belt based hydroEngine ?powertrain: 1. Can a belt handle the high torques and power loads demanded by the SLH? (Yes.) 2. Can the SLH blades be mounted to belt with a connection that can withstand the loads encountered in operation? (Yes.) 3. Can the belt, with blade attachments, live through the required cyclic loading? (Yes.) The research adds to the general understanding of sustainable small hydropower systems by using innovative system testing to develop and demonstrate performance of a novel powertrain solution, enabling a new type of hydroelectric turbine to be commercially developed. The technical effectiveness of the methods investigated has been shown to be positive through an extensive design and testing process accommodating many constraints and goals, with a major emphasis on high cycle fatigue life. Economic feasibility of the innovations has been demonstrated through many iterations of design for manufacturability and cost reduction. The project is of benefit to the public because it has helped to develop a solution to a major problem -- despite the large available potential for new low-head hydropower, high capital costs and high levelized cost of electricity (LCOE) continue to be major barriers to project development. The hydroEngine? represents a significant innovation, leveraging novel fluid mechanics and mechanical configuration to allow lower-cost turbine manufacture and development of low head hydropower resources.

  19. 1 INTRODUCTION Appalachian coal recovered during mining fre-

    E-Print Network [OSTI]

    of Appalachian underground coal mining (Newman 2003). Storage of coal processing waste is limited to above ground- ground room-and-pillar or longwall coal production do not allow for the separation of waste during coal. Such an analysis requires the ability to predict potential surface ground movements, both vertical (i

  20. IR Kuiper Belt Constraints

    E-Print Network [OSTI]

    Teplitz, V L; Anderson, J D; Rosenbaum, D C; Scalise, R J; Wentzler, P; Teplitz, Vigdor L.; Anderson, John D.; Rosenbaum, Doris; Scalise, Randall J.; Wentzler, Paul

    1999-01-01T23:59:59.000Z

    We compute the temperature and IR signal of particles of radius $a$ and albedo $\\alpha$ at heliocentric distance $R$, taking into account the emissivity effect, and give an interpolating formula for the result. We compare with analyses of COBE DIRBE data by others (including recent detection of the cosmic IR background) for various values of heliocentric distance, $R$, particle radius, $a$, and particle albedo, $\\alpha$. We then apply these results to a recently-developed picture of the Kuiper belt as a two-sector disk with a nearby, low-density sector (40belt IR spectra for various parameter v...

  1. All majors in geology are required to complete GLY 4750 (Field Methods) which includes classroom lectures on Appalachian Geology, a nine day trip to the Southern Appalachians, and

    E-Print Network [OSTI]

    Fernandez, Eduardo

    All majors in geology are required to complete GLY 4750 (Field Methods) which includes classroom lectures on Appalachian Geology, a nine day trip to the Southern Appalachians, and two oneday field trips geological data and interpretations, and requires the student to demonstrate proficiency in integrating

  2. Appalachian State University Water Resources Planning Committee Impacts of Urbanization on Headwater

    E-Print Network [OSTI]

    Thaxton, Christopher S.

    Temperature surges (Summer Months): Contact and runoff from impervious surfaces during afternoon rain storms by groundwater influx UPSTREAM MIDSTREAM DOWNSTREAM #12;Appalachian State University Water Resources Planning

  3. E-Print Network 3.0 - appalachian mountain region Sample Search...

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

    (GRAM) Program Award. Graduate School, Appalachian State University. "Arid region... of stream restoration on woody riparian vegetation of Southern ... Source: Collection:...

  4. Appalachian basin coal-bed methane: Elephant or flea

    SciTech Connect (OSTI)

    Hunt, A.M. (Dames and Moore, Cincinnati, OH (United States))

    1991-08-01T23:59:59.000Z

    Historically, interest in the Appalachian basin coal-bed methane resource extends at least over the last 50 years. The Northern and Central Appalachian basins are estimated to contain 61 tcf and 5 tcf of coal-bed methane gas, respectively. Development of this resource has not kept pace with that of other basins, such as the Black Warrior basin of Alabama of the San Juan basin of northern New Mexico and Colorado. Without the benefit of modern completion, stimulation, and production technology, some older Appalachian basin coal-bed methane wells were reported to have produced in excess of 150 used here to characterize some past projects and their results. This work is not intended to comprise a comprehensive survey of all Appalachian basin projects, but rather to provide background information from which to proceed for those who may be interested in doing so. Several constraints to the development of this resource have been identified, including conflicting legal rights of ownership of the gas produced from the coal seams when coal and conventional oil and gas rights are controlled by separate parties. In addition, large leaseholds have been difficult to acquire and finding costs have been high. However, the threshold of minimum economic production may be relatively low when compared with other areas, because low-pressures pipelines are available and gas prices are among the highest in the nation. Interest in the commercial development of the resource seems to be on the increase with several projects currently active and more reported to be planned for the near future.

  5. Opportunities for Visual Resource Management in the Southern Appalachian Coal Basin1

    E-Print Network [OSTI]

    Standiford, Richard B.

    Opportunities for Visual Resource Management in the Southern Appalachian Coal Basin1 John W) in the southern Appalachian coal basin resulting from the Surface Mining Control and Reclamation Act. It focuses been concerned with the visual impacts resulting from the surface mined coal the agency purchases

  6. Protein folding tames chaos

    E-Print Network [OSTI]

    Xia, Kelin

    2013-01-01T23:59:59.000Z

    Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to theoretical modeling and computer simulations. The present work introduces molecular nonlinear dynamics (MND), or molecular chaotic dynamics, as a theoretical framework for describing and analyzing protein folding. We unveil the existence of intrinsically low dimensional manifolds (ILDMs) in the chaotic dynamics of folded proteins. Additionally, we reveal that the transition from disordered to ordered conformations in protein folding increases the transverse stability of the ILDM. Stated differently, protein folding reduces the chaoticity of the nonlinear dynamical system, and a folded protein has the best ability to tame chaos. Additionally, we bring to light the connection between the ILDM stability and the thermodynamic stability, which enables us to quantify the disorderli...

  7. Geologic Controls of Hydrocarbon Occurrence in the Southern Appalachian Basin in Eastern Tennessee, Southwestern Virginia, Eastern Kentucky, and Southern West Virginia

    SciTech Connect (OSTI)

    Robert D. Hatcher

    2004-05-31T23:59:59.000Z

    This report summarizes the second-year accomplishments of a three-year program to investigate the geologic controls of hydrocarbon occurrence in the southern Appalachian basin in eastern Tennessee, southwestern Virginia, eastern Kentucky, and southern West Virginia. The project: (1) employs the petroleum system approach to understand the geologic controls of hydrocarbons; (2) attempts to characterize the T-P parameters driving petroleum evolution; (3) attempts to obtain more quantitative definitions of reservoir architecture and identify new traps; (4) is working with USGS and industry partners to develop new play concepts and geophysical log standards for subsurface correlation; and (5) is geochemically characterizing the hydrocarbons (cooperatively with USGS). Second-year results include: All current milestones have been met and other components of the project have been functioning in parallel toward satisfaction of year-3 milestones. We also have been effecting the ultimate goal of the project in the dissemination of information through presentations at professional meetings, convening a major workshop in August 2003, and the publication of results. Our work in geophysical log correlation in the Middle Ordovician units is bearing fruit in recognition that the criteria developed locally in Tennessee and southern Kentucky have much greater extensibility than anticipated earlier. We have identified a major 60 mi-long structure in the western part of the Valley and Ridge thrust belt that is generating considerable exploration interest. If this structure is productive, it will be one of the largest structures in the Appalachians. We are completing a more quantitative structural reconstruction of the Valley and Ridge than has been made before. This should yield major dividends in future exploration in the southern Appalachian basin. Our work in mapping, retrodeformation, and modeling of the Sevier basin is a major component of the understanding of the Ordovician petroleum system in this region. Prior to our undertaking this project, this system was the least understood in the Appalachian basin. We have made numerous presentations, convened a workshop, and are beginning to disseminate our results in print. This project, in contrast to many if not most programs undertaken in DOE laboratories, has a major educational component wherein three Ph.D. students have been partially supported by this grant, one M.S. student partially supported, and another M.S. student fully supported by the project. These students will be well prepared for professional careers in the oil and gas industry.

  8. New oilfield air bit improves drilling economics in Appalachian Basin

    SciTech Connect (OSTI)

    Brannon, K.C.; Grimes, R.E. [Hughes Christensen Co., Houston, TX (United States); Vietmeier, W.R. [Hughes Christensen Co., Imperial, PA (United States)

    1994-12-31T23:59:59.000Z

    Petroleum exploration in the Appalachian Basin of the northeastern United States has traditionally relied on compressed air, rather than drilling fluid, for its circulating medium. When compared to drilling mud, compressed air provides such advantages as increased rates of penetration, longer bit life, decreased formation damage, no lost circulation and saves the expense associated with mud handling equipment. Throughout the 1970s and early 1980s, roller cone mining bits and surplus oilfield bits were used to drill these wells. While the cutting structures of mining bits were well-suited for air drilling, the open roller bearings invariably shortened the useful life of the bit, particularly when water was present in the hole. This paper will highlight the development of a new IADC Class 539Y oilfield roller cone bit that is establishing performance records in air drilling applications throughout the Appalachian Basin. Essentially, the latest generation evolved from a roller cone bit successfully introduced in 1985 that combined a specialized non-offset cutting structure with a premium oilfield journal bearing package. Since its introduction, several sizes and types of oilfield air bits have been developed that have continually decreased drilling costs through enhanced performance and reliability. The design and evolution of rock bit cutting structures and bearing packages for high-performance oilfield air drilling applications will be detailed. Laboratory drilling test data will demonstrate the difference in drilling efficiencies between air drilling and conventional fluid drilling. Case studies taken from throughout the Appalachian Basin will be presented to illustrate the improvements in cost per foot, penetration rate, total footage drilled, drilling hours, and bit dull grades.

  9. Algorithmic folding complexity

    E-Print Network [OSTI]

    Cardinal, Jean

    2009-01-01T23:59:59.000Z

    How do we most quickly fold a paper strip (modeled as a line) to obtain a desired mountain-valley pattern of equidistant creases (viewed as a binary string)? Define the folding complexity of a mountain-valley string as the ...

  10. Appalachian Colleges Community Economic Development Partnership The Small Private Colleges Economic Development Toolkit

    E-Print Network [OSTI]

    Engel, Jonathan

    Partnerships o Evaluation: Measuring Effectiveness #12;The Small Private Colleges Economic Development ToolkitAppalachian Colleges Community Economic Development Partnership The Small Private Colleges Economic and sustainable economic development outreach programs. It contains carefully selected articles and case studies

  11. Microsoft PowerPoint - APPALACHIAN_STATE_Presentation 4 27 2015...

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

    Built Environment APPALACHIAN STATE UNIVERSITY 19 April 2015 2 The App State Team Jake Smith Chris Schoonover A.J. Smith Josh Brooks Chase Ambler Brad Painting Harrison Sytz...

  12. Native American Studies at West Virginia University: Continuing the Interactions of Native and Appalachian People

    E-Print Network [OSTI]

    High, Ellesa Clay; McNeil, Daniel W.

    2001-03-01T23:59:59.000Z

    Native American Studies at West Virginia University: Continuing the Interactions of Native and Appalachian People Ellesa Clay High and Daniel W. McNeil In the heart of Appalachia, Native American Studies has been growing for almost two decades.... West Virginia is the only state totally encompassed by the Appalachian region, the mountains of which stretch from Maine to Georgia. About the size of the Navajo Nation, "wild and wonderful" West Virginia is a place of intricate ridges, hollows...

  13. Synchronous and Cogged Fan Belt Performance Assessment

    SciTech Connect (OSTI)

    Cutler, D.; Dean, J.; Acosta, J.

    2014-02-01T23:59:59.000Z

    The GSA Regional GPG Team commissioned the National Renewable Energy Laboratory (NREL) to perform monitoring of cogged V-belts and synchronous belts on both a constant volume and a variable air volume fan at the Byron G. Rodgers Federal Building and U.S. Courthouse in Denver, Colorado. These motor/fan combinations were tested with their original, standard V-belts (appropriately tensioned by an operation and maintenance professional) to obtain a baseline for standard operation. They were then switched to the cogged V-belts, and finally to synchronous belts. The power consumption by the motor was normalized for both fan speed and air density changes. This was necessary to ensure that the power readings were not influenced by a change in rotational fan speed or by the power required to push denser air. Finally, energy savings and operation and maintenance savings were compiled into an economic life-cycle cost analysis of the different belt options.

  14. ACCEPTED MANUSCRIPT Fold interaction and wavelength selection

    E-Print Network [OSTI]

    Kaus, Boris

    simulations the lateral growth of folds is studied, in particular with respect to fold segments interactions; folding modes; fold interactions; 3D folding; numerical modelling 1 Introduction Buckling or folding

  15. 1. THE RADIATION BELTS The outer zone radiation belts consist of energetic elec-

    E-Print Network [OSTI]

    Elkington, Scot R.

    1. THE RADIATION BELTS The outer zone radiation belts consist of energetic elec- trons trapped in the geomagnetic field. The dynamics of the belts are dictated by the global and local electric and mag- netic electrons in the outer zone and electric and magnetic field variations occurring on ULF time scales

  16. Variation and Trends of Landscape Dynamics, Land Surface Phenology and Net Primary Production of the Appalachian Mountains

    SciTech Connect (OSTI)

    Wang, Yeqiao; Zhao, Jianjun; Zhou, Yuyu; Zhang, Hongyan

    2012-12-15T23:59:59.000Z

    The gradients of the Appalachian Mountains in elevations and latitudes provide a unique regional perspective of landscape variations in the eastern United States and a section of the southeastern Canada. This study reveals patterns and trends of landscape dynamics, land surface phenology and ecosystem production along the Appalachian Mountains using time series data from Global Inventory Modeling and Mapping Studies (GIMMS) and AVHRR Global Production Efficiency Model (GloPEM) datasets. We analyzed the spatial and temporal patterns of Normalized Difference Vegetation Index (NDVI), length of growing season (LOS) and net primary production (NPP) of selected ecoregions along the Appalachian Mountains regions. We compared the results out of the Appalachian Mountains regions in different spatial contexts including the North America and the Appalachian Trail corridor area. To reveal latitudinal variations we analyzed data and compared the results between 30N-40N and 40N-50N latitudes. The result revealed significant decreases in annual peak NDVI in the Appalachian Mountains regions. The trend for the Appalachian Mountains regions was -0.0018 (R2=0.55, P<0.0001) NDVI unit decrease per year during 25 years between 1982 and 2006. The LOS had prolonged 0.3 day yr-1 during 25 years over the Appalachian Mountains regions. The NPP increased by 2.68 gC m-2yr-2 in Appalachian Mountains regions from 1981 to 2000. The comparison with the North America reveals the effects of topography and ecosystem compositions of the Appalachian Mountains. The comparison with the Appalachian Trail corridor area provides a regional mega-transect view of the measured variables.

  17. Middle Paleozoic convergent orogenic belts in western Inner Mongolia (China)

    E-Print Network [OSTI]

    Paris-Sud XI, Universit de

    Middle Paleozoic convergent orogenic belts in western Inner Mongolia (China): framework, kinematics recognized in western Inner Mongolia (China), including, from south to north: North China Craton (NCC), Southern Orogenic Belt (SOB), Hunshandake Block (HB), Northern Orogenic Belt (NOB), South Mongolia

  18. INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION

    E-Print Network [OSTI]

    Halligan, Daniel

    INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION AND TIE KNOTS Thomas M. A. Fink st. john Introduction 3 1.1 Inverse Protein Folding 3 1.2 Hierarchical Optimisation 5 1.3 Tie Knots 6 1.4 Schematic Organisation 6 1.5 Publications 9 2 Protein Folding, Inverse Protein Folding and Energy Landscapes 10 2

  19. Simulations of Protein Folding

    E-Print Network [OSTI]

    Michael Cahill; Mark Fleharty; Kevin Cahill

    1999-09-17T23:59:59.000Z

    We have developed a simple, phenomenological, Monte-Carlo code that predicts the three-dimensional structure of globular proteins from the DNA sequences that define them. We have applied this code to two small proteins, the villin headpiece (1VII) and cole1 rop (1ROP). Our code folds both proteins to within 5 A rms of their native structures.

  20. Creating Artificial Radiation Belts in the Lab

    E-Print Network [OSTI]

    Mauel, Michael E.

    Current: Trapped, High- Protons (15-250 keV) Greatly intensified during geomagnetic storms Ti ~ 7Te Jeff #12;Outline The Earth's radiation belts and ring current Fast-electron interchange instability to measure the artificial radiation belt produced by the Argus explosions (1958). (Explosions continued

  1. Protein folding and cosmology

    E-Print Network [OSTI]

    P. F. Gonzalez-Diaz; C. L. Siguenza

    1997-06-04T23:59:59.000Z

    Protein denaturing induced by supercooling is interpreted as a process where some or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape becomes temperature-dependent and describes a phase transition. The idea that deformed vortices could be produced in the transition induced by temperature quenching, from native proteins to unfolded conformations is discussed in terms of the Zurek mechanism that implements the analogy between vortices, created in the laboratory at low energy, and the cosmic strings which are thought to have been left after symmetry breaking phase transitions in the early universe. An experiment is proposed to test the above idea which generalizes the cosmological analogy to also encompass biological systems and push a step ahead the view that protein folding is a biological equivalent of the big bang.

  2. Protein folding and heteropolymers

    E-Print Network [OSTI]

    T. Garel; H. Orland; E. Pitard

    1997-06-12T23:59:59.000Z

    We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random heteropolymeric description of these non random biomolecules. Various kinds of randomness are investigated, and the connection with disordered systems is discussed. We conclude by a brief study of the dynamics of proteins.

  3. Ab initio RNA folding

    E-Print Network [OSTI]

    Tristan Cragnolini; Philippe Derreumaux; Samuela Pasquali

    2014-12-30T23:59:59.000Z

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  4. Eastern Overthrust Belt. Signs of a hoped-for awakening

    SciTech Connect (OSTI)

    Bartlett, C.S. Jr.; Biggs, T.H.

    1982-06-01T23:59:59.000Z

    Exploration for oil and gas is on the upswing in the SW Virginia sector of the Eastern Overthrust Belt in the 200-mile long portion between Lee and Montgomery Counties. In the past several months one new oil field has been opened and the area's only gas field has been revived after lying idle for 23 yr. These signs of a hoped-for awakening have been accompanied by an intense leasing program by many oil companies. This review is confined to the geology of the strongly folded and faulted area of SW Virginia. In the Overthrust area, early studies indicated that oil would be found only in portions of Lee and Scott Counties, and that other areas would contain only natural gas because of the greater intensity of regional metamorphism. Drilling so far has confirmed these forecasts. This study will be divided in a similar manner.

  5. Electric filter with movable belt electrode

    DOE Patents [OSTI]

    Bergman, W.

    1983-09-20T23:59:59.000Z

    A method and apparatus for removing airborne contaminants entrained in a gas or airstream includes an electric filter characterized by a movable endless belt electrode, a grounded electrode, and a filter medium sandwiched there between. Inclusion of the movable, endless belt electrode provides the driving force for advancing the filter medium through the filter, and reduces frictional drag on the filter medium, thereby permitting a wide choice of filter medium materials. Additionally, the belt electrode includes a plurality of pleats in order to provide maximum surface area on which to collect airborne contaminants. 4 figs.

  6. Folding and binding Editorial overview

    E-Print Network [OSTI]

    is on the study of how protein folding, unfolding and aggregation reactions commence, and on the study of California, Berkeley. Her lab focuses on studies of protein folding and dynamics. Currently shebased kinetics. Much of the progress that has been made in the past fifty years in the study of protein folding

  7. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    Theoretical Perspectives on Protein Folding D. Thirumalai,1 Edward P. O'Brien,2 Greg Morrison,3 Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions remains to be done to solve the protein folding problem in the broadest sense. 159 Annu.Rev.Biophys.2010

  8. Computer Simulations of Protein Folding

    E-Print Network [OSTI]

    Sorin, Eric J.

    CHAPTER 8 Computer Simulations of Protein Folding VIJAY S. PANDE , ERIC J. SORIN , CHRISTOPHER D, CA 94305, USA 8.1 Introduction: Goals and Challenges of Simulating Protein Folding Computer as well as recent applications of this methodology. 8.1.1 Simulating Protein Folding Proteins play

  9. Petaflop Computing for Protein Folding

    E-Print Network [OSTI]

    Izaguirre, Jesús A.

    "SIAM01p 2000/12/4 page 1 Petaflop Computing for Protein Folding Shannon K. Kuntz, Richard C. Murphy, Michael T. Niemier, Jesus Izaguirre, and Peter M. Kogge 1 Introduction Protein Folding the protein folding problem, while Silicon Graphics has been continually working to produce more powerful

  10. Seat Belt Use Policy Outline the policy regarding use of seat belt in University of Michigan (U-M) vehicles.

    E-Print Network [OSTI]

    Kirschner, Denise

    Seat Belt Use Policy Objective Outline the policy regarding use of seat belt in University of Michigan (U-M) vehicles. Vehicle Use Policy 1. Staff members are responsible to operate U-M vehicles are adhering to the seat belt use laws when operating a U-M vehicle. 3. State of Michigan seat belt laws

  11. A study of binary Kuiper Belt objects

    E-Print Network [OSTI]

    Kern, Susan Diane

    2006-01-01T23:59:59.000Z

    About 105 bodies larger than 100km in diameter (Jewitt 1998) reside in the Kuiper Belt, beyond the orbit of Neptune. Since 1992 observational surveys have discovered over one thousand of these objects, believed to be fossil ...

  12. Protein folding in the ER.

    SciTech Connect (OSTI)

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

    1999-10-01T23:59:59.000Z

    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.

  13. Uncovering Allostery in a Uniquely Folded Metalloprotein /

    E-Print Network [OSTI]

    Baxter, Elizabeth Leigh

    2013-01-01T23:59:59.000Z

    M (2005) Downhill protein folding: evolution meets physics.based models for protein folding and function. Proteins:48-51). This is because protein folding and protein function

  14. 44 Journal of Student Research in Environmental Science at Appalachian Determining the viability of the practical

    E-Print Network [OSTI]

    Thaxton, Christopher S.

    of the practical application of solar electric systems in Boone, North Carolina April Lail Environmental Sciences44 Journal of Student Research in Environmental Science at Appalachian Determining the viability. Solar electric systems are a common renewable energy technology in households throughout the United

  15. CHARACTERIZATION OF CENTRAL APPALACHIAN BASIN CBM DEVELOPMENT: POTENTIAL FOR CARBON SEQUESTRATION

    E-Print Network [OSTI]

    of the carbon sequestration potential of the Pennsylvanian-age coalbeds in the Central Appalachian Basin favorable reservoirs for carbon sequestration due to their thickness, depth, rank, and permeability high gas content should provide the optimum reservoirs for carbon sequestration since these coals

  16. Spatio-temporal availability of soft mast in clearcuts in the Southern Appalachians

    E-Print Network [OSTI]

    Mitchell, Mike

    Spatio-temporal availability of soft mast in clearcuts in the Southern Appalachians Melissa J availability of soft mast though time is not fully understood. We tested a theoretical model of temporal availability of soft mast in clearcuts using empirical data on percent cover and berry production

  17. 96 Journal of Student Research in Environmental Science at Appalachian Genetically Modified Maize (Bt corn) and

    E-Print Network [OSTI]

    Thaxton, Christopher S.

    to produce their own pesticides or insecticides. The engineering of genetically modified food is a rel96 Journal of Student Research in Environmental Science at Appalachian Genetically Modified Maize the short-term effects of genetically modified (GM) maize, specifically MON810 and MON863, on laboratory

  18. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

    D. Thirumalai; Edward P. O'Brien; Greg Morrison; Changbong Hyeon

    2010-07-18T23:59:59.000Z

    Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing the folding mechanisms of globular proteins. The experimental data and theoretical methods have revealed the multifaceted character of proteins. Proteins exhibit universal features that can be determined using only the number of amino acid residues (N) and polymer concepts. The sizes of proteins in the denatured and folded states, cooperativity of the folding transition, dispersions in the melting temperatures at the residue level, and time scales of folding are to a large extent determined by N. The consequences of finite N especially on how individual residues order upon folding depends on the topology of the folded states. Such intricate details can be predicted using the Molecular Transfer Model that combines simulations with measured transfer free energies of protein building blocks from water to the desired concentration of the denaturant. By watching one molecule fold at a time, using single molecule methods, the validity of the theoretically anticipated heterogeneity in the folding routes, and the N-dependent time scales for the three stages in the approach to the native state have been established. Despite the successes of theory, of which only a few examples are documented here, we conclude that much remains to be done to solve the "protein folding problem" in the broadest sense.

  19. Graphene folding on flat substrates

    SciTech Connect (OSTI)

    Chen, Xiaoming; Zhao, Yadong; Ke, Changhong, E-mail: cke@binghamton.edu [Department of Mechanical Engineering, State University of New York at Binghamton, Binghamton, New York 13902 (United States); Zhang, Liuyang; Wang, Xianqiao [College of Engineering, University of Georgia, Athens, Georgia 30602 (United States)

    2014-10-28T23:59:59.000Z

    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.

  20. Mesoscale Folding: A Physical Realization of an Abstract, 2D Lattice Model for Molecular Folding

    E-Print Network [OSTI]

    Prentiss, Mara

    . Protein Folding: Theoretical Studies of Thermodynamics and Dynamics. In Protein Folding; Creighton, T. E

  1. Assessment of undiscovered carboniferous coal-bed gas resources of the Appalachian Basin and Black Warrior Basin Provinces, 2002

    SciTech Connect (OSTI)

    Milici, R.C.; Hatch, J.R.

    2004-09-15T23:59:59.000Z

    Coalbed methane (CBM) occurs in coal beds of Mississippian and Pennsylvanian (Carboniferous) age in the Appalachian basin, which extends almost continuously from New York to Alabama. In general, the basin includes three structural subbasins: the Dunkard basin in Pennsylvania, Ohio, and northern West Virginia; the Pocahontas basin in southern West Virginia, eastern Kentucky, and southwestern Virginia; and the Black Warrior basin in Alabama and Mississippi. For assessment purposes, the Appalachian basin was divided into two assessment provinces: the Appalachian Basin Province from New York to Alabama, and the Black Warrior Basin Province in Alabama and Mississippi. By far, most of the coalbed methane produced in the entire Appalachian basin has come from the Black Warrior Basin Province. 8 refs., 1 fig., 1 tab.

  2. Structural analysis of the perdido fold belt: timing, evolution, and structural style

    E-Print Network [OSTI]

    Waller, Troy Dale, II

    2007-09-17T23:59:59.000Z

    the upper portion consist of fine grained and muddy siliciclastics which are typical of turbidite and other typical deep water deposits. 2-D, prestacked, depth-migrated seismic data (TGS Phase 45) was interpreted in conjunction with Hess Corporation...

  3. Evolution and dynamics of a fold-thrust belt: the Sulaiman Range of Pakistan

    E-Print Network [OSTI]

    Reynolds, Kirsty; Copley, Alex; Hussain, Ekbal

    2015-03-09T23:59:59.000Z

    earthquakes (Szeliga et al. 2009) (solid yellow circles on Fig. 3a). The mechanism of the 1931 Sharigh event is not known (Quittmeyer & Jacob 1979). Remeasurement of a levelling line, together with structural interpretation of seismic reflection data suggests... that the seismic deformation in the range is concentrated in the thick pile of sediments overlying the underthrusting lithosphere of the Indian subcontinent. The slip vectors of the earthquakes vary in strike around the margin of the range, in tandem with the shape...

  4. Fast events in protein folding

    SciTech Connect (OSTI)

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

    1996-04-01T23:59:59.000Z

    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.

  5. Six Sigma Black Belts Fight For Quality

    E-Print Network [OSTI]

    Vardeman, Stephen B.

    Six Sigma Black Belts Fight For Quality Ron Scott Ross Finnestad Rodney Kalsow IE 361 mini-paper 9/22/00 #12;Six Sigma is a breakthrough management strategy that is revolutionizing the world's top corporations. So what is Six Sigma? "It is a business process that allows companies to drastically improve

  6. Impacts of Minnesota's Primary Seat Belt Law

    E-Print Network [OSTI]

    Minnesota, University of

    for Excellence in Rural Safety Humphrey School of Public Affairs #12;CERS's "Safe Six Regardless of Residence Urban/Small City Suburban Rural/Small Town Primary Seat; . . AND IN MINNESOTA #12;Predicted Impact 2009 and 2010 CERS Reports: Primary Seat Belt Laws

  7. Method for applying group selection in central appalachian hardwoods. Forest Service research paper (Final)

    SciTech Connect (OSTI)

    Miller, G.W.; Schuler, T.M.; Smith, H.C.

    1995-03-01T23:59:59.000Z

    Public concern over the adverse visual impact of clearcutting has heightened interest in developing and testing alternative regeneration practices for central Appalachian hardwoods. Group selection can meet aesthetic goals while providing suitable light conditions to reproduce shade-intolerant species. Volume control and residual stand density are used to reg8ulate periodic cuts. In central Appalachian hardwoods, openings must have a minimum size of 0.4 acre; all stems 1.0 inch d.b.h. and larger are cut to reproduce desirable shade-intollerant species. Openings should be located using the worst first approach to give the growing space occupied by mature trees or risky trees to faster growing, desirable regeneration.

  8. Sedimentology of gas-bearing Devonian shales of the Appalachian Basin

    SciTech Connect (OSTI)

    Potter, P.E.; Maynard, J.B.; Pryor, W.A.

    1981-01-01T23:59:59.000Z

    The Eastern Gas Shales Project (1976-1981) of the US DOE has generated a large amount of information on Devonian shale, especially in the western and central parts of the Appalachian Basin (Morgantown Energy Technology Center, 1980). This report summarizes this information, emphasizing the sedimentology of the shales and how it is related to gas, oil, and uranium. This information is reported in a series of statements each followed by a brief summary of supporting evidence or discussion and, where interpretations differ from our own, we include them. We believe this format is the most efficient way to learn about the gas-bearing Devonian shales of the Appalachian Basin and have organized our statements as follows: paleogeography and basin analysis; lithology and internal stratigraphy; paleontology; mineralogy, petrology, and chemistry; and gas, oil, and uranium.

  9. Introduction to Grid computing Protein folding

    E-Print Network [OSTI]

    Boyar, Joan

    Introduction to Grid computing Protein folding Protein folding is an extremely hot topic in medical research these days, unfortunately protein folding is extremely computationally demanding and requires a huge supercomputer to fold even the simplest proteins. Luckily the task of calculating protein foldings

  10. Protein Folding Sculpting Evolutionary Change

    E-Print Network [OSTI]

    Lindquist, Susan

    Our work suggests that the forces that govern protein folding exert a profound effect on how genotypes are translated into phenotypes and that this in turn has strong effects on evolutionary processes. Molecular chaperones, ...

  11. Eustatic and tectonic control of sedimentation in the Pennsylvanian strata of the Central Appalachian Basin

    SciTech Connect (OSTI)

    Chesnut, D.R. Jr. (Univ. of Kentucky, Lexington, KY (United States). Kentucky Geological Survey)

    1992-01-01T23:59:59.000Z

    Analysis of the Breathitt Group of the Central Appalachian Basin reveals three orders of depositional cycles or trends. The Breathitt coarsening-upward trend (20 million years (my)) represents increasing intensity of the Alleghenian Orogeny. The major transgression (MT) cycle (2.5 my) was controlled by an unknown eustatic or tectonic mechanism. The major coal beds and intervening strata make up the coal-clastic cycle (CC cycle) (=Appalachian cyclothem) which has a 0.4 my periodicity. This periodicity supports eustatic control of sedimentation modulated by an orbital periodicity. Extensive coastal peats deposited at lowstand (CC cycle) were preserved as coals, whereas highstand peats were eroded during the subsequent drop in sea level. Autocyclic processes such as delta switching and avulsion occurred within CC cycles. An Early Pennsylvanian unconformity represents uplift and erosion of mid-Carboniferous foreland basin deposits. Alluvial deposits (Breathitt Group) derived from the highlands were transported to the northwest toward the forebulge. During lowstand, the only outlet available to further sediment transport (Lee sandstones) was toward the southwest (Ouachita Trough), along the Black Warrior-Appalachian foreland basins. The Middle Pennsylvanian marks a period of intermittent overfilling of the foreland basin and cresting of the forebulge. Marine transgressions entered through the foreland basins and across saddles in the forebulge. After the Ouachita Trough was destroyed during the late Middle Pennsylvanian, marine transgressions migrated only across saddles in the forebulge. In the Late Pennsylvanian, marine waters entered the basin only across the diminished forebulge north of the Jessamine Dome.

  12. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01T23:59:59.000Z

    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.

  13. A motion planning approach to protein folding

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30T23:59:59.000Z

    Protein folding is considered to be one of the grand challenge problems in biology. Protein folding refers to how a protein's amino acid sequence, under certain physiological conditions, folds into a stable close-packed three-dimensional structure...

  14. A motion planning approach to protein folding

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30T23:59:59.000Z

    Protein folding is considered to be one of the grand challenge problems in biology. Protein folding refers to how a protein's amino acid sequence, under certain physiological conditions, folds into a stable close-packed ...

  15. Biophysical characterization of protein folding and misfolding.

    E-Print Network [OSTI]

    Schmittschmitt, Jason Peter

    2004-09-30T23:59:59.000Z

    The HPr proteins were characterized as folding by a two-state folding mechanism. Here, we present a comparison of the equilibrium and kinetic folding for the HPr protein from Bacillus subtilis, E coli and a key variant ...

  16. Search for: "protein folding" | DOE PAGES

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

    protein folding" Find + Advanced Search Advanced Search All Fields: "protein folding" Title: Full Text: Bibliographic Data: Creator Author: Name Name ORCID Search Authors...

  17. Population of the Scattered Kuiper Belt

    E-Print Network [OSTI]

    C. A. Trujillo; D. C. Jewitt; J. X. Luu

    1999-12-20T23:59:59.000Z

    We present the discovery of three new Scattered Kuiper Belt Objects (SKBOs) from a wide-field survey of the ecliptic. This continuing survey has to date covered 20.2 square degrees to a limiting red magnitude of 23.6. We combine the data from this new survey with an existing survey conducted at the University of Hawaii 2.2m telescope to constrain the number and mass of the SKBOs. The SKBOs are characterized by large eccentricities, perihelia near 35 AU, and semi-major axes > 50 AU. Using a maximum-likelihood model, we estimate the total number of SKBOs larger than 100 km in diameter to be N = 3.1 (+1.9/-1.3) x 10^4 (1 sigma) and the total mass of SKBOs to be about 0.05 Earth masses, demonstrating that the SKBOs are similar in number and mass to the Kuiper Belt inside 50 AU.

  18. Disulfide-Linked Protein Folding Pathways

    E-Print Network [OSTI]

    Bardwell, James

    Disulfide-Linked Protein Folding Pathways Bharath S. Mamathambika1,3 and James C. Bardwell2,3, 1 of protein folding is difficult because it involves the identification and characterization of folding to protein folding in vitro and in vivo. 211 Click here for quick links to Annual Reviews content online

  19. Replace V-Belts with Notched or Synchronous Belt Drives | Department of

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page onYouTube YouTube Note: Since the.pdfBreakingMay 2015 < prevQuickEnergy V-Belts with Notched or Synchronous Belt

  20. Dominant Pathways in Protein Folding

    E-Print Network [OSTI]

    P. Faccioli; M. Sega; F. Pederiva; H. Orland

    2006-07-27T23:59:59.000Z

    We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy between thermal and quantum diffusion: by writing the solution of the Fokker-Planck equation for the time-evolution of a protein in a viscous heat-bath in terms of a path integral, we derive a Hamilton-Jacobi variational principle from which we are able to compute the most probable pathway of folding. The method is applied to the folding of the Villin Headpiece Subdomain, in the framework of a Go-model. We have found that, in this model, the transition occurs through an initial collapsing phase driven by the starting coil configuration and a later rearrangement phase, in which secondary structures are formed and all computed paths display strong similarities. This method is completely general, does not require the prior knowledge of any reaction coordinate and represents an efficient tool to perfom ab-initio simulations of the entire folding process with available computers.

  1. Corn Belt Energy Corporation- Residential Energy Efficiency Rebate Program

    Broader source: Energy.gov [DOE]

    Corn Belt Energy Corporation (CBEC), in association with the Wabash Valley Power Association, provides its customers with the "Power Moves" energy efficiency rebate program. Through this program,...

  2. Geologic Setting of the Central Alaskan Hot Springs Belt: Implications...

    Open Energy Info (EERE)

    Sustainable Energy Production Jump to: navigation, search OpenEI Reference LibraryAdd to library Thesis: Geologic Setting of the Central Alaskan Hot Springs Belt: Implications for...

  3. Magnetic refrigeration apparatus with belt of ferro or paramagnetic material

    DOE Patents [OSTI]

    Barclay, John A. (Madison, WI); Stewart, Walter F. (Marshall, WI); Henke, Michael D. (Los Alamos, NM); Kalash, Kenneth E. (Los Alamos, NM)

    1987-01-01T23:59:59.000Z

    A magnetic refrigerator operating in the 12 to 77K range utilizes a belt which carries ferromagnetic or paramagnetic material and which is disposed in a loop which passes through the center of a solenoidal magnet to achieve cooling. The magnetic material carried by the belt, which can be blocks in frames of a linked belt, can be a mixture of substances with different Curie temperatures arranged such that the Curie temperatures progressively increase from one edge of the belt to the other. This magnetic refrigerator can be used to cool and liquefy hydrogen or other fluids.

  4. Magnetic refrigeration apparatus with belt of ferro or paramagnetic material

    DOE Patents [OSTI]

    Barclay, J.A.; Stewart, W.F.; Henke, M.D.; Kalash, K.E.

    1986-04-03T23:59:59.000Z

    A magnetic refrigerator operating in the 12 to 77 K range utilizes a belt which carries ferromagnetic or paramagnetic material and which is disposed in a loop which passes through the center of a solenoidal magnet to achieve cooling. The magnetic material carried by the belt, which can be blocks in frames of a linked belt, can be a mixture of substances with different Curie temperatures arranged such that the Curie temperatures progressively increase from one edge of the belt to the other. This magnetic refrigerator can be used to cool and liquefy hydrogen or other fluids.

  5. Feasibility study of heavy oil recovery in the Appalachian, Black Warrior, Illinois, and Michigan basins

    SciTech Connect (OSTI)

    Olsen, D.K.; Rawn-Schatzinger, V.; Ramzel, E.B.

    1992-07-01T23:59:59.000Z

    This report is one of a series of publications assessing the feasibility of increasing domestic heavy oil production. Each report covers select areas of the United States. The Appalachian, Black Warrior, Illinois, and Michigan basins cover most of the depositional basins in the Midwest and Eastern United States. These basins produce sweet, paraffinic light oil and are considered minor heavy oil (10{degrees} to 20{degrees} API gravity or 100 to 100,000 cP viscosity) producers. Heavy oil occurs in both carbonate and sandstone reservoirs of Paleozoic Age along the perimeters of the basins in the same sediments where light oil occurs. The oil is heavy because escape of light ends, water washing of the oil, and biodegradation of the oil have occurred over million of years. The Appalachian, Black Warrior, Illinois, and Michigan basins' heavy oil fields have produced some 450,000 bbl of heavy oil of an estimated 14,000,000 bbl originally in place. The basins have been long-term, major light-oil-producing areas and are served by an extensive pipeline network connected to refineries designed to process light sweet and with few exceptions limited volumes of sour or heavy crude oils. Since the light oil is principally paraffinic, it commands a higher price than the asphaltic heavy crude oils of California. The heavy oil that is refined in the Midwest and Eastern US is imported and refined at select refineries. Imports of crude of all grades accounts for 37 to >95% of the oil refined in these areas. Because of the nature of the resource, the Appalachian, Black Warrior, Illinois and Michigan basins are not expected to become major heavy oil producing areas. The crude oil collection system will continue to degrade as light oil production declines. The demand for crude oil will increase pipeline and tanker transport of imported crude to select large refineries to meet the areas' liquid fuels needs.

  6. Feasibility study of heavy oil recovery in the Appalachian, Black Warrior, Illinois, and Michigan basins

    SciTech Connect (OSTI)

    Olsen, D.K.; Rawn-Schatzinger, V.; Ramzel, E.B.

    1992-07-01T23:59:59.000Z

    This report is one of a series of publications assessing the feasibility of increasing domestic heavy oil production. Each report covers select areas of the United States. The Appalachian, Black Warrior, Illinois, and Michigan basins cover most of the depositional basins in the Midwest and Eastern United States. These basins produce sweet, paraffinic light oil and are considered minor heavy oil (10{degrees} to 20{degrees} API gravity or 100 to 100,000 cP viscosity) producers. Heavy oil occurs in both carbonate and sandstone reservoirs of Paleozoic Age along the perimeters of the basins in the same sediments where light oil occurs. The oil is heavy because escape of light ends, water washing of the oil, and biodegradation of the oil have occurred over million of years. The Appalachian, Black Warrior, Illinois, and Michigan basins` heavy oil fields have produced some 450,000 bbl of heavy oil of an estimated 14,000,000 bbl originally in place. The basins have been long-term, major light-oil-producing areas and are served by an extensive pipeline network connected to refineries designed to process light sweet and with few exceptions limited volumes of sour or heavy crude oils. Since the light oil is principally paraffinic, it commands a higher price than the asphaltic heavy crude oils of California. The heavy oil that is refined in the Midwest and Eastern US is imported and refined at select refineries. Imports of crude of all grades accounts for 37 to >95% of the oil refined in these areas. Because of the nature of the resource, the Appalachian, Black Warrior, Illinois and Michigan basins are not expected to become major heavy oil producing areas. The crude oil collection system will continue to degrade as light oil production declines. The demand for crude oil will increase pipeline and tanker transport of imported crude to select large refineries to meet the areas` liquid fuels needs.

  7. Appalachian Rivers II Conference: Technology for Monitoring, Assessing, and Restoring Streams, Rivers, and Watersheds

    SciTech Connect (OSTI)

    None available

    1999-07-29T23:59:59.000Z

    On July 28-29, 1999, the Federal Energy Technology Center (FETC) and the WMAC Foundation co-sponsored the Appalachian Rivers II Conference in Morgantown, West Virginia. This meeting brought together over 100 manufacturers, researchers, academicians, government agency representatives, watershed stewards, and administrators to examine technologies related to watershed assessment, monitoring, and restoration. Sessions included presentations and panel discussions concerning watershed analysis and modeling, decision-making considerations, and emerging technologies. The final session examined remediation and mitigation technologies to expedite the preservation of watershed ecosystems.

  8. Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways

    E-Print Network [OSTI]

    Plotkin, Steven S.

    Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways Ali induce dominant pathway mechanisms in protein folding. Citation: Mohazab AR, Plotkin SS (2013) Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways. PLoS ONE 8(1): e53642

  9. Corn Belt Power Coop | Open Energy Information

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page onYou are now leaving Energy.gov You are now leaving Energy.gov You are beingZealand JumpConceptual Model, clickInformationNew|Core Analysis At Geysers| Open EnergyAl.,A,CorixBelt

  10. Protein folding using contact maps

    E-Print Network [OSTI]

    Michele Vendruscolo; Eytan Domany

    1999-01-21T23:59:59.000Z

    We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three dimensional conformation from a contact map and the Monte Carlo dynamics in contact map space. We then discuss two approximations to the free energy of the contact maps and a method to derive energy parameters based on perceptron learning. Finally we present results, first for predictions based on threading and then for energy minimization of crambin and of a set of 6 immunoglobulins. The main result is that we proved that the two simple approximations we studied for the free energy are not suitable for protein folding. Perspectives are discussed in the last section.

  11. Changes in the extent of surface mining and reclamation in the Central Appalachians detected using a 19762006 Landsat time series

    E-Print Network [OSTI]

    Radeloff, Volker C.

    of surface mining using heavy equipment can produce dramatic alterations in land cover, both ecologicallyChanges in the extent of surface mining and reclamation in the Central Appalachians detected using of Forest and Wildlife Ecology, 1630 Linden Drive, Madison, WI 53706, United States b Virginia Polytechnic

  12. Investigating Protein Folding and Function by Manipulating Rare and Partially-Folded Conformations

    E-Print Network [OSTI]

    Horner, Geoffrey Ashworth

    2010-01-01T23:59:59.000Z

    Z. Zhou, and Y. Bai, A protein folding pathway with multipleintermediate state in protein folding by a hydrophobicAre there pathways for protein folding. J Chim Phys, 1968.

  13. Folding pathway of a lattice model for protein folding Vijay S. Pande1

    E-Print Network [OSTI]

    Croquette, Vincent

    Folding pathway of a lattice model for protein folding Vijay S. Pande1 and Daniel S. Rokhsar1 principles that describe protein folding, then one might expect them to apply to simplified models

  14. WATER ICE IN THE KUIPER BELT

    SciTech Connect (OSTI)

    Brown, M. E.; Fraser, W. C. [Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 (United States); Schaller, E. L., E-mail: mbrown@caltech.edu [NASA Dryden Aircraft Operations Facility, Palmdale, CA 93550 (United States)

    2012-06-15T23:59:59.000Z

    We examine a large collection of low-resolution near-infrared spectra of Kuiper Belt objects (KBOs) and centaurs in an attempt to understand the presence of water ice in the Kuiper Belt. We find that water ice on the surface of these objects occurs in three separate manners: (1) Haumea family members uniquely show surfaces of nearly pure water ice, presumably a consequence of the fragmentation of the icy mantle of a larger differentiated proto-Haumea; (2) large objects with absolute magnitudes of H < 3 (and a limited number to H = 4.5) have surface coverings of water ice-perhaps mixed with ammonia-that appears to be related to possibly ancient cryovolcanism on these large objects; and (3) smaller KBOs and centaurs which are neither Haumea family members nor cold-classical KBOs appear to divide into two families (which we refer to as 'neutral' and 'red'), each of which is a mixture of a common nearly neutral component and either a slightly red or very red component that also includes water ice. A model suggesting that the difference between neutral and red objects due to formation in an early compact solar system either inside or outside, respectively, of the {approx}20 AU methanol evaporation line is supported by the observation that methanol is only detected on the reddest objects, which are those which would be expected to have the most of the methanol containing mixture.

  15. Large Bodies in the Kuiper Belt

    E-Print Network [OSTI]

    Chadwick A. Trujillo; Jane X. Luu; Amanda S. Bosh; James L. Elliot

    2001-08-27T23:59:59.000Z

    We present a survey for bright Kuiper Belt Objects (KBOs) and Centaurs, conducted at the Kitt Peak National Observatory (KPNO) 0.9 m telescope with the KPNO 8k Mosaic CCD. The survey imaged 164 sq deg near opposition to a limiting red magnitude of 21.1. Three bright KBOs and one Centaur were found, the brightest KBO having red magnitude 19.7, about 700 km in diameter assuming a dark Centaur-like 4% albedo. We estimate the power-law differential size distribution of the Classical KBOs to have index q = 4.2 (+0.4)(-0.3), with the total number of Classical KBOs with diameters larger than 100 km equal to 4.7 (+1.6)(-1.0) x 10^4. Additionally, we find that if there is a maximum object size in the Kuiper Belt, it must be larger than 1000 km in diameter. By extending our model to larger size bodies, we estimate that 30 (+16)(-12) Charon-sized and 3.2 (+2.8)(-1.7) Pluto-sized Classical KBOs remain undiscovered.

  16. Higher coronary heart disease and heart attack morbidity in Appalachian coal mining regions

    SciTech Connect (OSTI)

    Hendryx, M.; Zullig, K.J. [West Virginia University, Morgantown, WV (United States). Dept. of Community Medicine

    2009-11-15T23:59:59.000Z

    This study analyzes the U.S. 2006 Behavioral Risk Factor Surveillance System survey data (N = 235,783) to test whether self-reported cardiovascular disease rates are higher in Appalachian coal mining counties compared to other counties after control for other risks. Dependent variables include self-reported measures of ever (1) being diagnosed with cardiovascular disease (CVD) or with a specific form of CVD including (2) stroke, (3) heart attack, or (4) angina or coronary heart disease (CHD). Independent variables included coal mining, smoking, BMI, drinking, physician supply, diabetes co-morbidity, age, race/ethnicity, education, income, and others. SUDAAN Multilog models were estimated, and odds ratios tested for coal mining effects. After control for covariates, people in Appalachian coal mining areas reported significantly higher risk of CVD (OR = 1.22, 95% CI = 1.14-1.30), angina or CHO (OR = 1.29, 95% C1 = 1.19-1.39) and heart attack (OR = 1.19, 95% C1 = 1.10-1.30). Effects were present for both men and women. Cardiovascular diseases have been linked to both air and water contamination in ways consistent with toxicants found in coal and coal processing. Future research is indicated to assess air and water quality in coal mining communities in Appalachia, with corresponding environmental programs and standards established as indicated.

  17. Geochemical analysis of crude oil from northern Appalachian, eastern Illinois, and southern Michigan basins

    SciTech Connect (OSTI)

    Noel, J.A.; Cole, J.; Innes, C.; Juzwick, S.

    1987-09-01T23:59:59.000Z

    In May 1986, the Ohio Board of Regents awarded a research grant to Ashland College to investigate the basinal origin of crude oil through trace-element analysis. The major thrust of the project was to attempt to finger print crude oils of various ages and depths from the northern Appalachian, eastern Illinois, and southern Michigan basins, to learn if the oldest crudes may have migrated among the basins. This in turn might give a more definitive time for the separation of the three basins. Nickel to vanadium ratios, were chosen to be the discriminators. Nickel to vanadium ratios show that the Trenton oil from the fields at Lima, Ohio; Oak Harbor in Ottawa County, Ohio; Urbana, Indiana; Peru, Indiana; and Albion, Michigan, are all different. The Trempealeau oils in Harmony and Lincoln Townships, Morrow County, are similar but they are different from those in Peru and Bennington Townships. The Devonian oils of the Illinois and Appalachian basins are distinctly different. The Berea oil shows little or no variability along strike. The Mississippian oils of the Illinois basin are different from the Berea oils and the Salem oil is different from the Chester. The only thing consistent about the Clinton is its inconsistency.

  18. Topology to geometry in protein folding: -Lactoglobulin

    E-Print Network [OSTI]

    Berry, R. Stephen

    Topology to geometry in protein folding: -Lactoglobulin Ariel Fernandez* , Andres Colubri , and R angles and at the -carbon atoms of the peptide backbone dominate protein folding. Next in importance

  19. Parametric analysis of RNA folding

    E-Print Network [OSTI]

    Hower, Valerie

    2009-01-01T23:59:59.000Z

    We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We use this polytope and its normal fan to study the effect of varying three parameters in the free energy model that are not determined experimentally. Our results indicate that variation of these specific parameters does not have a dramatic effect on the structures predicted by the free energy model. We additionally map a collection of known RNA secondary structures to the RNA polytope.

  20. Approximate Inference and Protein-Folding

    E-Print Network [OSTI]

    Weiss, Yair

    Approximate Inference and Protein-Folding Chen Yanover and Yair Weiss School of Computer Science Side-chain prediction is an important subtask in the protein-folding problem. We show that #12;nding algorithms, including a widely used protein-folding software (SCWRL). 1 Introduction Inference in graphical

  1. EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS

    E-Print Network [OSTI]

    Guibas, Leonidas J.

    EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS D. RUSSEL and L. GUIBAS Computer of secondary and tertiary structures as the protein folds. 1 Introduction There has been extensive work understanding of protein folding by studying their ensemble behaviors. Most currently used methods

  2. UNCORRECTED 3 Protein folding: Then and now

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    UNCORRECTED PROOF 1 2 Review 3 Protein folding: Then and now 4 Yiwen Chen 1 , Feng Ding 1 , Huifen 8 9 Abstract 10 Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how 11 a protein folds has now become vital

  3. Protein folding: not just another optimization

    E-Print Network [OSTI]

    Karplus, Kevin

    Protein folding: not just another optimization problem Kevin Karplus karplus of California, Santa Cruz protein-folding: not just opt p.1/68 #12;Outline of Talk What is Bioinformatics initio" methods Contact prediction protein-folding: not just opt p.2/68 #12;What is Bioinformatics

  4. Atomistic Protein Folding Simulations on the

    E-Print Network [OSTI]

    Snow, Christopher

    Atomistic Protein Folding Simulations on the Submillisecond Time Scale Using Worldwide Distributed Abstract: Atomistic simulations of protein folding have the potential to be a great complement. Biopolymers 68: 91109, 2003 Keywords: atomistic protein folding; microsecond time scale; computer hardware

  5. 272 Dispatch Protein folding: Chaperones get Hip

    E-Print Network [OSTI]

    Craig, Elizabeth A

    272 Dispatch Protein folding: Chaperones get Hip Thomas Ziegelhoffer, Jill L. Johnson and Elizabeth the complexity of the Hsp70 `chaperone machine' that mediates early steps of protein folding in cells. Address of protein folding and translocation through their ability to recognize non-native conformations of proteins

  6. Thermodynamics of Protein Folding Erik Sandelin

    E-Print Network [OSTI]

    Sandelin, Erik

    Thermodynamics of Protein Folding and Design Erik Sandelin Department of Theoretical Physics Lund Slvegatan 14A 223 62 LUND September 2000 Erik Sandelin Thermodynamics of Protein Folding and Design The protein folding and protein design problems are addressed, using coarse-grained models with only two types

  7. Geohydrologic feasibility study of the Northern and Central Appalachian basin areas for the potential application of a production process patented by Jack W. McIntyre

    SciTech Connect (OSTI)

    Kvasnicka, D.

    1994-03-01T23:59:59.000Z

    Geraghty & Miller, Inc. of Midland, Texas conducted geologic and hydrologic feasibility studies of the potential applicability of a patented (US Patent Office No. 4,766,957) process developed by Jack W. McIntyre for the recovery of natural gas from coalbed/sand formations in the Northern and Central Appalachian basin areas. General research, based on a review of published literature from both public and private sources, indicates that the generally thin, but numerous coalbeds found in the greater Appalachian Basin area do exhibit some potential for the application of this patented process. Estimates of total gas reserves in-place (Gas Research Institute, July 1991) for coalbeds in the Central and Northern Appalachian Basin areas are 5 trillion cubic feet (TCF) and 61 TCF respectively. Produced waters associated with coal deposits in the greater Appalachian Basin area can be characterized on the basis of established but limited production of coalbed methane. Central Appalachian coals generally produce small quantities of water (less than 50 barrels of water per day for the average producing well) which is high in total dissolved solids (TDS), greater than 30,000 parts per million (ppM). The chemical quality of water produced from these coal seams represents a significant disposal challenge to the operators of methane-producing wells in the Central Appalachian Basin. By contrast, water associated with the production of coalbed methane in the Northern Appalachian Basin is generally fair to good quality, and daily production volumes are low. However, the relatively slow desorption of methane gas from Northern Appalachian coals may result in a greater net volume of produced water over the economic life of the well. The well operator must respond to long-term disposal needs.

  8. Introducing Protein Folding Using Simple Models

    E-Print Network [OSTI]

    D. Thirumalai; D. K. Klimov

    2001-01-04T23:59:59.000Z

    We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use of lattice models to understand the selection of the limited set of viable protein folds; (ii) the relationship between structure and sequence spaces; (iii) the application of lattice models for studying folding mechanisms (topological frustration, kinetic partitioning mechanism). Classification of folding scenarios based on the intrinsic thermodynamic properties of a sequence (namely, the collapse and folding transition temperatures) is outlined. A brief discussion of random heteropolymer model is also presented.

  9. A review of recent advances in ab initio protein folding by the Folding@home project

    E-Print Network [OSTI]

    A review of recent advances in ab initio protein folding by the Folding@home project William Ito molecular simulations of protein folding. Thanks to engineering innovations like a Graphical Processing Unit power, allowing it to simulate longer and more complex protein folding mechanisms than ever before

  10. Protein Folding Trajectories Analysis: Summarization, Event Detection and Consensus Partial Folding Pathway

    E-Print Network [OSTI]

    Yang, Hui

    Protein Folding Trajectories Analysis: Summarization, Event Detection and Consensus Partial Folding in protein folding trajectories. We pro- pose an approach that employs the simplicity of contact maps and po- tentially cure diseases caused by misfolding. The protein folding problem is therefore one

  11. Computational investigations of folded self-avoiding walks related to protein folding

    E-Print Network [OSTI]

    Paris-Sud XI, Universit de

    Computational investigations of folded self-avoiding walks related to protein folding Jacques M, protein folding, protein structure prediction 1. Introduction Self-avoiding walks (SAWs) have been studied, 9], authors of this manuscript have investigated some dynamic protein folding models. They have

  12. CREATING A GEOLOGIC PLAY BOOK FOR TRENTON-BLACK RIVER APPALACHIAN BASIN EXPLORATION

    SciTech Connect (OSTI)

    Douglas G. Patchen; James Drahovzal; Larry Wickstrom; Taury Smith; Chris Laughery; Katharine Lee Avary

    2004-04-01T23:59:59.000Z

    Private- and public-sector stakeholders formed the new ''Trenton-Black River Appalachian Basin Exploration Consortium'' and began a two-year research effort that will lead to a play book for Trenton-Black River exploration throughout the Appalachian basin. The final membership of the Consortium includes 17 gas exploration companies and 6 research team members, including the state geological surveys in Kentucky, Ohio, Pennsylvania and West Virginia, the New York State Museum Institute and West Virginia University. Seven integrated research tasks are being conducted by basin-wide research teams organized from this large pool of experienced professionals. More than 3400 miles of Appalachian basin digital seismic data have been quality checked. In addition, inquiries have been made regarding the availability of additional seismic data from government and industry partners in the consortium. Interpretations of the seismic data have begun. Error checking is being performed by mapping the time to various prominent reflecting horizons, and analyzing for any anomalies. A regional geological velocity model is being created to make time-to-depth conversions. Members of the stratigraphy task team compiled a generalized, basin-wide correlation chart, began the process of scanning geophysical logs and laid out lines for 16 regional cross sections. Two preliminary cross sections were constructed, a database of all available Trenton-Black River cores was created, and a basin-wide map showing these core locations was produced. Two cores were examined, described and photographed in detail, and were correlated to the network of geophysical logs. Members of the petrology team began the process of determining the original distribution of porous and permeable facies within a sequence stratigraphic framework. A detailed sedimentologic and petrographic study of the Union Furnace road cut in central Pennsylvania was completed. This effort will facilitate the calibration of subsurface core and log data. A core-sampling plan was developed cooperatively with members of the isotope geochemistry and fluid inclusion task team. One hundred thirty (130) samples were prepared for trace element and stable isotope analysis, and six samples were submitted for strontium isotope analysis. It was learned that there is a good possibility that carbon isotope stratigraphy may be a useful tool to locate the top of the Black River Formation in state-to-state correlations. Gas samples were collected from wells in Kentucky, New York and West Virginia. These were sent to a laboratory for compositional, stable isotope and hydrogen and radiogenic helium isotope analysis. Decisions concerning necessary project hardware, software and configuration of the website and database were made by the data, GIS and website task team. A file transfer protocol server was established for project use. The project website is being upgraded in terms of security.

  13. Structural and Energetic Heterogeneity in Protein Folding

    E-Print Network [OSTI]

    Steven S. Plotkin; Jose N. Onuchic

    2000-09-27T23:59:59.000Z

    A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native stability, as well as entropic heterogeneity intrinsic to the topology of the native structure are both investigated as to their impact on the folding free energy landscape and resulting folding mechanism. Given a minimally frustrated protein, both structural and energetic heterogeneity lower the thermodynamic barrier to folding, and designing in sufficient heterogeneity can eliminate the barrier at the folding transition temperature. Sequences with different distributions of stability throughout the protein and correspondingly different folding mechanisms may still be good folders to the same structure. This theoretical framework allows for a systematic study of the coupled effects of energetics and topology in protein folding, and provides interpretations and predictions for future experiments which may investigate these effects.

  14. Electron loss rates from the outer radiation belt caused by the filling of the outer plasmasphere: the calm before the storm

    SciTech Connect (OSTI)

    Borovsky, Joseph E [Los Alamos National Laboratory; Denton, Michael H [LANCASTER UNIV

    2009-01-01T23:59:59.000Z

    Measurements from 7 spacecraft in geosynchronous orbit are analyzed to determine the decay rate of the number density of the outer electron radiation belt prior to the onset of high-speed-stream-driven geomagnetic storms. Superposed-data analysis is used wan(?) a collection of 124 storms. When there is a calm before the storm, the electron number density decays exponentially before the storm with a 3.4-day e-folding time: beginning about 4 days before storm onset, the density decreases from {approx}4x10{sup -4} cm{sup -3} to {approx}1X 10{sup -4} cm{sup -3}. When there is not a calm before the storm, the number-density decay is very smalL The decay in the number density of radiation-belt electrons is believed to be caused by pitch-angle scattering of electrons into the atmospheric loss cone as the outer plasmasphere fills during the calms. While the radiation-belt electron density decreases, the temperature of the electron radiation belt holds approximately constant, indicating that the electron precipitation occurs equally at all energies. Along with the number density decay, the pressure of the outer electron radiation belt decays and the specific entropy increases. From the measured decay rates, the electron flux to the atmosphere is calculated and that flux is 3 orders of magnitude less than thermal fluxes in the magnetosphere, indicating that the radiation-belt pitch-angle scattering is 3 orders weaker than strong diffusion. Energy fluxes into the atmosphere are calculated and found to be insufficient to produce visible airglow.

  15. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01T23:59:59.000Z

    Intermediates can accelerate protein folding. Proceedings ofunifying mechanism for protein folding? [Review]. Trends incoordinate for protein folding. Journal of Chemical Physics

  16. Folding amphipathic helices into membranes: Amphiphilicity trumps hydrophobicity

    E-Print Network [OSTI]

    Fernndez-Vidal, Mnica; Jayasinghe, Sajith; Ladokhin, Alexey S; White, Stephen H

    2007-01-01T23:59:59.000Z

    C. (1999). Membrane protein folding and stability: PhysicalA. S. & Hristova, K. (1998). Protein folding in membranes:Mutational analysis of protein folding and stability. In

  17. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01T23:59:59.000Z

    H. (2008). Understanding protein folding: small proteins inG. (1997). Theory of protein folding: the energy landscapeenergy landscape of protein folding: a synthesis. Proteins

  18. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01T23:59:59.000Z

    Stochastic Dynamics on a Protein Folding Energy Landscape .and J. N. Onuchic. Protein folding funnels: kinetic pathwaysthe energy landscape of protein folding. Proteins: Struct.

  19. Financial aspects of partial cutting practices in central Appalachian hardwoods. Forest Service research paper (Final)

    SciTech Connect (OSTI)

    Miller, G.W.

    1993-06-01T23:59:59.000Z

    Unveven-aged silvicultural practices can be used to regenerate and manage many eastern hardwood stands. Single-tree selection methods are feasible in stands where a desirable shade-tolerant commercial species can be regenerated following periodic harvests. A variety of partial cutting practices, including single-tree selection and diameter-limit cutting have been used for 30 years or more to manage central Appalachian hardwoods on the Fernow Experimental Forest near Parsons, West Virginia. Results from these research areas are presented to help forest managers evaluate financial aspects of partial cutting practices. Observed volume growth, product yields, changes in species composition, and changes in residual stand quality are used to evaluate potential financial returns. Also, practical economic considerations for applying partial cutting methods are discussed.

  20. Epicormic branching on Central Appalachian hardwoods 10 years after deferment cutting. Forest Service research paper

    SciTech Connect (OSTI)

    Miller, G.W.

    1996-03-01T23:59:59.000Z

    Epicormic branching as monitored over a 10-year period following deferment cutting in four central Appalachian hardwood stands in West Virginia. Data from 545 codominant residual trees indicated that the average number of epicormic branches on the butt and second 16-food log sections increased significantly for the first 2 years after treatment. For upper log sections of basswood, northern red oak, and black cherry, significant increases continued from the second to the tenth year. The net effect on quality was that 11 percent of residual trees exhibited a reduction in butt-log grade due to epicormic branching. Of the few grade reductions observed, white oak, northern red oak, and black cherry were the most susceptible. Less than 1 percent of yellow-poplar trees had lower grades due to epicormic branching.

  1. Relationship between bitumen maturity and organic facies in Devonian shales from the Appalachian basin

    SciTech Connect (OSTI)

    Daly, A.R.

    1988-01-01T23:59:59.000Z

    Variation in several bitumen maturity parameters was studied in a core of Devonian shale from the central Appalachian basin. Kerogens in the shales are at maturity levels equivalent to the early stages of oil generation and range in composition from Type III-IV to Type II-III. Maturity parameters based on steranes, terpanes, and n-alkanes exhibit fluctuations that are unrelated to thermal maturity changes in the core. The parameters correlate with one another to a high degree and appear to be directly or indirectly related to the organic facies of the shales. The maturity level indicated by each parameter increases with total organic carbon (TOC) content and hydrogen index value. The greatest variation occurs in rocks with TOC values below 2% and hydrogen index values below 250. The data provide a good opportunity to examine the dependency of bitumen maturity on organic facies, and they highlight a caveat to be considered during interpretation.

  2. abitibi greenstone belt: Topics by E-print Network

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

    belt object satellites, again pointing to possible differences in their origin. M. E. Brown; M. A. van Dam; A. H. Bouchez; D. Le Mignant; R. D. Campbell; J. C. Y. Chin; A....

  3. altai metallogenic belt: Topics by E-print Network

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

    belt object satellites, again pointing to possible differences in their origin. M. E. Brown; M. A. van Dam; A. H. Bouchez; D. Le Mignant; R. D. Campbell; J. C. Y. Chin; A....

  4. Corn Belt Energy Coop- Commercial Energy Efficiency Rebate Program (Illinois)

    Broader source: Energy.gov [DOE]

    Corn Belt Energy, through the Wabash Valley Power Association, offersbusiness, school, and farm customers a variety of energy efficient rebates and incentives through its "Power Moves" program....

  5. VP 100: Brevini Wind Factory Helps Rust Belt Town's Economy ...

    Energy Savers [EERE]

    450 jobs in next two years Faced with a recession and an auto industry that ran out gas, many manufacturing towns in the Rust Belt have reinvented themselves. Some found...

  6. Nanomaterial modifications on conductivity of coal conveyer belt

    SciTech Connect (OSTI)

    Zhang, J.C.; Zhang, Y.G.; Wang, T.T.; Yang, L.F.; Liu, S.M.; Yang, D.H.; Zhang, M.; Gao, X. [Zhongyuan University of Technology, Zhengzhou (China)

    2008-08-15T23:59:59.000Z

    By analyzing the macro electrical properties and the microscopic structure from SEM of nanomaterials modified mine transmission belt samples. The influences of the filling process of inorganic nano particle-filled rubber and PVC polymer on the physical properties of coal transmission belt is reviewed, as well as PTC and NTC effect on the stability of the physical properties and stability of materials. Influence of nano-materials and polymer materials for rubber and temperature changes in the plastic filled refining process. Crosslinker and major filler changes in the amount and filled plastic chain time on the conductivity of coal conveyer belt is studied. Influence of cure temperature. Cure time on the mechanical performance is studied. The microscopic mechanism of macro conductivity change of conveyer belt is discussed.

  7. automatic seat belts: Topics by E-print Network

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

    There is no agreement on the expansion time, which varies from 30 - 100 Myr. The inclination of the Gould belt is not explained by the above models of expansion. An oblique...

  8. allen radiation belt: Topics by E-print Network

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

    particles. Hudson, H S; Frewen, S F N; DeRosa, M L 2009-01-01 7 Drivers, Detection, and Impacts of Precipitation from the Radiation Belts C. J. Rodger1 Physics Websites Summary:...

  9. Stem cubic-foot volume tables for tree species in the Appalachian area. Forest Service research paper

    SciTech Connect (OSTI)

    Clark, A.; Souter, R.A.

    1996-03-01T23:59:59.000Z

    Steamwood cubic-foot volume inside bark tables are presented for 20 species and 8 species groups based on equations used to estimate timber sale volumes on national forests in the Appalachian Area. Tables are based on form class measurement data for 2,670 trees sampled in the Appalachian Area and taper data collected across the South. A series of tables is presented for each species based on diameter at breast height (d.b.h.) in combination with total height and height to a 4-inch diameter outside bark (d.o.b.) top. Volume tables are also presented based on d.b.h. in combination with height to a 7-inch d.o.b. top for softwoods and height to a 9-inch d.o.b. top for hardwoods.

  10. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect (OSTI)

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

    2010-05-25T23:59:59.000Z

    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.

  11. STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS

    E-Print Network [OSTI]

    Dinner, Aaron

    STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS AARON R. DINNER New Chemistry Laboratory for Protein Folding: Advances in Chemical Physics, Volume 120. Edited by Richard A. Friesner. Series Editors Experimental and theoretical studies have led to the emergence of a unified general mechanism for protein

  12. Sedimentation and basin-fill history of the Neogene clastic succession exposed in the southeastern fold belt of the

    E-Print Network [OSTI]

    Kulp, Mark

    and exploitation strategy for hydrocarbon plays that may prove vital to the oil companies engaged in exploration of reference for tide-dominated regressive shelf depositional systems. The top of the composite sequence B

  13. The sedimentological and geotechnical characteristics of the lower continental slope and rise of the Mississippi Fan fold belt

    E-Print Network [OSTI]

    Ramazanova, Rahila

    2001-01-01T23:59:59.000Z

    The study is based on geological and geotechnical laboratory testing data of 70 three inch diameter piston cores. Concentration is along the Sigsbee Escarpment in a grid area between 90? and 91?W and 26.7? and 27.3?N. Water depth ranges from 1...

  14. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1996-06-11T23:59:59.000Z

    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.

  15. Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and

    E-Print Network [OSTI]

    Pratt, Vaughan

    Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics for studying protein folding kinetics. It uses the recently intro- duced Stochastic Roadmap Simulation (SRS validate the SRS method and indicate its potential as a general tool for studying protein folding kinetics

  16. JOVIAN EARLY BOMBARDMENT: PLANETESIMAL EROSION IN THE INNER ASTEROID BELT

    SciTech Connect (OSTI)

    Turrini, D.; Coradini, A.; Magni, G., E-mail: diego.turrini@ifsi-roma.inaf.it [Istituto di Astrofisica e Planetologia Spaziali, INAF-IAPS, Via Fosso del Cavaliere 100, 00133, Rome (Italy)

    2012-05-01T23:59:59.000Z

    The asteroid belt is an open window on the history of the solar system, as it preserves records of both its formation process and its secular evolution. The progenitors of the present-day asteroids formed in the Solar Nebula almost contemporary to the giant planets. The actual process producing the first generation of asteroids is uncertain, strongly depending on the physical characteristics of the Solar Nebula, and the different scenarios produce very diverse initial size-frequency distributions (SFDs). In this work, we investigate the implications of the formation of Jupiter, plausibly the first giant planet to form, on the evolution of the primordial asteroid belt. The formation of Jupiter triggered a short but intense period of primordial bombardment, previously unaccounted for, which caused an early phase of enhanced collisional evolution in the asteroid belt. Our results indicate that this Jovian Early Bombardment caused the erosion or the disruption of bodies smaller than a threshold size, which strongly depends on the SFD of the primordial planetesimals. If the asteroid belt was dominated by planetesimals less than 100 km in diameter, the primordial bombardment would have caused the erosion of bodies smaller than 200 km in diameter. If the asteroid belt was instead dominated by larger planetesimals, the bombardment would have resulted in the destruction of bodies as big as 500 km.

  17. Angle stations in or for endless conveyor belts

    DOE Patents [OSTI]

    Steel, Alan (Glasgow, GB6)

    1987-04-07T23:59:59.000Z

    In an angle station for an endless conveyor belt, there are presented to each incoming run of the belt stationary curved guide members (18, 19) of the shape of a major segment of a right-circular cylinder and having in the part-cylindrical portion (16 or 17) thereof rectangular openings (15) arranged in parallel and helical paths and through which project small freely-rotatable rollers (14), the continuously-changing segments of the curved surfaces of which projecting through said openings (15) are in attitude to change the direction of travel of the belt (13) through 90.degree. during passage of the belt about the part-cylindrical portion (16 or 17) of the guide member (18 or 19). The rectangular openings (15) are arranged with their longer edges lengthwise of the diagonals representing the mean of the helix but with those of a plurality of the rows nearest to each end of the part-cylindrical portion (16 or 17) slightly out of axial symmetry with said diagonals, being slightly inclined in a direction about the intersections (40) of the diagonals of the main portion of the openings, to provide a "toe-in" attitude in relation to the line of run of the endless conveyor belt.

  18. Mechanical Models of Fault-Related Folding

    SciTech Connect (OSTI)

    Johnson, A. M.

    2003-01-09T23:59:59.000Z

    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).

  19. Protein Folding as a Physical Stochastic Process

    E-Print Network [OSTI]

    Kerson Huang

    2007-07-17T23:59:59.000Z

    We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as hydrogen bonding, which can be taken into account by imposing conditions on SAW. The resulting model is termed CSAW (conditioned self-avoiding walk. Conceptually, the mathematical basis is a generalized Langevin equation. In practice, the model is implemented on a computer by combining SAW and Monte Carlo. To illustrate the flexibility and capabilities of the model, we consider a number of examples, including folding pathways, elastic properties, helix formation, and collective modes.

  20. Mining conditions and deposition in the Amburgy (Westphalian B) coal, Breathitt Group, central Appalachian basin

    SciTech Connect (OSTI)

    Greb, S.F.; Eble, C.F. [Kentucky Geological Survey, Lexington, KY (United States); Hower, J.C. [Center for Applied Research, Lexington, KY (United States); Phillips, T.L. [Univ. of illinois, Urbana, IL (United States)

    1996-09-01T23:59:59.000Z

    Carbonate concretions called clay balls are rare in the Central Appalachian Basin, but were found in the Amburgy coal overlain by the Kendrick Shale Member. In the study area, the Amburgy coal is 0.7 to 0.9 meters thick, moderate to high in sulfur content, moderate to high in ash yield, and mostly bright clarain, except at the top near the area of coal balls, where durain of limited extent occurs. The coal is co-dominated by lycopod and cordaites; tree spores, with subordinate Calamites. The local durain layer is dominated by Densosporites, produced by the shrubby lycopod Ompbalophloios. Coal balls were encountered where the durain is immediately overlain by a coquinoid hash of broken and whole marine fossils, along a trend of coal thinning. The coal balls contain permineralized cordaites, lycopods, calamites, and ferns. The Amburgy coal accumulated as a succession of planar mires. Local splits in the seam are common, indicating contemporaneous clastic influx. The abundance of Cordaites may indicate brackish mire waters related to a coastal position and initial eustatic rise of the marginal Kendrick seas. Near the end of the Amburgy mires, the high ash-Omphalopbloios association is interpreted as a local area that was being drowned by the Kendrick transgression. Ravinement within this local embayment, rapid inundation by marine waters, and concentration of carbonate-bearing waters within transgressive scours may have contributed to the formation of coal balls and pyritic concretions in the upper part of the coal bed.

  1. Preliminary analysis of Devonian shale oil production in the Appalachian Basin

    SciTech Connect (OSTI)

    Duda, J.R.

    1985-12-01T23:59:59.000Z

    Devonian shale production has been continuous for many years in the Appalachian Basin. In the northwest portion of West Virginia and the southeast area of Ohio, the shale produces liquid hydrocarbons. A few wells have reported initial potentials (IP's) in excess of 1000 barrels per day (bpd). Inherent to this unconventional resource (low pressure, low permeability, low porosity, and naturally-fractured) is a rapid rate of production decline such that, after 4 to 6 months, many wells become inoperable. The US Department of Energy's (DOE's) Morgantown Energy technology Center. (METC) anticipates investigating the occurrence of liquid hydrocarbons in the shale, as well as the reservoir engineering and fluid properties aspects. DOE/METC intends to offer producers in the area information, techniques, and procedures that will optimize liquid production. Besides new well drilling ventures, results of the investigation should affect the approximately 2000 shale wells that are already completed but are plagued by a rapid decline in production. Ideally, these older wells will be regenerated, at least to some degree, leading to further resource exploitation. This report summarizes some of the available production data, characterizes decline rates for selected wells, and specifies a refined study area of high resource potential. 11 refs., 14 figs., 1 tab.

  2. Data Analysis of Villin Headpiece Subdomain Folding Simulations.

    E-Print Network [OSTI]

    seeks to understand the process of protein folding by analyzing the vast amount of data generated while simulating the folding of the villin headpiece. Introduction Protein folding has been called one proteins unlike homology or threading based approaches. Protein folding studies the folding trajectory

  3. DYNAMIC INVARIANTS IN PROTEIN FOLDING PATHWAYS REVEALED BY TENSOR ANALYSIS

    E-Print Network [OSTI]

    Langmead, Christopher James

    DYNAMIC INVARIANTS IN PROTEIN FOLDING PATHWAYS REVEALED BY TENSOR ANALYSIS Arvind Ramanathan Lane a spatio-temporal analysis of protein folding pathways. We applied our method to folding simulations of how a protein folds into its functionally relevant conformations. Protein folding pathways span over

  4. Hierarchical Protein Folding Pathways: A Computational Study of Protein Fragments

    E-Print Network [OSTI]

    Haspel, Nurit

    Hierarchical Protein Folding Pathways: A Computational Study of Protein Fragments Nurit Haspel,1 folding model. The model postulates that protein folding is a hierarchical top-down pro- cess. The basic words: protein folding; building blocks; pro- tein structure prediction; hierarchical folding; protein

  5. Predicting Protein Folding Mohammed J. Zaki, Vinay Nadimpally, Deb

    E-Print Network [OSTI]

    Zaki, Mohammed Javeed

    Predicting Protein Folding Pathways Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff 1. Predicting Protein Folding Pathways Summary. A structured folding pathway, which is a time ordered sequence of folding events, plays an important role in the protein folding process and hence

  6. FROM GENETIC CODING TO PROTEIN FOLDING Jean-Luc Jestin

    E-Print Network [OSTI]

    Paris-Sud XI, Universit de

    FROM GENETIC CODING TO PROTEIN FOLDING Jean-Luc Jestin ABSTRACT A discrete classical mechanics (DCM of the genetic code. A DCM model for protein folding allows a set of folding nuclei to be derived for each. A PROTEIN FOLDING MODEL Let us consider the following protein folding model. A chemical group of mass m

  7. DMBC: Web Planning & Layouts Above the Fold

    E-Print Network [OSTI]

    Stowell, Michael

    DMBC: Web Planning & Layouts Above the Fold · · Website Heig Website width ht Important content - lipsum.com) Media Placeholders g & Organization · · Triad C C S· hades · Custom F Web Layouts Photosho

  8. Mutagenic effects on protein folding and stability

    E-Print Network [OSTI]

    Anderson, Thomas Anthony, 1973-

    2002-01-01T23:59:59.000Z

    Knowing how sequence information dictates the formation of protein structure is critical for accurate prediction of structure, for de novo protein design, and for understanding protein folding and misfolding. Based on ...

  9. Cooperativity and Contact Order in Protein Folding

    E-Print Network [OSTI]

    Marek Cieplak

    2004-01-11T23:59:59.000Z

    The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as in the absence of cooperativity. For a fixed native geometry, small changes in the effective contact map may affect the folding times in a chance way and to the extent that is comparable to the shift in the folding times due to cooperativity. The contact order controlls folding scenarios: the average times necessary to bring pairs of amino acids into their near native separations depend on the sequential distances within the pairs. This dependence is largely monotonic, regardless of the cooperativity, and the dominant trend could be described by a single parameter like the average contact order. However, it is the deviations from the trend which are usually found to set the net folding times.

  10. Self-folding with shape memory composites

    E-Print Network [OSTI]

    Felton, Samuel M.

    Origami-inspired manufacturing can produce complex structures and machines by folding two-dimensional composites into three-dimensional structures. This fabrication technique is potentially less expensive, faster, and ...

  11. Toward a Theory on the Stability of Protein Folding: Challenges for Folding Models

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-12-28T23:59:59.000Z

    We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the progress from the random coil to the native state. In this paper we explore the stability of folding using established methods from physics and mathematics. Our result is a preliminary theory of the physics of folding. We suggest some tests of these ideas using folding simulations. We begin by supposing that folding events are related in some way to mechanical waves on the molecule. We adopt an analytical approach to the physics which was pioneered by M.V. Berry, (in another context), based upon mathematics developed mainly by R. Thom and V.I. Arnold. We find that the stability of the folding process can be understood in terms of structures known as caustics, which occur in many kinds of wave phenomena. The picture that emerges is that natural selection has given us a set of protein molecules which have mechanical waves that propagate according to several mathematically specific restrictions. Successful simulations of folding can be used to test and constrain these wave motions. With some additional assumptions the theory explains or is consistent with a number of experimental facts about folding. We emphasize that this wave-based approach is fundamentally different from energy-based approaches.

  12. Modeling the radiation belt electrons with radial diffusion driven by the solar wind

    E-Print Network [OSTI]

    Li, Xinlin

    in the enhancement of radiation belt electrons yet leaves a significant portion of the variance unaccounted for. We

  13. A phenomenological model of protein folding

    E-Print Network [OSTI]

    Danielsson, Ulf H; Niemi, Antti J

    2009-01-01T23:59:59.000Z

    We construct a phenomenological effective field theory model that describes the universality class of biologically active single-strand proteins. The model allows both for an explicit construction of native state protein conformations, and a dynamical description of protein folding and unfolding processes. The model reveals a connection between homochirality and protein collapse, and enables the theoretical investigation of various other aspects of protein folding even in the case of very long polypeptide chains where other methods are not available.

  14. Protein Folding: A Perspective From Statistical Physics

    E-Print Network [OSTI]

    Jinzhi Lei; Kerson Huang

    2010-02-26T23:59:59.000Z

    In this paper, we introduce an approach to the protein folding problem from the point of view of statistical physics. Protein folding is a stochastic process by which a polypeptide folds into its characteristic and functional 3D structure from random coil. The process involves an intricate interplay between global geometry and local structure, and each protein seems to present special problems. We introduce CSAW (conditioned self-avoiding walk), a model of protein folding that combines the features of self-avoiding walk (SAW) and the Monte Carlo method. In this model, the unfolded protein chain is treated as a random coil described by SAW. Folding is induced by hydrophobic forces and other interactions, such as hydrogen bonding, which can be taken into account by imposing conditions on SAW. Conceptually, the mathematical basis is a generalized Langevin equation. To illustrate the flexibility and capabilities of the model, we consider several examples, including helix formation, elastic properties, and the transition in the folding of myoglobin. From the CSAW simulation and physical arguments, we find a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. The elastic energy gives rise to scaling laws $R_{g}\\sim N^{\

  15. Are energetic electrons in the solar wind the source of the outer radiation belt?

    E-Print Network [OSTI]

    Li, Xinlin

    Are energetic electrons in the solar wind the source of the outer radiation belt? Xinlin Li,1 D. N in the solar wind are the source of the outer rela- tivistic electron radiation belt. Though there is some radiation belt, the phase space density of 20-200 keV electrons in the solar wind is not adequate to supply

  16. Radiation Belt Activity Indices and Solar Proton Event Alarm on the CRATERRE Project Web Site

    E-Print Network [OSTI]

    Radiation Belt Activity Indices and Solar Proton Event Alarm on the CRATERRE Project Web Site D--Two Radiation Belt Activity Indices, based on electron flux measurement >300 keV and >1.6 MeV, and one Solar updated. Index Terms- CRATERRE project, Radiation belts activity, Space environment I. INTRODUCTION

  17. Subsurface structure of the north Summit gas field, Chestnut Ridge anticline of the Appalachian Basin

    SciTech Connect (OSTI)

    Zhou, G.; Shumaker, R.C. [West Virginia Univ., Morgantown, WV (United States); Staub, W.K. [Consolidated Gas Transmission Co., Clarksburg, WV (United States)

    1996-09-01T23:59:59.000Z

    The Chestnut Ridge anticline is the westernmost of the High Plateau folds in southwestern Pennsylvania and north-central West Virginia that are detached primarily in the Marcellus Shale, and the Martinsburg, Salina, and Rome Formations. The primary, basal detachment at the Summit field occurs in the Salina salt. Production from fracture porosity in the Devonian Oriskany Sandstone commenced in 1936. During the late 1980s and early 1990s, 14 wells were drilled preparatory to conversion of the reservoir to gas storage. Schlumberger`s Formation MicroScanner (FMS) logs were run in each of these wells to provide information on the structural configuration and fracture patterns of the reservoir. These data indicate that two inward-facing, tight folds at the Oriskany level form the upper flanks and core of the anticline at the northern end of the field, whereas the main part of the field to the south is a comparatively simple, broad closure at the Oriskany level. The structure is a broad, slightly asymmetric open fold in the Mississippian Greenbrier Formation at the surface. Fracture patterns mapped using FMS logs indicate a complex fracture system which varies slightly along the trend of the fold and among the units analyzed, including the Helderberg Formation, Huntersville Chert, Oriskany Sandstone, and Onondaga Formation. An orthogonal joint system strikes toward the northwest and northeast slightly askew to the trend of the fold`s crestal trace. A similar, but more complex fracture pattern is found in an oriented core of these units.

  18. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01T23:59:59.000Z

    C. Are there pathways for protein folding? Journal de Chimieand the mechanism of protein folding. Ann Rev Biochem 1982;Baldwin RL. How does protein folding get started? TRENDS in

  19. Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding

    E-Print Network [OSTI]

    Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding Intermediate, the results show that protein folding intermediates are ensembles of different structural forms direct experi- mental evidence in support of a basic tenet of energy landscape theory for protein folding

  20. THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES

    E-Print Network [OSTI]

    Sosnick, Tobin R.

    THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES FOR DELINEATION ............................................................................................................ 1 1.1 Why study protein folding .............................................................................. 3 1.2.1 How fast should a protein fold ........................................................... 3

  1. Protein folding using contact maps Michele Vendruscolo and Eytan Domany

    E-Print Network [OSTI]

    Domany, Eytan

    Protein folding using contact maps Michele Vendruscolo and Eytan Domany Department of Physics 26 I. INTRODUCTION Computational approaches to protein folding are divided into two main categories protein fold prediction. Contact maps are a particularly manageable representation of protein structure

  2. Effective Conveyor Belt Inspection for Improved Mining Productivity

    SciTech Connect (OSTI)

    Chris Fromme

    2006-06-01T23:59:59.000Z

    This document details progress on the project entitled ''Effective Conveyor Belt Inspection for Improved Mining Productivity'' during the period from November 15, 2004 to May 14, 2004. Highlights include fabrication of low-cost prototype hardware, acquisition of infrared thermal data, and initial design of a Smart-Camera based system.

  3. Effective Conveyor Belt Inspection for Improved Mining Productivity

    SciTech Connect (OSTI)

    Chris Fromme

    2006-06-01T23:59:59.000Z

    This document details progress on the project entitled ''Effective Conveyor Belt Inspection for Improved Mining Productivity'' during the period from November 15, 2004 to May 14, 2004. Highlights include fabrication of an improved LED lightbar, fabrication of a line-scan sensor head for the Smart-Camera based prototype, and development of prototype vulcanized splice detection algorithms.

  4. Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios

    E-Print Network [OSTI]

    Berry, R. Stephen

    Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios Ariel Ferna presents a method to portray protein folding dynamics at a coarse resolution, based on a pattern

  5. Protein Folding: A New Geometric Analysis

    E-Print Network [OSTI]

    Walter A. Simmons; Joel L. Weiner

    2008-09-11T23:59:59.000Z

    A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it is possible that so many initial configurations proceed to fold to a unique final configuration. We put energy and dynamical considerations temporarily aside and focus upon the geometry alone. We parameterize the structure of an idealized protein using the concept of a ribbon from differential geometry. The deformation of the ribbon is described by introducing a generic twisting Ansatz. The folding process in this picture entails a change in shape guided by the local amino acid geometry. The theory is reparamaterization invariant from the start, so the final shape is independent of folding time. We develop differential equations for the changing shape. For some parameter ranges, a sine-Gordon torsion soliton is found. This purely geometric waveform has properties similar to dynamical solitons. Namely: A threshold distortion of the molecule is required to initiate the soliton, after which, small additional distortions do not change the waveform. In this analysis, the soliton twists the molecule until bonds form. The analysis reveals a quantitative relationship between the geometry of the amino acids and the folded form.

  6. Fractures in oriented Devonian-shale cores from the Appalachian Basin. Vol. 1

    SciTech Connect (OSTI)

    Evans, M.A.

    1980-01-01T23:59:59.000Z

    Examination of thirteen oriented Devonian-shale cores from the Appalachian Basin revealed considerable fracturing and shearing at depth. Fracture frequency and orientation measurements were made on the fractures in each core. Fractures and associated structures were differentiated into core-induced fractures, unmineralized natural fractures, mineralized natural fractures, slickensided fractures, and slickenlines. Core-induced fractures exhibit a consistent northeast orientation both areally and with depth. This consistency indicates the presence of an anisotropy which is interpreted to be related to an east to northeast trending maximum compressive stress developed in eastern North America by the convective flow in the mantle associated with spreading along the Mid-Atlantic Ridge. Natural fracture, slickenside, and slickenline orientations are related to: (1) northwest directed tectonic compressive stresses associated with Alleghenian deformation, (2) stresses associated with local faulting, and (3) the same east to northeast maximum compressive stress responsible for the core-induced fractures. Higher frequencies of natural fractures and slickensides are associated primarily with incompetent, high-organic shales. Natural fractures occur most frequently in the Marcellus Shale, Tully Limestone, Geneseo Shale, West Falls Formation, and the Lower Huron Member of the Ohio Shale. Slickensided fractures occur most frequently in the Marcellus Shale, Tully Limestone, Geneseo Shale, West Falls Formation, base of the Java Formation, and Lower Huron and Cleveland Members of the Ohio Shale. These observations are consistent with a fracture facies concept that proposes fracture development in shales that have acted as decollement zones during Alleghenian deformation. Detailed reports are included in Volume 2 for each of the thirteen cores investigated. 25 figures, 4 tables.

  7. Exploring the mechanisms of protein folding

    E-Print Network [OSTI]

    Xu, Ji; Ren, Ying; Li, Jinghai

    2013-01-01T23:59:59.000Z

    Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the exclusive dominant mechanism of protein folding, and attributes the structural transition from one characteristic state to another to energy barriers. Conversely, the concept of kinetic stability overemphasizes dominant mechanisms that are related to kinetic factors. This article explores the stability condition of protein structures from the viewpoint of meso-science, paying attention to the compromise in the competition between minimum free energy and other dominant mechanisms. Based on our study of complex systems, we propose that protein folding is a meso-scale, dissipative, nonlinear and non-equilibrium process that is dominated by the compromise between free energy and other dominant mechanisms such as environmental factors. Consequently, a protein shows dynamic structures,...

  8. What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs

    E-Print Network [OSTI]

    Tawfik, Dan S.

    What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade not trading off, but instead promoting the acquisition of new activities. Indeed, computational analysis. It is often the case that activity and stability trade off.10,22 Many enzymes were, however, dramatically

  9. Toward a Theory on the Stability of Protein Folding: Challenges for Folding Models

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01T23:59:59.000Z

    We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the progress from the random coil to the native state. In this paper we explore the stability of folding using established methods from physics and mathematics. Our result is a preliminary theory of the physics of folding. We suggest some tests of these ideas using folding simulations. We begin by supposing that folding events are related in some way to mechanical waves on the molecule. We adopt an analytical approach to the physics which was pioneered by M.V. Berry, (in another context), based upon mathematics developed mainly by R. Thom and V.I. Arnold. We find that the stability of the folding process can be understood in terms of structures known as caustics, which occur in many kinds of wave phenomena. The picture that emerges is that natural selection has given us a set of prot...

  10. Strontium isotope quantification of siderite, brine and acid mine drainage contributions to abandoned gas well discharges in the Appalachian Plateau

    SciTech Connect (OSTI)

    Chapman, Elizabeth C.; Capo, Rosemary C.; Stewart, Brian W.; Hedin, Robert S.; Weaver, Theodore J.; Edenborn, Harry M.

    2013-04-01T23:59:59.000Z

    Unplugged abandoned oil and gas wells in the Appalachian region can serve as conduits for the movement of waters impacted by fossil fuel extraction. Strontium isotope and geochemical analysis indicate that artesian discharges of water with high total dissolved solids (TDS) from a series of gas wells in western Pennsylvania result from the infiltration of acidic, low Fe (Fe < 10 mg/L) coal mine drainage (AMD) into shallow, siderite (iron carbonate)-cemented sandstone aquifers. The acidity from the AMD promotes dissolution of the carbonate, and metal- and sulfate-contaminated waters rise to the surface through compromised abandoned gas well casings. Strontium isotope mixing models suggest that neither upward migration of oil and gas brines from Devonian reservoirs associated with the wells nor dissolution of abundant nodular siderite present in the mine spoil through which recharge water percolates contribute significantly to the artesian gas well discharges. Natural Sr isotope composition can be a sensitive tool in the characterization of complex groundwater interactions and can be used to distinguish between inputs from deep and shallow contamination sources, as well as between groundwater and mineralogically similar but stratigraphically distinct rock units. This is of particular relevance to regions such as the Appalachian Basin, where a legacy of coal, oil and gas exploration is coupled with ongoing and future natural gas drilling into deep reservoirs.

  11. Fast Gravitational Wave Radiometry using Data Folding

    E-Print Network [OSTI]

    Anirban Ain; Prathamesh Dalvi; Sanjit Mitra

    2015-04-07T23:59:59.000Z

    Gravitational Waves (GWs) from the early universe and unresolved astrophysical sources are expected to create a stochastic GW background (SGWB). The GW radiometer algorithm is well suited to probe such a background using data from ground based laser interferometric detectors. Radiometer analysis can be performed in different bases, e.g., isotropic, pixel or spherical harmonic. Each of these analyses possesses a common temporal symmetry which we exploit here to fold the whole dataset for every detector pair, typically a few hundred to a thousand days of data, to only one sidereal day, without any compromise in precision. We develop the algebra and a software pipeline needed to fold data, accounting for the effect of overlapping windows and non-stationary noise. We implement this on LIGO's fifth science run data and validate it by performing a standard anisotropic SGWB search on both folded and unfolded data. Folded data not only leads to orders of magnitude reduction in computation cost, but it results in a conveniently small data volume of few gigabytes, making it possible to perform an actual analysis on a personal computer, as well as easy movement of data. A few important analyses, yet unaccomplished due to computational limitations, will now become feasible. Folded data, being independent of the radiometer basis, will also be useful in reducing processing redundancies in multiple searches and provide a common ground for mutual consistency checks. Most importantly, folded data will allow vast amount of experimentation with existing searches and provide substantial help in developing new strategies to find unknown sources.

  12. Energetic Components of Cooperative Protein Folding

    E-Print Network [OSTI]

    Huseyin Kaya; Hue Sun Chan

    2000-10-11T23:59:59.000Z

    A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative helical formation and contact energies based on a 5-letter alphabet are found to be insufficient to satisfy calorimetric and other experimental criteria for two-state folding. Such proteinlike behaviors are predicted, however, by models with polypeptide-like local conformational restrictions and environment-dependent hydrogen bonding-like interactions.

  13. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12T23:59:59.000Z

    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.

  14. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

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

    2011-06-14T23:59:59.000Z

    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.

  15. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16T23:59:59.000Z

    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.

  16. Circular permutant GFP insertion folding reporters

    SciTech Connect (OSTI)

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

    2008-06-24T23:59:59.000Z

    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.

  17. Nonlinear conformation of secondary protein folding

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2012-01-01T23:59:59.000Z

    A model to describe the mechanism of conformational dynamics in secondary protein based on matter interactions is proposed. The approach deploys the lagrangian method by imposing certain symmetry breaking. The protein backbone is initially assumed to be nonlinear and represented by the Sine-Gordon equation, while the nonlinear external bosonic sources is represented by $\\phi^4$ interaction. It is argued that the nonlinear source induces the folding pathway in a different way than the previous work with initially linear backbone. Also, the nonlinearity of protein backbone decreases the folding speed.

  18. CSAW: a dynamical model of protein folding

    E-Print Network [OSTI]

    Kerson Huang

    2006-01-12T23:59:59.000Z

    CSAW (conditioned self-avoiding walk) is a model of protein folding that combines SAW (self-avoiding walk) with Monte-Carlo. It simulates the Brownian motion of a chain molecule in the presence of interactions, both among chain residues, and with the environment. In a first model that includes the hydrophobic effect and hydrogen bonding, a chain of 30 residues folds into a native state with stable secondary and tertiary structures. The process starts with a rapid collapse into an intermediate "molten globule", which slowly decays into the native state afer a relatively long quiescent period. The behavior of the radius of gyration mimics experimental data.

  19. Automated Discovery of Structural Signatures of Protein Fold and Function

    E-Print Network [OSTI]

    Muggleton, Stephen H.

    Automated Discovery of Structural Signatures of Protein Fold and Function Marcel Turcotte1 sys- tematically for protein fold signatures, we have explored the use of Inductive Logic Programming fold. The work showed that signatures of protein folds exist, about half of rules discov- ered

  20. Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics

    E-Print Network [OSTI]

    Santiago, Juan G.

    Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics David E. Hertzog with numerical simulations to minimize the mixing time of a microfluidic mixer developed for protein folding reported continuous flow mixer for protein folding. Fast events in protein folding often occur

  1. Polypeptide chain collapse and protein folding Jayant B. Udgaonkar

    E-Print Network [OSTI]

    Review Polypeptide chain collapse and protein folding Jayant B. Udgaonkar National Centre is an integral component of a protein folding reaction. In this review, exper- imental characterization solvent [2]. A distinctive physical feature of any protein folding reaction is the greater than 3-fold

  2. Early Events in Protein Folding Explored by Rapid Mixing Methods

    E-Print Network [OSTI]

    Roder, Heinrich

    15 Early Events in Protein Folding Explored by Rapid Mixing Methods Heinrich Roder, Kosuke Maki for Understanding Protein Folding As with any complex reaction, time-resolved data are essential for elucidating the mechanism of protein folding. Even in cases where the whole process of folding occurs in a single step

  3. Nonlinear dynamics of secondary protein folding Natalia G. Berloff

    E-Print Network [OSTI]

    Nonlinear dynamics of secondary protein folding Natalia G. Berloff Department of Applied field varies. Pacs: 87.15.-v, 87.15By, 05.45.-a, 41.20Jb Keywords: Folding pathway, protein folding interaction and hydrophobic effects. The most common shapes of the protein folding are alpha () and beta

  4. Cellular mechanisms of membrane protein folding William R Skach

    E-Print Network [OSTI]

    Cai, Long

    Cellular mechanisms of membrane protein folding William R Skach The membrane proteinfolding. This Perspective will focus on emerging evidence that the RTC functions as a protein-folding machine that restricts. The process of polytopic (multispanning) membrane protein folding can be viewed as a series of sequential

  5. Protein folding by zipping and assembly S. Banu Ozkan*

    E-Print Network [OSTI]

    Southern California, University of

    Protein folding by zipping and assembly S. Banu Ozkan* , G. Albert Wu* , John D. Chodera, CA, May 2, 2007 (received for review April 13, 2006) How do proteins fold so quickly? Some denatured proteins fold to their native structures in only microseconds, on average, implying that there is a folding

  6. COMMUNICATION First Principles Prediction of Protein Folding Rates

    E-Print Network [OSTI]

    Goddard III, William A.

    COMMUNICATION First Principles Prediction of Protein Folding Rates Derek A. Debe and William A studies have demonstrated that many small, single-domain proteins fold via simple two-state kinetics. We. # 1999 Academic Press Keywords: protein folding; kinetics; diffusion; fold topology; nucleation

  7. Critical aspects of hierarchical protein folding

    E-Print Network [OSTI]

    Alex Hansen; Mogens H. Jensen; Kim Sneppen; Giovanni Zocchi

    1998-01-13T23:59:59.000Z

    We argue that the first order folding transitions of proteins observed at physiological chemical conditions end in a critical point for a given temperature and chemical potential of the surrounding water. We investigate this critical point using a hierarchical Hamiltonian and determine its universality class. This class differs qualitatively from those of other known models.

  8. On the Complexity of Protein Folding

    E-Print Network [OSTI]

    Pierluigi Crescenzi; Deborah Goldman; Christos Papadimitriou; Antonio Piccolboni; Mihalis Yannakakis

    We show that the protein folding problem in the two-dimensional H-P model is NP-complete. 1 Introduction Proteins are polymer chains consisting of monomers of twenty different kinds. Much of the genetic information in the DNA contains the sequence information of proteins, with three nucleotides

  9. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

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

    1995-08-08T23:59:59.000Z

    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.

  10. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

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

    1995-01-01T23:59:59.000Z

    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.

  11. Fast Gravitational Wave Radiometry using Data Folding

    E-Print Network [OSTI]

    Ain, Anirban; Mitra, Sanjit

    2015-01-01T23:59:59.000Z

    Gravitational Waves (GWs) from the early universe and unresolved astrophysical sources are expected to create a stochastic GW background (SGWB). The GW radiometer algorithm is well suited to probe such a background using data from ground based laser interferometric detectors. Radiometer analysis can be performed in different bases, e.g., isotropic, pixel or spherical harmonic. Each of these analyses possesses a common temporal symmetry which we exploit here to fold the whole dataset for every detector pair, typically a few hundred to a thousand days of data, to only one sidereal day, without any compromise in precision. We develop the algebra and a software pipeline needed to fold data, accounting for the effect of overlapping windows and non-stationary noise. We implement this on LIGO's fifth science run data and validate it by performing a standard anisotropic SGWB search on both folded and unfolded data. Folded data not only leads to orders of magnitude reduction in computation cost, but it results in a co...

  12. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

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

    1990-08-23T23:59:59.000Z

    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.

  13. RNAiFold: A web server for RNA inverse folding and molecular Juan Antonio Garcia-Martin, Peter Clote

    E-Print Network [OSTI]

    Clote, Peter

    RNAiFold: A web server for RNA inverse folding and molecular design Juan Antonio Garcia title: RNAiFold web server Key words: RNA, inverse folding, molecular design, synthetic biology, RNA to the 21st century. In this paper, we describe a new web server to support in silico RNA molecular design

  14. Heteropolymer Folding 9 1. C. Gh'elis and J. Yon, Protein Folding (Academic, New York, 1982).

    E-Print Network [OSTI]

    Roma "La Sapienza", Università di

    Heteropolymer Folding 9 References 1. C. Gh'elis and J. Yon, Protein Folding (Academic, New York, editor, The Protein Folding Problem (Westview, Boulder, 1984).. 5. N. G??o, Annu. Rev. Biophys. Bioeng. 12 for Protein Folding, Europhys. Lett. 6, 307 (1988). 14. G. Iori, E. Marinari, G. Parisi and M. V. Struglia

  15. ENHANCEMENT OF TERRESTRIAL CARBON SINKS THROUGH RECLAMATION OF ABANDONED MINE LANDS IN THE APPALACHIAN REGION

    SciTech Connect (OSTI)

    Gary D. Kronrad

    2002-12-01T23:59:59.000Z

    The U.S.D.I. Office of Surface Mining (OSM) estimates that there are approximately 1 million acres of abandoned mine land (AML) in the Appalachian region. AML lands are classified as areas that were inadequately reclaimed or were left unreclaimed prior to the passage of the 1977 Surface Mining Control and Reclamation Act, and where no federal or state laws require any further reclamation responsibility to any company or individual. Reclamation and afforestation of these sites have the potential to provide landowners with cyclical timber revenues, generate environmental benefits to surrounding communities, and sequester carbon in the terrestrial ecosystem. Through a memorandum of understanding, the OSM and the U.S. Department of Energy (DOE) have decided to investigate reclaiming and afforesting these lands for the purpose of mitigating the negative effects of anthropogenic carbon dioxide in the atmosphere. This study determined the carbon sequestration potential of northern red oak (Quercus rubra L.), one of the major reclamation as well as commercial species, planted on West Virginia AML sites. Analyses were conducted to (1) calculate the total number of tons that can be stored, (2) determine the cost per ton to store carbon, and (3) calculate the profitability of managing these forests for timber production alone and for timber production and carbon storage together. The Forest Management Optimizer (FORMOP) was used to simulate growth data on diameter, height, and volume for northern red oak. Variables used in this study included site indices ranging from 40 to 80 (base age 50), thinning frequencies of 0, 1, and 2, thinning percentages of 20, 25, 30, 35, and 40, and a maximum rotation length of 100 years. Real alternative rates of return (ARR) ranging from 0.5% to 12.5% were chosen for the economic analyses. A total of 769,248 thinning and harvesting combinations, net present worths, and soil expectation values were calculated in this study. Results indicate that the cost per ton to sequester carbon ranges from $6.54 on site index 80 land at a 12.5% ARR to $36.68 on site index 40 land at an ARR of 0.5%. Results also indicate that the amount of carbon stored during one rotation ranges between 38 tons per acre on site index 40 land to 58 tons per acre on site index 80 land. The profitability of afforestation on these AML sites in West Virginia increases as the market price for carbon increases from $0 to $100 per ton.

  16. STORMREADY! Winter weather at Appalachian usually includes snow, ice, freezing rain, and sleet from November through April. Those that have spent several years in the Boone area understand how quickly the weather can

    E-Print Network [OSTI]

    Rose, Annkatrin

    and signals. Inspect: Check your vehicle's tires, wiper blades, fluids, lights, belts and hoses. Time: Allow

  17. A simple theory of protein folding kinetics

    E-Print Network [OSTI]

    Pande, Vijay S

    2010-01-01T23:59:59.000Z

    We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical properties seen in detailed simulations as well as to serve as a model to easily compare why these simulations suggest a different kinetic mechanism than previous simple models. Specifically, we find that non-native contacts play a key role in determining the mechanism, which can shift dramatically as the energetic strength of non-native interactions is changed. For protein-like non-native interactions, our model finds that the native state is a kinetic hub, connecting the strength of relevant interactions directly to the nature of folding kinetics.

  18. Effects of interlayer slip on multilayered folds

    E-Print Network [OSTI]

    Casarta, Lawrence Joseph

    1980-01-01T23:59:59.000Z

    composed of Coconino Sandstone (brittle) or Indiana Limestone (ductile) interlayered with lead (very ductile) are folded by layer parallel compression at a confining pressure of 100 MPa, temperature of 24 C and axial displacement rate of 10 3 cm... differential stress-axial shortening curves. a, and b, specimens composed of Coconino Sandstone and lead. c, specimens composed of Indiana Limestone and lead. Each curve is for a different specimen a and b. Schematic illustration of double hinged...

  19. Simple Models of the Protein Folding Problem

    E-Print Network [OSTI]

    Chao Tang

    1999-12-26T23:59:59.000Z

    The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I will give an introduction to the problem, and then focus on some recent work concerning the so-called ``designability principle''. The designability of a structure is measured by the number of sequences that have that structure as their unique ground state. Structures differ drastically in terms of their designability; highly designable structures emerge with a number of associated sequences much larger than the average. These highly designable structures 1) possess ``proteinlike'' secondary structures and motifs, 2) are thermodynamically more stable, and 3) fold faster than other structures. These results suggest that protein structures are selected in nature because they are readily designed and stable against mutations, and that such selection simultaneously leads to thermodynamic stability and foldability. According to this picture, a key to the protein folding problem is to understand the emergence and the properties of the highly designable structures.

  20. CREATING A GEOLOGIC PLAY BOOK FOR TRENTON-BLACK RIVER APPALACHIAN BASIN EXPLORATION

    SciTech Connect (OSTI)

    Douglas G. Patchen; Katharine Lee Avary; John M. Bocan; Michael Hohn; John B. Hickman; Paul D. Lake; James A. Drahovzal; Christopher D. Laughrey; Jaime Kostelnik; Taury Smith; Ron Riley; Mark Baranoski

    2005-04-01T23:59:59.000Z

    The Trenton-Black River Appalachian Basin Research Consortium has made significant progress toward their goal of producing a geologic play book for the Trenton-Black River gas play. The final product will include a resource assessment model of Trenton-Black River reservoirs; possible fairways within which to concentrate further studies and seismic programs; and a model for the origin of Trenton-Black River hydrothermal dolomite reservoirs. All seismic data available to the consortium have been examined. Synthetic seismograms constructed for specific wells have enabled researchers to correlate the tops of 15 stratigraphic units determined from well logs to seismic profiles in New York, Pennsylvania, Ohio, West Virginia and Kentucky. In addition, three surfaces for the area have been depth converted, gridded and mapped. A 16-layer velocity model has been developed to help constrain time-to-depth conversions. Considerable progress was made in fault trend delineation and seismic-stratigraphic correlation within the project area. Isopach maps and a network of gamma-ray cross sections supplemented with core descriptions allowed researchers to more clearly define the architecture of the basin during Middle and Late Ordovician time, the control of basin architecture on carbonate and shale deposition and eventually, the location of reservoirs in Trenton Limestone and Black River Group carbonates. The basin architecture itself may be structurally controlled, and this fault-related structural control along platform margins influenced the formation of hydrothermal dolomite reservoirs in original limestone facies deposited in high energy environments. This resulted in productive trends along the northwest margin of the Trenton platform in Ohio. The continuation of this platform margin into New York should provide further areas with good exploration potential. The focus of the petrographic study shifted from cataloging a broad spectrum of carbonate rocks that occur in the Trenton-Black River interval to delineation of regional limestone diagenesis in the basin. A consistent basin-wide pattern of marine and burial diagenesis that resulted in relatively low porosity and permeability in the subtidal facies of these rocks has been documented across the study area. Six diagenetic stages have been recognized: four marine diagenesis stages and two burial diagenesis stages. This dominance of extensive marine and burial diagenesis yielded rocks with low reservoir potential, with the exception of fractured limestone and dolostone reservoirs. Commercial amounts of porosity, permeability and petroleum accumulation appear to be restricted to areas where secondary porosity developed in association with hydrothermal fluid flow along faults and fractures related to basement tectonics. A broad range of geochemical and fluid inclusion analyses have aided in a better understanding of the origin of the dolomites in the Trenton and Black River Groups over the study area. The results of these analyses support a hydrothermal origin for all of the various dolomite types found to date. The fluid inclusion data suggest that all of the dolomite types analyzed formed from hot saline brines. The dolomite is enriched in iron and manganese, which supports a subsurface origin for the dolomitizing brine. Strontium isotope data suggest that the fluids passed through basement rocks or immature siliciclastic rocks prior to forming the dolomites. All of these data suggest a hot, subsurface origin for the dolomites. The project database continued to be redesigned, developed and deployed. Production data are being reformatted for standard relational database management system requirements. Use of the project intranet by industry partners essentially doubled during the reporting period.

  1. CREATING A GEOLOGIC PLAY BOOK FOR TRENTON-BLACK RIVER APPALACHIAN BASIN EXPLORATION

    SciTech Connect (OSTI)

    Douglas G. Patchen; Chris Laughrey; Jaime Kostelnik; James Drahovzal; John B. Hickman; Paul D. Lake; John Bocan; Larry Wickstrom; Taury Smith; Katharine Lee Avary

    2004-10-01T23:59:59.000Z

    The ''Trenton-Black River Appalachian Basin Exploration Consortium'' has reached the mid-point in a two-year research effort to produce a play book for Trenton-Black River exploration. The final membership of the Consortium includes 17 exploration and production companies and 6 research team members, including four state geological surveys, the New York State Museum Institute and West Virginia University. Seven integrated research tasks and one administrative and technology transfer task are being conducted basin-wide by research teams organized from this large pool of experienced professionals. All seismic data available to the consortium have been examined at least once. Synthetic seismograms constructed for specific wells have enabled researchers to correlate the tops of 10 stratigraphic units determined from well logs to seismic profiles in New York and Pennsylvania. In addition, three surfaces in that area have been depth converted, gridded and mapped. In the Kentucky-Ohio-West Virginia portion of the study area, a velocity model has been developed to help constrain time-to-depth conversions. Fifteen formation tops have been identified on seismic in that area. Preliminary conclusions based on the available seismic data do not support the extension of the Rome Trough into New York state. Members of the stratigraphy task team measured, described and photographed numerous cores from throughout the basin, and tied these data back to their network of geophysical log cross sections. Geophysical logs were scanned in raster files for use in detailed well examination and construction of cross sections. Logs on these cross sections that are only in raster format are being converted to vector format for final cross section displays. The petrology team measured and sampled one classic outcrop in Pennsylvania and ten cores in four states. More than 600 thin sections were prepared from samples in those four states. A seven-step procedure is being used to analyze all thin sections, leading to an interpretation of the sequence of diagenetic events and development of porosity in the reservoir. Nearly 1000 stable isotope geochemistry samples have been collected from cores in four of the five states in the study area. More than 400 of these samples will be analyzed for fluid inclusion and/or strontium isotope analyses, as well. Gas samples have been collected from 21 wells in four states and analyzed for chemical content and isotope analyses of carbon and hydrogen. Because natural gases vary in chemical and isotope composition as a function of their formation and migration history, crossplots of these values can be very revealing. Gas from the Homer field in Kentucky indicates compartmentalization and at least two different sources. Gas from the York field in Ohio also came from at least two discrete compartments. Gas from the Cottontree field in West Virginia is very dry, probably generated from post-mature source rocks. Isotope reversals may be indicative of cracking of residual oil. Gas from Glodes Corners Road field in New York also is post-mature, dry gas, and again isotope reversals may indicate cracking of residual oil in the reservoir. Noble gases are predominantly of crustal origin, but a minor helium component was derived from the mantle. The project web server continues to evolve as the project progresses. The user/password authenticated website has 18 industry partner users and 20 research team users. Software has been installed to track website use. Two meetings of the research team were held to review the status of the project and prepare reports to be given to the full consortium. A meeting of the full consortium--industry partners and researchers--was very successful. However, the ultimate product of the research could be improved if industry members were more forthcoming with proprietary data.

  2. 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...

  3. Computational and experimental investigations of forces in protein folding

    E-Print Network [OSTI]

    Schell, David Andrew

    2005-02-17T23:59:59.000Z

    in protein folding is essential to the understanding and treatment of protein misfolding diseases. When proteins fold, a significant amount of surface area is buried in the protein interior. It has long been known that burial of hydrophobic surface area...

  4. Experimental and Computational Studies on Protein Folding, Misfolding and Stability

    E-Print Network [OSTI]

    Wei, Yun

    2010-07-14T23:59:59.000Z

    Proteins need fold to perform their biological function. Thus, understanding how proteins fold could be the key to understanding life. In the first study, the stability and structure of several !-hairpin peptide variants derived from the C...

  5. Why are MD simulated protein folding times wrong? Dmitry Nerukh

    E-Print Network [OSTI]

    Nerukh, Dmitry

    Why are MD simulated protein folding times wrong? Dmitry Nerukh Unilever Centre for Molecular.ac.uk The question of significant deviations of protein folding times simulated using molecular dynamics from

  6. Protein Folding Simulation in CCP Luca Bortolussi1

    E-Print Network [OSTI]

    Bortolussi, Luca

    Protein Folding Simulation in CCP Luca Bortolussi1 , Alessandro Dal Pal`u1 , Agostino Dovier1 as the protein folding. This problem is fundamental for biological and pharmaceutical research. Currently

  7. Folding simulations of small proteins Seung-Yeon Kima

    E-Print Network [OSTI]

    Lee, Jooyoung

    Abstract Understanding how a protein folds is a long-standing challenge in modern science. We have used-native conformations are carried out for each protein. In all cases, proteins fold into their native-like conformations, ~108 Monte Carlo steps). D 2004 Elsevier B.V. All rights reserved. Keywords: Protein folding; Computer

  8. Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding

    E-Print Network [OSTI]

    Michalet, Xavier

    Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding David E. Hertzog,, Xavier a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 s and sample) measurements of single-stranded DNA. We also demon- strate the feasibility of measuring fast protein folding

  9. COMMUNICATION Are Residues in a Protein Folding Nucleus

    E-Print Network [OSTI]

    Dai, Yang

    COMMUNICATION Are Residues in a Protein Folding Nucleus Evolutionarily Conserved? Yan Yuan Tseng is the hallmark of life. It is important to understand how protein folding and evolution influence each other in protein folding nucleus as measured by experi- mental f-value and selection pressure as measured by v

  10. Protein folding: Then and now Yiwen Chen 1

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    Review Protein folding: Then and now Yiwen Chen 1 , Feng Ding 1 , Huifen Nie 1 , Adrian W decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally

  11. Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives

    E-Print Network [OSTI]

    Janke, Wolfhard

    8 Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives Michael Bachmann applications. In this lecture, we focus on the anal- ysis of mesoscopic models for protein folding, aggregation for a more universal description of the notoriously difficult problem of protein fold- ing. In this approach

  12. Protein folding with stochastic L-systems Gemma Danks1

    E-Print Network [OSTI]

    Stepney, Susan

    Protein folding with stochastic L-systems Gemma Danks1 , Susan Stepney1 and Leo Caves1 1 University-like structures. Models of protein folding vary in complexity and the amount of prior knowledge they contain). The energy landscape theory of protein folding (Onuchic et al., 1997) predicts a rugged funnel-like energy

  13. Evolutionary Monte Carlo for protein folding simulations Faming Lianga)

    E-Print Network [OSTI]

    Liang, Faming

    Evolutionary Monte Carlo for protein folding simulations Faming Lianga) Department of Statistics to simulations of protein folding on simple lattice models, and to finding the ground state of a protein. In all structures in protein folding. The numerical results show that it is drastically superior to other methods

  14. John von Neumann Institute for Computing Monte Carlo Protein Folding

    E-Print Network [OSTI]

    Hsu, Hsiao-Ping

    John von Neumann Institute for Computing Monte Carlo Protein Folding: Simulations of Met://www.fz-juelich.de/nic-series/volume20 #12;#12;Monte Carlo Protein Folding: Simulations of Met-Enkephalin with Solvent-Accessible Area difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular

  15. Protein Folding Challenge and Theoretical Computer Science Somenath Biswas

    E-Print Network [OSTI]

    Biswas, Somenath

    Protein Folding Challenge and Theoretical Computer Science Somenath Biswas Department of Computer the chain of amino acids that defines a protein. The protein folding problem is: given a sequence of amino to use an efficient algorithm to carry out protein folding. The atoms in a protein molecule attract each

  16. Author's personal copy Protein folding: Then and now

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    Author's personal copy Review Protein folding: Then and now Yiwen Chen 1 , Feng Ding 1 , Huifen Nie Available online 8 June 2007 Abstract Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital

  17. Author's personal copy Protein folding in confined and crowded environments

    E-Print Network [OSTI]

    Weston, Ken

    Author's personal copy Review Protein folding in confined and crowded environments Huan-Xiang Zhou protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize

  18. Combinatorial Problems on Strings with Applications to Protein Folding

    E-Print Network [OSTI]

    Newman, Alantha

    Combinatorial Problems on Strings with Applications to Protein Folding Alantha Newman MIT San Jose, CA 95120, USA ruhl@almaden.ibm.com Abstract We consider the problem of protein folding in linear time. 1 Introduction We consider the problem of protein folding in the HP model on the three

  19. Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao

    E-Print Network [OSTI]

    Bystroff, Chris

    Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao Dept of Biology Rensselaer Polytechnic Institute, Troy, NY. e-mail:{bystrc, shaoy}@rpi.edu Summary Proteins fold through a series of intermediate states called a pathway. Protein folding pathways have been modeled using either simulations

  20. Polymer Collapse, Protein Folding, and the Percolation Threshold

    E-Print Network [OSTI]

    Meirovitch, Hagai

    Polymer Collapse, Protein Folding, and the Percolation Threshold HAGAI MEIROVITCH University (Macromolecules 1989, 22, 39863997) to study protein folding, where H and P are the hydrophobic and polar amino; computer simulation; collapse transition; protein folding Introduction The behavior of dilute polymer

  1. Steiner Minimal Trees, Twist Angles, and the Protein Folding Problem

    E-Print Network [OSTI]

    Smith, J. MacGregor

    Steiner Minimal Trees, Twist Angles, and the Protein Folding Problem J. MacGregor Smith, Yunho Jang. These properties should be ultimately useful in the ab ini- tio protein folding prediction. Proteins 2007;66:889 902. VVC 2006 Wiley-Liss, Inc. Key words: Steiner trees; twist angles; protein fold- ing; side chain

  2. MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix

    E-Print Network [OSTI]

    Dix, Daniel B.

    MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix Department of Mathematics University of South Carolina Abstract. We present an elementary introduction to the protein folding problem directed toward, and biological problem, protein folding can also be precisely formulated as a set of mathematics problems. We

  3. Protein Folding Simulation by Two-Stage Optimization

    E-Print Network [OSTI]

    Will, Sebastian

    Protein Folding Simulation by Two-Stage Optimization A. Dayem Ullah1 , L. Kapsokalivas1 , M. Mann2 propose a two-stage optimization approach for protein folding simulation in the FCC lattice, inspired from procedure based on simulated annealing alone. 1 Introduction The question of how proteins fold and whether

  4. Tolerance of combined salinity and O2 deficiency in Hordeum marinum accessions from the grain-belt of Western Australia

    E-Print Network [OSTI]

    Malik1,2,3, AI; English1,2, JP; Shepherd1,4, KA; Islam2,5, AKMR; Colmer1,2, TD

    2009-01-01T23:59:59.000Z

    from the grain-belt of Western Australia for tolerance toin the accessions from Western Australia, as well as K +from the grain-belt of Western Australia. Single heads were

  5. A parametric study of the source rate for outer radiation belt electrons using a Kalman filter

    E-Print Network [OSTI]

    Li, Xinlin

    A parametric study of the source rate for outer radiation belt electrons using a Kalman filter Q increasingly popular to describe the outer radiation belt energetic electron environment. We use a Kalman included. We augment the Kalman filter to include the intensity of local acceleration in the state vector

  6. Precambrian Research 136 (2005) 2750 The Wadi Mubarak belt, Eastern Desert of Egypt

    E-Print Network [OSTI]

    Fritz, Harald

    Precambrian Research 136 (2005) 27­50 The Wadi Mubarak belt, Eastern Desert of Egypt, Graz, Austria b Mansoura University, Faculty of Science, Geology Department, El Mansoura, Egypt c February 2003; accepted 3 September 2004 Abstract The Wadi Mubarak belt in Egypt strikes west­east (and

  7. Thermo-mechanical structure beneath the young orogenic belt of Taiwan

    E-Print Network [OSTI]

    Ma, Kuo-Fong

    Thermo-mechanical structure beneath the young orogenic belt of Taiwan Kuo-Fong Ma*, Teh-Ru Alex Abstract We investigate the thermo-mechanical properties beneath the young orogenic belt of Taiwan.V. All rights reserved. Keywords: Thermo-mechanical; Rheology; Seismicity; Strength profile; Composition

  8. Comparison of two approaches to automated PI controller tuning for an industrial weigh belt feeder

    E-Print Network [OSTI]

    Collins, Emmanuel

    Comparison of two approaches to automated PI controller tuning for an industrial weigh belt feeder, are applied to an industrial weigh belt feeder that has significant nonlinearities. Both methods do--The Instrumentation, Systems, and Automation Society. Keywords: Fuzzy logic control; Unfalsified control; PI control

  9. Introduction to protein folding for physicists

    E-Print Network [OSTI]

    Pablo Echenique

    2007-05-13T23:59:59.000Z

    The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.

  10. Green belts in the hands and minds of farmers: A socio-agronomical approach to farmers' practices

    E-Print Network [OSTI]

    Paris-Sud XI, Universit de

    1 Green belts in the hands and minds of farmers: A socio-agronomical approach to farmers' practices.alavoine-mornas@irstea.fr ; sabine.girard@irstea.fr Keywords: green belts - biodiversity farmers practices French Alps Abstract of intensive agriculture. In France, this topic is addressed by the "blue and green belts" measure, which

  11. Improving the Availability and Delivery of Critical Information for Tight Gas Resource Development in the Appalachian Basin

    SciTech Connect (OSTI)

    Mary Behling; Susan Pool; Douglas Patchen; John Harper

    2008-12-31T23:59:59.000Z

    To encourage, facilitate and accelerate the development of tight gas reservoirs in the Appalachian basin, the geological surveys in Pennsylvania and West Virginia collected widely dispersed data on five gas plays and formatted these data into a large database that can be accessed by individual well or by play. The database and delivery system that were developed can be applied to any of the 30 gas plays that have been defined in the basin, but for this project, data compilation was restricted to the following: the Mississippian-Devonian Berea/Murrysville sandstone play and the Upper Devonian Venango, Bradford and Elk sandstone plays in Pennsylvania and West Virginia; and the 'Clinton'/Medina sandstone play in northwestern Pennsylvania. In addition, some data were collected on the Tuscarora Sandstone play in West Virginia, which is the lateral equivalent of the Medina Sandstone in Pennsylvania. Modern geophysical logs are the most common and cost-effective tools for evaluating reservoirs. Therefore, all of the well logs in the libraries of the two surveys from wells that had penetrated the key plays were scanned, generating nearly 75,000 scanned e-log files from more than 40,000 wells. A standard file-naming convention for scanned logs was developed, which includes the well API number, log curve type(s) scanned, and the availability of log analyses or half-scale logs. In addition to well logs, other types of documents were scanned, including core data (descriptions, analyses, porosity-permeability cross-plots), figures from relevant chapters of the Atlas of Major Appalachian Gas Plays, selected figures from survey publications, and information from unpublished reports and student theses and dissertations. Monthly and annual production data from 1979 to 2007 for West Virginia wells in these plays are available as well. The final database also includes digitized logs from more than 800 wells, sample descriptions from more than 550 wells, more than 600 digital photos in 1-foot intervals from 11 cores, and approximately 260 references for these plays. A primary objective of the research was to make data and information available free to producers through an on-line data delivery model designed for public access on the Internet. The web-based application that was developed utilizes ESRI's ArcIMS GIS software to deliver both well-based and play-based data that are searchable through user-originated queries, and allows interactive regional geographic and geologic mapping that is play-based. System tools help users develop their customized spatial queries. A link also has been provided to the West Virginia Geological Survey's 'pipeline' system for accessing all available well-specific data for more than 140,000 wells in West Virginia. However, only well-specific queries by API number are permitted at this time. The comprehensive project web site (http://www.wvgs.wvnet.edu/atg) resides on West Virginia Geological Survey's servers and links are provided from the Pennsylvania Geological Survey and Appalachian Oil and Natural Gas Research Consortium web sites.

  12. Signatures of the protein folding pathway in two-dimensional ultraviolet spectroscopy

    E-Print Network [OSTI]

    Jiang, J; Lai, Z; Wang, J; Mukamel, S

    2014-01-01T23:59:59.000Z

    2) Dobson, C. M. Protein Folding and Misfolding. Naturethe Complexity of Protein Folding. Curr. Opin. Struct. Biol.Signatures of the Protein Folding Pathway in Two-Dimensional

  13. Microfluidic advantage : novel techniques for protein folding and oxygen control in cell cultures

    E-Print Network [OSTI]

    Polinkovsky, Mark E.; Polinkovsky, Mark E.

    2012-01-01T23:59:59.000Z

    Novel Techniques for Protein Folding and Oxygen Control inTemperature Jump System to Study Fast Protein FoldingNovel Techniques for Protein Folding and Oxygen Control in

  14. Carbon-deuterium bonds as an infrared probe of protein dynamics, local electrostatics and folding

    E-Print Network [OSTI]

    Sagle, Laura B.

    2006-01-01T23:59:59.000Z

    and Englander, W. S. , Protein Folding: A Stepwise AssemblyEnglander, S. W. , Protein Folding Intermediates NativeR. L. , How Does Protein Folding Get Started? Trends

  15. The folding energy landscape of Cytochrome c : theoretical and experimental investigations

    E-Print Network [OSTI]

    Weinkam, Patrick

    2009-01-01T23:59:59.000Z

    Chemical Frustration in the Protein Folding Landscape: GrandChemical Frustration in the Protein Folding Landscape: GrandEnzyme Catalysis and Protein Folding (Freeman, New York). [

  16. Topology, frustration, folding and function of the inflammatory cytokine Interleukin-1[beta

    E-Print Network [OSTI]

    Capraro, Dominique T.

    2008-01-01T23:59:59.000Z

    the features of protein folding, where proteins with manychain connectivity on protein folding (53). Application ofhave gone beyond protein folding and have characterized

  17. Energy landscapes for protein folding, binding, and aggregation : simple funnels and beyond

    E-Print Network [OSTI]

    Cho, Samuel Sung-Il

    2007-01-01T23:59:59.000Z

    coordinates capture protein folding on smooth landscapes.in the Prediction of Protein Folding Kinetics. Proc. Natl.Landscapes for Protein Folding, Binding, and Aggregation:

  18. 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

    2007-03-31T23:59:59.000Z

    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

  19. An energy landscape theory for cotranslational protein folding

    E-Print Network [OSTI]

    Tourigny, David S

    2013-01-01T23:59:59.000Z

    Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome, there have been few attempts to modify energy landscape theory by accounting for cotranslational folding. This paper introduces a model for cotranslational folding that leads to a natural definition of a nested energy landscapes. By applying concepts drawn from submanifold differential geometry, the dynamics of protein folding on the ribosome can be explored in a quantitative manner and conditions on the nested potential energy landscapes for a good cotranslational folder are obtained. A generalisation of diffusion rate theory using van Kampen's technique of composite stochastic processes is then used to account for entropic contributions and the effects of variable translation rates on cotranslational folding. This stochastic approach agrees well with experimental results...

  20. Inferring the Rate-Length Law of Protein Folding

    E-Print Network [OSTI]

    Lane, Thomas J

    2013-01-01T23:59:59.000Z

    We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. We demonstrate that chain length is a dominant factor determining folding times, and that the unambiguous determination of the way chain length corre- lates with folding times could provide key mechanistic insight into the folding process. Four specific proposed laws (power law, exponential, and two stretched exponentials) are tested against one an- other, and it is found that the power law best explains the data. At the same time, the fit power law results in rates that are very fast, nearly unreasonably so in a biological context. We show that any of the proposed forms are viable, conclude that more data is necessary to unequivocally infer the rate-length law, and that such data could be obtained through a small number of protein folding experiments on large protein domains.

  1. Accordian-folded boot shield for flexible swivel connection

    DOE Patents [OSTI]

    Hoh, Joseph C. (Naperville, IL)

    1986-01-01T23:59:59.000Z

    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.

  2. Variational theory for site resolved protein folding free energy surfaces

    E-Print Network [OSTI]

    John J. Portman; Shoji Takada; Peter G. Wolynes

    1999-01-18T23:59:59.000Z

    We present a microscopic variational theory for the free energy surface of a fast folding protein that allows folding kinetics to be resolved to the residue level using Debye-Waller factors as local order parameters. We apply the method to lambda-repressor and compare with site directed mutagenesis experiments. The formation of native structure and the free energy profile along the folding route are shown to be well described by the capillarity approximation but with some fine structure due to local folding topology.

  3. Topological complexity, contact order and protein folding rates

    E-Print Network [OSTI]

    P. F. N. Faisca; R. C. Ball

    2002-05-29T23:59:59.000Z

    Monte Carlo simulations of protein folding show the emergence of a strong correlation between the relative contact order parameter, CO, and the folding time, t, of two-state folding proteins for longer chains with number of amino acids, N>=54, and higher contact order, CO > 0.17. The correlation is particularly strong for N=80 corresponding to slow and more complex folding kinetics. These results are qualitatively compatible with experimental data where a general trend towards increasing t with CO is indeed observed in a set of proteins with chain length ranging from 41 to 154 amino acids.

  4. Mechanics of large folds in thin interfacial films

    E-Print Network [OSTI]

    Vincent Dmery; Benny Davidovitch; Christian D. Santangelo

    2014-07-16T23:59:59.000Z

    A thin film at a liquid interface responds to uniaxial confinement by wrinkling and then by folding; its shape and energy have been computed exactly before self contact. Here, we address the mechanics of large folds, i.e. folds that absorb a length much larger than the wrinkle wavelength. With scaling arguments and numerical simulations, we show that the antisymmetric fold is energetically favorable and can absorb any excess length at zero pressure. Then, motivated by puzzles arising in the comparison of this simple model to experiments on lipid monolayers and capillary rafts, we discuss how to incorporate film weight, self-adhesion and energy dissipation.

  5. affecting protein folding: Topics by E-print Network

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

    or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape becomes...

  6. assisted protein folding: Topics by E-print Network

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

    or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape becomes...

  7. arrestin fold variations: Topics by E-print Network

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

    25 Next Page Last Page Topic Index 1 Variational theory for site resolved protein folding free energy surfaces Condensed Matter (arXiv) Summary: We present a microscopic...

  8. Protein folding: A complex potential for the driving force

    E-Print Network [OSTI]

    Chekmarev, Sergei F

    2013-01-01T23:59:59.000Z

    Using the Helmholtz decomposition of the vector field of folding fluxes in a reduced space of collective variables, a potential of the driving force for protein folding is determined. The potential has two components and can be written as a complex function. One component is responsible for the source and sink of the folding flows (representing, respectively, the unfolded states and the native state of the protein), and the other accounts for the vorticity of the flow that is produced at the boundaries of the main flow by the contact of the moving folding "fluid" with the quiescent surroundings. The theoretical consideration is illustrated by calculations for a model $\\beta$-hairpin protein.

  9. 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...

  10. Thermodynamics of protein folding: a random matrix formulation

    E-Print Network [OSTI]

    Pragya Shukla

    2010-10-16T23:59:59.000Z

    The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows however that the evolution of the statistical measures e.g Gibbs free energy, heat capacity, entropy is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies.

  11. A dynamical approach to protein folding

    E-Print Network [OSTI]

    Alessandro Torcini; Roberto Livi; Antonio Politi

    2001-03-13T23:59:59.000Z

    In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the native configuration. The results reported in this paper have been obtained for a two-dimensional toy-model of amino acid sequences, whose native configurations were previously determined by Monte Carlo techniques. The somewhat controversial scenario emerging from the comparison among various thermodynamical indicators is definitely better resolved relying upon a truly dynamical description, that points out the crucial role played by long-range interactions in determining the characteristic step-wise evolution of ``good'' folders to their native state. It is worth stressing that this dynamical scenario is consistent with the information obtained by exploring the energy landscapes of different sequences. This suggests that even the identification of more efficient ``static'' indicators should take into account the peculiar features associated with the complex ``orography'' of the landscape.

  12. Thrust belt architecture of the central and southern Western Foothills of Taiwan

    E-Print Network [OSTI]

    Rodriguez-Roa, Fernando Antonio

    2009-05-15T23:59:59.000Z

    segments. The restored position of the preexisting normal faults places the current trace of the Western Foothills-Slate Belt boundary beneath the Coastal Range. The restoration of WFFTBs rocks to their depositional locations also supports the tectonic...

  13. Thermal and Structural Constraints on the Tectonic Evolution of the Idaho-Wyoming-Utah Thrust Belt

    E-Print Network [OSTI]

    Chapman, Shay Michael

    2013-08-09T23:59:59.000Z

    The timing of motion on thrust faults in the Idaho-Wyoming-Utah (IWU) thrust belt comes from synorogenic sediments, apatite thermochronology and direct dating of fault rocks coupled with good geometrical constraints of the subsurface structure...

  14. At several localities around the world, thrust belts have developed on both sides of

    E-Print Network [OSTI]

    ten Brink, Uri S.

    of the Eastern Greater Antilles arc (Hispaniola and Puerto Rico), whereas a south-verging thrust belt called; Fig. 2). The Eastern Greater Antilles arc (Hispaniola and Puerto Rico) of the northeastern Caribbean

  15. The Electric Field and Waves Instruments on the Radiation Belt Storm Probes Mission

    E-Print Network [OSTI]

    Wygant, J. R.

    The Electric Fields and Waves (EFW) Instruments on the two Radiation Belt Storm Probe (RBSP) spacecraft (recently renamed the Van Allen Probes) are designed to measure three dimensional quasi-static and low frequency ...

  16. The use of pre- and post-stimulation well test analysis in the evaluation of stimulation effectiveness in the Devonian Shales of the Appalachian Basin

    E-Print Network [OSTI]

    Lancaster, David Earl

    1988-01-01T23:59:59.000Z

    gas wells throughout the Appalachian Basin. The analysis of pre-stimulation well tests from four wells in Pike County, KY illustrates the practical difficulties in obtaining analyzable data from Devonian Shale wells. Fig. 1 shows the location... and requires that the flow periods prior to shut-in be even longer. The Martin 1 well located in Martin County, KY illustrates the problem of an insufficient flow period in a more typical Devonian Shale well test. The Martin 1 well was studied as part...

  17. The use of pre- and post-stimulation well test analysis in the evaluation of stimulation effectiveness in the Devonian Shales of the Appalachian Basin

    E-Print Network [OSTI]

    Lancaster, David Earl

    1988-01-01T23:59:59.000Z

    gas wells throughout the Appalachian Basin. The analysis of pre-stimulation well tests from four wells in Pike County, KY illustrates the practical difficulties in obtaining analyzable data from Devonian Shale wells. Fig. 1 shows the location... and requires that the flow periods prior to shut-in be even longer. The Martin 1 well located in Martin County, KY illustrates the problem of an insufficient flow period in a more typical Devonian Shale well test. The Martin 1 well was studied as part...

  18. Water Ice on the Satellite of Kuiper Belt Object 2003 EL61

    E-Print Network [OSTI]

    K. M Barkume; M. E. Brown; E. L. Schaller

    2006-01-24T23:59:59.000Z

    We have obtained a near infrared spectrum of the brightest satellite of the large Kuiper Belt Object, 2003 EL61. The spectrum has absorption features at 1.5 and 2.0 microns, indicating that water ice is present on the surface. We find that the satellite's absorption lines are much deeper than water ice features typically found on Kuiper Belt Objects. We argue that the unusual spectrum indicates that the satellite was likely formed by impact and not by capture.

  19. An economic analysis of sprinkler irrigation technology in the Texas Rice Belt

    E-Print Network [OSTI]

    Parker, Michael R

    1985-01-01T23:59:59.000Z

    AN ECONOMIC ANALYSIS OF SPRINKLER IRRIGATION TECHNOLOGY IN THE TEXAS RICE BELT A Thesis MICHAEL RAY PARKER Submitted to the Graduate College of Texas ASM University in partial fulfillment of the requirements for the degree of MASTER OP... SCIENCE December 1985 Major Subject: Agricultural Economics AN ECONOMIC ANALYSIS OF SPRINKLER IRRIGATION TECHNOLOGY IN THE TEXAS RICE BELT A Thesis MICHAEL R. PARKER Approved as to style and content by: M. Edward Rister (Co-Chairman) Ronald C...

  20. Thermodynamic control and dynamical regimes in protein folding

    E-Print Network [OSTI]

    P. F. N. Faisca; R. C. Ball

    2001-10-07T23:59:59.000Z

    Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be single exponential in nature, while the second regime is typical of sequences longer than 80 amino acids and the folding performance achievable is sensitive to target conformation. The extent to which stability, as measured by the energy of a sequence in the target, is an essential requirement and affects the folding dynamics of protein molecules in the first regime is investigated. The folding dynamics of sequences whose design stage was restricted to a certain fraction of randomly selected amino acids shows that while some degree of stability is a necessary and sufficient condition for successful folding, designing sequences that provide the lowest energy in the target seems to be a superfluous constraint. By studying the dynamics of under annealed but otherwise freely designed sequences we explore the relation between stability and kinetic accessibility. We find that there is no one-to-one correspondence between having low energy and folding quickly to the target, as only a small fraction of the most stable sequences were also found to fold relatively quickly.

  1. Multi-Agent Simulation of Protein Folding Luca Bortolussi1

    E-Print Network [OSTI]

    Bortolussi, Luca

    Multi-Agent Simulation of Protein Folding Luca Bortolussi1 , Agostino Dovier1 , and Federico residues) is known. The process for reaching this state is known as the protein fold- ing. This problem the feasibility and the power of the method. Keywords: Computational Biology, Agent-Based Technologies, Protein

  2. Statistical Analysis of Protein Folding Kinetics Aaron R. Dinner

    E-Print Network [OSTI]

    Dinner, Aaron

    Statistical Analysis of Protein Folding Kinetics Aaron R. Dinner , Sung-Sau So , and Martin and theoretical studies over several years have led to the emergence of a unified general mechanism for protein folding that serves as a framework for the design and interpretation of research in this area [1

  3. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1994-12-27T23:59:59.000Z

    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.

  4. Storm/substorm signatures in the outer belt

    SciTech Connect (OSTI)

    Korth, A.; Friedel, R.H.W.; Mouikis, C. [Max-Planck-Inst. fuer Aeronomie, Lindau (Germany); Fennell, J.F. [Aerospace Corp., El Segundo, CA (United States)

    1998-12-01T23:59:59.000Z

    The response of the ring current region is compared for periods of storm and substorm activity, with an attempt to isolate the contributions of both processes. The authors investigate CRRES particle data in an overview format that allows the display of long-term variations of the outer radiation belt. They compare the evolution of the ring current population to indicators of storm (Dst) and substorm (AE) activity and examine compositional changes. Substorm activity leads to the intensification of the ring current at higher L (L {approximately} 6) and lower ring current energies compared to storms (L {approximately} 4). The O{sup +}/H{sup +} ratio during substorms remains low, near 10%, but is much enhanced during storms (can exceed 100%). They conclude that repeated substorms with an AE {approximately} 900 nT lead to a {Delta}Dst of {approximately} 30 nT, but do not contribute to Dst during storm main phase as substorm injections do not form a symmetric ring current during such disturbed times.

  5. On the Plutinos and Twotinos of the Kuiper Belt

    E-Print Network [OSTI]

    E. I. Chiang; A. B. Jordan

    2002-10-18T23:59:59.000Z

    We illuminate dynamical properties of Kuiper Belt Objects (KBOs) in the 3:2 (``Plutino'') and 2:1 (``Twotino'') Neptunian resonances within the model of resonant capture and migration. We analyze a series of numerical integrations, each involving the 4 migratory giant planets and 400 test particles distributed throughout trans-Neptunian space, to measure efficiencies of capture as functions of migration speed. Snapshots of the spatial distribution of resonant KBOs reveal that Twotinos cluster +/- 75 degrees away from Neptune's longitude, while Plutinos cluster +/- 90 degrees away. Longitudinal clustering persists even for surveys that are not volume-limited in their ability to detect resonant KBOs. Remarkably, between -90 degrees and -60 degrees of Neptune's longitude, we find the sky density of Twotinos to nearly equal that of Plutinos, despite the greater average distance of Twotinos. We couple our findings to observations to crudely estimate that the intrinsic Twotino population is within a factor of 3 of the Plutino population. Most strikingly, the migration model predicts that more Twotinos may lie at longitudes behind that of Neptune than ahead of it. The magnitude of the asymmetry amplifies dramatically with faster rates of migration and can be as large as 300%. A differential measurement of the sky density of 2:1 resonant objects behind of and in front of Neptune's longitude would powerfully constrain the migration history of that planet.

  6. Initial highlights from the Herschel Gould Belt survey

    E-Print Network [OSTI]

    Andr, Ph; Bontemps, S; Knyves, V; Motte, F; Schneider, N; Didelon, P; Minier, V; Saraceno, P; Ward-Thompson, D; Di Francesco, J; White, G; Molinari, S; Testi, L; Abergel, A; Griffin, M; Henning, Th; Royer, P; Mern, B; Vavrek, R; Attard, M; Arzoumanian, D; Wilson, C D; Ade, P; Aussel, H; Baluteau, J -P; Benedettini, M; Bernard, J -Ph; Blommaert, J A D L; Cambrsy, L; Cox, P; Di Giorgio, A; Hargrave, P; Hennemann, M; Huang, M; Kirk, J; Krause, O; Launhardt, R; Leeks, S; Pennec, J Le; Li, J Z; Martin, P; Maury, A; Olofsson, G; Omont, A; Peretto, N; Pezzuto, S; Prusti, T; Roussel, H; Russeil, D; Sauvage, M; Sibthorpe, B; Sicilia-Aguilar, A; Spinoglio, L; Waelkens, C; Woodcraft, A; Zavagno, A

    2010-01-01T23:59:59.000Z

    We summarize the first results from the Gould Belt survey, obtained toward the Aquila Rift and Polaris Flare regions during the 'science demonstration phase' of Herschel. Our 70-500 micron images taken in parallel mode with the SPIRE and PACS cameras reveal a wealth of filamentary structure, as well as numerous dense cores embedded in the filaments. Between ~ 350 and 500 prestellar cores and ~ 45-60 Class 0 protostars can be identified in the Aquila field, while ~ unbound starless cores and no protostars are observed in the Polaris field. The prestellar core mass function (CMF) derived for the Aquila region bears a strong resemblance to the stellar initial mass function (IMF), already confirming the close connection between the CMF and the IMF with much better statistics than earlier studies. Comparing and contrasting our Herschel results in Aquila and Polaris, we propose an observationally-driven scenario for core formation according to which complex networks of long, thin filaments form first within molecul...

  7. Volatile Loss and Classification of Kuiper Belt Objects

    E-Print Network [OSTI]

    Johnson, R E; Young, L A; Volkov, A N; Schmidt, C

    2015-01-01T23:59:59.000Z

    Observations indicate that some of the largest Kuiper Belt Objects (KBOs) have retained volatiles in the gas phase, which implies the presence of an atmosphere that can affect their reflectance spectra and thermal balance. Volatile escape rates driven by solar heating of the surface were estimated by Schaller and Brown (2007) (SB) and Levi and Podolak (2009)(LP) using Jeans escape from the surface and a hydrodynamic model respectively. Based on recent molecular kinetic simulations these rates can be hugely in error (e.g., a factor of $\\sim 10^{16}$ for the SB estimate for Pluto). In this paper we estimate the loss of primordial N$_2$ for several large KBOs guided by recent molecular kinetic simulations of escape due to solar heating of the surface and due to UV/EUV heating of the upper atmosphere. For the latter we extrapolate simulations of escape from Pluto (Erwin et al. 2013) using the energy limited escape model recently validated for the KBOs of interest by molecular kinetic simulations (Johnson et al. 2...

  8. Planar resonant periodic orbits in Kuiper belt dynamics

    E-Print Network [OSTI]

    George Voyatzis; Thomas Kotoulas

    2005-02-28T23:59:59.000Z

    In the framework of the planar restricted three body problem we study a considerable number of resonances associated to the Kuiper Belt dynamics and located between 30 and 48 a.u. Our study is based on the computation of resonant periodic orbits and their stability. Stable periodic orbits are surrounded by regular librations in phase space and in such domains the capture of trans-Neptunian object is possible. All the periodic orbits found are symmetric and there is evidence for the existence of asymmetric ones only in few cases. In the present work first, second and third order resonances are under consideration. In the planar circular case we found that most of the periodic orbits are stable. The families of periodic orbits are temporarily interrupted by collisions but they continue up to relatively large values of the Jacobi constant and highly eccentric regular motion exists for all cases. In the elliptic problem and for a particular eccentricity value of the primary bodies the periodic orbits are isolated. The corresponding families, where they belong to, bifurcate from specific periodic orbits of the circular problem and seem to continue up to the rectilinear problem. Both stable and unstable orbits are obtained for each case. In the elliptic problem the unstable orbits found are associated with narrow chaotic domains in phase space. The evolution of the orbits, which are located in such chaotic domains, seems to be practically regular and bounded for long time intervals.

  9. Kuiper belt structure around nearby super-Earth host stars

    E-Print Network [OSTI]

    Kennedy, Grant M; Marmier, Maxime; Greaves, Jane S; Wyatt, Mark C; Bryden, Geoffrey; Holland, Wayne; Lovis, Christophe; Matthews, Brenda C; Pepe, Francesco; Sibthorpe, Bruce; Udry, Stphane

    2015-01-01T23:59:59.000Z

    We present new observations of the Kuiper belt analogues around HD 38858 and HD 20794, hosts of super-Earth mass planets within 1 au. As two of the four nearby G-type stars (with HD 69830 and 61 Vir) that form the basis of a possible correlation between low-mass planets and debris disc brightness, these systems are of particular interest. The disc around HD 38858 is well resolved with Herschel and we constrain the disc geometry and radial structure. We also present a probable JCMT sub-mm continuum detection of the disc and a CO J=2-1 upper limit. The disc around HD 20794 is much fainter and appears marginally resolved with Herschel, and is constrained to be less extended than the discs around 61 Vir and HD 38858. We also set limits on the radial location of hot dust recently detected around HD 20794 with near-IR interferometry. We present HARPS upper limits on unseen planets in these four systems, ruling out additional super-Earths within a few au, and Saturn-mass planets within 10 au. We consider the disc st...

  10. RESTORING SUSTAINABLE FORESTS ON APPALACHIAN MINED LANDS FOR WOOD PRODUCTS, RENEWABLE ENERGY, CARBON SEQUESTRATION, AND OTHER ECOSYSTEM SERVICES

    SciTech Connect (OSTI)

    Jonathan Aggett

    2003-12-15T23:59:59.000Z

    The overall purpose of this project is to evaluate the biological and economic feasibility of restoring high-quality forests on mined land, and to measure carbon sequestration and wood production benefits that would be achieved from forest restoration procedures. In this segment of work, our goal was to review methods for estimating tree survival, growth, yield and value of forests growing on surface mined land in the eastern coalfields of the USA, and to determine the extent to which carbon sequestration is influenced by these factors. Public Law 95-87, the Surface Mining Control and Reclamation Act of 1977 (SMCRA), mandates that mined land be reclaimed in a fashion that renders the land at least as productive after mining as it was before mining. In the central Appalachian region, where prime farmland and economic development opportunities for mined land are scarce, the most practical land use choices are hayland/pasture, wildlife habitat, or forest land. Since 1977, the majority of mined land has been reclaimed as hayland/pasture or wildlife habitat, which is less expensive to reclaim than forest land, since there are no tree planting costs. As a result, there are now hundreds of thousands of hectares of grasslands and scrublands in various stages of natural succession located throughout otherwise forested mountains in the U.S. A literature review was done to develop the basis for an economic feasibility study of a range of land-use conversion scenarios. Procedures were developed for both mixed hardwoods and white pine under a set of low product prices and under a set of high product prices. Economic feasibility is based on land expectation values. Further, our review shows that three types of incentive schemes might be important: (1) lump sum payment at planting (and equivalent series of annual payments); (2) revenue incentive at harvest; and (3) benefit based on carbon volume.

  11. Sedimentology, petrology, and gas potential of the Brallier Formation: upper Devonian turbidite facies of the Central and Southern Appalachians

    SciTech Connect (OSTI)

    Lundegard, P.D.; Samuels, N.D.; Pryor, W.A.

    1980-03-01T23:59:59.000Z

    The Upper Devonian Brallier Formation of the central and southern Appalachian basin is a regressive sequence of siltstone turbidites interbedded with mudstones, claystones, and shales. It reaches 1000 meters in thickness and overlies basinal mudrocks and underlies deltaic sandstones and mudrocks. Facies and paleocurrent analyses indicate differences between the depositional system of the Brallier Formation and those of modern submarine fans and ancient Alpine flysch-type sequences. The Brallier system is of finer grain size and lower flow intensity. In addition, the stratigraphic transition from turbidites to deltaic sediments is gradual and differs in its facies succession from the deposits of the proximal parts of modern submarine fans. Such features as massive and pebbly sandstones, conglomerates, debris flows, and massive slump structures are absent from this transition. Paleocurrents are uniformly to the west at right angles to basin isopach, which is atypical of ancient turbidite systems. This suggests that turbidity currents had multiple point sources. The petrography and paleocurrents of the Brallier Formation indicate an eastern source of sedimentary and low-grade metasedimentary rocks with modern relief and rainfall. The depositional system of the Brallier Formation is interpreted as a series of small ephemeral turbidite lobes of low flow intensity which coalesced in time to produce a laterally extensive wedge. The lobes were fed by deltas rather than submarine canyons or upper fan channel systems. This study shows that the present-day turbidite facies model, based mainly on modern submarine fans and ancient Alpine flysch-type sequences, does not adequately describe prodeltaic turbidite systems such as the Brallier Formation. Thickly bedded siltstone bundles are common features of the Brallier Formation and are probably its best gas reservoir facies, especially when fracture porosity is well developed.

  12. Multi-scale and Integrated Characterization of the Marcellus Shale in the Appalachian Basin: From Microscopes to Mapping

    SciTech Connect (OSTI)

    Crandall, Dustin; Soeder, Daniel J; McDannell, Kalin T.; Mroz, Thomas

    2010-01-01T23:59:59.000Z

    Historic data from the Department of Energy Eastern Gas Shale Project (ESGP) were compiled to develop a database of geochemical analyses, well logs, lithological and natural fracture descriptions from oriented core, and reservoir parameters. The nine EGSP wells were located throughout the Appalachian Basin and intercepted the Marcellus Shale from depths of 750 meters (2500 ft) to 2500 meters (8200 ft). A primary goal of this research is to use these existing data to help construct a geologic framework model of the Marcellus Shale across the basin and link rock properties to gas productivity. In addition to the historic data, x-ray computerized tomography (CT) of entire cores with a voxel resolution of 240mm and optical microscopy to quantify mineral and organic volumes was performed. Porosity and permeability measurements in a high resolution, steady-state flow apparatus are also planned. Earth Vision software was utilized to display and perform volumetric calculations on individual wells, small areas with several horizontal wells, and on a regional basis. The results indicate that the lithologic character of the Marcellus Shale changes across the basin. Gas productivity appears to be influenced by the properties of the organic material and the mineral composition of the rock, local and regional structural features, the current state of in-situ stress, and lithologic controls on the geometry of induced fractures during stimulations. The recoverable gas volume from the Marcellus Shale is variable over the vertical stratigraphic section, as well as laterally across the basin. The results from this study are expected to help improve the assessment of the resource, and help optimize the recovery of natural gas.

  13. Structural mapping of the ClpB ATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design.

    E-Print Network [OSTI]

    Ah Young, AP; Koehl, A; Cascio, D; Egea, PF

    2015-01-01T23:59:59.000Z

    falciparum: Targeting protein folding and secretion forfalciparum: targeting protein folding and secretion for

  14. Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways

    E-Print Network [OSTI]

    Mohazab, Ali R

    2012-01-01T23:59:59.000Z

    We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold $\\alpha$, $\\beta$, $\\alpha/\\beta$, and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other order parameters. It was seen that non-crossing distance over chain length provided the best discrimination between structural and kinetic classes. The scaling of non-crossing distance with chain length implies an inevitable crossover to entanglement-do...

  15. 52 Journal of Student Research in Environmental Science at Appalachian F A C U L T Y C O N T R I B U T I O N

    E-Print Network [OSTI]

    Thaxton, Christopher S.

    52 Journal of Student Research in Environmental Science at Appalachian F A C U L T Y C O N T R I B U T I O N Call for Papersongoing The Journal of Student Research in Environmental Science. This journal will annually publish a collection of non-peer reviewed student and faculty articles based

  16. Conditions during syntectonic vein formation in the footwall of the Absaroka thrust fault of the Idaho-Wyoming-Utah fold and thrust belt

    E-Print Network [OSTI]

    Lambert, George Randall

    1993-01-01T23:59:59.000Z

    the calcite strain gauge technique of Groshong (1972, 1974). 14 Scatter plot of all measured homogenization (Th) and melting temperature (Tm) pairs. . 30 15 P-T diagram used to calculate inclusion entrapment temperatures. . . . . . 31 16 The equilibrium... types of equations of state for the chemical system under scrutiny. Variables associated with a typical equation of state include the measured Th, the measured Tm and a computed fluid density. The microcomputer program FLINCOR (Brown, 1989) was used...

  17. Solid bitumen at Atigun Gorge, central Brooks Range front: Implications for oil exploration in the North Slope fold and thrust belt

    SciTech Connect (OSTI)

    Howell, D.G.; Johnsson, M.J.; Bird, K.J. (U.S. Geological Survey, Menlo Park, CA (United States))

    1991-03-01T23:59:59.000Z

    The Atigun Gorge area of the north-central Brooks range is a structurally complex region in which a sequence of north-verging duplex structures involving Paleozoic and Mesozoic Ellesmerian continental margin deposits are structurally overlain by a south-verging thrust of Brookian foreland basin deposits of Albian age. The resulting structural triangle zone is marked by numerous small-scale thrusts involving Permian and Triassic strata in which solid bitumen, occupying fissures up to 10 cm wide and several meters in length, has been found. The presence of aromatics in the odorless, black material was confirmed by ultraviolet fluorescence following extraction in dichloromethane. The occurrence of solid bitumen at Atigun Gorge adds to a growing inventory of hydrocarbon-filled fractures found mostly in Cretaceous rocks in the Brooks Range foothills. These occurrences are consistent with a model of hydrocarbon generation beneath the northern margin of the Brooks Range. The regional distribution of vitrinite reflectance isograds suggests that the northern margin of the Brooks Range and the adjoining foreland basin deposits of the North Slope have experienced similar thermal histories. The 0.6% vitrinite reflectance isograd intersects the land surface along the southern margin of the foreland and the 2.0% isograd lies within the northern part of the range. Although these relations suggest the possibility of petroleum resources at shallow depths beneath the Brooks Range foothills, they also indicate that a considerable amount of differential uplift has occurred, probably resulting in redistribution and some leakage of any oil and gas accumulations.

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

    SciTech Connect (OSTI)

    Robert Jacobi; John Fountain

    2002-01-30T23:59:59.000Z

    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.

  19. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-08-13T23:59:59.000Z

    The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how energy from diverse small sources can drive a complex molecule to a unique state. We explore the possibility that the missing factor is in the geometry. A comparison of folding with other physical phenomena, together with analytic modeling of a molecule, led us to analyze the physics of optical caustic formation and of folding behavior side-by-side. The physics of folding and caustics is ostensibly very different but there are several strong parallels. This comparison emphasizes the mathematical similarity and also identifies differences. Since the 1970's, the physics of optical caustics has been developed to a very high degree of mathematical sophistication using catastrophe theory. That kind of quantitative application of catastrophe theory has not previously been applied to folding nor have the points of similarity with optics been identified or exploited. A putative underlying physical link between caustics and folding is a torsion wave of non-constant wave speed, propagating on the dihedral angles and $\\Psi$ found in an analytical model of the molecule. Regardless of whether we have correctly identified an underlying link, the analogy between caustic formation and folding is strong and the parallels (and differences) in the physics are useful.

  20. Modeling two-state cooperativity in protein folding

    E-Print Network [OSTI]

    K. Fan; J. Wang; W. Wang

    2001-03-19T23:59:59.000Z

    A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical characteristics and free energy profile show a well-defined two-state behavior and cooperativity of folding for such a model. As a comparison, related simulations for the usual G\\={o} model, where the interaction energies are independent of the local conformations, are also made. Our results indicate that the evolution of interactions during the folding process plays an important role in the two-state cooperativity in protein folding.

  1. 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)

    2010-01-29T23:59:59.000Z

    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.

  2. Computational investigations of folded self-avoiding walks related to protein folding

    E-Print Network [OSTI]

    Bahi, Jacques M; Mazouzi, Kamel; Philippe, Laurent

    2013-01-01T23:59:59.000Z

    Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are studied computationally in this article. We show that these two sets are equal and correspond to the whole $n$-step self-avoiding walks for $n\\leqslant 14$, but that they are different for numerous $n \\geqslant 108$, which are common protein lengths. Concrete counterexamples are provided and the computational methods used to discover them are completely detailed. A tool for studying these subsets of walks related to both pivot moves and proteins conformations is finally presented.

  3. Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude

    E-Print Network [OSTI]

    Mochrie, Simon

    Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds. Introduction When a protein folds, the backbone and sidechain atoms organize from the extensive number protein folding usually occurs on the order of milliseconds to seconds, it is gener- ally accepted

  4. DOI: 10.1002/cphc.200700247 Collapsed But Not Folded: Looking with

    E-Print Network [OSTI]

    Enderlein, Jrg

    at Protein Folding Jrg Enderlein*[a] Protein folding, that is, the organization of proteins into a highly folded structure. To solve Levinthal's paradox it was postulated that proteins fold along specific path- ways (older view), or follow one of many parallel paths down the now famous protein folding funnel

  5. RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki

    E-Print Network [OSTI]

    Kavraki, Lydia E.

    RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki Abstract--Protein folding, and get a coarse view of the energy landscape. Keywords: protein folding, folding kinetics, roadmap methods, conformation sampling techniques, energy landscape. 1 Introduction Protein folding refers

  6. Kinetic Studies of the Folding of Heterodimeric Monellin: Evidence for Switching between Alternative

    E-Print Network [OSTI]

    Keywords: monellin; heterodimeric protein; folding kinetics; parallel pathways Determining whether or not a protein uses multiple pathways to fold is an important goal in protein folding studies. When multiple to the protein folding reaction, and the utilization of more than one pathway would speed protein folding.2

  7. Protein Quaternary Fold Recognition Using Conditional Graphical Models Yan Liu Jaime Carbonell

    E-Print Network [OSTI]

    Carbonell, Jaime

    02139 pweigele@mit.edu Abstract Protein fold recognition is a crucial step in infer- ring biological- acid sequences is protein fold recognition and alignment. Given a target protein fold 1 , the task-to-topology alignment against the fold. There are different kinds of protein folds based on their structural properties

  8. DOI: 10.1002/ijch.201300141 Exploring the Protein Folding Dynamics of Beta3s with

    E-Print Network [OSTI]

    Mukamel, Shaul

    DOI: 10.1002/ijch.201300141 Exploring the Protein Folding Dynamics of Beta3s with Two folding process. Howev- er, monitoring protein folding dynamics is still challeng- ing. Experiments of protein folding. However, most folding processes of interest occur on timescales (microsecond to second

  9. Using Bit-Vector Decision Procedures for Analysis of Protein Folding Pathways

    E-Print Network [OSTI]

    Langmead, Christopher James

    Using Bit-Vector Decision Procedures for Analysis of Protein Folding Pathways Christopher James-vector decision procedures for the analysis of protein folding pathways. We argue that the protein fold- ing by the different nature of the protein folding problem, we present a translation of the protein folding pathways

  10. PCB origami : folding circuit boards into electronic products

    E-Print Network [OSTI]

    Sterman, Yoav

    2013-01-01T23:59:59.000Z

    PCB origami is a concept for an alternative manufacturing process of electronic products, in which the electronic material will be manufactured flat and folded into functional 3D graspable products by the user. PCBs will ...

  11. Probing the Origins of Two-State Folding

    E-Print Network [OSTI]

    Lane, Thomas J; Beauchamp, Kyle A; Pande, Vijay S

    2013-01-01T23:59:59.000Z

    Many protein systems fold in a two-state manner. Random models, however, rarely display two-state kinetics and thus such behavior should not be accepted as a default. To date, many theories for the prevalence of two-state kinetics have been presented, but none sufficiently explain the breadth of experimental observations. A model, making a minimum of assumptions, is introduced that suggests two-state behavior is likely for any system with an overwhelmingly populated native state. We show two-state folding is emergent and strengthened by increasing the occupancy population of the native state. Further, the model exhibits a hub-like behavior, with slow interconversions between unfolded states. Despite this, the unfolded state equilibrates quickly relative to the folding time. This apparent paradox is readily understood through this model. Finally, our results compare favorable with experimental measurements of protein folding rates as a function of chain length and Keq, and provide new insight into these result...

  12. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01T23:59:59.000Z

    The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how energy from diverse small sources can drive a complex molecule to a unique state. We explore the possibility that the missing factor is in the geometry. A comparison of folding with other physical phenomena, together with analytic modeling of a molecule, led us to analyze the physics of optical caustic formation and of folding behavior side-by-side. The physics of folding and caustics is ostensibly very different but there are several strong parallels. This comparison emphasizes the mathematical similarity and also identifies differences. Since the 1970's, the physics of optical caustics has been developed to a very high degree of mathematical sophistication using catastrophe theory. That kind of quantitative application of catastrophe theory has not previously been applied ...

  13. Low energy pathways for reproducible in vivo protein folding

    E-Print Network [OSTI]

    Leonor Cruzeiro

    2011-01-03T23:59:59.000Z

    Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for those two proteins, starting from two well defined initial conformations: a fully extended and a alpha-helical conformation. The results show that for both proteins the alpha-helical initial conformation provides overall lower energy pathways to the native state. For the alpha/beta protein, 30 % (40%) of the pathways from an initial alpha-helix (fully extended) structure lead to unentangled native folds, a success rate that can be increased to 85 % by the introduction of a well-defined intermediate structure. These results open up a new direction in which to look for a solution to the protein folding problem, as detailed at the end.

  14. 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)

    1999-07-01T23:59:59.000Z

    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.

  15. UFO (UnFold Operator) computer program abstract

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F.

    1982-11-01T23:59:59.000Z

    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.

  16. Characterization of the vocal fold lamina propria towards voice restoration

    E-Print Network [OSTI]

    Hahn, Mariah S

    2004-01-01T23:59:59.000Z

    During normal speech, human vocal folds sustain greater than 100 high impact collisions each second. When the pliability of this complex biomechanical system is reduced by scarring, voice quality may be compromised. ...

  17. Master equation approach to protein folding and kinetic traps

    E-Print Network [OSTI]

    Marek Cieplak; Malte Henkel; Jan Karbowski; Jayanth R. Banavar

    1998-04-21T23:59:59.000Z

    The master equation for 12-monomer lattice heteropolymers is solved numerically and the time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time follows the Arrhenius law and is governed by the longest relaxation time. For good folders, significant kinetic traps appear in the folding funnel whereas for bad folders, the traps also occur in non-native energy valleys.

  18. Examining the coupling of carbon and nitrogen cycles in Southern Appalachian streams: Understanding the role of dissolved organic nitrogen

    SciTech Connect (OSTI)

    Lutz, Brian D [Duke University; Bernhardt, Emily [Duke University; Roberts, Brian [Louisiana Universities Marine Consortium; Mulholland, Patrick J [ORNL

    2011-01-01T23:59:59.000Z

    Although regional and global models of nitrogen (N) cycling typically focus on nitrate, dissolved organic nitrogen (DON) is the dominant form of nitrogen export from many watersheds and thus the dominant form of dissolved N in many streams. Our understanding of the processes controlling DON export from temperate forests is poor. In pristine systems, where biological N limitation is common, N contained in recalcitrant organic matter (OM) can dominate watershed N losses. This recalcitrant OM often has moderately constrained carbon:nitrogen (C:N) molar ratios ({approx}25-55) and therefore, greater DON losses should be observed in sites where there is greater total dissolved organic carbon (DOC) loss. In regions where anthropogenic N pollution is high, it has been suggested that increased inorganic N availability can reduce biological demand for organic N and therefore increase watershed DON losses. This would result in a positive correlation between inorganic and organic N concentrations across sites with varying N availability. In four repeated synoptic surveys of stream water chemistry from forested watersheds along an N loading gradient in the southern Appalachians, we found surprisingly little correlation between DON and DOC concentrations. Further, we found that DON concentrations were always significantly correlated with watershed N loading and stream water [NO{sub 3}{sup -}] but that the direction of this relationship was negative in three of the four surveys. The C:N molar ratio of dissolved organic matter (DOM) in streams draining watersheds with high N deposition was very high relative to other freshwaters. This finding, together with results from bioavailability assays in which we directly manipulated C and N availabilities, suggests that heterotrophic demand for labile C can increase as a result of dissolved inorganic N (DIN) loading, and that heterotrophs can preferentially remove N-rich molecules from DOM. These results are inconsistent with the two prevailing hypotheses that dominate interpretations of watershed DON loss. Therefore, we propose a new hypothesis, the indirect carbon control hypothesis, which recognizes that heterotrophic demand for N-rich DOM can keep stream water DON concentrations low when N is not limiting and heterotrophic demand for labile C is high.

  19. RESTORING SUSTAINABLE FORESTS ON APPALACHIAN MINED LANDS FOR WOOD PRODUCTS, RENEWABLE ENERGY, CARBON SEQUESTRATION, AND OTHER ECOSYSTEM SERVICES

    SciTech Connect (OSTI)

    James A. Burger; J. Galbraith; T. Fox; G. Amacher; J. Sullivan; C. Zipper

    2005-02-15T23:59:59.000Z

    The overall purpose of this project is to evaluate the biological and economic feasibility of restoring high-quality forests on mined land, and to measure carbon sequestration and wood production benefits that would be achieved from forest restoration procedures. During the reporting period (October-December 2004) we completed the validation of a forest productivity classification model for mined land. A coefficient of determination (R{sup 2}) of 0.68 confirms the model's ability to predict SI based on a selection of mine soil properties. To determine carbon sequestration under different forest management scenarios, a field study was installed as a 3 x 3 factorial in a random complete block design with three replications at each of three locations, Ohio (Figure 1), West Virginia (Figure 2), and Virginia (Figure 3). The treatments included three forest types (white pine, hybrid poplar, mixed hardwood) and three silvicultural regimes (competition control, competition control plus tillage, competition control plus tillage plus fertilization). For hybrid poplar, total plant biomass differences increased significantly with the intensity of silvicultural input. Root, stem, and foliage biomass also increased with the level of silvicultural intensity. Financial feasibility analyses of reforestation on mined lands previously reclaimed to grassland have been completed for conversion to white pine and mixed hardwood species. Examination of potential policy instruments for promoting financial feasibility also have been completed, including lump sum payments at time of conversion, annual payments through the life of the stand, and payments based on carbon sequestration that provide both minimal profitability and fully offset initial reforestation outlays. We have compiled a database containing mine permit information obtained from permitting agencies in Virginia, West Virginia, Pennsylvania, Ohio, and Kentucky. Due to differences and irregularities in permitting procedures between states, we found it necessary to utilize an alternative method to determine mined land acreages in the Appalachian region. We have initiated a proof of concept study, focused in the State of Ohio, to determine the feasibility of using images from the Landsat Thematic Mapper (TM) and/or Enhanced Thematic Mapper Plus (ETM+) to accurately identify mined lands.

  20. Detection and characterization of partially folded forms on the protein energy landscape

    E-Print Network [OSTI]

    Bernstein, Rachel Simma

    2011-01-01T23:59:59.000Z

    and the mechanism of protein folding in cytochrome C. Int Jstructure analysis of a protein folding transition state;of a three-state protein folding pathway by NMR relaxation

  1. Beyond the native state: Exploring the role of partially folded conformations on the protein energy landscape

    E-Print Network [OSTI]

    Connell, Katelyn Blair

    2010-01-01T23:59:59.000Z

    intermediate state in protein folding by a hydrophobicThe Yin and Yang of protein folding. FEBS J Varley, P. ,H. (2006). Early events in protein folding explored by rapid

  2. Parallel ContinuationBased Global Optimization for Molecular Conformation and Protein Folding \\Lambda

    E-Print Network [OSTI]

    Neumaier, Arnold

    Parallel ContinuationBased Global Optimization for Molecular Conformation and Protein Folding pecially protein folding. Global minimization problems are difficult to solve when the objective functions cluding energy functions for molecular conformation and protein folding. Mathematical theory

  3. On the Complexity of Protein Folding Pierluigi Crescenzi, Deborah Goldman, Christos Papadimitriou

    E-Print Network [OSTI]

    California at Irvine, University of

    On the Complexity of Protein Folding Pierluigi Crescenzi, Deborah Goldman, Christos Papadimitriou Antonio Piccolboni, Mihalis Yannakakis Abstract We show that the protein folding problem in the two protein folding are the interactions between their monomers; recently, the view that non

  4. Long-time protein folding dynamics from short-time molecular dynamics simulations

    E-Print Network [OSTI]

    Chodera, J D; Swope, W C; Pitera, J W; Dill, Ken A

    2006-01-01T23:59:59.000Z

    On the simulation of protein folding by short time scaleand W. A. Eaton, The protein folding speed limit, Curr.and T. Head-Gordon, Protein folding by distributed computing

  5. Crucial stages of protein folding through a solvable model: Predicting target sites

    E-Print Network [OSTI]

    Cecconi, Fabio

    Crucial stages of protein folding through a solvable model: Predicting target sites for enzyme. Keywords: Protein-folding modeling; prediction of key folding sites; HIV-1 protease; drug resistance One

  6. THE UNIVERSITY OF CHICAGO UNIFYING FRAMEWORK FOR THE PREDICTION OF PROTEIN FOLDING

    E-Print Network [OSTI]

    Sosnick, Tobin R.

    THE UNIVERSITY OF CHICAGO UNIFYING FRAMEWORK FOR THE PREDICTION OF PROTEIN FOLDING PATHWAYS the protein folding problem challenging? . . . . . . . . . . . . . 5 1.2 Some essential concepts: Ingredients of a protein folding algorithm . . . . . . . 15 1.4 Some useful formalisms regarding protein

  7. Parallel ContinuationBased Global Optimization for Molecular Conformation and Protein Folding

    E-Print Network [OSTI]

    Neumaier, Arnold

    Parallel ContinuationBased Global Optimization for Molecular Conformation and Protein Folding protein folding. Global minimization problems are difficult to solve when the objective functions have energy functions for molecular conformation and protein folding. Mathematical theory for the method

  8. Growth of asteroids, planetary embryos and Kuiper belt objects by chondrule accretion

    E-Print Network [OSTI]

    Johansen, Anders; Lacerda, Pedro; Bizzarro, Martin

    2015-01-01T23:59:59.000Z

    Chondrules are millimeter-sized spherules that dominate primitive meteorites (chondrites) originating from the asteroid belt. The incorporation of chondrules into asteroidal bodies must be an important step in planet formation, but the mechanism is not understood. We show that the main growth of asteroids can result from gas-drag-assisted accretion of chondrules. The largest planetesimals of a population with a characteristic radius of 100 km undergo run-away accretion of chondrules within ~3 Myr, forming planetary embryos up to Mars sizes along with smaller asteroids whose size distribution matches that of main belt asteroids. The aerodynamical accretion leads to size-sorting of chondrules consistent with chondrites. Accretion of mm-sized chondrules and ice particles drives the growth of planetesimals beyond the ice line as well, but the growth time increases above the disk life time outside of 25 AU. The contribution of direct planetesimal accretion to the growth of both asteroids and Kuiper belt objects is...

  9. The Antarctic Circumpolar Productivity Belt Joint Institute for the Study of the Atmosphere and Ocean, University of Washington, Seattle, Washington, USA

    E-Print Network [OSTI]

    Follows, Mick

    The Antarctic Circumpolar Productivity Belt T. Ito Joint Institute for the Study of the Atmosphere] We illustrate the mechanisms controlling the spatial patterns of biological productivity of enhanced export production, figuratively termed as the Antarctic Circumpolar Productivity Belt. As observed

  10. Planck intermediate results. XII: Diffuse Galactic components in the Gould Belt System

    E-Print Network [OSTI]

    Ade, P A R; Alves, M I R; Arnaud, M; Ashdown, M; Atrio-Barandela, F; Aumont, J; Baccigalupi, C; Banday, A J; Barreiro, R B; Bartlett, J G; Battaner, E; Bedini, L; Benabed, K; Benot, A; Bernard, J -P; Bersanelli, M; Bonaldi, A; Bond, J R; Borrill, J; Bouchet, F R; Boulanger, F; Burigana, C; Butler, R C; Chen, X; Chiang, L -Y; Christensen, P R; Clements, D L; Colombi, S; Colombo, L P L; Coulais, A; Cuttaia, F; Davies, R D; Davis, R J; de Bernardis, P; de Zotti, G; Delabrouille, J; Dickinson, C; Diego, J M; Dobler, G; Dole, H; Donzelli, S; Dor, O; Douspis, M; Dupac, X; Enlin, T A; Finelli, F; Forni, O; Frailis, M; Franceschi, E; Galeotta, S; Ganga, K; Gnova-Santos, R T; Ghosh, T; Giard, M; Giardino, G; Giraud-Hraud, Y; Gonzlez-Nuevo, J; Grski, K M; Gregorio, A; Gruppuso, A; Hansen, F K; Harrison, D; Hernndez-Monteagudo, C; Hildebrandt, S R; Hivon, E; Hobson, M; Holmes, W A; Hornstrup, A; Hovest, W; Huffenberger, K M; Jaffe, T R; Jaffe, A H; Juvela, M; Keihnen, E; Keskitalo, R; Kisner, T S; Knoche, J; Kunz, M; Kurki-Suonio, H; Lagache, G; Lhteenmki, A; Lamarre, J -M; Lasenby, A; Lawrence, C R; Leach, S; Leonardi, R; Lilje, P B; Linden-Vrnle, M; Lubin, P M; Macas-Prez, J F; Maffei, B; Maino, D; Mandolesi, N; Maris, M; Marshall, D J; Martin, P G; Martnez-Gonzlez, E; Masi, S; Massardi, M; Matarrese, S; Mazzotta, P; Melchiorri, A; Mennella, A; Mitra, S; Miville-Deschnes, M -A; Moneti, A; Montier, L; Morgante, G; Mortlock, D; Munshi, D; Murphy, J A; Naselsky, P; Nati, F; Natoli, P; Nrgaard-Nielsen, H U; Noviello, F; Novikov, D; Novikov, I; Osborne, S; Oxborrow, C A; Pajot, F; Paladini, R; Paoletti, D; Peel, M; Perotto, L; Perrotta, F; Piacentini, F; Piat, M; Pierpaoli, E; Pietrobon, D; Plaszczynski, S; Pointecouteau, E; Polenta, G; Popa, L; Poutanen, T; Pratt, G W; Prunet, S; Puget, J -L; Rachen, J P; Reach, W T; Rebolo, R; Reinecke, M; Renault, C; Ricciardi, S; Ristorcelli, I; Rocha, G; Rosset, C; Rubio-Martn, J A; Rusholme, B; Salerno, E; Sandri, M; Savini, G; Scott, D; Spencer, L; Stolyarov, V; Sudiwala, R; Suur-Uski, A -S; Sygnet, J -F; Tauber, J A; Terenzi, L; Tibbs, C T; Toffolatti, L; Tomasi, M; Tristram, M; Valenziano, L; Van Tent, B; Varis, J; Vielva, P; Villa, F; Vittorio, N; Wade, L A; Wandelt, B D; Ysard, N; Yvon, D; Zacchei, A; Zonca, A

    2013-01-01T23:59:59.000Z

    We perform an analysis of the diffuse low-frequency Galactic components in the Southern part of the Gould Belt system ($130^\\circ\\leq l\\leq 230^\\circ$ and $-50^\\circ\\leq b\\leq -10^\\circ$). Strong UV flux coming from the Gould Belt super-association is responsible for bright diffuse foregrounds that we observe from our position inside the system and that can help us improve our knowledge of the Galactic emission. Free-free emission and anomalous microwave emission (AME) are the dominant components at low frequencies ($\

  11. E-Print Network 3.0 - acids detection folding Sample Search Results

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

    Medicine 4 International Scientific Conference Computer Science'2008 Near-Native Protein Folding Summary: folded proteins generally have polar amino acids on the outside of their...

  12. E-Print Network 3.0 - ab initio folding Sample Search Results

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

    fold recogniion Ab initio Methods... Methods Ab initio methods: solution of a protein folding problem search in conformational space Energy... Protein Structure Analysis...

  13. Topological Aspects of DNA Function and Protein Folding 523 Knotting pathways in proteins

    E-Print Network [OSTI]

    Bigelow, Stephen

    Topological Aspects of DNA Function and Protein Folding 523 Knotting pathways in proteins Joanna I Key words: artificial knot, chaperone, free energy landscape, knotted protein, protein folding

  14. The effect of consensus mutation on the folding and binding kinetics of I(kappa)B(alpha)

    E-Print Network [OSTI]

    DeVries, Ingrid L.

    2011-01-01T23:59:59.000Z

    in the transition state of protein folding: alternativeet al. (2008). "Protein folding and stability usingH. Rosner, et al. (2002). "Protein folding and stability of

  15. Intermediates and the folding of proteins L and G

    SciTech Connect (OSTI)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01T23:59:59.000Z

    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.

  16. Concentration-Temperature Superposition of Helix Folding Rates in Gelatin

    E-Print Network [OSTI]

    J. L. Gornall; E. M. Terentjev

    2006-03-05T23:59:59.000Z

    We study the kinetics of helix-coil transition in water solutions of gelatin (collagen protein) by optical rotation techniques combined with thermal characterization. By examining the rates of secondary helix folding, and covering a very wide range of solution concentrations, we are able to identify a universal exponential dependence of folding rate on concentration and quench temperature. We demonstrate a new concentration-temperature superposition of data at all temperatures and concentrations, and build the corresponding master curve. The results support the concept of a diffuse helix-coil transition. We find no concentration dependance of the normalized rate constant, suggesting first order (single) kinetics of secondary helix folding dominate in the early stages of renaturation.

  17. 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)

    2000-01-01T23:59:59.000Z

    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.

  18. 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)

    1995-09-01T23:59:59.000Z

    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.

  19. Enhanced sampling and applications in protein folding in explicit solvent

    E-Print Network [OSTI]

    Zhang, Cheng

    2010-01-01T23:59:59.000Z

    We report a single-copy tempering method for enhancing sampling in simulating large complex systems. A continuous temperature space random walk is achieved by a Langevin equation, which is guided by a runtime estimate of the thermal average energy through a novel integral identity. We first validated the method in a two-dimensional Ising model and a Lennard-Jones liquid system. Then the method was applied to folding of three small proteins, trpzip2, trp-cage, and villin headpiece in explicit solvent. Within 0.5~1 microsecond, all three systems were folded into atomic accuracy: the alpha carbon root mean square deviation of the best folded conformations from the native states are 0.2 A, 0.4 A, and 0.4 A, for trpzip2, trp-cage, and villin headpiece, respectively.

  20. Folded Compact Range Development and Coherent Change Detection Measurement Project

    SciTech Connect (OSTI)

    Sorensen, K.W.

    1995-03-01T23:59:59.000Z

    A novel, folded compact range configuration has been developed at the Sandia National Laboratories compact range antenna and radar cross section measurement facility, operated by the Radar/Antenna Department 2343, as a means of performing indoor, environmentally-controlled, far-field simulations of synthetic aperture radar (SAR) coherent change detection (CCD) measurements. This report describes the development of the folded compact range configuration, as well as the initial set of coherent change detection measurements made with the system. These measurements have been highly successful, and have demonstrated the viability of the folded compact range concept in simulating SAR CCD measurements. It is felt that follow-on measurements have the potential of contributing significantly to the body of knowledge available to the scientific community involved in CCD image generation and processing, and that this tool will be a significant aid in the research and development of change detection methodologies.

  1. Ultraviolet resonance Raman spectroscopy of the integral membrane protein OmpA : elucidating structure and tryptophan microenvironment of folded and unfolded states

    E-Print Network [OSTI]

    Neary, Tiffany Jonean

    2008-01-01T23:59:59.000Z

    Intermediates in Membrane Protein Folding, Biochemistry (Intermediates in Membrane Protein Folding, Biochemistry (Engelman. Membrane-Protein Folding and Oligomerization -

  2. The role of the energy gap in protein folding dynamics

    E-Print Network [OSTI]

    Estelle Pitard; Henri Orland

    1998-11-17T23:59:59.000Z

    The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The influence of the gap on the folding dynamics is studied, for various models of the transition probabilities between the different states of the protein. We show that for certain models, the relaxation to the native state is accelerated by increasing the gap, whereas for others it is slowed down .

  3. Energy landscapes, folding mechanisms and kinetics of RNA tetraloop hairpins

    E-Print Network [OSTI]

    Chakraborty, Debayan; Collepardo-Guevara, Rosana; Wales, David J.

    2014-12-02T23:59:59.000Z

    41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 model, with the existence of several intermediates along the folding pathway. Recently, temper- ature jump in combination with microfluidic mixing techniques have revealed that the relaxation... with the recent experimental findings (for DNA hairpins) of Ansari and co-workers.41 In their study, the authors employed a combination of laser induced temperature jump and microfluidic techniques to initiate folding from different start- ing conditions...

  4. Topology, Geometry, and Stability: Protein Folding and Evolution

    E-Print Network [OSTI]

    Simmons, Walter

    2015-01-01T23:59:59.000Z

    The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows that features without length scales, i.e. topological features, are potentially of central importance. Topology is a natural mathematical tool for the study of shape and we avail ourselves of that tool to examine the relationship between the amino acid sequence and the shapes of protein molecules. We apply what we learn to conjectures about their biological evolution.

  5. Characterization of Protein Folding by Dominant Reaction Pathways

    E-Print Network [OSTI]

    Pietro Faccioli

    2008-06-23T23:59:59.000Z

    We assess the reliability of the recently developed approach denominated Dominant Reaction Pathways (DRP) by studying the folding of a 16-residue beta-hairpin, within a coarse-grained Go-type model. We show that the DRP predictions are in quantitative agreement with the results of Molecular Dynamics simulations, performed in the same model. On the other hand, in the DRP approach, the computational difficulties associated to the decoupling of time scales are rigorously bypassed. The analysis of the important transition pathways supports a picture of the beta-hairpin folding in which the reaction is initiated by the collapse of the hydrophobic cluster.

  6. Petrofabric analysis of experimentally folded multilithologic, layered rocks

    E-Print Network [OSTI]

    Pattison, Linda Jean

    1972-01-01T23:59:59.000Z

    of shortening and elongation parallel to the layering and normal to the fold axis and regions of relatively small differen- tial stress are located from the study of the orientations and positions of small thrust and normal faults, macro- and microfrac... to the bottom layer of the fold in the central anticline or to the top layer of the syncline. Movement on type G fractures creates a 0 thrust fault, and the displacement is at 20 to the direction of 25 loading (F'igure 6, p. 27 ). Type G fractures do...

  7. From genes to folds: a review of cortical gyrification theory

    E-Print Network [OSTI]

    Ronan, Lisa; Fletcher, Paul C

    2014-12-16T23:59:59.000Z

    REVIEW From genes to folds: a review of cortical gyrification theory Lisa Ronan Paul C. Fletcher Received: 5 September 2014 / Accepted: 6 December 2014 #2; The Author(s) 2014. This article is published with open access at Springerlink.com Abstract... microcephaly. Curr Opin Neurol 14:151 Nonaka-Kinoshita M, Reillo I, Artegiani B, Martinez-Martinez MA, Nelson M, Borrell V, Calegari F (2013) Regulation of cerebral cortex size and folding by expansion of basal progenitors. EMBO J 32:18171828 OLeary DDM, Chou...

  8. Precipitation of relativistic electrons of the Van Allen belts into the proton aurora

    SciTech Connect (OSTI)

    Jordanova, Vania K [Los Alamos National Laboratory; Miyoshi, Y [NAGOYA UNIV; Sakaguchi, K [NAGOYA UNIV; Shiokawa, K [NAGOYA UNIV; Evans, D S [SEC/NOAA; Albert, Jay [AFRL; Connors, M [UNIV OF ATHABASCA

    2008-01-01T23:59:59.000Z

    The Van Allen electron belts consist of two regions encircling the earth in which relativistic electrons are trapped in the earth's magnetic field. Populations of relativistic electrons in the Van Allen belts vary greatly with geomagnetic disturbance and they are a major source of damage to space vehicles. In order to know when and by how much these populations of relativistic electrons increase, it is important to elucidate not only the cause of acceleration of relativistic electrons but also the cause of their loss from the Van Allen belts. Here we show the first evidence that left-hand polarized electromagnetic ion cyclotron (EMIC) plasma waves can cause the loss of relativistic electrons into the atmosphere, on the basis of results of an excellent set of ground and satellite observations showing coincident precipitation of ions with energies of tens of keV and of relativistic electrons into an isolated proton aurora. The proton aurora was produced by precipitation of ions with energies of tens of keV due to EMIC waves near the plasma pause, which is a manifestation of wave-particle interactions. These observations clarify that ions with energies of tens of keV affect the evolution of relativistic electrons in the Van Allen belts via parasitic resonance with EMIC waves, an effect that was first theoretically predicted in the early 1970's.

  9. Modeling the deep penetration of outer belt electrons during the ``Halloween'' magnetic storm in 2003

    E-Print Network [OSTI]

    Li, Xinlin

    of this model is that the inputs are solely from measurements of current solar wind and energetic electrons. During the geomagnetic storm of October/November 2003, the intensity peak of the outer radiation belt model is developed, using the measurements of relativistic electrons at geosynchronous orbit

  10. Rayleigh-Taylor instability, lithospheric dynamics, surface topography at convergent mountain belts, and gravity anomalies

    E-Print Network [OSTI]

    Mojzsis, Stephen J.

    Rayleigh-Taylor instability, lithospheric dynamics, surface topography at convergent mountain belts; accepted 25 April 2013; published 24 May 2013. [1] Surface topography and associated gravity anomalies of surface topography, with negative (positive) free-air anomalies over regions of descent (ascent

  11. GEOSPATIAL DECISION SUPPORT FOR SEED COMPANIES IN THE CORN BELT Marcus E. Tooze1

    E-Print Network [OSTI]

    Reichenbach, Stephen E.

    GEOSPATIAL DECISION SUPPORT FOR SEED COMPANIES IN THE CORN BELT Marcus E. Tooze1 , S. Hatten2 , W in the seed industry, new applications emerge for mapping, analysis, and interpretation of cultivar. In addition, a geospatial framework was developed to identify the soil landscapes that had the best soil

  12. Incorporating spectral characteristics of Pc5 waves into three-dimensional radiation belt

    E-Print Network [OSTI]

    Elkington, Scot R.

    . This is the first analysis in three dimensions utilizing model ULF wave electric and magnetic fields on the guiding losses at MeV energies. This inner electron belt resides mainly below 2 RE geocen- tric distance center trajectories of relativistic electrons. A model is developed, describing magnetic and electric

  13. Energetic outer radiation-belt electron precipitation during recurrent solar activity

    E-Print Network [OSTI]

    Otago, University of

    on the atmosphere [Seppälä et al., 2004]. During some intense solar storms solar protons in the energy range 1Energetic outer radiation-belt electron precipitation during recurrent solar activity Mark A and Physical Sciences, University of Newcastle, Callaghan, Australia. Russell S. Grew School of Mathematical

  14. High-temperature deformation in the Neoproterozoic transpressional Ribeira belt, southeast Brazil

    E-Print Network [OSTI]

    Bascou, Jrme

    High-temperature deformation in the Neoproterozoic transpressional Ribeira belt, southeast Brazil^ncias da Universidade de Sa~o Paulo, Rua do Lago 562, Cep: 05508-080, Sa~o Paulo, SP, Brazil b Laboratoire Geologia, Universidade Federal de Ouro Preto, 35400-000, Ouro Pre^to, MG, Brazil Received 5 April 2001

  15. Analysis of Heavy Oil Recovery by Thermal EOR in a Meander Belt: From Geological

    E-Print Network [OSTI]

    Paris-Sud XI, Universit de

    Analysis of Heavy Oil Recovery by Thermal EOR in a Meander Belt: From Geological to Reservoir Energies nouvelles2 INTRODUCTION SAGD will become increasingly important for heavy oil recovery because assessment, well placement and production performance prediction. One of the most famous heavy oil provinces

  16. Tuesday, 31 July, 2012 Rapid radiation belt losses occurring during high speed solar wind stream1

    E-Print Network [OSTI]

    Otago, University of

    Tuesday, 31 July, 2012 1 Rapid radiation belt losses occurring during high speed solar wind stream1 Raita11 Sodankylä Geophysical Observatory, University of Oulu, Sodankylä, Finland12 Abstract. Recent geomagnetic disturbances triggered by the arrival of a Solar14 Wind Stream Interface (SWSI). In the current

  17. Power Line Damage, Electrical Outages Reduced in the ''Sleet Belt'': NICE3 Steel Project Fact Sheet

    SciTech Connect (OSTI)

    NONE

    2000-04-25T23:59:59.000Z

    The AR Windamper System was developed through a grant from the Inventions and Innovation Program, to protect power transmission lines in sleet belt states and provinces by eliminating the ''galloping'' phenomenon. Wind damping products minimize power outages and reduce repair costs to transmission lines.

  18. A VR-BASED TRAINING PROGRAM FOR CONVEYOR BELT SAFETY SUBMITTED: June 2007

    E-Print Network [OSTI]

    which has forced its adoption of large and fast moving equipment for transporting bulk material. Belt as their economy of operation, reliability, versatility, and practically unlimited range of capabilities. With all of these factors comes an inherent danger. From 1995 to 2007 there have been a total of 534 equipment related fatal

  19. Seismological evidence for crustal-scale thrusting in the Zagros mountain belt (Iran)

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Seismological evidence for crustal-scale thrusting in the Zagros mountain belt (Iran) Anne Paul 1 Grenoble Cedex, France 2 International Institute of Earthquake Engineering and Seismology, Tehran, Iran 3 that the crust of Zagros underthrusts the crust of central Iran along the MZT considered as a crustal

  20. Seismic imaging of the lithospheric structure of the Zagros mountain belt (Iran)

    E-Print Network [OSTI]

    Hatzfeld, Denis

    Seismic imaging of the lithospheric structure of the Zagros mountain belt (Iran) ANNE PAUL1*, DENIS International Institute of Earthquake Engineering and Seismology, Tehran, Iran 3 Institute for Advanced Studies in Basic Sciences (IASBS), PO Box 45195-1159, Zanjan, Iran *Corresponding author (e-mail: Anne

  1. Holocene vegetation and fire dynamics in the supra-mediterranean belt of the Nebrodi Mountains

    E-Print Network [OSTI]

    Bern, Universität

    and the Mediterranean region. Copyright # 2012 John Wiley & Sons, Ltd. KEYWORDS: climate change; human impact; Ilex TINNER1 1 Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of BernHolocene vegetation and fire dynamics in the supra-mediterranean belt of the Nebrodi Mountains

  2. Method for determining molten metal pool level in twin-belt continuous casting machines

    DOE Patents [OSTI]

    Kaiser, Timothy D. (Colchester, VT); Daniel, Sabah S. (Pittsburgh, PA); Dykes, Charles D. (Milton, VT)

    1989-03-21T23:59:59.000Z

    A method for determining level of molten metal in the input of a continuous metal casting machine having at least one endless, flexible, revolving casting belt with a surface which engages the molten metal to be cast and a reverse, cooled surface along which is directed high velocity liquid coolant includes the steps of predetermining the desired range of positions of the molten metal pool and positioning at least seven heat-sensing transducers in bearing contact with the moving reverse belt surface and spaced in upstream-downstream relationship relative to belt travel spanning the desired pool levels. A predetermined temperature threshold is set, somewhat above coolant temperature and the output signals of the transducer sensors are scanned regarding their output signals indicative of temperatures of the moving reverse belt surface. Position of the molten pool is determined using temperature interpolation between any successive pair of upstream-downstream spaced sensors, which follows confirmation that two succeeding downstream sensors are at temperature levels exceeding threshold temperature. The method accordingly provides high resolution for determining pool position, and verifies the determined position by utilizing full-strength signals from two succeeding downstream sensors. In addition, dual sensors are used at each position spanning the desired range of molten metal pool levels to provide redundancy, wherein only the higher temperature of each pair of sensors at a station is utilized.

  3. Restoring Sustainable Forests on Appalachian Mined Lands for Wood Products, Renewable Energy, Carbon Sequestration, and Other Ecosystem Services

    SciTech Connect (OSTI)

    Burger, James A

    2005-07-20T23:59:59.000Z

    The overall purpose of this project is to evaluate the biological and economic feasibility of restoring high-quality forests on mined land, and to measure carbon sequestration and wood production benefits that would be achieved from forest restoration procedures. We are currently estimating the acreage of lands in Virginia, West Virginia, Kentucky, Ohio, and Pennsylvania mined under SMCRA and reclaimed to non-forested post-mining land uses that are not currently under active management, and therefore can be considered as available for carbon sequestration. To determine actual sequestration under different forest management scenarios, a field study was installed as a 3 x 3 factorial in a random complete block design with three replications at each of three locations, one each in Ohio, West Virginia, and Virginia. The treatments included three forest types (white pine, hybrid poplar, mixed hardwood) and three silvicultural regimes (competition control, competition control plus tillage, competition control plus tillage plus fertilization). Each individual treatment plot is 0.5 acres. Each block of nine plots is 4.5 acres, and the complete installation at each site is 13.5 acres. During the reporting period we determined that by grinding the soil samples to a finer particle size of less than 250 ?m (sieve No. 60), the effect of mine soil coal particle size on the extent to which these particles will be oxidized during the thermal treatment of the carbon partitioning procedure will be eliminated, thus making the procedure more accurate and precise. In the second phase of the carbon sequestration project, we focused our attention on determining the sample size required for carbon accounting on grassland mined fields in order to achieve a desired accuracy and precision of the final soil organic carbon (SOC) estimate. A mine land site quality classification scheme was developed and some field-testing of the methods of implementation was completed. The classification model has been validated for softwoods (white pine) on several reclaimed mine sites in the southern Appalachian coal region. The classification model is a viable method for classifying post-SMCRA abandoned mined lands into productivity classes for white pine. A thinning study was established as a random complete block design to evaluate the response to thinning of a 26-year-old white pine stand growing on a reclaimed surface mine in southwest Virginia. Stand parameters were projected to age 30 using a stand table projection. Site index of the stand was found to be 32.3 m at base age 50 years. Thinning rapidly increased the diameter growth of the residual trees to 0.84 cm yr{sup -1} compared to 0.58 cm yr{sup -1} for the unthinned treatment; however, at age 26, there was no difference in volume or value per hectare. At age 30, the unthinned treatment had a volume of 457.1 m{sup 3} ha{sup -1} but was only worth $8807 ha{sup -1}, while the thinned treatment was projected to have 465.8 m{sup 3} ha{sup -1}, which was worth $11265 ha{sup -1} due to a larger percentage of the volume being in sawtimber size classes.

  4. An Outer Planet Beyond Pluto and Origin of the Trans-Neptunian Belt Architecture

    E-Print Network [OSTI]

    Patryk Sofia Lykawka; Tadashi Mukai

    2007-12-13T23:59:59.000Z

    Trans-Neptunian objects (TNOs) are remnants of a collisionally and dynamically evolved planetesimal disk in the outer solar system. This complex structure, known as the trans-Neptunian belt (or Edgeworth-Kuiper belt), can reveal important clues about disk properties, planet formation, and other evolutionary processes. In contrast to the predictions of accretion theory, TNOs exhibit surprisingly large eccentricities, e, and inclinations, i, which can be grouped into distinct dynamical classes. Several models have addressed the origin and orbital evolution of TNOs, but none have reproduced detailed observations, e.g., all dynamical classes and peculiar objects, or provided insightful predictions. Based on extensive simulations of planetesimal disks with the presence of the four giant planets and massive planetesimals, we propose that the orbital history of an outer planet with tenths of Earth's mass can explain the trans-Neptunian belt orbital structure. This massive body was likely scattered by one of the giant planets, which then stirred the primordial planetesimal disk to the levels observed at 40-50 AU and truncated it at about 48 AU before planet migration. The outer planet later acquired an inclined stable orbit (>100 AU; 20-40 deg) because of a resonant interaction with Neptune (an r:1 or r:2 resonance possibly coupled with the Kozai mechanism), guaranteeing the stability of the trans-Neptunian belt. Our model consistently reproduces the main features of each dynamical class with unprecedented detail; it also satisfies other constraints such as the current small total mass of the trans-Neptunian belt and Neptune's current orbit at 30.1 AU. We also provide observationally testable predictions.

  5. Pairwise contact potentials are unsuitable for protein folding Michele Vendruscolo and Eytan Domany

    E-Print Network [OSTI]

    Domany, Eytan

    Pairwise contact potentials are unsuitable for protein folding Michele Vendruscolo and Eytan Domany: protein folding; protein folding potential; contact map; neural networks; per ceptron. I. INTRODUCTION of protein folding [1] is to predict proteins' native structures from their amino acid sequences; solution

  6. Autotransporters: The Cellular Environment Reshapes a Folding Mechanism to Promote Protein Transport

    E-Print Network [OSTI]

    Clark, Patricia L.

    the cellular environment affects protein folding mechanisms. Here, we focus on one unique aspect affect protein folding kinetics and the conformations of folding intermediates? We focus on recent have been made to understand the mechanisms by which proteins fold to their native conformations.3

  7. A New Method for Modeling and Solving the Protein Fold Recognition Problem

    E-Print Network [OSTI]

    Istrail, Sorin

    Idstract A New Method for Modeling and Solving the Protein Fold Recognition Problem (Extended}@ornl.gov Computational recognition of native-like folds from a protein fold database is considered to be a promising recog- nition through optimally aligning (threading) an amino acid sequence and a protein fold (template

  8. Internal friction in the ultrafast folding of the tryptophan cage q Linlin Qiu 1

    E-Print Network [OSTI]

    Hagen, Stephen J.

    Internal friction in the ultrafast folding of the tryptophan cage q Linlin Qiu 1 , Stephen J. Hagen is a diffusional process, and the speed of folding is controlled by the frictional forces that act important source of friction in folding reactions. By contrast, our studies of the folding dynamics

  9. J. Mol. Biol. (1996) 264, 11641179 How to Derive a Protein Folding Potential? A New

    E-Print Network [OSTI]

    Mirny, Leonid

    J. Mol. Biol. (1996) 264, 1164­1179 How to Derive a Protein Folding Potential? A New Approach of deriving a pairwise potentialHarvard University Department of Chemistry for protein folding. The potential of accuracy. 7 1996 Academic Press Limited *Corresponding author Keywords: protein folding; protein folding

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

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM)

    2007-09-18T23:59:59.000Z

    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.

  11. Funnel-Like Organization in Sequence Space Determines the Distributions of Protein Stability and Folding Rate

    E-Print Network [OSTI]

    Levitt, Michael

    determinants of protein folding, we map out the complete organization of thermody- namic and kinetic properties simplified models of protein folding. We obtain a stability map and a folding rate map in sequence space. Proteins 2004;55:107­114. © 2004 Wiley-Liss, Inc. Key words: protein folding; protein sequence struc- ture

  12. Folding Reporter Not 4 Profit BMTA LANL Agreement Number: LOS ALAMOS NATIONAL SECURITY, LLC

    E-Print Network [OSTI]

    , Berendzen J, Terwilliger TC (1999) "Rapid protein folding assay using Green Fluorescent Protein" Nat Biotech

  13. Folding Reporter Foreign Not 4 Profit BMTA LANL Agreement Number: LOS ALAMOS NATIONAL SECURITY, LLC

    E-Print Network [OSTI]

    , Berendzen J, Terwilliger TC (1999) "Rapid protein folding assay using Green Fluorescent Protein" Nat Biotech

  14. Structural Basis of Folding Cooperativity in Model Proteins: Insights from a Microcanonical Perspective

    E-Print Network [OSTI]

    Bachmann, Michael

    characteristic in protein folding. It is defined by a depletion of states that lie energetically between folded have been observed only in lattice models. INTRODUCTION Two-state protein folding is characterized (19,20), and protein folding (2127). Two remarks are worthwhile: 1. If the transition

  15. Author's personal copy The Limited Role of Nonnative Contacts in the Folding

    E-Print Network [OSTI]

    Garrahan, Juan P.

    influential ideas on protein folding. Implicit in this simplification is a crucial assumption that has never been critically evaluated in a broad context: Detailed mechanisms of protein folding are not biased folding; principle of minimum frustration Introduction The current understanding of protein folding has

  16. Identifying the importance of amino acids for protein folding from crystal structures

    E-Print Network [OSTI]

    Stanley, H. Eugene

    Identifying the importance of amino acids for protein folding from crystal structures Nikolay V and characterizing protein folding kinetics from crystal structures using computational techniques. We also describe as the protein folding prob- lem [125], is of great importance because understanding protein folding mechanisms

  17. A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model

    E-Print Network [OSTI]

    Istrail, Sorin

    Article A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model Mao tool for the protein folding problem. Key words: protein folding, HP model, branch and bound, lattice Introduction The protein folding problem, or the protein struc- ture prediction problem, is one of the most

  18. Low-Dimensional Free Energy Landscapes of Protein Folding Reactions by Nonlinear Dimensionality Reduction

    E-Print Network [OSTI]

    Kavraki, Lydia E.

    Low-Dimensional Free Energy Landscapes of Protein Folding Reactions by Nonlinear Dimensionality(26):9885-9890, 2006 #12;Abstract The definition of reaction coordinates for the characterization of a protein folding along the main folding route. These results clearly show that a complex process such as protein folding

  19. Predicting Experimental Quantities in Protein Folding Kinetics using Stochastic Roadmap Simulation

    E-Print Network [OSTI]

    Pratt, Vaughan

    Predicting Experimental Quantities in Protein Folding Kinetics using Stochastic Roadmap Simulation the transition state ensemble (TSE) and predict the rates and -values for protein folding. The new method as a gen- eral tool for studying protein folding kinetics. 1 Introduction Protein folding is a crucial

  20. In and Out of the ER: Protein Folding, Quality Control, Degradation, and Related Human Diseases

    E-Print Network [OSTI]

    Hebert, Daniel N.

    In and Out of the ER: Protein Folding, Quality Control, Degradation, and Related Human Diseases 1377 C. Protein folding 1378 II. Protein Translocation, Folding, and Quality Control in the Endoplasmic Reticulum 1379 A. Protein targeting to the ER 1379 B. Chaperone-assisted protein folding in the ER 1379 C

  1. A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate

    E-Print Network [OSTI]

    Lebendiker, Mario

    A new protein folding screen: Application to the ligand binding domains of a glutamate and kainate of determining and evaluating protein folding conditions, we have designed a new fractional factorial protein folding screen. The screen includes 12 factors shown by previous experiments to enhance protein folding

  2. Estimates of the Loss of Main-Chain Conformational Entropy of Different Residues on Protein Folding

    E-Print Network [OSTI]

    Pal, Debnath

    Estimates of the Loss of Main-Chain Conformational Entropy of Different Residues on Protein Folding energy of protein folding is not well understood. We have developed empirical scales for the loss; protein folding; pro- tein engineering INTRODUCTION When a protein folds into a compact globule, the resi

  3. A New Algorithm for Protein Folding in the HP Model Alantha Newman *

    E-Print Network [OSTI]

    Istrail, Sorin

    876 A New Algorithm for Protein Folding in the HP Model Alantha Newman * Abstract We consider the problem of protein folding in the HP model ozt the two-dimensional square lattice. This problem.e.pairsof H's that are adjacent in the folding but not in the string) are present. The protein folding problem

  4. International Scientific Conference Computer Science'2008 Near-Native Protein Folding

    E-Print Network [OSTI]

    Fidanova, Stefka

    International Scientific Conference Computer Science'2008 61 Near-Native Protein Folding Stefka: The protein folding problem is a fundamental problem in computational molecular biology. The high resolution 3. After that the folding problem is de- fined like optimization problem. Keywords: Protein folding

  5. Identification of characteristic protein folding channels in a coarse-grained hydrophobic-polar peptide model

    E-Print Network [OSTI]

    Bachmann, Michael

    Identification of characteristic protein folding channels in a coarse-grained hydrophobic of protein folding is one of the major challenges of modern interdisciplinary science. Proteins are linear simulations of protein folding are difficult, mainly for two reasons. Firstly, the folding process is so slow

  6. Genetic Algorithm for Predicting Protein Folding in the 2D HP Model

    E-Print Network [OSTI]

    Emmerich, Michael

    Genetic Algorithm for Predicting Protein Folding in the 2D HP Model A Parameter Tuning Case Study of a protein, predicting its tertiary structure is known as the protein folding problem. This problem has been. The protein folding problem in the HP model is to find a conformation (a folded sequence) with the lowest

  7. The energy landscape for protein folding and possible connections to function

    E-Print Network [OSTI]

    Onuchic, Jos

    The energy landscape for protein folding and possible connections to function Margaret S. Cheunga to study protein folding. As good agreement between computational/theoretical studies and experimental-state proteins and larger proteins with more complex folding kinetics. How proteins fold from one

  8. BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum

    E-Print Network [OSTI]

    Petzold, Linda R.

    BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum Marc Griesemer1. *, Carissa (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness

  9. John von Neumann Institute for Computing Different Types of Protein Folding Identified with

    E-Print Network [OSTI]

    Janke, Wolfhard

    John von Neumann Institute for Computing Different Types of Protein Folding Identified://www.fz-juelich.de/nic-series/volume40 #12;Different Types of Protein Folding Identified with a Coarse-Grained Heteropolymer Model Stefan The identification of folding channels is one of the key tasks of protein folding studies. While secondary structures

  10. Constrained Proper Sampling of Conformations of Transition State Ensemble during Protein Folding

    E-Print Network [OSTI]

    Dai, Yang

    Constrained Proper Sampling of Conformations of Transition State Ensemble during Protein Folding) is important for studying protein folding. A promising approach pioneered by Vendruscolo et al40 to study TSE to understand how proteins fold to its native state8,29,37 . Protein folding is a complex process that involves

  11. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Studying submicrosecond protein folding

    E-Print Network [OSTI]

    proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Studying submicrosecond protein folding kinetics INTRODUCTION To understand the intrinsic principles of protein folding, the events in the folding process have to be systematically explored from small to large time scales. Tradi- tional methods for triggering protein folding

  12. Protein folding, the Levinthal paradox and rapidly mixing Markov chains

    E-Print Network [OSTI]

    Clote, Peter

    passage time) and (P) denote the energy gap between the lowest energy Ei0 (native state) and second lowest on a cubic lattice with normally distributed contact energies. Using a Monte-Carlo folding algorithm energy Ei1 of protein P with normally dis- tributed contact energy, Sali, Shakhnovich and Karplus

  13. Folding model description of reactions with exotic nuclei

    SciTech Connect (OSTI)

    Ibraheem, Awad A., E-mail: awad_ah_eb@hotmail.com [Al-Azhar University, Assiut Branch, Physics Department (Egypt); Hassanain, M. A. [King Khalid University, Physics Department (Saudi Arabia); Mokhtar, S. R. [Assiut University, Physics Department (Egypt); Zaki, M. A. [South-Valley University, Physics Department (Egypt); Mahmoud, Zakaria M. M. [Assiut University, Sciences Department, New-Valley Faculty of Education (Egypt); Farid, M. El-Azab [Assiut University, Physics Department (Egypt)

    2012-08-15T23:59:59.000Z

    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.

  14. The Highly Cooperative Folding of Small Naturally Occurring Proteins Is

    E-Print Network [OSTI]

    Baker, David

    Varani,2,3 Tobin Sosnick,4 and David Baker3,5, * 1 Molecular and Cellular Biology Program 2 Department 60637, USA 5 Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA 6 Present, this is now possible for protein folding (Kuhlman and Baker, 2004). Protein structures are stabilized

  15. Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives

    E-Print Network [OSTI]

    Michael Bachmann; Wolfhard Janke

    2007-10-25T23:59:59.000Z

    Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and function of complex macromolecules. This is reasoned by the interdisciplinary character of the associated questions ranging from the molecular origin of the loss of biological functionality as, for example, in Alzheimer's disease to the development of organic circuits for biosensory applications. In this lecture, we focus on the analysis of mesoscopic models for protein folding, aggregation, and hybrid systems of soft and solid condensed matter. The simplicity of the coarse-grained models allows for a more universal description of the notoriously difficult problem of protein folding. In this approach, classifications of structure formation processes with respect to the conformational pseudophases are possible. This is similar in aggregation and adsorption processes, where the individual folding propensity is influenced by external forces. The main problem in studies of conformational transitions is that the sequences of amino acids proteins are built up of are necessarily of finite length and, therefore, a thermodynamic limit does not exist. Thus, structural transitions are not phase transitions in the strict thermodynamic sense and the analysis of pseudouniversal aspects is intricate, as apparently small-system effects accompany all conformational transitions and cannot be neglected.

  16. * Corresponding author. : Primary student contributor. Folding-aware and Structure-conscious 3D Substructures in Folding Data: Identification and Applications

    E-Print Network [OSTI]

    Yang, Hui

    employed by biologists to study the protein folding problem. Such simulations have resulted in a large number of protein folding trajectories, each of which consists of a sequence of three, and cross-trajectory comparison. Key Words: protein folding trajectories, 3D substructure identification

  17. The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom

    E-Print Network [OSTI]

    Zhou, Yaoqi

    structures of proteins, has been extensively investigated to examine its role in protein folding. However the important role of sidechain packing in determining the specific pathway of protein folding. Additional 96 of Physics. DOI: 10.1063/1.1514574 I. INTRODUCTION Theoretical/computational studies of protein folding

  18. Different Kinds of Protein Folding Identified with a Coarse-Grained Heteropolymer Model

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2009-02-16T23:59:59.000Z

    Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing the equilibrium conformations with the folded state in terms of an angular overlap parameter. Although all investigated heteropolymer sequences contain the same content of hydrophobic and polar monomers, our analysis of the folding channels reveals a variety of characteristic folding behaviors known from realistic peptides.

  19. Former presence of thick post-Devonian strata in northern Appalachian basin: Evidence from fluid-inclusion studies

    SciTech Connect (OSTI)

    Sarwar, G.; Friedman, G.M. (Brooklyn College of the City Univ. of New York, NY (USA))

    1989-08-01T23:59:59.000Z

    Along an 80-km long belt south of Syracuse, New York, the maximum fluid-inclusion homogenization temperatures (T{sub max}) of late-stage cements of the lower Middle Devonian Onondaga Limestone show a local high of 150{degree}-160{degree}C in central New York. T{sub max} decreases both west and east of this area reaching about 100{degree}C in outcrops near Buffalo and Albany, respectively. Southward from Albany, along the western margin of the Hudson Valley, T{sub max} again rises sharply to 170{degree}-180{degree}C in the Kingston area. The thermal alteration index (TAI) and vitrinite reflectance of the overlying Marcellus-Bakoven (Middle Devonian) black shales in central and eastern New York show a comparable trend. The east-west profile of T{sub max} of the Onondaga rocks as well as thermal maturity of the black shales show excellent correlation with similar profiles of authigenic magnetite in the Onondaga Limestone and of clay diagenesis and fission-track ages of the Middle Devonian Tioga Metabentonite Bed, as reported by others. The T{sub max} of the Onondaga Limestone is believed to have been attained during maximum burial, the extent of which can not be accounted for by the present thickness of post-Onondaga strata. As a result of an inferred late Paleozoic uplift, in western and eastern New York, 2-3 km of post-Devonian strata were removed, in central New York 4-5 km, and in southeastern New York 5-6 km were removed. The north-south variation in maximum burial along the Hudson Valley may be explained by additional impact of tectonic loading in the south.

  20. Factors determining the adoption or non-adoption of precision agriculture by producers across the cotton belt

    E-Print Network [OSTI]

    Lavergne, Christopher Bernard

    2006-04-12T23:59:59.000Z

    The purpose of this study was to determine factors influencing cotton producer adoption of Precision Agriculture in the cotton belt according to members of the American Cotton Producers of the National Cotton Council. The National Research Council...

  1. Factors determining the adoption or non-adoption of precision agriculture by producers across the cotton belt

    E-Print Network [OSTI]

    Lavergne, Christopher Bernard

    2006-04-12T23:59:59.000Z

    The purpose of this study was to determine factors influencing cotton producer adoption of Precision Agriculture in the cotton belt according to members of the American Cotton Producers of the National Cotton Council. The ...

  2. The competition between surface adsorption and folding of fibril-forming polypeptides

    E-Print Network [OSTI]

    Ni, Ran; Abeln, Sanne; Stuart, Martien A Cohen; Bolhuis, Peter G

    2015-01-01T23:59:59.000Z

    Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse grained model, we systematically studied the folding and adsorption behavior of a $\\beta$-roll forming polypeptide. We find that there are two different folding pathways depending on the temperature: (i) at low temperature, the polypeptide folds in solution into a $\\beta$-roll before adsorbing onto the attractive surface, (ii) at higher temperature, the polypeptide first adsorbs in a disordered state, and folds while on the surface. The folding temperature increases with increasing attraction, as the folded $\\beta$-roll is stabilized by the surface. Surprisingly, further increasing the attraction lowers the folding temperature again, as strong attraction also stabilizes the adsorbed disordered state, which competes with folding of the polypeptide. Our results suggest that to enhance the folding, one should use a weakly attractive surface. They also explain t...

  3. Strong Nernst-Ettingshausen effect in folded graphene

    E-Print Network [OSTI]

    Friedemann Queisser; Ralf Schtzhold

    2013-01-17T23:59:59.000Z

    We study electronic transport in graphene under the influence of a transversal magnetic field $\\f{B}(\\f{r})=B(x)\\f{e}_z$ with the asymptotics $B(x\\to\\pm\\infty)=\\pm B_0$, which could be realized via a folded graphene sheet in a constant magnetic field, for example. By solving the effective Dirac equation, we find robust modes with a finite energy gap which propagate along the fold -- where particles and holes move in opposite directions. Exciting these particle-hole pairs with incident photons would then generate a nearly perfect charge separation and thus a strong magneto-thermoelectric (Nernst-Ettingshausen) or magneto-photoelectric effect -- even at room temperature.

  4. A coarse-grained, ``realistic'' model for Protein Folding

    E-Print Network [OSTI]

    Pierpaolo Bruscolini

    1997-07-24T23:59:59.000Z

    A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the number of secondary structure elements rather than with the number of residues. The hamiltonian presents both local (i.e. single helix, accounting for the stiffness of the chain) and non local (interactions between hydrophobically-charged helices) terms, and is expected to provide a first tool for studying the folding of real proteins. The partition function for a simplified, but by no means trivial, version of the model is calculated almost completely in an analytical way. The latter simplified model is also applied to the study of a synthetic protein, and some preliminary results are shown.

  5. Learning to Fold Proteins Using Energy Landscape Theory

    E-Print Network [OSTI]

    Schafer, N P; Zheng, W; Wolynes, P G

    2014-01-01T23:59:59.000Z

    This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy landscape theory of protein folding. We also present a review of the results of the AMH/AMC/AMW/AWSEM family of coarse-grained molecular dynamics protein folding models to illustrate the points covered in the first part of the article. Accurate coarse-grained structure prediction models can be used to investigate a wide range of conceptual and mechanistic issues outside of protein structure prediction; specifically, the paper concludes by reviewing how AWSEM has in recent years been able to elucidate questions related to the unusual kinetic behavior of artificially designed proteins, multidomain protein misfolding, and the initial stages of protein aggregation.

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

    SciTech Connect (OSTI)

    HART,WILLIAM E.; ISTRAIL,SORIN

    2000-06-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Hart, W.E.; Istrail, S.

    1995-12-11T23:59:59.000Z

    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.

  8. Elastic energy of proteins and the stages of protein folding

    E-Print Network [OSTI]

    Lei, Jinzhi

    2010-01-01T23:59:59.000Z

    We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable parameters are fitted to data from the computer simulation of the folding of a set of proteins using the CSAW (conditioned self-avoiding walk) model. The elastic energy gives rise to scaling relations of the form $R_{g}\\sim N^{\

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

    SciTech Connect (OSTI)

    Ruben A. Abagyan

    2000-06-01T23:59:59.000Z

    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).

  10. Restoring Sustainable Forests on Appalachian Mined Lands for Wood Product, Renewable Energy, Carbon Sequestration, and Other Ecosystem Services

    SciTech Connect (OSTI)

    Burger, James A

    2006-09-30T23:59:59.000Z

    Concentrations of CO{sub 2} in the Earths atmosphere have increased dramatically in the past 100 years due to deforestation, land use change, and fossil fuel combustion. These humancaused, higher levels of CO{sub 2} may enhance the atmospheric greenhouse effect and may contribute to climate change. Many reclaimed coal-surface mine areas in the eastern U.S. are not in productive use. Reforestation of these lands could provide societal benefits, including sequestration of atmospheric carbon. The goal of this project was to determine the biological and economic feasibility of restoring high-quality forests on the tens of thousands of hectares of mined land and to measure carbon sequestration and wood production benefits that would be achieved from large-scale application of forest restoration procedures. We developed a mine soil quality model that can be used to estimate the suitability of selected mined sites for carbon sequestration projects. Across the mine soil quality gradient, we tested survival and growth performance of three species assemblages under three levels of silvicultural. Hardwood species survived well in WV and VA, and survived better than the other species used in OH, while white pine had the poorest survival of all species at all sites. Survival was particularly good for the site-specific hardwoods planted at each site. Weed control plus tillage may be the optimum treatment for hardwoods and white pine, as any increased growth resulting from fertilization may not offset the decreased survival that accompanied fertilization. Grassland to forest conversion costs may be a major contributor to the lack of reforestation of previously reclaimed mine lands in the Appalachian coal-mining region. Otherwise profitable forestry opportunities may be precluded by these conversion costs, which for many combinations of factors (site class, forest type, timber prices, regeneration intensity, and interest rate) result in negative land expectation values. Improved technology and/or knowledge of reforestation practices in these situations may provide opportunities to reduce the costs of converting many of these sites as research continues into these practices. It also appears that in many cases substantial payments, non-revenue values, or carbon values are required to reach profitability under the present circumstances. It is unclear when, or in what form, markets will develop to support any of these add-on values to supplement commercial forestry revenues. However, as these markets do develop, they will only enhance the viability of forestry on reclaimed mined lands, although as we demonstrate in our analysis of carbon payments, the form of the revenue source may itself influence management, potentially mitigating some of the benefits of reforestation. For a representative mined-land resource base, reforestation of mined lands with mixed pine-hardwood species would result in an average estimated C accumulation in forms that can be harvested for use as wood products or are likely to remain in the soil C pool at ~250 Mg C ha{sup -1} over a 60 year period following reforestation. The additionality of this potential C sequestration was estimated considering data in scientific literature that defines C accumulation in mined-land grasslands over the long term. Given assumptions detailed in the text, these lands have the potential to sequester ~180 Mg C ha{sup -1}, a total of 53.5 x 10{sup 6} Mg C, over 60 years, an average of ~900,000 Mg C / yr, an amount equivalent to about 0.04% of projected US C emissions at the midpoint of a 60-year period (circa 2040) following assumed reforestation. Although potential sequestration quantities are not great relative to potential national needs should an energy-related C emissions offset requirement be developed at some future date, these lands are available and unused for other economically valued purposes and many possess soil and site properties that are well-suited to reforestation. Should such reforestation occur, it would also produce ancillary benefits by providing env

  11. A density-temperature description of the outer electron radiation belt during geomagnetic storms

    SciTech Connect (OSTI)

    Borovsky, Joseph E [Los Alamos National Laboratory; Cayton, Thomas E [Los Alamos National Laboratory; Denton, Michael H [LANCASTER UNIV

    2009-01-01T23:59:59.000Z

    Electron flux measurements from 7 satellites in geosynchronous orbit from 1990-2007 are fit with relativistic bi-Maxwellians, yielding a number density n and temperature T description of the outer electron radiation belt. For 54.5 spacecraft years of measurements the median value ofn is 3.7x10-4 cm-3 and the median value ofT is 142 keY. General statistical properties of n, T, and the 1.1-1.5 MeV flux J are investigated, including local-time and solar-cycle dependencies. Using superposed-epoch analysis triggered on storm onset, the evolution of the outer electron radiation belt through high-speed-steam-driven storms is investigated. The number density decay during the calm before the storm is seen, relativistic-electron dropouts and recoveries from dropout are investigated, and the heating of the outer electron radiation belt during storms is examined. Using four different triggers (SSCs, southward-IMF CME sheaths, southward-IMF magnetic clouds, and minimum Dst), CME-driven storms are analyzed with superposed-epoch techniques. For CME-driven storms an absence of a density decay prior to storm onset is found, the compression of the outer electron radiation belt at time of SSC is analyzed, the number-density increase and temperature decrease during storm main phase is seen, and the increase in density and temperature during storm recovery phase is observed. Differences are found between the density-temperature and the flux descriptions, with more information for analysis being available in the density-temperature description.

  12. Examining the specific entropy (density of adiabatic invariants) of the outer electron radiation belt

    SciTech Connect (OSTI)

    Borovsky, Joseph E [Los Alamos National Laboratory; Denton, Michael H [LANCASTER UNIV

    2008-01-01T23:59:59.000Z

    Using temperature and number-density measurements of the energetic-electron population from multiple spacecraft in geosynchronous orbit, the specific entropy S = T/n{sup 2/3} of the outer electron radiation belt is calculated. Then 955,527 half-hour-long data intervals are statistically analyzed. Local-time and solar-cycle variations in S are examined. The median value of the specific entropy (2.8 x 10{sup 7} eVcm{sup 2}) is much larger than the specific entropy of other particle populations in and around the magnetosphere. The evolution of the specific entropy through high-speed-stream-driven geomagnetic storms and through magnetic-cloud-driven geomagnetic storms is studied using superposed-epoch analysis. For high-speed-stream-driven storms, systematic variations in the entropy associated with electron loss and gain and with radiation-belt heating are observed in the various storm phases. For magnetic-cloud-driven storms, multiple trigger choices for the data superpositions reveal the effects of interplanetary shock arrival, sheath driving, cloud driving, and recovery phase. The specific entropy S = T/n{sup 2/3} is algebraically expressed in terms of the first and second adiabatic invariants of the electrons: this allows a relativistic expression for S in terms of T and n to be derived. For the outer electron radiation belt at geosynchronous orbit, the relativistic corrections to the specific entropy expression are -15%.

  13. A Correlation Between Inclination and Color in the Classical Kuiper Belt

    E-Print Network [OSTI]

    Chadwick A. Trujillo; Michael E. Brown

    2002-01-04T23:59:59.000Z

    We have measured broadband optical BVR photometry of 24 Classical and Scattered Kuiper belt objects (KBOs), approximately doubling the published sample of colors for these classes of objects. We find a statistically significant correlation between object color and inclination in the Classical Kuiper belt using our data. The color and inclination correlation increases in significance after the inclusion of additional data points culled from all published works. Apparently, this color and inclination correlation has not been more widely reported because the Plutinos show no such correlation, and thus have been a major contaminant in previous samples. The color and inclination correlation excludes simple origins of color diversity, such as the presence of a coloring agent without regard to dynamical effects. Unfortunately, our current knowledge of the Kuiper belt precludes us from understanding whether the color and inclination trend is due to environmental factors, such as collisional resurfacing, or primordial population effects. A perihelion and color correlation is also evident, although this appears to be a spurious correlation induced by sampling bias, as perihelion and inclination are correlated in the observed sample of KBOs.

  14. A Wide-Field CCD Survey for Centaurs and Kuiper Belt Objects

    E-Print Network [OSTI]

    S. Sheppard; D. Jewitt; C. Trujillo; M. Brown; M. Ashley

    2000-08-29T23:59:59.000Z

    A modified Baker-Nunn camera was used to conduct a wide-field survey of 1428 square degrees of sky near the ecliptic in search of bright Kuiper Belt objects and Centaurs. This area is an order of magnitude larger than any previously published CCD survey for Centaurs and Kuiper Belt Objects. No new objects brighter than red magnitude m=18.8 and moving at a rate 1"/hr to 20"/hr were discovered, although one previously discovered Centaur 1997 CU26 Chariklo was serendipitously detected. The parameters of the survey were characterized using both visual and automated techniques. From this survey the empirical projected surface density of Centaurs was found to be SigmaCentaur(m 1 km) assuming a geometric albedo of 0.04. About 100 Centaurs are larger than 50 km in radius, of which only 4 are presently known. The current total mass of the Centaurs is 10^-4 Earth Masses. No dust clouds were detected resulting from Kuiper Belt object collisions, placing a 3sigma upper limit <600 collisionally produced clouds of m<18.8 per year.

  15. THE COLOR DIFFERENCES OF KUIPER BELT OBJECTS IN RESONANCE WITH NEPTUNE

    SciTech Connect (OSTI)

    Sheppard, Scott S., E-mail: sheppard@dtm.ciw.edu [Department of Terrestrial Magnetism, Carnegie Institution of Washington, 5241 Broad Branch Road NW, Washington, DC 20015 (United States)

    2012-12-01T23:59:59.000Z

    The optical colors of 58 objects in mean motion resonance with Neptune were obtained. The various Neptune resonant populations were found to have significantly different surface color distributions. The 5:3 and 7:4 resonances have semimajor axes near the middle of the main Kuiper Belt and both are dominated by ultra-red material (spectral gradient: S {approx}> 25). The 5:3 and 7:4 resonances have statistically the same color distribution as the low-inclination 'cold' classical belt. The inner 4:3 and distant 5:2 resonances have objects with mostly moderately red colors (S {approx} 15), similar to the scattered and detached disk populations. The 2:1 resonance, which is near the outer edge of the main Kuiper Belt, has a large range of colors with similar numbers of moderately red and ultra-red objects at all inclinations. The 2:1 resonance was also found to have a very rare neutral colored object showing that the 2:1 resonance is really a mix of all object types. The inner 3:2 resonance, like the outer 2:1, has a large range of objects from neutral to ultra-red. The Neptune Trojans (1:1 resonance) are only slightly red (S {approx} 9), similar to the Jupiter Trojans. The inner 5:4 resonance only has four objects with measured colors but shows equal numbers of ultra-red and moderately red objects. The 9:5, 12:5, 7:3, 3:1, and 11:3 resonances do not have reliable color distribution statistics since few objects have been observed in these resonances, though it appears noteworthy that all three of the measured 3:1 objects have only moderately red colors, similar to the 4:3 and 5:2 resonances. The different color distributions of objects in mean motion resonance with Neptune are likely a result from the disruption of the primordial Kuiper Belt from the scattering and migration of the giant planets. The few low-inclination objects known in the outer 2:1 and 5:2 resonances are mostly only moderately red. This suggests if the 2:1 and 5:2 have a cold low-inclination component, the objects likely had a significantly different origin than the ultra-red-dominated cold components of the cold classical belt and 5:3 and 7:4 resonances.

  16. Self-organization and mismatch tolerance in protein folding: General theory and an application

    E-Print Network [OSTI]

    Berry, R. Stephen

    Self-organization and mismatch tolerance in protein folding: General theory and an application approaches to the so-called protein folding problem, mainly because the microscopic models have no explicit

  17. Techniques for modeling and analyzing RNA and protein folding energy landscapes

    E-Print Network [OSTI]

    Tang, Xinyu

    2009-05-15T23:59:59.000Z

    RNA and protein molecules undergo a dynamic folding process that is important to their function. Computational methods are critical for studying this folding pro- cess because it is difficult to observe experimentally. In ...

  18. Optimal fold symmetry of LH2 rings on a photosynthetic membrane

    E-Print Network [OSTI]

    Cleary, Liam

    An intriguing observation of photosynthetic light-harvesting systems is the N-fold symmetry of light-harvesting complex 2 (LH2) of purple bacteria. We calculate the optimal rotational configuration of N-fold rings on a ...

  19. Protein folding and phylogenetic tree reconstruction using stochastic approximation Monte Carlo

    E-Print Network [OSTI]

    Cheon, Sooyoung

    2007-09-17T23:59:59.000Z

    folding problems. The numerical results indicate that it outperforms simulated annealing and conventional Monte Carlo algorithms as a stochastic optimization algorithm. We also propose one method for the use of secondary structures in protein folding...

  20. Identification of Characteristic Protein Folding Channels in a Coarse-Grained Hydrophobic-Polar Peptide Model

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2007-10-25T23:59:59.000Z

    Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a heteropolymer sequence lead to completely different folding behaviors. Studying three exemplified sequences with the same content of hydrophobic and polar residues, we can reproduce within this simple model two-state folding, folding through intermediates, as well as metastability.

  1. Conformation changes and protein folding induced by \\phi^4 interaction

    E-Print Network [OSTI]

    Januar, M; Handoko, L T; 10.1142/9789814335614_0047

    2011-01-01T23:59:59.000Z

    A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected non-linear sources are represented by the bosonic lagrangian with an additional \\phi^4 interaction for the sources. In the model the spring tension of protein representing the internal hydrogen bonds is realized as the interactions between individual amino acids and nonlinear sources. The folding pathway is determined by the strength of nonlinear sources that propagate through the protein backbone. It is also shown that the model reproduces the results in some previous works.

  2. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect (OSTI)

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

    2005-02-10T23:59:59.000Z

    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.

  3. Directed transport as a mechanism for protein folding in vivo

    E-Print Network [OSTI]

    Ernesto Gonzalez-Candela; Victor Romero-Rochin

    2009-09-23T23:59:59.000Z

    We propose a model for protein folding in vivo based on a Brownian-ratchet mechanism in the multidimensional energy landscape space. The device is able to produce directed transport taking advantage of the assumed intrinsic asymmetric properties of the proteins and employing the consumption of energy provided by an external source. Through such a directed transport phenomenon, the polypeptide finds the native state starting from any initial state in the energy landscape with great efficacy and robustness, even in the presence of different type of obstacles. This model solves Levinthal's paradox without requiring biased transition probabilities but at the expense of opening the system to an external field.

  4. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect (OSTI)

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

    2003-06-25T23:59:59.000Z

    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.

  5. Directed transport as a mechanism for protein folding in vivo

    E-Print Network [OSTI]

    Gonzalez-Candela, Ernesto

    2009-01-01T23:59:59.000Z

    We propose a model for protein folding in vivo based on a Brownian-ratchet mechanism in the multidimensional energy landscape space. The device is able to produce directed transport taking advantage of the assumed intrinsic asymmetric properties of the proteins and employing the consumption of energy provided by an external source. Through such a directed transport phenomenon, the polypeptide finds the native state starting from any initial state in the energy landscape with great efficacy and robustness, even in the presence of different type of obstacles. This model solves Levinthal's paradox without requiring biased transition probabilities but at the expense of opening the system to an external field.

  6. Monitoring the Folding of Trp-Cage Peptide by Two-Dimensional Infrared (2DIR) Spectroscopy

    E-Print Network [OSTI]

    Mukamel, Shaul

    of China ABSTRACT: Protein folding is one of the most fundamental problems in modern molecular biology protein folding dynamics which accompany nanometer-scale conformational changes in the pico- to nanosecond bonding dynamics,17 fast chemical exchange in molecular complexes,18 and protein folding.7 According

  7. RESEARCH ARTICLE Open Access Probing the folding of mini-protein Beta3s by

    E-Print Network [OSTI]

    Mukamel, Shaul

    of the protein folding mechanism is of importance to pharmaceutical design and molecular biology [1-5]. Our understanding of protein folding has largely remained elusive due to the vast potential complexity framework for under- standing the global principles of protein folding in terms of funnels [9]. A greater

  8. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear

    E-Print Network [OSTI]

    Moll, Mark

    Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality) The definition of reaction coordinates for the characterization of a protein-folding reaction has long been-dimensional represen- tation of a complex process such as protein folding. reaction coordinate transition state

  9. Analysis of Methods for Predicting Protein Fold and Remote Homologue Recognition

    E-Print Network [OSTI]

    Analysis of Methods for Predicting Protein Fold and Remote Homologue Recognition Prepared by Sanjay Stanford University #12;1. PROTEIN FOLD AND REMOTE HOMOLOGS 1.1 INTRODUCTION Life is a complex system-going efforts to learn biology, the protein folding has been one of those challenging areas in computational

  10. Mechanical Properties of Bovine Rhodopsin and Bacteriorhodopsin: Possible Roles in Folding and Function

    E-Print Network [OSTI]

    Palczewski, Krzysztof

    in rhodopsin but not in bacteriorhodopsin. This core may reflect differences in mechanisms of protein folding their adaptation to differing functions. Introduction Protein folding is one of the most challenging problems protein folding. For more than a decade, the atomic force microscope (AFM) has permitted the use of single

  11. Within the folds, outside the box Susan Lindquist uncovers the roles that misshapen proteins

    E-Print Network [OSTI]

    Lindquist, Susan

    a com- mon thread. "The one universal theme in our lab is protein folding and how changes in protein on a hazy day. "People didn't realize how broad the protein folding problems are. A lot of things that started out as basic research into protein folding are now translating into a direct interest in human

  12. Multi-class Protein Fold Recognition Through a Symbolic-Statistical Framework

    E-Print Network [OSTI]

    Di Mauro, Nicola

    Multi-class Protein Fold Recognition Through a Symbolic-Statistical Framework Marenglen Biba, University of Bari, Italy {biba,esposito,ferilli,basile,ndm}@di.uniba.it Abstract. Protein fold recognition to a multi-class protein fold recognition problem. We compare the proposed approach to a symbolic

  13. Molecular Dynamics Simulations: Methods and Value in the Folding Problem Devon Chandler-Brown

    E-Print Network [OSTI]

    March 2013 Introduction The protein folding has been an outstanding problem in molecular biology for a long period of time. Stated simply, the question of protein folding is that of how the primary amino that govern protein folding are thought to be well established. Forces driven by ionic, Van der Waals

  14. Fluctuations of primary ubiquitin folding intermediates in a force clamp Frauke Grater, Helmut Grubmuller *

    E-Print Network [OSTI]

    Grter, Frauke

    function of which is determined by their three-dimensional struc- ture, the protein fold. Understanding the basic mechanism and associated driving forces of protein folding remains a major task in biology and has., 1997; Marszalek et al., 1999). Along these lines, new insights into protein folding have been recently

  15. Implementation and Characterization of Protein Folding on a Desktop Computational Grid

    E-Print Network [OSTI]

    Taufer, Michela

    Implementation and Characterization of Protein Folding on a Desktop Computational Grid Is CHARMM such as protein folding, desktop grids could become viable alter- natives to clusters of PCs. In this paper, we present a prototype and discuss the viabil- ity of a protein folding application with CHARMM on the United

  16. Long Proteins with Unique Optimal Foldings in the H-P Model ?

    E-Print Network [OSTI]

    state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state model designed to answer qualitative questions about the protein folding process. In this paper we; 1 Introduction Protein folding [14,22,30] is a central problem in molecular and computational

  17. Some New Features for Protein Fold Prediction Nikhil Ranjan Pal and Debrup Chakraborty

    E-Print Network [OSTI]

    Chakraborty, Debrup

    Some New Features for Protein Fold Prediction Nikhil Ranjan Pal and Debrup Chakraborty Electronics}@isical.ac.in Abstract. In this paper we propose several sets of new features for protein fold prediction. The first discriminating powers in predicting protein folds. 1 Introduction One of the most important and challenging

  18. Face-centered cubic (FCC) lattice models for protein folding: energy function inference and biplane packing

    E-Print Network [OSTI]

    Istrail, Sorin

    Face-centered cubic (FCC) lattice models for protein folding: energy function inference and biplane simplified. The objective of PSP (also known as protein folding) is to select the molecule conformation which to infer general energy functions for the protein folding problem. While the general problem is intractable

  19. Predicting Protein Folds with Structural Repeats Using a Chain Graph Model

    E-Print Network [OSTI]

    Xing, Eric P.

    Predicting Protein Folds with Structural Repeats Using a Chain Graph Model Yan Liu yanliu, Carnegie Mellon University, Pittsburgh, PA 15213 USA Abstract Protein fold recognition is a key step to to accurately identify protein folds aris- ing from typical spatial arrangements of well-defined secondary

  20. Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential

    E-Print Network [OSTI]

    Chan, Hue Sun

    the important contributions that computational methods can make in providing insights into protein folding. Understanding protein folding at the atomic level is a critical but elusive goal in structural biology. A protein's folded state can often be studied by x-ray crystallography or NMR spectroscopy, and recent

  1. Title: The automatic discovery of structural principles describing protein fold space

    E-Print Network [OSTI]

    Muggleton, Stephen H.

    Title: The automatic discovery of structural principles describing protein fold space Adrian P author Short title Describing protein fold space #12;Summary The study of protein structure has largely arrangements and in the wider context of protein folding, function and evolution. Given the complicated nature

  2. J. Mol. Biol. (1996) 259, 988994 Local Interactions Dominate Folding in a Simple

    E-Print Network [OSTI]

    Unger, Ron

    1996-01-01T23:59:59.000Z

    Unger1,2 * and John Moult2 Recent computational studies of simple models of protein folding have1 Press Limited Keywords: protein folding; lattice models; local interactions*Corresponding author Introduction What are the dominant contributions guiding the process of protein folding? The short life

  3. THESIS FOR THE DEGREE OF LICENTIATE OF ENGINEERING Numerical Folding of Airbags

    E-Print Network [OSTI]

    Patriksson, Michael

    THESIS FOR THE DEGREE OF LICENTIATE OF ENGINEERING Numerical Folding of Airbags Based of Technology and G¨oteborg University G¨oteborg, Sweden 2007 #12;Numerical Folding of Airbags Based¨oteborg, Sweden 2007 #12;Numerical Folding of Airbags Based on Optimization and Origami Christoffer Cromvik

  4. Topological Aspects of DNA Function and Protein Folding 533 Identifying knots in proteins

    E-Print Network [OSTI]

    Bigelow, Stephen

    Topological Aspects of DNA Function and Protein Folding 533 Identifying knots in proteins Kenneth C proteins. How these knotted proteins fold and finding the evolutionary advantage provided by these knots are among some of the key questions currently being studied in the protein folding field. The detection

  5. Self-Folding Origami: Shape Memory Composites Activated by Uniform Heating

    E-Print Network [OSTI]

    Wood, Robert

    Self-Folding Origami: Shape Memory Composites Activated by Uniform Heating Michael T. Tolley1 systems. Here, self- folding origami are presented, which consist of shape memory composites materials and tools. The folding mechanism based on the in-plane contraction of a sheet of shape memory

  6. Temperature dependence of the folding rate in a simple protein model: Search for a ``glass'' transition

    E-Print Network [OSTI]

    Sali, Andrej

    the thermodynamics and kinetics of protein folding over a wide range of temperatures. Both random sequences are in qualitative disagreement with the conclusions of a theoretical analysis of protein folding kinetics based. INTRODUCTION The protein folding problem has both thermodynamic and kinetic aspects. The existence of a unique

  7. Kinetics of Folding of Proteins and RNA D. THIRUMALAI* AND S. A. WOODSON

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    protein folding is a self-assembly process; i.e., the information needed for obtaining the three of protein folding came from Levinthal6 who wondered how a protein molecule searches the astronomically large to general kinetic scenarios for protein folding which are just beginning to be con- firmed experimentally

  8. How the diffusivity profile reduces the arbitrariness of protein folding free energies

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    How the diffusivity profile reduces the arbitrariness of protein folding free energies M 2010 The concept of a protein diffusing in its free-energy folding landscape has been fruitful for both as it stochastically folds and unfolds. The free-energy profiles for different RCs exhibit significant variations, some

  9. Cooperativity, Smooth Energy Landscapes and the Origins of Topology-dependent Protein Folding Rates

    E-Print Network [OSTI]

    Levine, Alex J.

    folding of simple proteins. We demonstrate that tra- ditional Go polymers lack the extreme cooperativityCooperativity, Smooth Energy Landscapes and the Origins of Topology-dependent Protein Folding Rates Barbara Santa Barbara, CA 93106-9510 USA The relative folding rates of simple, single-domain proteins

  10. Using Loop Length Variants to Dissect the Folding Pathway of a Four-helix-bundle Protein

    E-Print Network [OSTI]

    Mochrie, Simon

    . These observations show that loop alteration may be useful as a general tech- nique for dissecting protein folding pathways. # 1999 Academic Press Keywords: protein folding; kinetics; Rop; loops; four-helix-bundle*Corresponding author Introduction A frequently debated question in the eld of protein folding is the importance

  11. Discrete molecular dynamics studies of the folding of a protein-like model

    E-Print Network [OSTI]

    Buldyrev, Sergey

    for studying theoretical aspects of protein folding. The MC algorithm is based on a set of rules, it is useful to study off-lattice models of protein folding. Thus far, several off-lattice simulations have been performed [1921] that demonstrate the ability of the sim- plified models to study protein folding

  12. Characterization of folding the four-helix bundle protein Rop by real-time NMR

    E-Print Network [OSTI]

    Mochrie, Simon

    -loop-helix monomers. Protein folding moni- tored by stopped-flow fluorescence or CD exhibits biphasic kinetics when: protein folding/real-time NMR Introduction Rop is an RNA-binding protein that is involved in the regu of the effect on protein folding of the length of the connecting loop between the helices, led us to suggest

  13. Combining Task-and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform

    E-Print Network [OSTI]

    Taufer, Michela

    Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform Is efficient protein folding possible with CHARMM on the United Devices MetaProcessor? B. Uk1 , M. Taufer1 parallelism and might not fit the needs for protein folding simulations with explicit water molecules. A short

  14. [25] Identifying Importance of Amino Acids for Protein Folding from Crystal Structures

    E-Print Network [OSTI]

    Dokholyan, Nikolay V.

    [25] Identifying Importance of Amino Acids for Protein Folding from Crystal Structures By Nikolay V their unique three-dimensional structure. This ques- tion, known as the protein-folding problem,125 is of great importance because understanding protein-folding mechanisms is a key to success- ful manipulation

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

    E-Print Network [OSTI]

    Shorter, James

    Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level coupled to the process of protein folding in vivo. While previous studies have provided invaluable insight about how crowding affects protein folding dynamics at the secondary structure level. In this study, we

  16. From residue matching patterns to protein folding topographies: General model and bovine

    E-Print Network [OSTI]

    Berry, R. Stephen

    From residue matching patterns to protein folding topographies: General model and bovine pancreatic-grained model for protein-folding dynamics is introduced based on a discretized representation of torsional, pattern recognition, and general characteristics of protein folding kinetics. Topology here implies

  17. Is Protein Unfolding the Reverse of Protein Folding? A Lattice Simulation Analysis

    E-Print Network [OSTI]

    Dinner, Aaron

    Is Protein Unfolding the Reverse of Protein Folding? A Lattice Simulation Analysis Aaron R. Dinner1- turing conditions are commonly employed to study the mechanism by which a protein folds to its native of determining the mechanism by which a protein folds would be to use an accurate high-resolution model

  18. Task-parallel global optimization with application to protein folding C. Voglis, P. E. Hadjidoukas,

    E-Print Network [OSTI]

    Dimakopoulos, Vassilios

    Task-parallel global optimization with application to protein folding C. Voglis, P. E. Hadjidoukas parallelization of a real application case that concerns the protein folding problem. The experimental evaluation, cluster programming, numerical differentiation, global optimization, protein folding. 1. INTRODUCTION Many

  19. Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast

    E-Print Network [OSTI]

    Fayer, Michael D.

    Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR in the folded configuration. The dynamics of the folded HP35-CN2 are compared to that of the guanidine to differentiate the peptide dynamic contributions to the observables from those of the water solvent. Because

  20. Lattice Protein Folding With Two and Four-Body Statistical Hin Hark Gan,1

    E-Print Network [OSTI]

    Schlick, Tamar

    Lattice Protein Folding With Two and Four-Body Statistical Potentials Hin Hark Gan,1 Alexander/sequence compatibility of proteins,5,6 homology modeling,7 and protein folding simulations.8 10 Currently, most structures. Multibody potentials may help improve our understanding of the cooperativity of protein folding

  1. Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics

    E-Print Network [OSTI]

    Takada, Shoji

    Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics John involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the preceding

  2. Signatures of the Protein Folding Pathway in Two-Dimensional Ultraviolet Spectroscopy

    E-Print Network [OSTI]

    Mukamel, Shaul

    Signatures of the Protein Folding Pathway in Two-Dimensional Ultraviolet Spectroscopy Jun Jiang of the signals provides a quantitative marker of protein folding status, accessible by both theoretical calculations and experiments. SECTION: Biophysical Chemistry and Biomolecules Protein folding is an important

  3. AN ANALYSIS OF PROTEIN FOLDING BY DECODING THE HIERARCHY OF NATIVE-STATE STRUCTURAL INTERACTIONS

    E-Print Network [OSTI]

    Thorpe, Michael

    AN ANALYSIS OF PROTEIN FOLDING BY DECODING THE HIERARCHY OF NATIVE-STATE STRUCTURAL INTERACTIONS and Department of Physics and Astronomy 2002 #12;ABSTRACT AN ANALYSIS OF PROTEIN FOLDING BY DECODING by which proteins fold is one of the most intensely studied prob- lems in science. Here, an analysis

  4. Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines

    E-Print Network [OSTI]

    Cheng, Jianlin Jack

    Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support, Columbia, Missouri * Corresponding author: chengji@missouri.edu Abstract Predicting protein folding rate is useful for understanding protein folding process and guiding protein design. Here we developed a method

  5. Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies

    E-Print Network [OSTI]

    Croquette, Vincent

    Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies for protein folding studies and has been extensively stud- ied, both experimentally (at the ensemble level concentration. It is shown that new infor- mation about different aspects of the protein folding reaction can

  6. Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete

    E-Print Network [OSTI]

    Istrail, Sorin

    Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete Bonnie Berger* Tom Leightont Abstract One of the simplest and most popular biophysical mod- els of protein folding is the hydrophobic-hydrophilic (HP) model. The HP model abstracts the hydrophobic in- teraction in protein folding

  7. A new approach to multi-modal diffusions with applications to protein folding

    E-Print Network [OSTI]

    Srensen, Michael

    A new approach to multi-modal diffusions with applications to protein folding Julie Lyng Forman1 rates are estimated. The new models provide a better fit to this type of protein folding data than time; measurement error; martingale estimating func- tion; multi-modality; protein folding; stochastic

  8. Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity

    E-Print Network [OSTI]

    Bachmann, Michael

    Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativitylich, 52425 Julich, Germany Received June 14, 2010; E-mail: deserno@andrew.cmu.edu Abstract: Protein folding be difficult to measure. Therefore, protein folding cooperativity is often probed using the calorimetric

  9. Pathways for protein folding: is a "new view" needed? Vijay S Pande1

    E-Print Network [OSTI]

    Croquette, Vincent

    Pathways for protein folding: is a "new view" needed? Vijay S Pande1 , Alexander Yu Grosberg2 energy MG Molten globule Introduction How do proteins fold? While the thirty five years since Anfinsen has demonstrated the complexity of protein folding, the search continues for the general principles

  10. Single-molecule spectroscopy of protein folding in a chaperonin cage

    E-Print Network [OSTI]

    Lipman, Everett A.

    Single-molecule spectroscopy of protein folding in a chaperonin cage Hagen Hofmanna , Frank for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms In the recent past, a large number of components have been identified that control and modulate protein folding

  11. Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent

    E-Print Network [OSTI]

    Berne, Bruce J.

    Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent protein folding in explicit solvent. This method is based on exaggerating the hydrophobic effect understanding of protein folding and misfolding is critical to many problems in computational biology.1 Many

  12. A New Algorithm for Protein Folding in the HP Model Alantha Newman

    E-Print Network [OSTI]

    Newman, Alantha

    A New Algorithm for Protein Folding in the HP Model Alantha Newman #3; Abstract We consider the problem of protein folding in the HP model on the two-dimensional square lattice. This problem but not in the string) are present. The protein folding problem in the hydrophobic-hydrophilic (HP) model on the 2D

  13. Reliable Protein Folding on Complex Energy Landscapes: The Free Energy Reaction Path

    E-Print Network [OSTI]

    Gelfond, Michael

    Reliable Protein Folding on Complex Energy Landscapes: The Free Energy Reaction Path Gregg Lois the dynamics of protein folding. The key insight is that the search for the native protein conformation. In the ``new view'' of protein folding (3,7), statistical fluctuations on an energy landscape give rise

  14. Protein Folding and Misfolding in Disease Instructors: Jean Baum and Ron Levy

    E-Print Network [OSTI]

    Chen, Kuang-Yu

    Protein Folding and Misfolding in Disease Instructors: Jean Baum and Ron Levy Tuesday 2:30-5:00 PDB Training Room Syllabus Part I: Protein Folding 9/4: Introduction to Protein Architecture 9/11: Cooperative Transitions in Protein Molecules 9/16: Kinetics of Protein Folding and the Energy Landscape Model 9

  15. Techniques for modeling and analyzing RNA and protein folding energy landscapes

    E-Print Network [OSTI]

    Tang, Xinyu

    2009-05-15T23:59:59.000Z

    techniques can be used to study RNA and protein fold- ing kinetics such as population kinetics, folding rates, and the folding of particular subsequences. In particular, a map-based Master Equation (MME) method can be used to analyze the population kinetics...

  16. Protein Folding, Spin Glass and Computational Complexity 1 Aviezri S. Fraenkel

    E-Print Network [OSTI]

    Fraenkel, Aviezri

    Protein Folding, Spin Glass and Computational Complexity 1 Aviezri S. Fraenkel Abstract of protein folding to solve computationally intractable problems. One way of investigating this idea is to encode known NP­complete problems in terms of protein folding. The main content of this paper is to do

  17. Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study

    E-Print Network [OSTI]

    Levine, Alex J.

    Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study Re October 1998 In the framework of a lattice-model study of protein folding, we investigate the interplay model. Lattice models have been widely used in the study of protein folding dynamics.28 The main

  18. An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem

    E-Print Network [OSTI]

    Hoos, Holger H.

    An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem Alena hydrophobic-polar (2D HP) protein folding problem. We present an improved version of our recently proposed Ant search. Overall, the results presented here establish our new ACO algorithm for 2D HP protein folding

  19. An Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem

    E-Print Network [OSTI]

    Hoos, Holger H.

    An Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem Alena Shmygelska, Rosal, the two dimensional hydrophobic-polar (2D HP) protein folding problem. We introduce an ant colony algorithm closely approaches that of specialised, state-of-the methods for 2D HP protein folding. 1

  20. Cotranslational protein folding with L-systems Gemma B. Danks1,2

    E-Print Network [OSTI]

    Stepney, Susan

    Cotranslational protein folding with L-systems Gemma B. Danks1,2 , Susan Stepney2 , and Leo S. D-systems, parallel rewriting rules, to modelling protein folding using two complementary approaches: a physics an adaptive stochas- tic open L-systems model of protein folding. L-systems were originally developed to model

  1. Predicting protein folding rates from geometric contact and amino acid sequence

    E-Print Network [OSTI]

    Dai, Yang

    Predicting protein folding rates from geometric contact and amino acid sequence ZHENG OUYANG structural properties. Keywords: protein folding; geometric contact number; zippers model; folding rate, USA (RECEIVED January 22, 2008; FINAL REVISION April 4, 2008; ACCEPTED April 7, 2008) Abstract Protein

  2. Semi-deterministic and genetic algorithms for global optimization of microfluidic protein folding

    E-Print Network [OSTI]

    Santiago, Juan G.

    Semi-deterministic and genetic algorithms for global optimization of microfluidic protein folding of a fast microfluidic protein folding device. The aim of the latter design is to reduce mixing times protein folding devices design. Section 3 presents three global optimization algorithms with associated

  3. Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results

    E-Print Network [OSTI]

    Istrail, Sorin

    Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results a comprehensive survey of combinatorial algorithms and theorems about lattice protein folding models obtained in the almost 15 years since the publication in 1995 of the first protein folding approximation algorithm

  4. Using Motion Planning to Study Protein Folding Pathways Department of Computer Science

    E-Print Network [OSTI]

    LaValle, Steven M.

    Using Motion Planning to Study Protein Folding Pathways #3; Guang Song Department of Computer a framework for studying protein folding path- ways and potential landscapes which is based on techniques and study with other methods. Our focus in this work is to study the protein folding mech- anism assuming we

  5. The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding

    E-Print Network [OSTI]

    Fleming, Patrick

    coil theories and protein folding. Contrary to the hypothesis, we find that systematic local steric effects can). The central thermodynamic question in protein folding is: How can a polypeptide chain overcome conformational6) and protein-folding theories (7). It follows from the hypothesis that local structural transitions are ruled

  6. Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics

    E-Print Network [OSTI]

    Morozov, Alexandre V.

    Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics Eric Alm1 underlying the protein-folding problem can be tested by developing and characterizing simple models that make prefactor for protein folding. Finally, we discuss the limitations of simple native-state-based models

  7. A minimum-reaction-flux solution to master-equation models of protein folding

    E-Print Network [OSTI]

    Weston, Ken

    A minimum-reaction-flux solution to master-equation models of protein folding Huan-Xiang Zhoua; published online 20 May 2008 Master equations are widely used for modeling protein folding. Here- ceptual and quantitative models for protein folding.115 In such models, the conformational space

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

    E-Print Network [OSTI]

    Weston, Ken

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

  9. Relationship between protein folding thermodynamics and the energy landscape Jaegil Kim,* Thomas Keyes,

    E-Print Network [OSTI]

    Straub, John E.

    Relationship between protein folding thermodynamics and the energy landscape Jaegil Kim,* Thomas Received 23 September 2008; published 4 March 2009 The origin of protein folding thermodynamics is examined.15.Cc, 05.70. a, 87.15.A Protein folding--i.e., how a polypeptide chain reaches a unique native state

  10. Gibbs Adsorption Isotherm Combined with Monte Carlo Sampling to See Action of Cosolutes on Protein Folding

    E-Print Network [OSTI]

    Harries, Daniel

    Driven by conditions set by smaller solutes, proteins fold and unfold. Experimentally, these conditions stability. Proteins 2004;57:311321. 2004 Wiley-Liss, Inc. INTRODUCTION Inside cells, proteins fold poten- tials, to follow the process of protein folding or unfolding in response to its environment

  11. ORIGINAL RESEARCH PAPER Canyon-infilling and gas hydrate occurrences in the frontal fold

    E-Print Network [OSTI]

    Lin, Andrew Tien-Shun

    ORIGINAL RESEARCH PAPER Canyon-infilling and gas hydrate occurrences in the frontal fold to infer the canyon-infilling, fold uplift, and gas hydrate occurrences beneath the frontal fold at the toe simu- lating reflector (BSR) on seismic sections indicates the base of gas hydrate stability zone

  12. Ultraviolet resonance Raman and fluorescence studies of folded and unfolded conformations of the membrane protein OmpA

    E-Print Network [OSTI]

    Sanchez, Katheryn Marie

    2010-01-01T23:59:59.000Z

    Thermodynamics of Membrane Protein Folding: Lessons from theA Model for Membrane Protein Folding, H. S. Shafaat, K. M.goals of membrane protein folding studies is to ascertain

  13. YidC protein, a molecular chaperone for LacY protein folding via the SecYEG protein machinery

    E-Print Network [OSTI]

    Zhu, L; Kaback, HR; Dalbey, RE

    2013-01-01T23:59:59.000Z

    GroEL-GroES- mediated protein folding. Chem. Rev. 106, 1917of chaperone-mediated protein folding in the cytosol. Nat.that impair membrane protein folding and generate a membrane

  14. Exploring the protein folding dynamics of beta3s with two-dimensional ultraviolet (2DUV) spectroscopy

    E-Print Network [OSTI]

    Lai, Z; Jiang, J; Mukamel, S; Wang, J

    2014-01-01T23:59:59.000Z

    Wang* Exploring the Protein Folding Dynamics of Beta3s withExploring the Protein Folding Dynamics of Beta3s with Two-echo signals to monitor the protein folding pro- cess of the

  15. The impact of main belt asteroids on infrared--submillimetre photometry and source counts

    E-Print Network [OSTI]

    Cs. Kiss; A. Pal; Th. G. Mueller; P. Abraham

    2007-11-28T23:59:59.000Z

    > Among the components of the infrared and submillimetre sky background, the closest layer is the thermal emission of dust particles and minor bodies in the Solar System. This contribution is especially important for current and future infrared and submillimetre space instruments --like those of Spitzer, Akari and Herschel -- and must be characterised by a reliable statistical model. > We describe the impact of the thermal emission of main belt asteroids on the 5...1000um photometry and source counts, for the current and future spaceborne and ground-based instruments, in general, as well as for specific dates and sky positions. > We used the statistical asteroid model (SAM) to calculate the positions of main belt asteroids down to a size of 1km, and calculated their infrared and submillimetre brightness using the standard thermal model. Fluctuation powers, confusion noise values and number counts were derived from the fluxes of individual asteroids. > We have constructed a large database of infrared and submillimetre fluxes for SAM asteroids with a temporal resolution of 5 days, covering the time span January 1, 2000 -- December 31, 2012. Asteroid fluctuation powers and number counts derived from this database can be obtained for a specific observation setup via our public web-interface. > Current space instruments working in the mid-infrared regime (Akari and Spitzer Space Telescopes) are affected by asteroid confusion noise in some specific areas of the sky, while the photometry of space infrared and submillimetre instruments in the near future (e.g. Herschel and Planck Space Observatories) will not be affected by asteroids. Faint main belt asteroids might also be responsible for most of the zodiacal emission fluctuations near the ecliptic.

  16. New Horizons Science Photos from NASA's Pluto-Kuiper Belt Mission

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

    DOE provided the power supply for NASA's New Horizons Mission, a mission to the Pluto and Charon, a double-planet system, and the Kuiper Belt. There are 61 science photos posted on the New Horizons website, along with mission photos, spacecraft images, launch photos, posters and renderings that are both scientific and artistic. Dates range from June of 2006 to February of 2008. The images can be searched by keywords, by date, or by subject topic. They can also be browsed as an entire list. Each image has a detailed description.

  17. Water Ice in 2060 Chiron and its Implications for Centaurs and Kuiper Belt Objects

    E-Print Network [OSTI]

    J. X. Luu; D. C. Jewitt; C. Trujillo

    2000-02-04T23:59:59.000Z

    We report the detection of water ice in the Centaur 2060 Chiron, based on near-infrared spectra (1.0 - 2.5 micron) taken with the 3.8-meter United Kingdom Infrared Telescope (UKIRT) and the 10-meter Keck Telescope. The appearance of this ice is correlated with the recent decline in Chiron's cometary activity: the decrease in the coma cross-section allows previously hidden solid-state surface features to be seen. We predict that water ice is ubiquitous among Centaurs and Kuiper Belt objects, but its surface coverage varies from object to object, and thus determines its detectability and the occurrence of cometary activity.

  18. Emplacement of the Moxa Arch and interaction with the Western Overthrust Belt, Wyoming

    E-Print Network [OSTI]

    Kraig, David Harry

    1986-01-01T23:59:59.000Z

    of MASTER OF SCIENCE May 1986 Major Subject: Geology EMPLACEMENT OF THE MOXA ARCH AND INTERACTION WITH THE WESTERN OVERTHRUST BELT, WYOMING A Thesis by DAVID HARRY KRAIG Approved as to style and content by: David V. Wiltschko (Chairman of Committee... College B. S. The University of New Mexico Chairman of Advisory Committee: Dr. David V. Wiltschko The northern segment of the Moxa Arch is modeled as uplifted along a low-angle thrust (Moxa thrust, MT). The west-verging MT cuts up section from...

  19. Development and application of all-atom structure-based models for studying the role of geometry in biomolecular folding and function

    E-Print Network [OSTI]

    Noel, Jeffrey Kenneth

    2012-01-01T23:59:59.000Z

    in Protein Folding . . . . . . . . . . . . . . . . . . . . .P. G. (2004) Theory of protein folding. Curr. Opin. Struct.statistical mechanics of protein folding. Proc. Nat. Acad.

  20. Regional geological assessment of the Devonian-Mississippian shale sequence of the Appalachian, Illinois, and Michigan basins relative to potential storage/disposal of radioactive wastes

    SciTech Connect (OSTI)

    Lomenick, T.F.; Gonzales, S.; Johnson, K.S.; Byerly, D.

    1983-01-01T23:59:59.000Z

    The thick and regionally extensive sequence of shales and associated clastic sedimentary rocks of Late Devonian and Early Mississippian age has been considered among the nonsalt geologies for deep subsurface containment of high-level radioactive wastes. This report examines some of the regional and basin-specific characteristics of the black and associated nonblack shales of this sequence within the Appalachian, Illinois, and Michigan basins of the north-central and eastern United States. Principal areas where the thickness and depth of this shale sequence are sufficient to warrant further evaluation are identified, but no attempt is made to identify specific storage/disposal sites. Also identified are other areas with less promise for further study because of known potential conflicts such as geologic-hydrologic factors, competing subsurface priorities involving mineral resources and groundwater, or other parameters. Data have been compiled for each basin in an effort to indicate thickness, distribution, and depth relationships for the entire shale sequence as well as individual shale units in the sequence. Included as parts of this geologic assessment are isopach, depth information, structure contour, tectonic elements, and energy-resource maps covering the three basins. Summary evaluations are given for each basin as well as an overall general evaluation of the waste storage/disposal potential of the Devonian-Mississippian shale sequence,including recommendations for future studies to more fully characterize the shale sequence for that purpose. Based on data compiled in this cursory investigation, certain rock units have reasonable promise for radioactive waste storage/disposal and do warrant additional study.