Sample records for faults folds grabens

  1. Genesis of fault hosted carbonate fracture cements in a naturally high CO2 province, South Viking Graben, UK North Sea 

    E-Print Network [OSTI]

    Lee, David Robert

    2013-07-01T23:59:59.000Z

    The Late Jurassic Brae oilfields in the South Viking Graben of the northern North Sea contain naturally high concentrations of carbon dioxide (up to 35 mol %). Fields immediately adjacent to the graben bounding fault ...

  2. 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).

  3. The effects of lithology and initial fault angle in physical models of fault-propagation folds

    E-Print Network [OSTI]

    McLain, Christopher Thomas

    2001-01-01T23:59:59.000Z

    Experimentally deformed physical rock models are used to examine the effects of changing mechanical stratigraphy and initial fault angle on the development of fault-propagation folds over a flat-ramp-flat thrust geometry. This study also...

  4. Analysis of monoclinal folds associated with the Brittmore fault in northwest Houston, Texas

    E-Print Network [OSTI]

    Jones, Jayne Ann

    1988-01-01T23:59:59.000Z

    ANALYSIS OF MONOCLINAL FOLDS ASSOCIATED WITH THE BRITTMORE FAULT IN NORTHWEST HOUSTON, TEXAS A Thesis by JAYNE ANN JONES Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirements for the degree... of MASTER OF SCIENCE August t988 Major Subject: Geology ANALYSIS OF MONOCUNAL FOLDS ASSOCIATED WITH THE BRITTMORE FAULT IN NORTHWEST HOUSTON, TEXAS A Thesis by JAYNE AhlN JONES Approved as to style and content by: Christ her C. Mathewson (Chairman...

  5. 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.

  6. Tectonic evolution of the Thakkahola Graben and Dhaulagiri Himalaya, Central Nepal

    E-Print Network [OSTI]

    Hurtado, José Miguel, 1974-

    2002-01-01T23:59:59.000Z

    Three extensional fault systems intersect in the central Nepal Himalaya: the South Tibetan fault system (STFS); the Thakkhola graben; and structures bounding the Upper Mustang Massif (UMM). Interactions between these systems ...

  7. 3D numericalmodellingof grabeninteraction and linkage: a case studyof the Canyonlands grabens,

    E-Print Network [OSTI]

    Fossen, Haakon

    alongside each other with limited segment interaction; and (4) an abandoned graben segment in a system we understand fault growth in general and structurally complex hydrocarbon reservoirs in particular

  8. 3D numericalmodellingof grabeninteraction and linkage: a case studyof the Canyonlands grabens,

    E-Print Network [OSTI]

    Fossen, Haakon

    with limited segment interaction and (4) an abandoned graben segment in a sys- tem of multiple competing fault growth in general and structurally complex hydrocarbon reservoirs in particular (e.g., Morley

  9. Geometric analysis of faulted rollovers: Contrasting styles of extensional growth folding in the Gulf of Mexico and Offshore Trinidad

    SciTech Connect (OSTI)

    Bentham, P.A. (Amoco Corp., Houston, TX (United States))

    1996-01-01T23:59:59.000Z

    Rapid sedimentation rates combined with the presences of seaward-dipping detachment levels in both the U.S. Gulf of Mexico (GOM) and the Columbus Basin (Offshore Trinidad) have facilitated the development of large extensional growth faults and their associated hanging-wall rollover folds. While detachment in the GOM is often associated with salt and/or overpresurred shale, shale is believed to be responsible for detachment and translation of large structural blocks within the Columbus Basin. Although, gravity-driven extension seems to be the primary mechanism driving structural development in both regions, the detailed structural geometries and deformational mechanisms present seem to be quite different. In the Columbus Basin, extensional rollovers are generally dominated by the presence of pervasive synthetic faults. Restoration of these structures suggests that these synthetic faults are accomodating the bulk hanging-wall deformation as the hanging-wall slides basinwards above an underlying listric fault surface. This synthetic simple shear deformation is not typically observed in Gulf of Mexico rollovers. In contrast, although synthetic faults are present, often observed in Gulf of Mexico rollovers. In contrast, although synthetic faults are present, often spatially associated with the master growth fault, antithetic or mixed antithetic/synthetic faulting dominates the crest of the structures. An antithetic simple shear deformation is borne out by simple geometric modeling and restoration. The synthetic faulting seem in Trinidadian rollovers to be influenced by the presence of important vertical pressure seals (major unconformities) that may act as internal detachment levels within the larger folds. Synthetic faults are often observed to sole or die downwards into these intervals. Generally, lateral closure of rollover anticlines in the GOM is controlled by the underlying scoop-like shape of the major listric growth faults.

  10. Geometric analysis of faulted rollovers: Contrasting styles of extensional growth folding in the Gulf of Mexico and Offshore Trinidad

    SciTech Connect (OSTI)

    Bentham, P.A. [Amoco Corp., Houston, TX (United States)

    1996-12-31T23:59:59.000Z

    Rapid sedimentation rates combined with the presences of seaward-dipping detachment levels in both the U.S. Gulf of Mexico (GOM) and the Columbus Basin (Offshore Trinidad) have facilitated the development of large extensional growth faults and their associated hanging-wall rollover folds. While detachment in the GOM is often associated with salt and/or overpresurred shale, shale is believed to be responsible for detachment and translation of large structural blocks within the Columbus Basin. Although, gravity-driven extension seems to be the primary mechanism driving structural development in both regions, the detailed structural geometries and deformational mechanisms present seem to be quite different. In the Columbus Basin, extensional rollovers are generally dominated by the presence of pervasive synthetic faults. Restoration of these structures suggests that these synthetic faults are accomodating the bulk hanging-wall deformation as the hanging-wall slides basinwards above an underlying listric fault surface. This synthetic simple shear deformation is not typically observed in Gulf of Mexico rollovers. In contrast, although synthetic faults are present, often observed in Gulf of Mexico rollovers. In contrast, although synthetic faults are present, often spatially associated with the master growth fault, antithetic or mixed antithetic/synthetic faulting dominates the crest of the structures. An antithetic simple shear deformation is borne out by simple geometric modeling and restoration. The synthetic faulting seem in Trinidadian rollovers to be influenced by the presence of important vertical pressure seals (major unconformities) that may act as internal detachment levels within the larger folds. Synthetic faults are often observed to sole or die downwards into these intervals. Generally, lateral closure of rollover anticlines in the GOM is controlled by the underlying scoop-like shape of the major listric growth faults.

  11. GEOLOGIC NOTE Fault linkage and graben

    E-Print Network [OSTI]

    Fossen, Haakon

    . Schultz $ Geomechanics-Rock Fracture Group, Department of Geological Sciences and Engineering/172 (1982), and his Ph.D. in geomechanics from Purdue University (1987). He worked at the Lunar

  12. Volcanic rifting at Martian grabens Daniel Me`ge,1

    E-Print Network [OSTI]

    Mege, Daniel

    Volcanic rifting at Martian grabens Daniel Me`ge,1 Anthony C. Cook,2,3 Erwan Garel,4 Yves: Solar System Objects: Mars; 8121 Tectonophysics: Dynamics, convection currents and mantle plumes; 8010: Me`ge, D., A. C. Cook, E. Garel, Y. Lagabrielle, and M.-H. Cormier, Volcanic rifting at Martian

  13. Triassic/Jurassic faulting patterns of Conecuh Ridge, southwest Alabama

    SciTech Connect (OSTI)

    Hutley, J.K.

    1985-02-01T23:59:59.000Z

    Two major fault systems influenced Jurassic structure and deposition on the Conecuh Ridge, southwest Alabama. Identification and dating of these fault systems are based on seismic-stratigraphic interpretation of a 7-township grid in Monroe and Conecuh Counties. Relative time of faulting is determined by fault geometry and by formation isopachs and isochrons. Smackover and Norphlet Formations, both Late Jurassic in age, are mappable seismic reflectors and are thus reliable for seismicstratigraphic dating. The earlier of the 2 fault systems is a series of horsts and grabens that trends northeast-southwest and is Late Triassic to Early Jurassic in age. The system formed in response to tensional stress associated with the opening of the Atlantic Ocean. The resulting topography was a series of northeast-southwest-trending ridges. Upper Triassic Eagle Mills and Jurassic Werner Formations were deposited in the grabens. The later fault system is also a series of horsts and grabens trending perpendicular to the first. This system was caused by tensional stress related to a pulse in the opening of the Gulf of Mexico. Faulting began in Early Jurassic and continued into Late Jurassic, becoming progressively younger basinward. At the basin margin, faulting produced a very irregular shoreline. Submerged horst blocks became centers for shoaling or carbonate buildups. Today, these blocks are exploration targets in southwest Alabama.

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

    SciTech Connect (OSTI)

    Bruno, Michael

    2014-12-08T23:59:59.000Z

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

  15. Analysis of faults using gravity methods in Mason County, Texas

    E-Print Network [OSTI]

    Milligan, Michael Glen

    1992-01-01T23:59:59.000Z

    Committee: Dr. D. A. Fahlquist Dr. B. Johnson The objective of this study is to determine the applicability of gravity profiling methods for determining the location and throw of a series of faults related to a structural graben in northern Mason County... profiles. For two faults with the best geologic control, the best-fit gravity models compared favorably with the the geologic model constructed by Randolph (1991) on the basis of surface mapping, structural control and well control. The gravity models...

  16. Regional seismic reflection line, southern Illinois Basin, provides new data on Cambrian rift geometry, Hicks Dome genesis, and the Fluorspar Area Fault Complex

    SciTech Connect (OSTI)

    Potter, C.J.; Goldhaber, M.B.; Taylor, C.D. (U.S. Geological Survey, Denver, CO (United States)); Heigold, P.C. (Illinois State Geological Survey, Champaign, IL (United States))

    1992-01-01T23:59:59.000Z

    Detailed studies of the subsurface structure of the Cambrian Reelfoot rift (RFR) in the Midwestern US provide important insights into continental rifting processes and into the structural fabric of a zone of modern intracratonic seismicity (New Madrid zone). High-quality oil industry seismic reflection data show that in the area of transition between the RFR and the Rough Creek Graben (RCG) the geometry of the Cambrian rift system is that of a half-graben that thickens to the southeast. This contrasts with the northward-thickening half-graben observed to the east in the RCG and with the more symmetric graben to the south in the RFR. An 82.8-km segment of a northwest-southeast seismic reflection profile in southeastern Illinois and western Kentucky shows that near Hicks Dome, Illinois, Middle and Lower Cambrian syn-rift sedimentary rocks occupy about 0.35 s (two-way travel time) on the seismic reflection section (corresponding to a thickness of about 970 m). This stratigraphic interval occupies about 0.45 s (1,250 m) near the Ohio river and is thickest against the Tabb Fault System (TFS) in Kentucky, where it occupies 0.7 s (1,940 m). The seismic data show that in this part of the Cambrian rift the master fault was part of the TFS and that normal displacement on the TFS continued through middle Paleozoic time. The seismic data also provide new information on the late Paleozoic development of Hicks-Dome and the surrounding Fluorspar Area Fault Complex (FAFC) in southeastern Illinois and western Kentucky. A series of grabens and horsts in the FAFC document a late Paleozoic reactivation of the RFR. Comparison of the reflection data with surface mineralization patterns shows that in most cases mineralized graben-bounding faults clearly cut basement or are splays from faults that cut basement.

  17. Post-Cretaceous faulting at head of Mississippi embayment

    SciTech Connect (OSTI)

    Nelson, W.J. (Illinois State Geological Survey, Champaign, IL (United States)); Harrison, R.W. (Geological Survey, Reston, VA (United States))

    1993-03-01T23:59:59.000Z

    Recent mapping in southernmost Illinois and southeastern Missouri has revealed numerous faults that displace Cretaceous and Tertiary strata. Units as young as the Pliocene-Pleistocene( ) Mounds Gravel are deformed; some faults possibly displace Quaternary sediments. The faults strike northeast, dip nearly vertically, and exhibit characteristics of dextral strike-slip. Pull-apart grabens occur along right-stepping fault strands, they contain chaotically jumbled blocks of Paleozoic, Cretaceous and Tertiary rocks downdropped as much as 800 m relative to wall rocks. Faults at the head of the Mississippi embayment probably originated during Cambrian rifting (Reelfoot rift) and have a long, complex history of reactivation under different stress fields. Some faults are on strike with faults in the New Madrid seismic zone. Kinematics of post-Cretaceous displacements fit the contemporary stress regime of ENE-WSW compression. Similar fault orientations and kinematics, as well as close proximity, suggest a close link between faulting at the head of the embayment and ongoing tectonism in the New Madrid seismic zone.

  18. 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...

  19. Fluid-rock interactions in the Rhine Graben: A thermodynamic model of the hydrothermal alteration observed in deep drilling

    SciTech Connect (OSTI)

    Komninou, A.; Yardley, B.W.D. [Univ. of Leeds (United Kingdom)] [Univ. of Leeds (United Kingdom)

    1997-02-01T23:59:59.000Z

    Deep drilling at Soultz-sous-Forets, France, on the western flanks of the Rhine Graben, has penetrated Hercynian granite underlying Mesozoic sediments. Veins are present throughout the drilled granite, and there are flows of warm water localized in fractures within the granite. Detailed mineralogical study of core material from the research drillhole EPSI has been carried out in order to assess the alteration history of the Soultz granite, part of the crystalline basement of the Rhine Graben. The results of the study have been used, in conjunction with analyses of present-day fluids from deep drilling in the Rhine Graben reported in the literature, to model thermodynamically the alteration process, and in particular to evaluate if it is likely to be continuing today. Reaction-path calculations show that if deep basinal brines, such as are known from sediments of the central Rhine Graben, react with Hercynian granite, they will form different alteration assemblages depending on both the path that the fluid follows (e.g., descending through sediments or through granite) and the extent of preexisting alteration of the granite. The calculations suggest that fluid now sampled from granite in EPS-1 achieved its peak temperature, c. 200{degrees}C while within Permo-Triassic sandstone. The modeling also indicates that present-day fluids from the Rhine Graben system are capable of producing the vein quartz and possibly also the baryte veins, seen in the EPSI core. Much of the alteration present in the granite in the vicinity of veins and fractures may have been produced by a flow regime similar to that prevailing today. 48 refs., 15 figs., 4 tabs.

  20. 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...

  1. 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...

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

    SciTech Connect (OSTI)

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

    1997-08-01T23:59:59.000Z

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

  3. 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 ...

  4. 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

  5. The Influence of Fold and Fracture Development on Reservoir Behavior of the Lisburne Group of Northern Alaska

    SciTech Connect (OSTI)

    Wallace, Wesley K.; Hanks, Catherine L.; Whalen, Michael T.; Jensen1, Jerry; Shackleton, J. Ryan; Jadamec, Margarete A.; McGee, Michelle M.; Karpov1, Alexandre V.

    2001-07-23T23:59:59.000Z

    The Carboniferous Lisburne Group is a major carbonate reservoir unit in northern Alaska. The lisburne is detachment folded where it is exposed throughout the northeastern Brooks Range, but is relatively underformed in areas of current production in the subsurface of the North Slope. The objectives of this study are to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults, (2) The influence of folding on fracture patterns, (3) The influence of deformation on fluid flow, and (4) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics.

  6. 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

  7. 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.

  8. The aftermath of silurian faulting in southeast Michigan, and its effect on oil and gas exploration

    SciTech Connect (OSTI)

    Fowler, J.H. (Polaris Energy, Jackson, MI (United States))

    1994-08-01T23:59:59.000Z

    In Macomb Township of Macomb County, southeast Michigan, is found a sinuous normal fault extending along a N82[degrees]W strike, from end to end only 6 mi long, but with more than 260 ft of maximum displacement at the Trenton level. Through about 3 mi of its midsection extent, the main fault is paired with another normal fault with opposite displacement sense, forming a very narrow graben. The timing of development of this divergent wrench feature coincides with Caledonian tectonic activity, a period of intense structural disturbance and regional subsidence throughout the Michigan basin. The fault appears to cut no higher than A[sub 1] Carbonate, although relationships are obscured by subsequent dissolution of more than 500 ft of Salina A[sub 1], A[sub 2], B, D, and F salts along and beyond the trace of the fault. Collapse of interbedded carbonates and shales is evident, although the apparent lack of brecciation indicates salt removal was not rapid. Further, salt removal proceeded throughout the Devonian, producing dramatic compensatory thickening in overlying units. The development of this large feature in prime Niagaran reef territory may have prevented the discovery of reefs by obscuring what is otherwise well-known stratigraphy and seismic signature. The presence of oil production in dolomitized fracture zones in the Trenton/Black River rocks of nearby Ontario may point to similar potential yet remaining along the Macomb faulted trend.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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

  16. Structural relations along the western end of the Arrowhead Fault, Muddy Mountains, Nevada

    E-Print Network [OSTI]

    Temple, Vernon James Jay

    1977-01-01T23:59:59.000Z

    , resembling "drag" effects related to horizontal movement on the Arrowhead fault, are interpreted as the re- sult of a drape-folded fold. The Summit thrust, a local northwesterly trending fault at the eastern end of the study area, is interpreted... Bonanza King Formation Dunderb erg Shale Buffington Formation Ordovician System Monocline Valley Formation Devonian System Muddy Peak Limestone Mississippian Series Rogers Spring Limestone vii xiii 12 12 12 12 13 1) 23 25 25 26 26 26...

  17. Deformation of layered rocks in the ramp regions of thrust faults: a study with rock models

    E-Print Network [OSTI]

    Chester, Judith Savaso

    1985-01-01T23:59:59.000Z

    and thrust belts for example, thrust faults commonly occur along specific stratigraphic horizons, and folding and faulting within thrust sheets often involves slip along bedding planes (e. g. , Rich, 1934; Douglas, 1950; Dahl str om, 1970; Price, 1981...). With the regional framework of many fold and thrust belts well estab- lished, the current emphasis of many studies has turned to defining the geometries, kinematics, and deformation mechanisms of individual thrust belt structures, and the intrinsic and extrinsic...

  18. Recurrent faulting and petroleum accumulation, Cat Creek Anticline, central Montana

    SciTech Connect (OSTI)

    Nelson, W.J. (Illinois State Geological Survey, Champaign (United States))

    1991-06-01T23:59:59.000Z

    The Cat Creek anticline, scene of central Montana's first significant oil discovery, is underlain by a south-dipping high-angle fault (Cat Creek fault) that has undergone several episodes of movement with opposite sense of displacement. Borehole data suggest that the Cat Creek fault originated as a normal fault during Proterozoic rifting concurrent with deposition of the Belt Supergroup. Reverse faulting took place in Late Cambrian time, and again near the end of the Devonian Period. The Devonian episode, coeval with the Antler orogeny, raised the southern block several hundred feet. The southern block remained high through Meramecian time, then began to subside. Post-Atokan, pre-Middle Jurassic normal faulting lowered the southern block as much as 1,500 ft. During the Laramide orogeny (latest Cretaceous-Eocene) the Cat Creek fault underwent as much as 4,000 ft of reverse displacement and a comparable amount of left-lateral displacement. The Cat Creek anticline is a fault-propagation fold; en echelon domes and listric normal faults developed along its crest in response to wrenching. Oil was generated mainly in organic-rich shales of the Heath Formation (upper Chesterian Series) and migrated upward along tectonic fractures into Pennsylvanian, Jurassic, and Cretaceous reservoir rocks in structural traps in en echelon domes. Production has been achieved only from those domes where structural closure was retained from Jurassic through Holocene time.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. Fault tolerant pulse synchronization 

    E-Print Network [OSTI]

    Deconda, Keerthi

    2009-05-15T23:59:59.000Z

    FFC n=4 orig alg n=4 ft alg n=7 orig alg n=7 ft alg n=10 orig alg n=10 ft alg 24 (a) n=4, f=1. (b) n=7, f=2. Fig. 5: Convergence Time with No Jump faults. 0 50 100 150 200 250 70 100 250 500 Tim e to co nv erg e FFC orig alg: no faults... orig alg: NoJump faults ft alg:NoJump faults 0 50 100 150 200 250 300 350 400 450 70 100 250 500 Tim e to co nv erg e FFC orig alg: no faults orig alg: NoJump faults ft alg:NoJump faults 25 (c) n=10, f=3. Fig. 5 (Continued) Fig. 5(a...

  5. Active folding of fluvial terraces across the Siwaliks Hills, Himalayas of central Nepal

    E-Print Network [OSTI]

    Avouac, Jean-Philippe

    Active folding of fluvial terraces across the Siwaliks Hills, Himalayas of central Nepal J. Lave´1 of central Nepal, south of the Kathmandu Basin. The Main Frontal Thrust fault (MFT), which marks the southern analysis, complemented by geological investiga- tions in central Nepal. Active deformation in the Himalaya

  6. Fault simulation and test generation for small delay faults

    E-Print Network [OSTI]

    Qiu, Wangqi

    2007-04-25T23:59:59.000Z

    Delay faults are an increasingly important test challenge. Traditional delay fault models are incomplete in that they model only a subset of delay defect behaviors. To solve this problem, a more realistic delay fault model has been developed which...

  7. Optimal fault location

    E-Print Network [OSTI]

    Knezev, Maja

    2009-05-15T23:59:59.000Z

    are triggered. Protection system consisting of protection relays and circuit breakers (CBs) will operate in order to de-energize faulted line. Different Intelligent Electronic Devices (IEDs) located in substations for the purpose of monitoring... in the control center by an operator who will mark fault event in a spreadsheet and inform other staff responsible for dealing with fault analysis and repair such as protection group or maintenance respectively. Protective relaying staff will be ready...

  8. Optimal fault location

    E-Print Network [OSTI]

    Knezev, Maja

    2008-10-10T23:59:59.000Z

    are triggered. Protection system consisting of protection relays and circuit breakers (CBs) will operate in order to de-energize faulted line. Different Intelligent Electronic Devices (IEDs) located in substations for the purpose of monitoring... in the control center by an operator who will mark fault event in a spreadsheet and inform other staff responsible for dealing with fault analysis and repair such as protection group or maintenance respectively. Protective relaying staff will be ready...

  9. 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.

  10. Oil springs and flat top anticlines, Carbon County Wyoming: An unusual fold pair

    SciTech Connect (OSTI)

    Blackstone, D.L. Jr. (Univ. of Wyoming, Laramie, WY (United States))

    1994-04-01T23:59:59.000Z

    Oil Springs Anticline, northwest of Medicine Bow, Wyoming, and located at the northeast corner of the Hanna Basin, lies near the junction of the Freezeout Hills Anticline, the Shirley thrust fault and the Flat Top Anticline. The surface fold as defined by the outcrop of the Wall Creek Sandstone Member of the Frontier Formation is disharmonic to deeper structure at the level of the Jurassic Sundance Formation. The fold is wedged between two major folds and is the result of a space problem between larger structural elements. The controlling Flat Top Anticline is an excellent example of a fold controlled by a well constrained fault in the Precambrian crystalline basement. The basement is bowed upward and outward to the northwest in the hanging wall of the Flat Top Anticline. The purpose of this paper is to describe the geologic structure of the Oil Springs and Flat Top anticlines and their relationship to the Freezeout Hills and the Hanna Basin. Commercial production of petroleum and natural gas occurs on the west flank of the Laramie-Cooper Lake Basin as far north as the northeast corner of the Hanna Basin. Stone reviewed the producing formations in the Laramie and eastern Hanna basins and noted that 11 commercial accumulations of petroleum and natural gas are directly related to anticlinal structures. Production derived from the Permian-Pennsylvanian Tensleep Sandstone in this region has a special geologic framework. Fields that produce from the Tensleep Sandstone are well defined anticlines bounded by faults or fault systems, a situation also reported by Biggs and Espach, Blackstone and in the Wyoming Geological Association Symposium. The Tensleep Sandstone reservoirs in these faulted anticlines are in juxtaposition to potential source rocks of either Jurassic or Cretaceous age in the footwalls of the faults. 17 refs., 9 figs., 1 tab.

  11. 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

  12. 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, ...

  13. Structural geometry, strain distribution, and mechanical evolution of eastern Umtanum Ridge and a comparison with other selected localities within Yakima fold structures, south-central Washington

    SciTech Connect (OSTI)

    Price, E.H.

    1982-01-01T23:59:59.000Z

    The Yakima fold system of south-central Washington and north-central Oregon is a series of megascopic anticlinal ridge of multilayered basalt. Cross-sectional strain analyses were performed at five localities within three anticlines. The analyses show that the strain is consistent both laterally along a fold and within different folds. Folding strain is localized layer-internal faulting, extensive shattering, and limited layer-parallel faulting. Most strain is cataclastic, but glassy flow tops appear to have been more ductile. The strain distributions and structural geometries accord well with a flexural flow buckle model; however, the internal cataclastic flow is not inherently penetrative and limited flexural slip has occurred. This fold model suggests that most strain in the fold is by simple shear and it took place above the topographic surface of adjacent synclinal valleys. Large reverse faults associated with the anticlines are interpreted to be folding strain required by the concentric folding and their displacement is interpreted to have reached the surface late in the folding process. Therefore, the observed strain and its distribution are interpreted to be not directly the result of regional plateau shortening, but of local stresses and resultant strains related to fold geometry. A mechanical analysis of the Umtanum structure termination geometry, combined with slickenside striae movement directions from the study areas suggests that the Palouse slope has behaved as a rigid buttress around which the basalt has rotated clockwise into the folds from the southeast. Compression-box clay modeling of the Yakima fold system within the Pasco Basin shows that the buttress edge orientations control the localization and orientations of buckle folds. Fold orientations and three-dimensional shapes remarkably resembling the Yakima fold system in the Pasco Basin were produced under north-south compression.

  14. 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.

  15. Solar system fault detection

    DOE Patents [OSTI]

    Farrington, R.B.; Pruett, J.C. Jr.

    1984-05-14T23:59:59.000Z

    A fault detecting apparatus and method are provided for use with an active solar system. The apparatus provides an indication as to whether one or more predetermined faults have occurred in the solar system. The apparatus includes a plurality of sensors, each sensor being used in determining whether a predetermined condition is present. The outputs of the sensors are combined in a pre-established manner in accordance with the kind of predetermined faults to be detected. Indicators communicate with the outputs generated by combining the sensor outputs to give the user of the solar system and the apparatus an indication as to whether a predetermined fault has occurred. Upon detection and indication of any predetermined fault, the user can take appropriate corrective action so that the overall reliability and efficiency of the active solar system are increased.

  16. 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...

  17. 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 ...

  18. 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 ...

  19. 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...

  20. 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

  1. 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.

  2. 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

  3. THE INFLUENCE OF FOLD AND FRACTURE DEVELOPMENT ON RESERVOIR BEHAVIOR OF THE LISBURNE GROUP OF NORTHERN ALASKA

    SciTech Connect (OSTI)

    Wesley K. Wallace; Catherine L. Hanks; Jerry Jensen; Michael T. Whalen

    2002-01-01T23:59:59.000Z

    The Carboniferous Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is detachment folded where it is exposed throughout the northeastern Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study are to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults. (2) The influence of folding on fracture patterns. (3) The influence of deformation on fluid flow. (4) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics. The Lisburne in the main axis of the Brooks Range is characteristically deformed into imbricate thrust sheets with asymmetrical hanging wall anticlines and footwall synclines. In contrast, the Lisburne in the northeastern Brooks Range is characterized by symmetrical detachment folds. The focus of our 2000 field studies was at the boundary between these structural styles in the vicinity of Porcupine Lake, in the Arctic National Wildlife Refuge. The northern edge of thrust-truncated folds in Lisburne is marked by a local range front that likely represents an eastward continuation of the central Brooks Range front. This is bounded to the north by a gently dipping panel of Lisburne with local asymmetrical folds. The leading edge of the flat panel is thrust over Permian to Cretaceous rocks in a synclinal depression. These younger rocks overlie symmetrically detachment-folded Lisburne, as is extensively exposed to the north. Six partial sections were measured in the Lisburne of the flat panel and local range front. The Lisburne here is about 700 m thick and is interpreted to consist primarily of the Wachsmuth and Alapah Limestones, with only a thin veneer of Wahoo Limestone. The Wachsmuth (200 m) is gradational between the underlying Missippian Kayak Shale and the overlying Mississippian Alapah, and increases in resistance upward. The Alapah consists of a lower resistant member (100 m) of alternating limestone and chert, a middle recessive member (100 m), and an upper resistant member (260 m) that is similar to Wahoo in the northeastern Brooks Range. The Wahoo is recessive and is thin (30 m) due either to non-deposition or erosion beneath the sub-Permian unconformity. The Lisburne of the area records two major episodes of transgression and shallowing-upward on a carbonate ramp. Thicknesses and facies vary along depositional strike. Asymmetrical folds, mostly truncated by thrust faults, were studied in and south of the local range front. Fold geometry was documented by surveys of four thrust-truncated folds and two folds not visibly cut by thrusts. A portion of the local range front was mapped to document changes in fold geometry along strike in three dimensions. The folds typically display a long, non-folded gently to moderately dipping backlimbs and steep to overturned forelimbs, commonly including parasitic anticline-syncline pairs. Thrusts commonly cut through the anticlinal forelimb or the forward synclinal hinge. These folds probably originated as detachment folds based on their mechanical stratigraphy and the transition to detachment folds to the north. Their geometry indicates that they were asymmetrical prior to thrust truncation. This asymmetry may have favored accommodation of increasing shortening by thrust breakthrough rather than continued folding. Fracture patterns were documented in the gently dipping panel of Lisburne and the asymmetrical folds within it. Four sets of steeply dipping extension fractures were identified, with strikes to the (1) N, (2) E, (3) N to NW, and (4) NE. The relative timing of these fracture sets is complex and unclear. En echelon sets of fractures are common, and display normal or strike-slip sense. Mesoscopic and penetrative structures are locally well developed, and indicate bed-parallel shear within the flat panel and strain within folds. Three sets of normal faults are well developed in the area, and are unusual

  4. 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.

  5. 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.

  6. 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

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

    SciTech Connect (OSTI)

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

    2004-07-01T23:59:59.000Z

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

  8. Transition-fault test generation

    E-Print Network [OSTI]

    Cobb, Bradley Douglas

    2013-02-22T23:59:59.000Z

    . One way to detect these timing defects is to apply test patterns to the integrated circuit that are generated using the transition-fault model. Unfortunately, industry's current transition-fault test generation schemes produce test sets that are too...

  9. Fault tolerant linear actuator

    DOE Patents [OSTI]

    Tesar, Delbert

    2004-09-14T23:59:59.000Z

    In varying embodiments, the fault tolerant linear actuator of the present invention is a new and improved linear actuator with fault tolerance and positional control that may incorporate velocity summing, force summing, or a combination of the two. In one embodiment, the invention offers a velocity summing arrangement with a differential gear between two prime movers driving a cage, which then drives a linear spindle screw transmission. Other embodiments feature two prime movers driving separate linear spindle screw transmissions, one internal and one external, in a totally concentric and compact integrated module.

  10. Computer hardware fault administration

    DOE Patents [OSTI]

    Archer, Charles J. (Rochester, MN); Megerian, Mark G. (Rochester, MN); Ratterman, Joseph D. (Rochester, MN); Smith, Brian E. (Rochester, MN)

    2010-09-14T23:59:59.000Z

    Computer hardware fault administration carried out in a parallel computer, where the parallel computer includes a plurality of compute nodes. The compute nodes are coupled for data communications by at least two independent data communications networks, where each data communications network includes data communications links connected to the compute nodes. Typical embodiments carry out hardware fault administration by identifying a location of a defective link in the first data communications network of the parallel computer and routing communications data around the defective link through the second data communications network of the parallel computer.

  11. Topology to geometry in protein folding: -Lactoglobulin

    E-Print Network [OSTI]

    Berry, R. Stephen

    Topology to geometry in protein folding: -Lactoglobulin Ariel Ferna´ndez* , Andre´s Colubri , and R angles and at the -carbon atoms of the peptide backbone dominate protein folding. Next in importance

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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 Sölvegatan 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

  20. Fault Tolerant Quantum Filtering and Fault Detection for Quantum Systems

    E-Print Network [OSTI]

    Qing Gao; Daoyi Dong; Ian R. Petersen

    2015-04-26T23:59:59.000Z

    This paper aims to determine the fault tolerant quantum filter and fault detection equation for a class of open quantum systems coupled to laser fields and subject to stochastic faults. In order to analyze open quantum systems where the system dynamics involve both classical and quantum random variables, a quantum-classical probability space model is developed. Using a reference probability approach, a fault tolerant quantum filter and a fault detection equation are simultaneously derived for this class of open quantum systems. An example of two-level open quantum systems subject to Poisson-type faults is presented to illustrate the proposed method. These results have the potential to lead to a new fault tolerant control theory for quantum systems.

  1. Row fault detection system

    DOE Patents [OSTI]

    Archer, Charles Jens (Rochester, MN); Pinnow, Kurt Walter (Rochester, MN); Ratterman, Joseph D. (Rochester, MN); Smith, Brian Edward (Rochester, MN)

    2010-02-23T23:59:59.000Z

    An apparatus and program product check for nodal faults in a row of nodes by causing each node in the row to concurrently communicate with its adjacent neighbor nodes in the row. The communications are analyzed to determine a presence of a faulty node or connection.

  2. Row fault detection system

    DOE Patents [OSTI]

    Archer, Charles Jens (Rochester, MN); Pinnow, Kurt Walter (Rochester, MN); Ratterman, Joseph D. (Rochester, MN); Smith, Brian Edward (Rochester, MN)

    2012-02-07T23:59:59.000Z

    An apparatus, program product and method check for nodal faults in a row of nodes by causing each node in the row to concurrently communicate with its adjacent neighbor nodes in the row. The communications are analyzed to determine a presence of a faulty node or connection.

  3. Characteristics of displacement transfer zones associated with thrust faults / by Arthur Francis Xavier O'Keefe

    E-Print Network [OSTI]

    O'Keefe, Arthur Francis Xavier

    1980-01-01T23:59:59.000Z

    back limb fault and then develops into s. drag fold on the underlying plate. The lower thrust dies by losing displacement until it becomes a fore-limb . hrust in a mino" anticline which plunges out under . he higher thrust (Figure 2). drag olo... is compared with two physical models developed by Gardner and Spang (1973). Their fi. st model involves a conical fold in the upper plate of the lowez- thzust with the point of the cone at the termination of the higher thrust . The fold then opens along...

  4. 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.

  5. Evaluating the Effectiveness of Fault Tolerance in Replicated Database Management Systems

    E-Print Network [OSTI]

    -Olaf.Hvasshovd@idi.ntnu.no Abstract Database management systems (DBMS) achieve high availabilityand faulttolerance usuallyby of this study is two-fold. It eval- uates the effectiveness of DBMS fault tolerance in the pres- ence on database integrity, performance, and availability on a replicated DBMS, ClustRa[6], in the presence

  6. 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

  7. 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

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

    E-Print Network [OSTI]

    Paris-Sud XI, Université 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

  9. 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.

  10. 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

  11. Folding amphipathic helices into membranes: Amphiphilicity trumps hydrophobicity

    E-Print Network [OSTI]

    Fernández-Vidal, Mónica; 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

  12. 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

  13. 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.

  14. Stress and fault rock controls on fault zone hydrology, Coso...

    Open Energy Info (EERE)

    rock controls on fault zone hydrology, Coso geothermal field, CA Abstract In crystalline rock of the Coso Geothermal Field, CA, fractures are the primary source of permeability....

  15. 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.

  16. Fault interaction near Hollister, California

    SciTech Connect (OSTI)

    Mavko, G.M.

    1982-09-10T23:59:59.000Z

    A numerical model is used to study fault stress slip near Hollister, California. The geometrically complex system of interacting faults, including the San Andreas, Calaveras, Sargent, and Busch faults, is approximated with a two-dimensional distribution of short planar fault segments in an elastic medium. The steady stress and slip rate are simulated by specifying frictional strength and stepping the remote stress ahead in time. The resulting computed fault stress is roughly proportional to the observed spatial density of small earthquakes, suggesting that the distinction between segments characterized by earthquakes and those with aseismic creep results, in part, from geometry. A nonsteady simulation is made by introducing, in addition, stress drops for individual moderate earthquakes. A close fit of observed creep with calculated slip on the Calaveras and San Andreas faults suggests that many changes in creep rate (averaged over several months) are caused by local moderate earthquakes. In particular, a 3-year creep lag preceding the August 6, 1979, Coyote Lake earthquake on the Calaveras fault seems to have been a direct result of the November 28, 1974, Thanksgiving Day earthquake on the Busch fault. Computed lags in slip rate preceding some other moderate earthquakes in the area are also due to earlier earthquakes. Although the response of the upper 1 km of the fault zone may cause some individual creep events and introduce delays in others, the long-term rate appears to reflect deep slip.

  17. Fault current limiter

    DOE Patents [OSTI]

    Darmann, Francis Anthony

    2013-10-08T23:59:59.000Z

    A fault current limiter (FCL) includes a series of high permeability posts for collectively define a core for the FCL. A DC coil, for the purposes of saturating a portion of the high permeability posts, surrounds the complete structure outside of an enclosure in the form of a vessel. The vessel contains a dielectric insulation medium. AC coils, for transporting AC current, are wound on insulating formers and electrically interconnected to each other in a manner such that the senses of the magnetic field produced by each AC coil in the corresponding high permeability core are opposing. There are insulation barriers between phases to improve dielectric withstand properties of the dielectric medium.

  18. Fault Current Limiters

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742Energy Chinaof EnergyImpactOnSTATEMENT OF DAVID GEISEREnergy1DNVDOE'sUAfter 12Fault

  19. 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

  20. Observer-based fault detection for nuclear reactors

    E-Print Network [OSTI]

    Li, Qing, 1972-

    2001-01-01T23:59:59.000Z

    This is a study of fault detection for nuclear reactor systems. Basic concepts are derived from fundamental theories on system observers. Different types of fault- actuator fault, sensor fault, and system dynamics fault ...

  1. 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.

  2. 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

  3. Colorado Regional Faults

    SciTech Connect (OSTI)

    Hussein, Khalid

    2012-02-01T23:59:59.000Z

    Citation Information: Originator: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Originator: Colorado Geological Survey (CGS) Publication Date: 2012 Title: Regional Faults Edition: First Publication Information: Publication Place: Earth Science & Observation Center, Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder Publisher: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Description: This layer contains the regional faults of Colorado Spatial Domain: Extent: Top: 4543192.100000 m Left: 144385.020000 m Right: 754585.020000 m Bottom: 4094592.100000 m Contact Information: Contact Organization: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Contact Person: Khalid Hussein Address: CIRES, Ekeley Building Earth Science & Observation Center (ESOC) 216 UCB City: Boulder State: CO Postal Code: 80309-0216 Country: USA Contact Telephone: 303-492-6782 Spatial Reference Information: Coordinate System: Universal Transverse Mercator (UTM) WGS’1984 Zone 13N False Easting: 500000.00000000 False Northing: 0.00000000 Central Meridian: -105.00000000 Scale Factor: 0.99960000 Latitude of Origin: 0.00000000 Linear Unit: Meter Datum: World Geodetic System 1984 (WGS ’984) Prime Meridian: Greenwich Angular Unit: Degree Digital Form: Format Name: Shape file

  4. Synchronized sampling improves fault location

    SciTech Connect (OSTI)

    Kezunovic, M. [Texas A and M Univ., College Station, TX (United States)] [Texas A and M Univ., College Station, TX (United States); Perunicic, B. [Lamar Univ., Beaumont, TX (United States)] [Lamar Univ., Beaumont, TX (United States)

    1995-04-01T23:59:59.000Z

    Transmission line faults must be located accurately to allow maintenance crews to arrive at the scene and repair the faulted section as soon as possible. Rugged terrain and geographical layout cause some sections of power transmission lines to be difficult to reach. In the past, a variety of fault location algorithms were introduced as either an add-on feature in protective relays or stand-alone implementation in fault locators. In both cases, the measurements of current and voltages were taken at one terminal of a transmission line only. Under such conditions, it may become difficult to determine the fault location accurately, since data from other transmission line ends are required for more precise computations. In the absence of data from the other end, existing algorithms have accuracy problems under several circumstances, such as varying switching and loading conditions, fault infeed from the other end, and random value of fault resistance. Most of the one-end algorithms were based on estimation of voltage and current phasors. The need to estimate phasors introduces additional difficulty in high-speed tripping situations where the algorithms may not be fast enough in determining fault location accurately before the current signals disappear due to the relay operation and breaker opening. This article introduces a unique concept of high-speed fault location that can be implemented either as a simple add-on to the digital fault recorders (DFRs) or as a stand-alone new relaying function. This advanced concept is based on the use of voltage and current samples that are synchronously taken at both ends of a transmission line. This sampling technique can be made readily available in some new DFR designs incorporating receivers for accurate sampling clock synchronization using the satellite Global Positioning System (GPS).

  5. 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.

  6. Automated Fault Location In Smart Distribution Systems 

    E-Print Network [OSTI]

    Lotfifard, Saeed

    2012-10-19T23:59:59.000Z

    ............................................................................................................................ 88 x LIST OF FIGURES Page Figure 1 Multiple possible fault location estimation for a fault at node A ........................ 7 Figure 2 Simple faulted network model [1] © [2011] IEEE ............................................ 40 Figure 3... Types C and D voltage sags for different phases [51] © [2003] IEEE .............. 42 Figure 4 Rf estimation procedure [1] © [2011] IEEE ...................................................... 45 Figure 5 Flow chart of the fault location algorithm [1...

  7. Hot Pot Detail - Evidence of Quaternary Faulting

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

    Lane, Michael

    Compilation of published data, field observations and photo interpretation relevant to Quaternary faulting at Hot Pot.

  8. Hot Pot Detail - Evidence of Quaternary Faulting

    SciTech Connect (OSTI)

    Lane, Michael

    2013-06-27T23:59:59.000Z

    Compilation of published data, field observations and photo interpretation relevant to Quaternary faulting at Hot Pot.

  9. Arc fault detection system

    DOE Patents [OSTI]

    Jha, Kamal N. (Bethel Park, PA)

    1999-01-01T23:59:59.000Z

    An arc fault detection system for use on ungrounded or high-resistance-grounded power distribution systems is provided which can be retrofitted outside electrical switchboard circuits having limited space constraints. The system includes a differential current relay that senses a current differential between current flowing from secondary windings located in a current transformer coupled to a power supply side of a switchboard, and a total current induced in secondary windings coupled to a load side of the switchboard. When such a current differential is experienced, a current travels through a operating coil of the differential current relay, which in turn opens an upstream circuit breaker located between the switchboard and a power supply to remove the supply of power to the switchboard.

  10. Arc fault detection system

    DOE Patents [OSTI]

    Jha, K.N.

    1999-05-18T23:59:59.000Z

    An arc fault detection system for use on ungrounded or high-resistance-grounded power distribution systems is provided which can be retrofitted outside electrical switchboard circuits having limited space constraints. The system includes a differential current relay that senses a current differential between current flowing from secondary windings located in a current transformer coupled to a power supply side of a switchboard, and a total current induced in secondary windings coupled to a load side of the switchboard. When such a current differential is experienced, a current travels through a operating coil of the differential current relay, which in turn opens an upstream circuit breaker located between the switchboard and a power supply to remove the supply of power to the switchboard. 1 fig.

  11. 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

  12. 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

  13. 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

  14. 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

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

    E-Print Network [OSTI]

    Paris-Sud XI, Université 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

  16. Relationship of compaction bands in Utah to Laramide fault-related folding Richard A. Schultz

    E-Print Network [OSTI]

    Geomechanics--Rock Fracture Group, Department of Geological Sciences and Engineering/172, University of Nevada localization in rock that can impede subsurface uid ow and thus are also important to groundwater and petroleum

  17. 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

  18. 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 ...

  19. 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.

  20. 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 ...

  1. 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.

  2. 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.

  3. 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^{\

  4. Internal structure of the Kern Canyon Fault, California: a deeply exhumed strike-slip fault

    E-Print Network [OSTI]

    Neal, Leslie Ann

    2002-01-01T23:59:59.000Z

    Deformation and mineral alteration adjacent to a 2 km long segment of the Kern Canyon fault near Lake Isabella, California are studied to characterize the internal structure of the fault zone and to understand the development of fault structure...

  5. Fault-tolerant rotary actuator

    SciTech Connect (OSTI)

    Tesar, Delbert

    2006-10-17T23:59:59.000Z

    A fault-tolerant actuator module, in a single containment shell, containing two actuator subsystems that are either asymmetrically or symmetrically laid out is provided. Fault tolerance in the actuators of the present invention is achieved by the employment of dual sets of equal resources. Dual resources are integrated into single modules, with each having the external appearance and functionality of a single set of resources.

  6. 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

  7. 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

  8. 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

  9. 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

  10. Development of Characterization Technology for Fault Zone Hydrology

    E-Print Network [OSTI]

    Karasaki, Kenzi

    2010-01-01T23:59:59.000Z

    TECHNOLOGY FOR FAULT ZONE HYDROLOGY Kenzi Karasaki Lawrencefor characterizing the hydrology of fault zones, recognizingstructure of faults to hydrology, that it still may be

  11. active fault diagnosis: Topics by E-print Network

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

    Harrold, Mary Jean 453 Fault Tolerant Control with Additive Compensation for Faults in an Automotive Damper Physics Websites Summary: Fault Tolerant Control with Additive...

  12. Passive fault current limiting device

    DOE Patents [OSTI]

    Evans, Daniel J. (Wheeling, IL); Cha, Yung S. (Darien, IL)

    1999-01-01T23:59:59.000Z

    A passive current limiting device and isolator is particularly adapted for use at high power levels for limiting excessive currents in a circuit in a fault condition such as an electrical short. The current limiting device comprises a magnetic core wound with two magnetically opposed, parallel connected coils of copper, a high temperature superconductor or other electrically conducting material, and a fault element connected in series with one of the coils. Under normal operating conditions, the magnetic flux density produced by the two coils cancel each other. Under a fault condition, the fault element is triggered to cause an imbalance in the magnetic flux density between the two coils which results in an increase in the impedance in the coils. While the fault element may be a separate current limiter, switch, fuse, bimetal strip or the like, it preferably is a superconductor current limiter conducting one-half of the current load compared to the same limiter wired to carry the total current of the circuit. The major voltage during a fault condition is in the coils wound on the common core in a preferred embodiment.

  13. Passive fault current limiting device

    DOE Patents [OSTI]

    Evans, D.J.; Cha, Y.S.

    1999-04-06T23:59:59.000Z

    A passive current limiting device and isolator is particularly adapted for use at high power levels for limiting excessive currents in a circuit in a fault condition such as an electrical short. The current limiting device comprises a magnetic core wound with two magnetically opposed, parallel connected coils of copper, a high temperature superconductor or other electrically conducting material, and a fault element connected in series with one of the coils. Under normal operating conditions, the magnetic flux density produced by the two coils cancel each other. Under a fault condition, the fault element is triggered to cause an imbalance in the magnetic flux density between the two coils which results in an increase in the impedance in the coils. While the fault element may be a separate current limiter, switch, fuse, bimetal strip or the like, it preferably is a superconductor current limiter conducting one-half of the current load compared to the same limiter wired to carry the total current of the circuit. The major voltage during a fault condition is in the coils wound on the common core in a preferred embodiment. 6 figs.

  14. 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

  15. 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.

  16. 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,...

  17. 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

  18. 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...

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Condition Assessment and Fault Prognostics of Microelectromechanical Systems

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    monitoring, Condition assessment, Fault detection, Fault diagnostics, Fault prognostics. Corresponding, batteries, etc.) to complete machines (wind turbines, electrical motors, machining tools, etc.). SeveralCondition Assessment and Fault Prognostics of Microelectromechanical Systems K. Medjaher , H. Skima

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. Sensor Fault Detection and Isolation System

    E-Print Network [OSTI]

    Yang, Cheng-Ken

    2014-08-01T23:59:59.000Z

    The purpose of this research is to develop a Fault Detection and Isolation (FDI) system which is capable to diagnosis multiple sensor faults in nonlinear cases. In order to lead this study closer to real world applications in oil industries...

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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...

  2. 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.

  3. A Rectilinear-Monotone Polygonal Fault Block Model for Fault-Tolerant Minimal Routing

    E-Print Network [OSTI]

    Wang, Dajin

    ]. In rectangular model, all faulty nodes are grouped in dis- jointed, rectangular areas, called fault blocksA Rectilinear-Monotone Polygonal Fault Block Model for Fault-Tolerant Minimal Routing in Mesh Dajin Wang, Member, IEEE Abstract--We propose a new fault block model, Minimal-Connected-Component (MCC

  4. 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

  5. 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. Gâ??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

  6. FAULT & COORDINATION STUDY FOR T PLANT COMPLEX

    SciTech Connect (OSTI)

    MCDONALD, G.P.; BOYD-BODIAU, E.A.

    2004-09-01T23:59:59.000Z

    A short circuit study is performed to determine the maximum fault current that the system protective devices, transformers, and interconnections would he subject to in event of a three phase, phase-to-phase, or phase-to-ground fault. Generally, the short circuit study provides the worst case fault current levels at each bus or connection point of the system.

  7. High temperature superconducting fault current limiter

    DOE Patents [OSTI]

    Hull, J.R.

    1997-02-04T23:59:59.000Z

    A fault current limiter for an electrical circuit is disclosed. The fault current limiter includes a high temperature superconductor in the electrical circuit. The high temperature superconductor is cooled below its critical temperature to maintain the superconducting electrical properties during operation as the fault current limiter. 15 figs.

  8. High temperature superconducting fault current limiter

    DOE Patents [OSTI]

    Hull, John R. (Hinsdale, IL)

    1997-01-01T23:59:59.000Z

    A fault current limiter (10) for an electrical circuit (14). The fault current limiter (10) includes a high temperature superconductor (12) in the electrical circuit (14). The high temperature superconductor (12) is cooled below its critical temperature to maintain the superconducting electrical properties during operation as the fault current limiter (10).

  9. Using Fault Model Enforcement to Improve Availability

    E-Print Network [OSTI]

    instead that a new approach, called fault model enforcement, that maps actual faults to expected faults on a constellation of interconnected systems--a typical example is cluster-based systems [4]. Traditional database centers around a set of closely guarded racks and data closets woven together by intricate networks

  10. Using Fault Model Enforcement to Improve Availability

    E-Print Network [OSTI]

    Martin, Richard P.

    that a new approach, called fault model enforcement, that maps actual faults to expected faults on a constellation of interconnected systems--a typical example is cluster-based systems [4]. Traditional database centers around a set of closely guarded racks and data closets woven together by intricate networks

  11. Cell boundary fault detection system

    DOE Patents [OSTI]

    Archer, Charles Jens (Rochester, MN); Pinnow, Kurt Walter (Rochester, MN); Ratterman, Joseph D. (Rochester, MN); Smith, Brian Edward (Rochester, MN)

    2011-04-19T23:59:59.000Z

    An apparatus and program product determine a nodal fault along the boundary, or face, of a computing cell. Nodes on adjacent cell boundaries communicate with each other, and the communications are analyzed to determine if a node or connection is faulty.

  12. Software Fault Diagnosis Peter Zoeteweij

    E-Print Network [OSTI]

    Zoeteweij, Peter

    Lab, Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University-to-day basis is constantly growing. Combined with a practically constant rate of faults per line of code in the software development cycle, which aim at exposing such discrepancies. In this context, automated diagnosis

  13. Development of a bridge fault extractor tool

    E-Print Network [OSTI]

    Bhat, Nandan D.

    2005-02-17T23:59:59.000Z

    as interlayer faults. An example of an intralayer fault is a bridge between two adjacent metal1 lines. An example of an interlayer fault is a short between overlapping polysilicon and metal1 lines. The rest of this thesis is organized as follows: Chapter 2... between two adjacent 6 metal1 lines. An example of an interlayer fault is a short between overlapping polysilicon and metal1 lines. A recent survey of fault extractors describes their different features [15]. Some tools such as VLASIC [16] attempt...

  14. 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.

  15. 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...

  16. 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.

  17. The detection of high impedance faults using random fault behavior

    E-Print Network [OSTI]

    Carswell, Patrick Wayne

    1988-01-01T23:59:59.000Z

    In response to an Electric Power Research Institute (EPRI) request for pro- posed solutions for the detection of high impedance faults, the Hughes Aircraft Corporation developed a detection technique based solely on the level of the third harmonic current... for proposed solutions from EPRI that brought the Hughes technique, Power Technologies Incorporated (PTI) proposed a technique which statistically monitors the first, third, and fifth harmonics of current to make a, determination as to the presence of a high...

  18. Development of secondary faults between en echelon, oblique-slip faults: examples from basement controlled, small-fault systems in the Llano Uplift of central Texas

    E-Print Network [OSTI]

    Hedgcoxe, Howard Reiffert

    1987-01-01T23:59:59.000Z

    correspond to the NE trending set of faults and the secondary antithetic faults corre- spond to the N to NNE set (Figure 12). Fractures, represented by the dashed lines in Figure 12, occur in direct association with the primary and secondary faults...DEVELOPMENT OF SECONDARY FAULTS BETWEEN EN ECHELON, OBLIQUE-SLIP FAULTS: EXAMPLES FROM BASEMENT CONTROLLED, SMALL-FAULT SYSTEMS IN THE LLANO UPLIFT OF CENTRAL TEXAS A Thesis by HOWARD REIFFERT HEDGCOXE Submitted to the Graduate College...

  19. New Crystal Structures Lift Fog around Protein Folding

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

    New Crystal Structures Lift Fog around Protein Folding New Crystal Structures Lift Fog around Protein Folding Print Wednesday, 25 July 2012 00:00 Nature's proteins set a high bar...

  20. 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...

  1. 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...

  2. 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

  3. 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

  4. 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...

  5. 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

  6. 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 µs and sample) measurements of single-stranded DNA. We also demon- strate the feasibility of measuring fast protein folding

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. Fault prophet : a fault injection tool for large scale computer systems

    E-Print Network [OSTI]

    Tchwella, Tal

    2014-01-01T23:59:59.000Z

    In this thesis, I designed and implemented a fault injection tool, to study the impact of soft errors for large scale systems. Fault injection is used as a mechanism to simulate soft errors, measure the output variability ...

  3. Realistic fault modeling and quality test generation of combined delay faults 

    E-Print Network [OSTI]

    Thadhlani, Ajaykumar A

    2001-01-01T23:59:59.000Z

    With increasing operating speed and shrinking technology, timing defects in integrated circuits are becoming increasingly important. The well established stuck-at-fault model is not sufficient because it is a static fault ...

  4. Collateral damage: Evolution with displacement of fracture distribution and secondary fault strands in fault damage zones

    E-Print Network [OSTI]

    Savage, Heather M.; Brodsky, Emily E.

    2011-01-01T23:59:59.000Z

    E. McCallum (1999), Reservoir damage around faults: OutcropSkar (2005), Controls on damage zone asymmetry of a normal2007), The evolution of the damage zone with fault growth in

  5. Collateral damage: Evolution with displacement of fracture distribution and secondary fault strands in fault damage zones

    E-Print Network [OSTI]

    Savage, Heather M.; Brodsky, Emily E.

    2011-01-01T23:59:59.000Z

    8 m fault 14 m fault Lonewolf Wadi Araba Carboneras Caletasiltstone, conglomerate Wadi As Sir Limestone gneiss schistFaulkner et al. , 2003], and Wadi Araba [Du Bernard et al. ,

  6. Fault-tolerant dynamic task graph scheduling

    SciTech Connect (OSTI)

    Kurt, Mehmet C.; Krishnamoorthy, Sriram; Agrawal, Kunal; Agrawal, Gagan

    2014-11-16T23:59:59.000Z

    In this paper, we present an approach to fault tolerant execution of dynamic task graphs scheduled using work stealing. In particular, we focus on selective and localized recovery of tasks in the presence of soft faults. We elicit from the user the basic task graph structure in terms of successor and predecessor relationships. The work stealing-based algorithm to schedule such a task graph is augmented to enable recovery when the data and meta-data associated with a task get corrupted. We use this redundancy, and the knowledge of the task graph structure, to selectively recover from faults with low space and time overheads. We show that the fault tolerant design retains the essential properties of the underlying work stealing-based task scheduling algorithm, and that the fault tolerant execution is asymptotically optimal when task re-execution is taken into account. Experimental evaluation demonstrates the low cost of recovery under various fault scenarios.

  7. 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.

  8. Automated Fault Location In Smart Distribution Systems

    E-Print Network [OSTI]

    Lotfifard, Saeed

    2012-10-19T23:59:59.000Z

    Quality Meters (PQM), are installed to capture harmonics and certain disturbances for analyzing the power quality indices. Digital Protective Relays are utilized to detect occurrence of the faults and isolate faulted section as fast as possible. Digital... Protective Relays) use synchronous methods [28]. Therefore, if the available data is provided by RTUs, fault location methods that operate based on direct comparison of the input samples cannot be 17 utilized. However, if the data could be gathered from...

  9. Detachment Faulting & Geothermal Resources - Pearl Hot Spring...

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

    Faulting & Geothermal Resources - Pearl Hot Spring, NV Conducting a 3D Converted Shear Wave Project to Reduce Exploration Risk at Wister, CA Crump Geyser: High Precision...

  10. Towards Fault-Tolerant Digital Microfluidic Lab-on-Chip: Defects, Fault Modeling, Testing, and Reconfiguration

    E-Print Network [OSTI]

    Chakrabarty, Krishnendu

    Towards Fault-Tolerant Digital Microfluidic Lab-on-Chip: Defects, Fault Modeling, Testing, NC 27708, USA Abstract Dependability is an important attribute for microfluidic lab-on-chip devices microfluidic lab-on-chip systems. Defects are related to logical fault models that can be viewed not only

  11. Contribution of Identified Active Faults to Near Fault Seismic Hazard in the Flinders Ranges

    E-Print Network [OSTI]

    Sandiford, Mike

    Somerville1 , Peggy Quijada1 , Hong Kie Thio1 , Mike Sandiford2 and Mark Quigley2 1. URS Corporation estimates of fault slip rate from Quigley et al. (2006) to quantify the seismic activity rate on the faults of these models was used in conjunction with the active fault model. Quigley et al. (2006) identified a system

  12. A fault location approach for fuzzy fault section estimation on radial distribution feeders

    E-Print Network [OSTI]

    Andoh, Kwame Sarpong

    2000-01-01T23:59:59.000Z

    was involved in the fault was evaluated using the event-phase possibility values and line section phase topology information. The fault distance algorithm was used to eliminate sections of the feeder that were not likely to be possible faulted section...

  13. Shallow faults mapped with seismic reflections: Lost River Fault, Idaho

    E-Print Network [OSTI]

    Mubarik, Ali; Miller, Richard D.; Steeples, Don W.

    1991-09-01T23:59:59.000Z

    stations 132 and 160. Total bedrock dis?lace- ment interpreted along this seismic survey line is approxa- mately 6 m, representing 4 to 6 times more displacement than is observed on either the common offset refraction section or at the surface..., vol. A, U.S. Geological Survey Open-file Report 85-290, 182-194, 1985. Crone, A. J., and M. N. Macbette, Surface faulting accompa- nying the Borah Peak earthquake, central Idaho, Geology, 12, 664-667, 1984. Crone, A. J., M. N. Macbette, M. G...

  14. Accurate resistive bridge fault modeling, simulation, and test generation 

    E-Print Network [OSTI]

    Sar-Dessai, Vijay Ramesh

    1999-01-01T23:59:59.000Z

    Resistive bridging faults in CMOS combinational circuits are studied in this work. Bridging faults are modeled using HSPICE circuit simulation of the various types of bridging faults that can occur in CMOS combinational ...

  15. Earthquake behavior and structure of oceanic transform faults

    E-Print Network [OSTI]

    Roland, Emily Carlson

    2012-01-01T23:59:59.000Z

    Oceanic transform faults that accommodate strain at mid-ocean ridge offsets represent a unique environment for studying fault mechanics. Here, I use seismic observations and models to explore how fault structure affects ...

  16. Low-cost motor drive embedded fault diagnosis systems

    E-Print Network [OSTI]

    Akin, Bilal

    2009-05-15T23:59:59.000Z

    Electric motors are used widely in industrial manufacturing plants. Bearing faults, insulation faults, and rotor faults are the major causes of electric motor failures. Based on the line current analysis, this dissertation mainly deals with the low...

  17. Accurate resistive bridge fault modeling, simulation, and test generation

    E-Print Network [OSTI]

    Sar-Dessai, Vijay Ramesh

    1999-01-01T23:59:59.000Z

    Resistive bridging faults in CMOS combinational circuits are studied in this work. Bridging faults are modeled using HSPICE circuit simulation of the various types of bridging faults that can occur in CMOS combinational circuits. The results...

  18. 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

  19. 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

  20. 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

  1. 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). [

  2. 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

  3. 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:

  4. Off-fault Damage Associated with a Localized Bend in the North Branch San Gabriel Fault, California

    E-Print Network [OSTI]

    Becker, Andrew 1987-

    2012-08-15T23:59:59.000Z

    Structures within very large displacement, mature fault zones, such as the North Branch San Gabriel Fault (NBSGF), are the product of a complex combination of processes. Off-fault damage within a damage zone and first-order geometric asperities...

  5. Improving Distribution System Reliability Through Risk-base Doptimization of Fault Management and Improved Computer-based Fault Location

    E-Print Network [OSTI]

    Dong, Yimai

    2013-11-07T23:59:59.000Z

    )’s regulation on power quality. Optimization in fault management tasks has the potential of improving system reliability by reducing the duration and scale of outages caused by faults through fast fault isolation and service restoration. The research reported...

  6. Evaluation of faulting characteristics and ground acceleration associated with recent movement along the Meers Fault, Southwestern Oklahoma

    E-Print Network [OSTI]

    Burrell, Richard Dennis

    1997-01-01T23:59:59.000Z

    Recent studies have shown that a 27 km section of the Meers Fault was reactivated during Holocene time. Although these studies have proven the occurrence of recent fault activity, many basic characteristics of the faulting remain unresolved...

  7. An algorithm for faulted phase and feeder selection under high impedance fault conditions

    E-Print Network [OSTI]

    Benner, Carl Lee

    1988-01-01T23:59:59.000Z

    proximate lines served by the same substation. Because of this signal propagation, a fault will be detected simultaneously on the faulted line and possibly several other lines served by the substation. Since it would not be plausible for a utility company... to deenergize the entire area served by a substation due to a high impedance fault on one lateral, a technique is needed to discriminate the faulted line from neighboring healthy feeders and healthy phases of the faulted feeder. Such a technique would also...

  8. active fault segments: Topics by E-print Network

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

    Fault activation Kuzmanov, Georgi 140 Early stage evolution of growth faults: 3D seismic insights from the Levant Basin, Eastern Mediterranean Materials Science Websites...

  9. Modeling and Measurement Constraints in Fault Diagnostics for HVAC Systems

    E-Print Network [OSTI]

    Najafi, Massieh

    2010-01-01T23:59:59.000Z

    in Fault Diagnostics for HVAC Systems Massieh Najafi 1 ,tools for determining HVAC diagnostics, methods todetect faults in HVAC systems are still generally

  10. Fault-tolerant TCP mechanisms 

    E-Print Network [OSTI]

    Satapati, Suresh Kumar

    2000-01-01T23:59:59.000Z

    point (TSAPs). In BSD, a service access point is a TCP socket identified by an IP address and port number, A TCP based fault-tolerant service is realized by replicating a server program onto one or more hosts and by having all replicas bind... backup sends the SEQUENCE NUMBER of the segment it recently sent. Since the primary server doesn't exist, the client does not acknowledge. The TCP on backup server keeps retransmitting the same segment, which can be counted to initiate a...

  11. Fault Controlled | 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,DOEHazelPennsylvania: EnergyExolisFairway,FarmersFastcap SystemsShear Zone:Fault

  12. Spatial analysis of hypocenter to fault relationships for determining fault process zone width in Japan.

    SciTech Connect (OSTI)

    Arnold, Bill Walter; Roberts, Barry L.; McKenna, Sean Andrew; Coburn, Timothy C. (Abilene Christian University, Abilene, TX)

    2004-09-01T23:59:59.000Z

    Preliminary investigation areas (PIA) for a potential repository of high-level radioactive waste must be evaluated by NUMO with regard to a number of qualifying factors. One of these factors is related to earthquakes and fault activity. This study develops a spatial statistical assessment method that can be applied to the active faults in Japan to perform such screening evaluations. This analysis uses the distribution of seismicity near faults to define the width of the associated process zone. This concept is based on previous observations of aftershock earthquakes clustered near active faults and on the assumption that such seismic activity is indicative of fracturing and associated impacts on bedrock integrity. Preliminary analyses of aggregate data for all of Japan confirmed that the frequency of earthquakes is higher near active faults. Data used in the analysis were obtained from NUMO and consist of three primary sources: (1) active fault attributes compiled in a spreadsheet, (2) earthquake hypocenter data, and (3) active fault locations. Examination of these data revealed several limitations with regard to the ability to associate fault attributes from the spreadsheet to locations of individual fault trace segments. In particular, there was no direct link between attributes of the active faults in the spreadsheet and the active fault locations in the GIS database. In addition, the hypocenter location resolution in the pre-1983 data was less accurate than for later data. These pre-1983 hypocenters were eliminated from further analysis.

  13. Physiochemical Evidence of Faulting Processes and Modeling of Fluid in Evolving Fault Systems in Southern California

    SciTech Connect (OSTI)

    Boles, James [Professor

    2013-05-24T23:59:59.000Z

    Our study targets recent (Plio-Pleistocene) faults and young (Tertiary) petroleum fields in southern California. Faults include the Refugio Fault in the Transverse Ranges, the Ellwood Fault in the Santa Barbara Channel, and most recently the Newport- Inglewood in the Los Angeles Basin. Subsurface core and tubing scale samples, outcrop samples, well logs, reservoir properties, pore pressures, fluid compositions, and published structural-seismic sections have been used to characterize the tectonic/diagenetic history of the faults. As part of the effort to understand the diagenetic processes within these fault zones, we have studied analogous processes of rapid carbonate precipitation (scaling) in petroleum reservoir tubing and manmade tunnels. From this, we have identified geochemical signatures in carbonate that characterize rapid CO2 degassing. These data provide constraints for finite element models that predict fluid pressures, multiphase flow patterns, rates and patterns of deformation, subsurface temperatures and heat flow, and geochemistry associated with large fault systems.

  14. Optimized Fault Location Final Project Report

    E-Print Network [OSTI]

    Engineering Research Center Optimized Fault Location Concurrent Technologies Corporation Final Project Report by the Concurrent Technologies Corporation (CTC) and the Power Systems Engineering Research Center (PSERC). NeitherOptimized Fault Location Final Project Report Power Systems Engineering Research Center A National

  15. Sensor Fault Diagnosis Using Principal Component Analysis 

    E-Print Network [OSTI]

    Sharifi, Mahmoudreza

    2010-07-14T23:59:59.000Z

    The purpose of this research is to address the problem of fault diagnosis of sensors which measure a set of direct redundant variables. This study proposes: 1. A method for linear senor fault diagnosis 2. An analysis of isolability and detectability...

  16. Sensor Fault Diagnosis Using Principal Component Analysis

    E-Print Network [OSTI]

    Sharifi, Mahmoudreza

    2010-07-14T23:59:59.000Z

    The purpose of this research is to address the problem of fault diagnosis of sensors which measure a set of direct redundant variables. This study proposes: 1. A method for linear senor fault diagnosis 2. An analysis of isolability and detectability...

  17. INDUCTION MOTOR FAULT DIAGNOSTIC AND MONITORING METHODS

    E-Print Network [OSTI]

    Povinelli, Richard J.

    INDUCTION MOTOR FAULT DIAGNOSTIC AND MONITORING METHODS by Aderiano M. da Silva, B.S. A Thesis;i Abstract Induction motors are used worldwide as the "workhorse" in industrial applications material. However, induction motor faults can be detected in an initial stage in order to prevent

  18. Self-triggering superconducting fault current limiter

    DOE Patents [OSTI]

    Yuan, Xing (Albany, NY); Tekletsadik, Kasegn (Rexford, NY)

    2008-10-21T23:59:59.000Z

    A modular and scaleable Matrix Fault Current Limiter (MFCL) that functions as a "variable impedance" device in an electric power network, using components made of superconducting and non-superconducting electrically conductive materials. The matrix fault current limiter comprises a fault current limiter module that includes a superconductor which is electrically coupled in parallel with a trigger coil, wherein the trigger coil is magnetically coupled to the superconductor. The current surge doing a fault within the electrical power network will cause the superconductor to transition to its resistive state and also generate a uniform magnetic field in the trigger coil and simultaneously limit the voltage developed across the superconductor. This results in fast and uniform quenching of the superconductors, significantly reduces the burnout risk associated with non-uniformity often existing within the volume of superconductor materials. The fault current limiter modules may be electrically coupled together to form various "n" (rows).times."m" (columns) matrix configurations.

  19. The Starr fault system of southeastern Ohio

    SciTech Connect (OSTI)

    Brannock, M.C. (Qauker State Corp., Belpre, OH (United States))

    1993-08-01T23:59:59.000Z

    The Starr fault system is a series of east-west-trending faults located in southeastern Ohio. This fault system was discovered by mapping the anomalous sedimentary sequence of the [open quotes]Big Lime[close quotes]. The Big Lime is a driller's term for the stratigraphic section that includes the Lower Devonian Onondaga through Middle Silurian Lockport formations. The use of trend-surface analysis identified the probable fault orientation, which was then verified by seismic. The system is a series of high-angle faults, originating in the Precambrian, that occur along a narrow corridor traversing several townships. Analysis of the sedimentary section preserved by faulting indicates fault movement after the deposition of the Bass Island Formation, which was followed by a regional unconformity that removed the Bass Islands and a part of the upper Salina Formation. The Onondaga subsequently was deposited, masking fault movement evidence in the shallower formations. Some minor movement occurred later, as evidenced by the expansion in the Devonian shale sequence. The geometry of the fault system and other data suggest a pattern similar to the Albio-Scipio field of southern Michigan. A group of wells were drilled to test the Ordovician Trenton and Black River formations to determine the existence of secondary dolomite, which could be a potential reservoir. Secondary dolomite was encountered, but no commercial hydrocarbons were found in either the Trenton or Black River. Other formations produced hydrocarbons and water from fractured zones that were not known for this behavior. Other probable fault systems in southern Ohio, identified by using the same mapping techniques, may provide deeper targets for future drilling.

  20. 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...

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Mechanics of large folds in thin interfacial films

    E-Print Network [OSTI]

    Vincent Démery; 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.

  6. 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...

  7. 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...

  8. 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...

  9. 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.

  10. 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...

  11. 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.

  12. 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.

  13. Fault-Tolerant CCM Middleware for Embedded Adaptive Dependability (MEAD)

    E-Print Network [OSTI]

    Narasimhan, Priya

    Fault-Tolerant CCM Middleware for Embedded Adaptive Dependability (MEAD) Real-Time Fault Narasimhan Carnegie Mellon University CCM Workshop, Nashville, TN December 10, 2003 #12;12/11/2003 Page 2 Model precursor to a real-time fault tolerant CCM ­ Real-Time Fault Tolerant CORBA Standard RFP launched

  14. 1. Detect ground faults in PV arrays mounted on the roofs of 2. Interrupt the fault current

    E-Print Network [OSTI]

    Johnson, Eric E.

    1. Detect ground faults in PV arrays mounted on the roofs of dwellings 2. Interrupt the fault current 3. Indicate that a ground fault had occurred 4. Disconnect the faulted part of the PV array 5. "Crowbar" (short-circuit) the PV array The original GFPD prototype was developed in two versions that were

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. Structure of the eastern Red Rocks and Wind Ridge thrust faults, Wyoming: how a thrust fault gains displacement along strike 

    E-Print Network [OSTI]

    Huntsman, Brent Stanley

    1983-01-01T23:59:59.000Z

    OF FIELD MAPPING Methods . Thrust Faults . The Wind Ridge Thrust Fault System The Red Rocks Thrust Fault System CLAY MODEL STUDIES Purpose and Description Model Results DISCUSSION OF RESULTS Kinematics of the Red Rocks Thrust Fault Termination... . Kinematics of the Southern Wind Ridge Thrust Fault . . . A Conceptual Model of the Red Rocks Thrust Fault Termination Implications of the Red Rocks Fault Termination . . . . . . Page V1 V11 1X X1 X11 7 9 17 18 18 21 24 27 35 35 38 49 49...

  20. Fault Tolerant Control using Cartesian Genetic Programming

    E-Print Network [OSTI]

    Fernandez, Thomas

    Fault Tolerant Control using Cartesian Genetic Programming Yoshikazu Hirayama University of York]: Robotics-- Sensors; F.2.2 [Analysis of Algorithms and Problem Complexity]: Nonnumerical Algorithms and Problems General Terms Algorithms, Reliability Keywords cartesian genetic programming, evolutionary

  1. Microscopic feather fractures in the faulting process

    E-Print Network [OSTI]

    Conrad, Robert Eugene

    1974-01-01T23:59:59.000Z

    . Naximum compressive stress trajectories in a photoelastic model are shown by solid lines. Short lines are drawn on isoclinics in crossed polarized light at 10' intervals of rotation. Load axis is N-S. stress (o'I) trajectories curve near the fault..., maximum compressive stress, trajectories to a two dimensional during sliding along (dashed lines) in a cylindrical specimen reduced elastic problem. (b) Expected ol trajectories a fault. crack by shear along the crack surfaces (Bieniawski, 1967...

  2. 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

  3. 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...

  4. 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.

  5. Fault Detection and Load Distribution for the Wind Farm Challenge

    SciTech Connect (OSTI)

    Borchehrsen, Anders B.; Larsen, Jesper A.; Stoustrup, Jakob

    2014-08-24T23:59:59.000Z

    In this paper a fault detection system and a fault tolerant controller for a wind farm model. The wind farm model used is the one proposed as a public challenge. In the model three types of faults are introduced to a wind farm consisting of nine turbines. A fault detection system designed, by taking advantage of the fact that within a wind farm several wind turbines will be operating under all most identical conditions. The turbines are then grouped, and then turbines within each group are used to generate residuals for turbines in the group. The generated residuals are then evaluated using dynamical cumulative sum. The designed fault detection system is cable of detecting all three fault types occurring in the model. But there is room for improving the fault detection in some areas. To take advantage of the fault detection system a fault tolerant controller for the wind farm has been designed. The fault tolerant controller is a dispatch controller which is estimating the possible power at each individual turbine and then setting the reference accordingly. The fault tolerant controller has been compared to a reference controller. And the comparison shows that the fault tolerant controller performance better in all measures. The fault detection and a fault tolerant controller has been designed, and based on the simulated results the overall performance of the wind farm is improved on all measures. Thereby this is a step towards improving the overall performance of current and future wind farms.

  6. 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.

  7. 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.

  8. Collateral damage: Evolution with displacement of fracture distribution and secondary fault strands in fault

    E-Print Network [OSTI]

    Savage, Heather M.

    Collateral damage: Evolution with displacement of fracture distribution and secondary fault strands in fault damage zones Heather M. Savage1,2 and Emily E. Brodsky1 Received 22 April 2010; revised 10 of fracture distributions as a function of displacement to determine whether damage around small and large

  9. Fault-tolerant Sensor Network based on Fault Evaluation Matrix and Compensation for Intermittent Observation

    E-Print Network [OSTI]

    Fault-tolerant Sensor Network based on Fault Evaluation Matrix and Compensation for Intermittent-tolerant sensor network configuration problem for a target navigation. A sensor network system consists of many sensor nodes and its network connections. Each sensor node can exchange information by wireless

  10. Measuring and Modeling Fault Density for Plume-Fault Encounter Probability Estimation

    SciTech Connect (OSTI)

    Jordan, P.D.; Oldenburg, C.M.; Nicot, J.-P.

    2011-05-15T23:59:59.000Z

    Emission of carbon dioxide from fossil-fueled power generation stations contributes to global climate change. Storage of this carbon dioxide within the pores of geologic strata (geologic carbon storage) is one approach to mitigating the climate change that would otherwise occur. The large storage volume needed for this mitigation requires injection into brine-filled pore space in reservoir strata overlain by cap rocks. One of the main concerns of storage in such rocks is leakage via faults. In the early stages of site selection, site-specific fault coverages are often not available. This necessitates a method for using available fault data to develop an estimate of the likelihood of injected carbon dioxide encountering and migrating up a fault, primarily due to buoyancy. Fault population statistics provide one of the main inputs to calculate the encounter probability. Previous fault population statistics work is shown to be applicable to areal fault density statistics. This result is applied to a case study in the southern portion of the San Joaquin Basin with the result that the probability of a carbon dioxide plume from a previously planned injection had a 3% chance of encountering a fully seal offsetting fault.

  11. 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.

  12. Structural geology of the Huldra Field, northern North Sea--a major tilted fault block at the eastern edge of the Horda Platform

    E-Print Network [OSTI]

    Fossen, Haakon

    at the eastern edge of the Horda Platform Haakon Fossena,*, Jonny Hesthammera , Tord Erlend Skeie Johansena of the Viking Graben in the northern North Sea. Unlike the rest of the Horda Platform area, the Jurassic section of the Horda Platform after relief along the eastern margin of the Viking Graben built up in early parts

  13. Fault Locating, Prediction and Protection (FLPPS)

    SciTech Connect (OSTI)

    Yinger, Robert, J.; Venkata, S., S.; Centeno, Virgilio

    2010-09-30T23:59:59.000Z

    One of the main objectives of this DOE-sponsored project was to reduce customer outage time. Fault location, prediction, and protection are the most important aspects of fault management for the reduction of outage time. In the past most of the research and development on power system faults in these areas has focused on transmission systems, and it is not until recently with deregulation and competition that research on power system faults has begun to focus on the unique aspects of distribution systems. This project was planned with three Phases, approximately one year per phase. The first phase of the project involved an assessment of the state-of-the-art in fault location, prediction, and detection as well as the design, lab testing, and field installation of the advanced protection system on the SCE Circuit of the Future located north of San Bernardino, CA. The new feeder automation scheme, with vacuum fault interrupters, will limit the number of customers affected by the fault. Depending on the fault location, the substation breaker might not even trip. Through the use of fast communications (fiber) the fault locations can be determined and the proper fault interrupting switches opened automatically. With knowledge of circuit loadings at the time of the fault, ties to other circuits can be closed automatically to restore all customers except the faulted section. This new automation scheme limits outage time and increases reliability for customers. The second phase of the project involved the selection, modeling, testing and installation of a fault current limiter on the Circuit of the Future. While this project did not pay for the installation and testing of the fault current limiter, it did perform the evaluation of the fault current limiter and its impacts on the protection system of the Circuit of the Future. After investigation of several fault current limiters, the Zenergy superconducting, saturable core fault current limiter was selected for installation. Because of some testing problems with the Zenergy fault current limiter, installation was delayed until early 2009 with it being put into operation on March 6, 2009. A malfunction of the FCL controller caused the DC power supply to the superconducting magnet to be turned off. This inserted the FCL impedance into the circuit while it was in normal operation causing a voltage resonance condition. While these voltages never reached a point where damage would occur on customer equipment, steps were taken to insure this would not happen again. The FCL was reenergized with load on December 18, 2009. A fault was experienced on the circuit with the FCL in operation on January 14, 2010. The FCL operated properly and reduced the fault current by about 8%, what was expected from tests and modeling. As of the end of the project, the FCL was still in operation on the circuit. The third phase of the project involved the exploration of several advanced protection ideas that might be at a state where they could be applied to the Circuit of the Future and elsewhere in the SCE electrical system. Based on the work done as part of the literature review and survey, as well as a number of internal meetings with engineering staff at SCE, a number of ideas were compiled. These ideas were then evaluated for applicability and ability to be applied on the Circuit of the Future in the time remaining for the project. Some of these basic ideas were implemented on the circuit including measurement of power quality before and after the FCL. It was also decided that we would take what was learned as part of the Circuit of the Future work and extend it to the next generation circuit protection for SCE. Also at this time, SCE put in a proposal to the DOE for the Irvine Smart Grid Demonstration using ARRA funding. SCE was successful in obtaining funding for this proposal, so it was felt that exploration of new protection schemes for this Irvine Smart Grid Demonstration would be a good use of the project resources. With this in mind, a protection system that uses fault interrupting switches, hi

  14. 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

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

    E-Print Network [OSTI]

    Enderlein, Jörg

    at Protein Folding Jçrg 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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 ...

  2. 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...

  3. 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 ...

  4. 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.

  5. 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.

  6. 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.

  7. 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. ...

  8. Faulted joints: kinematics, displacementlength scaling relations and criteria for their identication

    E-Print Network [OSTI]

    Engelder, Terry

    and kinematics based on two sets of joints, pinnate joints and fault striations, reveal that some mesoscale faults (i.e., faults without linked fault segments) at the mesoscale: ªneoformed faultsº which form

  9. Microfracture fabric of the Punchbowl fault zone, San Andreas System, California

    E-Print Network [OSTI]

    Wilson, Jennifer Elizabeth

    1999-01-01T23:59:59.000Z

    The origin of fault zone structure is not completely understood. On the basis of mechanistic models of faulting, the characteristic internal structure of faults may largely be established early during growth of the fault, or it may develop...

  10. Robust Condition Monitoring and Fault Diagnosis of Variable Speed Induction Motor Drives

    E-Print Network [OSTI]

    Choi, Seungdeog

    2012-02-14T23:59:59.000Z

    The main types of faults studied in the literature are commonly categorized as electrical faults and mechanical faults. In addition to well known faults, the performance of a diagnostic algorithm and its operational reliability in harsh environments...

  11. A Hybrid Model Based and Statistical Fault Diagnosis System for Industrial Process

    E-Print Network [OSTI]

    Lin, Chen-Han

    2014-11-21T23:59:59.000Z

    This thesis presents a hybrid model based and statistical fault diagnosis system, which applied on the nonlinear three-tank model. The purpose of fault diagnosis is generating and analyzing the residual to find out the fault occurrence. This fault...

  12. 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.

  13. Synthesis and evaluation of fault-tolerant quantum computer architectures

    E-Print Network [OSTI]

    Cross, Andrew W. (Andrew William), 1979-

    2005-01-01T23:59:59.000Z

    Fault-tolerance is the cornerstone of practical, large-scale quantum computing, pushed into its prominent position with heroic theoretical efforts. The fault-tolerance threshold, which is the component failure probability ...

  14. FEATURE BASED HANDLING OF SURFACE FAULTS IN COMPACT DISC PLAYERS

    E-Print Network [OSTI]

    Wickerhauser, M. Victor

    two photo detectors. The distances are the distance from the actual position of the OPU such surface faults. The core idea is not to rely on sensor information during the fault. The sensor signals

  15. Observations on the capability of the Criner fault, southern Oklahoma

    E-Print Network [OSTI]

    Williamson, Shawn Collin

    1996-01-01T23:59:59.000Z

    of the present study suggest that the Criner fault is an old tectonic feature with a deceptively youthful geomorphic appearance. Differential erosion has likely exhumed the Criner fault-line scarp in the resistant Ordovician limestone of the Criner Hills...

  16. Design and analysis of a fault tolerant network processor

    E-Print Network [OSTI]

    Desai, Shaishav A

    1998-01-01T23:59:59.000Z

    This thesis investigates the effect of transient faults on a processor and proposes on-chip fault tolerant design techniques to improve its reliability. The target processor is a general 32-bit, four stage pipeline, dual context RISC style design...

  17. Frictional properties of faults: from observation on the

    E-Print Network [OSTI]

    Winfree, Erik

    Frictional properties of faults: from observation on the Longitudinal Valley Fault, Taiwan myself lucky to do what I love and to wake up every day, happy and excited about the day to come

  18. East-west faults due to planetary contraction

    E-Print Network [OSTI]

    Beuthe, Mikael

    2010-01-01T23:59:59.000Z

    Contraction, expansion and despinning have been common in the past evolution of Solar System bodies. These processes deform the lithosphere until it breaks along faults. The type and orientation of faults are usually determined under the assumption of a constant lithospheric thickness, but lithospheric thinning can occur at the equator or at the poles due either to latitudinal variation in solar insolation or to localized tidal dissipation. Using thin elastic shells with variable thickness, I show that the equatorial thinning of the lithosphere transforms the homogeneous and isotropic fault pattern caused by contraction/expansion into a pattern of faults striking east-west, preferably formed in the equatorial region. By contrast, lithospheric thickness variations only weakly affect the despinning faulting pattern consisting of equatorial strike-slip faults and polar normal faults. If contraction is added to despinning, the despinning pattern first shifts to thrust faults striking north-south and then to thrus...

  19. New approach to the fault location problem using synchronized sampling

    E-Print Network [OSTI]

    Mrkic, Jasna

    1994-01-01T23:59:59.000Z

    This thesis presents a new approach to solving the problem of fault location on a transmission line using synchronized data from both ends of the line. The synchronized phase voltage and current samples taken during the fault transient are used...

  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. VCSEL fault location apparatus and method

    DOE Patents [OSTI]

    Keeler, Gordon A. (Albuquerque, NM); Serkland, Darwin K. (Albuquerque, NM)

    2007-05-15T23:59:59.000Z

    An apparatus for locating a fault within an optical fiber is disclosed. The apparatus, which can be formed as a part of a fiber-optic transmitter or as a stand-alone instrument, utilizes a vertical-cavity surface-emitting laser (VCSEL) to generate a test pulse of light which is coupled into an optical fiber under test. The VCSEL is subsequently reconfigured by changing a bias voltage thereto and is used as a resonant-cavity photodetector (RCPD) to detect a portion of the test light pulse which is reflected or scattered from any fault within the optical fiber. A time interval .DELTA.t between an instant in time when the test light pulse is generated and the time the reflected or scattered portion is detected can then be used to determine the location of the fault within the optical fiber.

  9. Experimental characterization of faults on low-voltage systems

    E-Print Network [OSTI]

    Ahmed, Jubayer

    1992-01-01T23:59:59.000Z

    was to simulate a con- trolled arcing fault. Hence, the arcgap was maintained constant for a particular test. A tungsten welding rod was used as the electrode because it does not melt easily. This test was performed on a. single-phase system with 240 volts... better understanding of the problem. These arcing faults and high impedance and incipient faults constitute the previously mentioned low-current faults. Journal model is IEEE Transactions on Power Delivery. Although these problems have been...

  10. Fault seal analysis of Okan and Meren fields, Nigeria

    SciTech Connect (OSTI)

    Eisenberg, R.A. [Chevron Petroleum Technology Co., La Habra, CA (United States); Brenneman, R.J. [Chevron Overseas Petroleum Co., San Ramon, CA (United States); Adeogba, A.A. [Chevron Nigeria Ltd., Lagos (Nigeria)

    1995-08-01T23:59:59.000Z

    The sealing capacity and the dynamic seal behavior of faults between juxtaposed reservoirs were analyzed for Okan and Meren fields, offshore Nigeria. In both fields correlations were found between reservoir performance, juxtaposed fluid types, oil geochemistry, interpreted fluid contact relationships, fault sealing/leaking condition, and calculated smear gouge ratios. Integration of these data has been invaluable in quantifying fault seal risk and may effect depletion strategies for fault-juxtaposed reservoirs within these fields. Fault plane sections defined reservoir juxtapositions and aided visualization of potential cross-fault spill points. Smear gouge ratios calculated from E-logs were used to estimate the composition of fault-gouge materials between the juxtaposed reservoirs. These tools augmented interpretation of seal/nonseal character based on fluid contact relationships in proved reservoirs and, in addition, were used to quantify fault seal risk of untested fault-dependent closures in Okan. The results of these analyses were then used to interpret production-induced fault seal breakdown within the G-sands and also to risk seal integrity of fault dependent closures within the untested O-sands in an adjacent, upthrown fault block. Within this fault block the presence of potential fault intersection leak points and large areas of sand/sand juxtaposition with high smear gouge ratios (low sealing potential) limits potential reserves within the O-sand package. In Meren Field the E- and G-sands are juxtaposed, on different pressure decline, geochemically distinct, and are characterized by low smear gouge ratios. In contrast, specific G- and H-sands, juxtaposed across the same fault, contain similar OOWCs and are characterized by high smear gouge ratios. The cross-sealing and/or cross-leaking nature of compartment boundaries at Meren is related to fault displacement variation and the composition of displaced stratigraphy.

  11. Detachment Faulting & Geothermal Resources- Pearl Hot Spring, NV

    Broader source: Energy.gov [DOE]

    Detachment Faulting & Geothermal Resources - Pearl Hot Spring, NV presentation at the April 2013 peer review meeting held in Denver, Colorado.

  12. Photovoltaic ground fault and blind spot electrical simulations.

    SciTech Connect (OSTI)

    Flicker, Jack David; Johnson, Jay

    2013-06-01T23:59:59.000Z

    Ground faults in photovoltaic (PV) systems pose a fire and shock hazard. To mitigate these risks, AC-isolated, DC grounded PV systems in the United States use Ground Fault Protection Devices (GFPDs), e.g., fuses, to de-energize the PV system when there is a ground fault. Recently the effectiveness of these protection devices has come under question because multiple fires have started when ground faults went undetected. In order to understand the limitations of fuse-based ground fault protection in PV systems, analytical and numerical simulations of different ground faults were performed. The numerical simulations were conducted with Simulation Program with Integrated Circuit Emphasis (SPICE) using a circuit model of the PV system which included the modules, wiring, switchgear, grounded or ungrounded components, and the inverter. The derivation of the SPICE model and the results of parametric fault current studies are provided with varying array topologies, fuse sizes, and fault impedances. Closed-form analytical approximations for GFPD currents from faults to the grounded current carrying conductor-known as %E2%80%9Cblind spot%E2%80%9D ground faults-are derived to provide greater understanding of the influence of array impedances on fault currents. The behavior of the array during various ground faults is studied for a range of ground fault fuse sizes to determine if reducing the size of the fuse improves ground fault detection sensitivity. The results of the simulations show that reducing the amperage rating of the protective fuse does increase fault current detection sensitivity without increasing the likelihood of nuisance trips to a degree. Unfortunately, this benefit reaches a limit as fuses become smaller and their internal resistance increases to the point of becoming a major element in the fault current circuit.

  13. Understanding Fault Characteristics of Inverter-Based Distributed Energy Resources

    SciTech Connect (OSTI)

    Keller, J.; Kroposki, B.

    2010-01-01T23:59:59.000Z

    This report discusses issues and provides solutions for dealing with fault current contributions from inverter-based distributed energy resources.

  14. Experimental wrench faulting at confining pressure

    E-Print Network [OSTI]

    Bartlett, Wendy Louise

    1980-01-01T23:59:59.000Z

    along the precut, resembling the "flower or palm tree" structure noted by Sylvester and Smith (1976), in the Salton Sea area, California. The bounding fault above the down-dropped block dips at a lower angle to the forcing block-veneer interface than..., the oeometries, ori- gins, and sequence of development of structural elements comprising the fault zones. Specimens (2. 8 or 3. 4 x 3. 4 x 9. 4 cm) are loaded parallel to their longest dimension, at an average displacement rate -3 -1 of 7. 3 x 10 cm sec...

  15. UNSUPERVISED CLUSTERING FOR FAULT DIAGNOSIS IN NUCLEAR POWER PLANT COMPONENTS

    E-Print Network [OSTI]

    Boyer, Edmond

    1 UNSUPERVISED CLUSTERING FOR FAULT DIAGNOSIS IN NUCLEAR POWER PLANT COMPONENTS Piero Baraldi1 of prototypical behaviors. Its performance is tested with respect to an artificial case study and then applied on transients originated by different faults in the pressurizer of a nuclear power reactor. Key Words: Fault

  16. On Distributed Fault-Tolerant Detection in Wireless Sensor Networks

    E-Print Network [OSTI]

    Huang, Yinlun

    On Distributed Fault-Tolerant Detection in Wireless Sensor Networks Xuanwen Luo, Student Member problems for distributed fault-tolerant detection in wireless sensor networks: 1) how to address both it possible to perform energy- efficient fault-tolerant detection in a wireless sensor network. Index Terms

  17. Outlier Detection Rules for Fault Detection in Solar Photovoltaic Arrays

    E-Print Network [OSTI]

    Lehman, Brad

    , MPPT of the PV inverters, high fault impedance, or degradation of solar cells [1]. Without proper fault Abstract-- Solar photovoltaic (PV) arrays are unique power sources that may have uncleared fault current when utilizing conventional overcurrent protection devices. To monitor the PV operation and detect

  18. A Parametric Spectral Estimator for Faults Detection in Induction Machines

    E-Print Network [OSTI]

    Boyer, Edmond

    since their frequency resolution is limited and additional post-processing algorithms are required of bearing faults. Index Terms--Induction machine, faults detection, bearing faults, stator current that avoids the use of extra sensors since the stator currents are usually available and inexpensive

  19. RIS-M-2311 AUTOMATIC FAULT TREE CONSTRUCTION WITH RIKKE

    E-Print Network [OSTI]

    RISØ-M-2311 AUTOMATIC FAULT TREE CONSTRUCTION WITH RIKKE A COMPENDIUM OF EXAMPLES, VOLUME I BASIC MODELS J.R. Taylor Abstract. Examples of automatically constructed fault trees are given. In this first are intended to illustrate the prin- ciples of fault tree construction using the RIKKE failure analysis system

  20. Ris-M-2311 AUTOMATIC FAULT TREE CONSTRUCTION WITH RIKKE

    E-Print Network [OSTI]

    Risø-M-2311 Vol. 2 AUTOMATIC FAULT TREE CONSTRUCTION WITH RIKKE A COMPENDIUM OF EXAMPLES. VOLUME 2. CONTROL AND SAFETY LOOPS. J.R. Taylor Abstract. This second volume describes the construction of fault In this volume, examples of HIKKE fault tree construction including loops are given. The principles involved were

  1. Statistical estimation of multiple faults in aircraft gas turbine engines

    E-Print Network [OSTI]

    Ray, Asok

    415 Statistical estimation of multiple faults in aircraft gas turbine engines S Sarkar, C Rao of multiple faults in aircraft gas-turbine engines, based on a statistical pattern recognition tool called commercial aircraft engine. Keywords: aircraft propulsion, gas turbine engines, multiple fault estimation

  2. Identifying Security Fault Reports via Text Mining Michael Gegick, 2

    E-Print Network [OSTI]

    Young, R. Michael

    Identifying Security Fault Reports via Text Mining 1 Michael Gegick, 2 Pete Rotella, 1 Tao Xie 1 contains fault reports (FRs) collected from various sources such as development teams, test teams, and end-users. Software or security engineers manually analyze the FRs to label the subset of FRs that are security fault

  3. Diverse neural net solutions to a fault diagnosis problem \\Lambda

    E-Print Network [OSTI]

    Sharkey, Amanda

    Abstract The development of a neural net system for fault diagnosis in a mar­ ine diesel engine system solution to a problem of fault diagnosis in a four­stroke marine diesel engine; that of early to recognise faults in simulated data from a diesel engine; specifically to classify combustion condition

  4. 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...

  5. 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...

  6. 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

  7. A Summary of Fault Recurrence and Strain Rates in the Vicinity of the Hanford Site--Topical Report

    SciTech Connect (OSTI)

    Bjornstad, Bruce N.; Winsor, Kelsey; Unwin, Stephen D.

    2012-08-01T23:59:59.000Z

    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 available data and analyses relevant to fault recurrence and strain rates within the Yakima Fold Belt. Strain rates have met with contention in the expert community and may have a significant potential for impact on the seismic hazard estimate at the Hanford Site. This report identifies the alternative conceptual models relevant to this technical issue and the arguments and data that support those models. It provides a brief description of the technical issue and principal uncertainties; a general overview on the nature of the technical issue, along with alternative conceptual models, supporting arguments and information, and uncertainties; and finally, suggests some prospective approaches to reducing uncertainties about earthquake recurrence rates for the Yakima Fold Belt.

  8. 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

  9. 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.

  10. An algorithm for faulted phase and feeder selection under high impedance fault conditions 

    E-Print Network [OSTI]

    Benner, Carl Lee

    1988-01-01T23:59:59.000Z

    . One method based on increases in third and fifth harmonic symmetrical current components under high impedance fault conditions has been proposed by Balser et. Journal model is IEEE Transactions on Power Delivery. al, of Power Technologies Inc [1...

  11. Realistic fault modeling and quality test generation of combined delay faults

    E-Print Network [OSTI]

    Thadhlani, Ajaykumar A

    2001-01-01T23:59:59.000Z

    coupled lines. To cope up with these realistic testing problems, it is necessary to model the circuit defects by considering the capacitively coupling between lines. This needs a better fault model which can incorporate the local defects (such...

  12. Seismoelectric Imaging of a Shallow Fault System Employing Fault Guided Waves

    E-Print Network [OSTI]

    Cohrs, Frelynn Joseph Reese

    2012-07-16T23:59:59.000Z

    Independent sets of reflection seismic and seismoelectric data were collected, processed, and interpreted with the aim of generating and studying guided waves within a fault zone. While seismic surveys have recently been utilized to investigate...

  13. Clay fabric intensity in natural and artificial fault gouges: Implications for brittle fault zone processes and sedimentary

    E-Print Network [OSTI]

    Clay fabric intensity in natural and artificial fault gouges: Implications for brittle fault zone processes and sedimentary basin clay fabric evolution Samuel H. Haines,1 Ben A. van der Pluijm,1 Matt J intensity measurements using X-ray texture goniometry on 22 natural clay-rich fault gouges from low

  14. We develop a microprocessor design that tolerates hard faults, including fabrication defects and in-field faults,

    E-Print Network [OSTI]

    Sorin, Daniel J.

    1 Abstract We develop a microprocessor design that tolerates hard faults, including fabrication defects and in-field faults, by leveraging existing microprocessor redundancy. To do this, we must: detect FDUs with hard faults. In our reliable microprocessor design, we use DIVA dynamic verification

  15. Thermal anomaly near the Aigio fault, Gulf of Corinth, Greece, maybe due to convection below the fault

    E-Print Network [OSTI]

    Thermal anomaly near the Aigio fault, Gulf of Corinth, Greece, maybe due to convection below intersecting the active Aigio fault, Corinth Rift, Greece. The heat flow is 53 mW/m2 , indicating of Corinth, Greece, maybe due to convection below the fault, Geophys. Res. Lett., 34, L06314, doi:10

  16. Fault Tolerant CORBASpecification, OMG document: ptc/20000404

    E-Print Network [OSTI]

    Roma "La Sapienza", Università di

    Fault Tolerant CORBASpecification, V1.0 OMG document: ptc/2000­04­04 replaces draft adopted specification ptc/2000­03­04 and submission document orbos/00­01­19 This document is an OMG Final Adopted in the finalization phase. Comments on the content of this document are welcomed, and should be directed to issues

  17. All row, planar fault detection system

    DOE Patents [OSTI]

    Archer, Charles Jens; Pinnow, Kurt Walter; Ratterman, Joseph D; Smith, Brian Edward

    2013-07-23T23:59:59.000Z

    An apparatus, program product and method for detecting nodal faults may simultaneously cause designated nodes of a cell to communicate with all nodes adjacent to each of the designated nodes. Furthermore, all nodes along the axes of the designated nodes are made to communicate with their adjacent nodes, and the communications are analyzed to determine if a node or connection is faulty.

  18. Multi-directional fault detection system

    DOE Patents [OSTI]

    Archer, Charles Jens (Rochester, MN); Pinnow, Kurt Walter (Rochester, MN); Ratterman, Joseph D. (Rochester, MN); Smith, Brian Edward (Rochester, MN)

    2010-11-23T23:59:59.000Z

    An apparatus, program product and method checks for nodal faults in a group of nodes comprising a center node and all adjacent nodes. The center node concurrently communicates with the immediately adjacent nodes in three dimensions. The communications are analyzed to determine a presence of a faulty node or connection.

  19. Multi-directional fault detection system

    DOE Patents [OSTI]

    Archer, Charles Jens; Pinnow, Kurt Walter; Ratterman, Joseph D.; Smith, Brian Edward

    2010-06-29T23:59:59.000Z

    An apparatus, program product and method checks for nodal faults in a group of nodes comprising a center node and all adjacent nodes. The center node concurrently communicates with the immediately adjacent nodes in three dimensions. The communications are analyzed to determine a presence of a faulty node or connection.

  20. Global Trajectory Planning for Fault Tolerant Manipulators

    E-Print Network [OSTI]

    . Khosla Department of Electrical and Computer Engineering and The Robotics Institute, Carnegie Mellon attribute of robot manipulators in a growing range of applications such as space missions, nuclear waste retrieval, and medical robot­ ics. This trend has spawned a research effort in fault toler­ ant robotics

  1. Fault-tolerant, Universal Adiabatic Quantum Computation

    E-Print Network [OSTI]

    Ari Mizel

    2014-03-30T23:59:59.000Z

    Quantum computation has revolutionary potential for speeding computational tasks such as factoring and simulating quantum systems, but the task of constructing a quantum computer is daunting. Adiabatic quantum computation and other ``hands-off" approaches relieve the need for rapid, precise pulsing to control the system, inspiring at least one high-profile effort to realize a hands-off quantum computing device. But is hands-off incompatible with fault-tolerant? Concerted effort and many innovative ideas have not resolved this question but have instead deepened it, linking it to fundamental problems in quantum complexity theory. Here we present a hands-off approach that is provably (a) capable of scalable universal quantum computation in a non-degenerate ground state and (b) fault-tolerant against an analogue of the usual local stochastic fault model. A satisfying physical and numerical argument indicates that (c) it is also fault-tolerant against thermal excitation below a threshold temperature independent of the computation size.

  2. 54 MAY | 2012 Gearbox Fault Detection

    E-Print Network [OSTI]

    Kusiak, Andrew

    , research in fault identification and condition monitoring is war- ranted. In this study, detecting wind of a test wind turbine. The gearbox was retested at the Dynamometer Test Facility (DTF) at NREL. To retest the gearbox, the complete nacelle, and the drive train of the test wind turbine were installed at the DTF

  3. Fault-tolerant quantum computation by anyons

    E-Print Network [OSTI]

    A. Yu. Kitaev

    1997-07-09T23:59:59.000Z

    A two-dimensional quantum system with anyonic excitations can be considered as a quantum computer. Unitary transformations can be performed by moving the excitations around each other. Measurements can be performed by joining excitations in pairs and observing the result of fusion. Such computation is fault-tolerant by its physical nature.

  4. Fault-Tolerant Spanners: Better and Simpler

    E-Print Network [OSTI]

    Dinitz, Michael

    2011-01-01T23:59:59.000Z

    A natural requirement of many distributed structures is fault-tolerance: after some failures, whatever remains from the structure should still be effective for whatever remains from the network. In this paper we examine spanners of general graphs that are tolerant to vertex failures, and significantly improve their dependence on the number of faults $r$, for all stretch bounds. For stretch $k \\geq 3$ we design a simple transformation that converts every $k$-spanner construction with at most $f(n)$ edges into an $r$-fault-tolerant $k$-spanner construction with at most $O(r^3 \\log n) \\cdot f(2n/r)$ edges. Applying this to standard greedy spanner constructions gives $r$-fault tolerant $k$-spanners with $\\tilde O(r^{2} n^{1+\\frac{2}{k+1}})$ edges. The previous construction by Chechik, Langberg, Peleg, and Roddity [STOC 2009] depends similarly on $n$ but exponentially on $r$ (approximately like $k^r$). For the case $k=2$ and unit-length edges, an $O(r \\log n)$-approximation algorithm is known from recent work of D...

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Coordinated Fault Tolerance for High-Performance Computing

    SciTech Connect (OSTI)

    Dongarra, Jack; Bosilca, George; et al.

    2013-04-08T23:59:59.000Z

    Our work to meet our goal of end-to-end fault tolerance has focused on two areas: (1) improving fault tolerance in various software currently available and widely used throughout the HEC domain and (2) using fault information exchange and coordination to achieve holistic, systemwide fault tolerance and understanding how to design and implement interfaces for integrating fault tolerance features for multiple layers of the software stack—from the application, math libraries, and programming language runtime to other common system software such as jobs schedulers, resource managers, and monitoring tools.

  11. Probabilistic model of fault detection in quantum circuits

    E-Print Network [OSTI]

    Anindita Banerjee; Anirban Pathak

    2009-05-12T23:59:59.000Z

    It is shown that the fault testing for quantum circuits does not follow conventional classical techniques. If probabilistic gate like Hadamard gate is included in a circuit then the classical notion of test vector is shown to fail. We have reported several new and distinguishing features of quantum fault and also presented a general methodology for detection of functional faults in a quantum circuit. The technique can generate test vectors for detection of different kinds of fault. Specific examples are given and time complexity of the proposed quantum fault detection algorithm is reported.

  12. 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 -

  13. 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 .

  14. 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...

  15. 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.

  16. 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.

  17. 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 32:1817–1828 O’Leary DDM, Chou...

  18. Horst and Graben | 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: navigation, search OpenEIHesperia, California: EnergyHoloceneHonestHoosacHorseHorst and

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

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

    E-Print Network [OSTI]

    Onuchic, José

    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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. * 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

  11. 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

  12. 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.

  13. Completing fault models for abductive diagnosis

    SciTech Connect (OSTI)

    Knill, E. (Los Alamos National Lab., NM (United States)); Cox, P.T.; Pietrzykowski, T. (Technical Univ., NS (Canada))

    1992-11-05T23:59:59.000Z

    In logic-based diagnosis, the consistency-based method is used to determine the possible sets of faulty devices. If the fault models of the devices are incomplete or nondeterministic, then this method does not necessarily yield abductive explanations of system behavior. Such explanations give additional information about faulty behavior and can be used for prediction. Unfortunately, system descriptions for the consistency-based method are often not suitable for abductive diagnosis. Methods for completing the fault models for abductive diagnosis have been suggested informally by Poole and by Cox et al. Here we formalize these methods by introducing a standard form for system descriptions. The properties of these methods are determined in relation to consistency-based diagnosis and compared to other ideas for integrating consistency-based and abductive diagnosis.

  14. Stuck-at-fault test set compaction

    E-Print Network [OSTI]

    Vanfickell, Jason Michael

    2013-02-22T23:59:59.000Z

    of sltcp g(0. 5-ones~robo~, ~) Exc Bal, = 0. 25 ? of sites Figure 1. Formula for computation of the excitation balance Excitation balance is a metric computed for every detectable fault in the entire circuit. It is intended to provide a measure... Sigma ~ National Society of Collegiate Scholars Activities: ~ Texas A&M University Institute of Electrical and Electronic Engineers IT/Technology Chair and Webmaster, Fall 2003 ? Spring 2004 ~ Texas A&M University Student Engineers' Council...

  15. Undulator Hall Air Temperature Fault Scenarios

    SciTech Connect (OSTI)

    Sevilla, J.; Welch, J.; /SLAC; ,

    2010-11-17T23:59:59.000Z

    Recent experience indicates that the LCLS undulator segments must not, at any time following tuning, be allowed to change temperature by more than about {+-}2.5 C or the magnetic center will irreversibly shift outside of acceptable tolerances. This vulnerability raises a concern that under fault conditions the ambient temperature in the Undulator Hall might go outside of the safe range and potentially could require removal and retuning of all the segments. In this note we estimate changes that can be expected in the Undulator Hall air temperature for three fault scenarios: (1) System-wide power failure; (2) Heating Ventilation and Air Conditioning (HVAC) system shutdown; and (3) HVAC system temperature regulation fault. We find that for either a system-wide power failure or an HVAC system shutdown (with the technical equipment left on), the short-term temperature changes of the air would be modest due to the ability of the walls and floor to act as a heat ballast. No action would be needed to protect the undulator system in the event of a system-wide power failure. Some action to adjust the heat balance, in the case of the HVAC power failure with the equipment left on, might be desirable but is not required. On the other hand, a temperature regulation failure of the HVAC system can quickly cause large excursions in air temperature and prompt action would be required to avoid damage to the undulator system.

  16. Pressure test data reveal reservoir barriers/faults

    SciTech Connect (OSTI)

    Hurd, J.D.

    1984-07-30T23:59:59.000Z

    A review of transient pressure test data from an oil reservoir in Libya indicated not only the suspected fault barriers, but also the non-sealing portions of the faults. Extensive seismic data indicated much faulting, and directional trends had been interpreted to be generally northwest-southeast. The reservoir is a heterogeneous dolomite with average permeability of 40 to 50 md and contains neither natural fractures not stratification. Vertical displacement (throw) of each fault block is indicated to be within the range of the dolomite thickness, i.e., 40 to 180 ft. Therefore, when the fault throw is greater than reservoir thickness there is sealing, and when the throw is less than reservoir thickness the faults are non-sealing.

  17. Fibre bundle framework for unitary quantum fault tolerance

    E-Print Network [OSTI]

    Daniel Gottesman; Lucy Liuxuan Zhang

    2013-09-26T23:59:59.000Z

    We introduce a differential geometric framework for describing families of quantum error-correcting codes and for understanding quantum fault tolerance. This work unifies the notion of topological fault tolerance with fault tolerance in other kinds of quantum error-correcting codes. In particular, we use fibre bundles with a natural flat projective connection to study the transformation of codewords under unitary fault-tolerant evolutions. We show that the fault-tolerant logical operations are given by the monodromy group for either of two bundles, both of which have flat projective connections. As concrete realizations of the general framework, we construct the bundles explicitly for two examples of fault-tolerant families of operations, the qudit transversal gates and the string operators in the toric code.

  18. Similarity Matching Techniques for Fault Diagnosis in Automotive Infotainment Electronics

    E-Print Network [OSTI]

    Kabir, Mashud

    2009-01-01T23:59:59.000Z

    Fault diagnosis has become a very important area of research during the last decade due to the advancement of mechanical and electrical systems in industries. The automobile is a crucial field where fault diagnosis is given a special attention. Due to the increasing complexity and newly added features in vehicles, a comprehensive study has to be performed in order to achieve an appropriate diagnosis model. A diagnosis system is capable of identifying the faults of a system by investigating the observable effects (or symptoms). The system categorizes the fault into a diagnosis class and identifies a probable cause based on the supplied fault symptoms. Fault categorization and identification are done using similarity matching techniques. The development of diagnosis classes is done by making use of previous experience, knowledge or information within an application area. The necessary information used may come from several sources of knowledge, such as from system analysis. In this paper similarity matching tec...

  19. 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...

  20. Investigation of the Meers fault in southwestern Oklahoma

    SciTech Connect (OSTI)

    Luza, K.V.; Madole, R.F.; Crone, A.J.

    1987-08-01T23:59:59.000Z

    The Meers fault is part of a major system of NW-trending faults that form the boundary between the Wichita Mountains and the Anadarko basin in southwestern Oklahoma. A portion of the Meers fault is exposed at the surface in northern Comanche County and strikes approximately N. 60/sup 0/ W. where it offsets Permian conglomerate and shale for at least 26 km. The scarp on the fault is consistently down to the south, with a maximum relief of 5 m near the center of the fault trace. Quaternary stratigraphic relationships and 10 /sup 14/C age dates constrain the age of the last movement of the Meers fault. The last movement postdates the Browns Creek Alluvium, late Pleistocene to early Holocene, and predates the East Cache Alluvium, 100 to 800 yr B.P. Fan alluvium, produced by the last fault movement, buried a soil that dates between 1400 and 1100 yr B.P. Two trenches excavated across the scarp near Canyon Creek document the near-surface deformation and provide some general information on recurrence. Trench 1 was excavated in the lower Holocene part of the Browns Creek Alluvium, and trench 2 was excavated in unnamed gravels thought to be upper Pleistocene. Flexing and warping was the dominant mode of deformation that produced the scarp. The stratigraphy in both trenches indicates one surface-faulting event, which implies a lengthy recurrence interval for surface faulting on this part of the fault. Organic-rich material from two samples that postdate the last fault movement yielded /sup 14/C ages between 1600 and 1300 yr B.P. These dates are in excellent agreement with the dates obtained from soils buried by the fault-related fan alluvium.

  1. A Turing Machine Resisting Isolated Bursts Of Faults

    E-Print Network [OSTI]

    Capuni, Ilir

    2012-01-01T23:59:59.000Z

    We consider computations of a Turing machine under noise that causes consecutive violations of the machine's transition function. Given a constant upper bound B on the size of bursts of faults, we construct a Turing machine M(B) subject to faults that can simulate any fault-free machine under the condition that bursts are not closer to each other than V for an appropriate V = O(B^2).

  2. Strong Nernst-Ettingshausen effect in folded graphene

    E-Print Network [OSTI]

    Friedemann Queisser; Ralf Schützhold

    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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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^{\

  8. 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).

  9. Upper crustal faulting in an obliquely extending orogen, structural...

    Open Energy Info (EERE)

    faulting in an obliquely extending orogen, structural control on permeability and production in the Coso Geothermal Field, eastern California Jump to: navigation, search OpenEI...

  10. Active Fault Controls At High-Temperature Geothermal Sites- Prospectin...

    Open Energy Info (EERE)

    the level of unrecognized active faults present in these areas. Analysis of low-sun-angle aerial photography acquired over the Needle Rocks, Astor Pass, Empire, and Lee...

  11. Fault-tolerant distributed transactions for partitioned OLTP databases

    E-Print Network [OSTI]

    Jones, Evan P. C. (Evan Philip Charles), 1981-

    2012-01-01T23:59:59.000Z

    This thesis presents Dtxn, a fault-tolerant distributed transaction system designed specifically for building online transaction processing (OLTP) databases. Databases have traditionally been designed as general purpose ...

  12. atera fault central: Topics by E-print Network

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

    deformation and creep along the central section of the North Anatolian Fault (Turkey): InSAR observations Geosciences Websites Summary: Interseismic deformation and creep...

  13. Checksum-Based Fault Tolerance for LU Factorization

    E-Print Network [OSTI]

    Davies, Teresa

    2014-01-01T23:59:59.000Z

    study of failures in high-performance computing systems. InFault tolerant high performance computing by a codingfor large-scale high- performance computing. In 2012

  14. PV Arc Fault Detector Challenges Due to Module Frequency Response...

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

    This poster does not contain any proprietary or confidential information. Introduction PV system arc faults have led to a number of rooftop fires which have caused significant...

  15. Dating of major normal fault systems using thermochronology-...

    Open Energy Info (EERE)

    faults, timing of ductile mylonite formation and passage of rocks through the crystal-plastic to brittle transition, and multiple events of extensional unroofing. Here we...

  16. MICRO-SEISMICITY, FAULT STRUCTURE AND HYDRAULIC COMPARTMENTALIZATION...

    Open Energy Info (EERE)

    GETHERMAL FIELD, CALIFORNIA Jump to: navigation, search OpenEI Reference LibraryAdd to library Conference Proceedings: MICRO-SEISMICITY, FAULT STRUCTURE AND HYDRAULIC...

  17. PHOTOVOLTAIC DC ARC FAULT DETECTOR TESTING AT SANDIA NATIONAL

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

    PHOTOVOLTAIC DC ARC FAULT DETECTOR TESTING AT SANDIA NATIONAL LABORATORIES Jay Johnson 1 , Birger Pahl 2 , Charles Luebke 2 , Tom Pier 2 , Theodore Miller 3 , Jason Strauch 1 ,...

  18. Fault tolerant Quantum Information Processing with Holographic control

    E-Print Network [OSTI]

    G. A. Paz-Silva; G. K. Brennen; J. Twamley

    2010-08-10T23:59:59.000Z

    We present a fault-tolerant semi-global control strategy for universal quantum computers. We show that N-dimensional array of qubits where only (N-1)-dimensional addressing resolution is available is compatible with fault-tolerant universal quantum computation. What is more, we show that measurements and individual control of qubits are required only at the boundaries of the fault-tolerant computer, i.e. holographic fault-tolerant quantum computation. Our model alleviates the heavy physical conditions on current qubit candidates imposed by addressability requirements and represents an option to improve their scalability.

  19. Fault Tolerant Evaluation of Continuous Selection Queries over Sensor Data

    E-Print Network [OSTI]

    Lazaridis, Iosif; Han, Qi; Mehrotra, Sharad; Venkatasubramanian, Nalini

    2009-01-01T23:59:59.000Z

    Evaluation of Continuous Selection Queries over Sensor Dataevaluation of continuous selection queries (CSQs) over sensor-sensor suffices and there is no Fault Tolerant Evaluation of

  20. Aksaray And Ecemis Faults - Diapiric Salt Relationships- Relevance...

    Open Energy Info (EERE)

    Aksaray And Ecemis Faults - Diapiric Salt Relationships- Relevance To The Hydrocarbon Exploration In The Tuz Golu (Salt Lake) Basin, Central Anatolia, Turkey Jump to: navigation,...

  1. Wrench faulting and cavity concentration ; Dollarhide Field, Andrews County, Texas

    E-Print Network [OSTI]

    Dygert, Todd Charles

    1992-01-01T23:59:59.000Z

    structure map for the Devonian horizon 20 7. Seismic time slice taken at 1010 ms 8. Seismic line 190 9. Seismic line 108 10. Seismic line 40 22 25 27 11. Cross-sectional view of a wrench fault 31 12. Pure shear fault model for strike- slip.... The Clearfork horizon was mapped first since it was shallow, strong and continuous. The faults and Devonian horizon were interpreted simultaneously, Adjacent lines were interpreted together throughout the survey to insure consistent fault and horizon picks...

  2. Fault simulation of combinational circuits based on critical path tracing

    E-Print Network [OSTI]

    Burnett, Charles James

    1992-01-01T23:59:59.000Z

    advantage of the computer's internal architecture and does not intelligently analyze the CUT. The deductive simulator traverses the good circuit to determine the value of each line. At the same time, every fault that causes a line to have a different... of the faults on a line within the circuit is detected for a given test vector, the line is marked as critical [10]. These faults that are detected are marked as covered. This very quickly gathers faults without direct simulation to the outputs, however...

  3. Effects of Volcanism, Crustal Thickness, and Large Scale Faulting...

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

    of Volcanism, Crustal Thickness, and Large Scale Faulting on the Development and Evolution of Geothermal Systems: Collaborative Project in Chile Effects of Volcanism, Crustal...

  4. automatic fault management: Topics by E-print Network

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

    Software Fault Diagnosis by Exploiting Application Signatures Xiaoning Ding - The Ohio - The Ohio State University ABSTRACT Application problem diagnosis in complex...

  5. automatic fault tree: Topics by E-print Network

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

    Software Fault Diagnosis by Exploiting Application Signatures Xiaoning Ding - The Ohio - The Ohio State University ABSTRACT Application problem diagnosis in complex...

  6. automatical adaptive fault: Topics by E-print Network

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

    Software Fault Diagnosis by Exploiting Application Signatures Xiaoning Ding - The Ohio - The Ohio State University ABSTRACT Application problem diagnosis in complex...

  7. Recent earthquake sequences at Coso: Evidence for conjugate faulting...

    Open Energy Info (EERE)

    of faulting along conjugate planes. We present results from analyzing an earthquake sequence occurring in 1998 and compare it with a similar sequence that occurred in 1996. The...

  8. Direct dating of Eocene reverse faulting in northeastern Tibet using Ar-dating of fault clays and low-temperature thermochronometry

    E-Print Network [OSTI]

    Direct dating of Eocene reverse faulting in northeastern Tibet using Ar-dating of fault clays fault of northeastern Tibet by dating several size fractions of fault gouge clay that represent variable Ma and continued until at least Middle Miocene time and that authigenic clay growth occurred

  9. Evaluation of faulting characteristics and ground acceleration associated with recent movement along the Meers Fault, Southwestern Oklahoma 

    E-Print Network [OSTI]

    Burrell, Richard Dennis

    1997-01-01T23:59:59.000Z

    Exposures. 14 Diagram illustrating the effects of the Meers Fault scarp on stream channel pathways. 16 Tors on the western side of Elk Mountain, 17 Tors in Wichita Mountains known as Twin Rocks . . . 10 Tor Analysis Log utilized during fteld... and the adjacent petroleum rich Anadarko Basin. Moody and Hill (1956) identified the presence of a scarp along a section of the Meers Fault which deforms Quaternary deposits during a study of wrench fault tectonics. However, it was not until further observations...

  10. Treanmission Line Fault Location using Interoperability and Integration of Data and Model 

    E-Print Network [OSTI]

    Dutta, Papiya

    2014-01-10T23:59:59.000Z

    , classify and locate transmission line faults using synchronous samples of voltages and currents captured during fault transients from both ends of the transmission line of interest. The method is tested for several faults simulated on IEEE 118 bus test...

  11. Fault tolerant control of homopolar magnetic bearings and circular sensor arrays 

    E-Print Network [OSTI]

    Li, Ming-Hsiu

    2006-04-12T23:59:59.000Z

    Fault tolerant control can accommodate the component faults in a control system such as sensors, actuators, plants, etc. This dissertation presents two fault tolerant control schemes to accommodate the failures of power ...

  12. A Comparison of Fault Detection Methods For a Transcritical Refrigeration System

    E-Print Network [OSTI]

    Janecke, Alex Karl

    2012-10-19T23:59:59.000Z

    pairings of four faults: over/undercharge, evaporator fouling, gas cooler fouling, and compressor valve leakage. This technique allows for low cost measurement and independent detection of individual faults even when multiple faults are present. Results...

  13. Early Holocene and Late Pleistocene slip rates of the southern Dead Sea Fault determined from 10

    E-Print Network [OSTI]

    Klinger, Yann

    sites located along the Wadi Araba Fault (WAF) segment of the Dead Sea Fault are targeted on the DSF, focusing on the Wadi Araba Fault (WAF) segment (Figure 1b). The WAF strikes N12°E for about 160

  14. Data-Based Monitoring and Fault-Tolerant Control of Nonlinear Processes

    E-Print Network [OSTI]

    Chilin, David

    2012-01-01T23:59:59.000Z

    with a fault in the heat input/removal actuator to vessel 2with a fault in the heat input/removal actuator to vessel 2with a fault in the heat input/removal actuator to vessel 2

  15. Research on Fault Analysis and Fault-Tolerant Control of EV/HEV Powertrain

    E-Print Network [OSTI]

    Brest, Université de

    power industries, interests in diagnostics and fault-tolerant control of nuclear power plants have been industrial systems. To achieve these goals, monitoring and supervision are embedded in the electrical energy, FTC has been implemented in sensible applications such as aerospace, nuclear power, automotive

  16. Efficient Fault Tolerance: an Approach to Deal with Transient Faults in Multiprocessor Architectures

    E-Print Network [OSTI]

    Firenze, Università degli Studi di

    , 36, 56126 Pisa, Italy ** IEI/CNR, Via S. Maria, 46, 56126 Pisa, Italy Abstract Dynamic error, while making efficient use of the available resources. To this end, dynamic error processing must is integrated with a mechanism for dynamic error processing in a complete fault tolerance strategy. Reliability

  17. A core-based assessment of the spatial relationship of small faults associated with a basement-controlled, large normal fault in the Hickory Sandstone

    E-Print Network [OSTI]

    Graff, Mitchell C

    2006-10-30T23:59:59.000Z

    Measures of Small Faults??????????????? Page iii v vi viii xiv 1 3 3 5 7 10 10 10 12 14 18 20 26 28 vii 4. ESTIMATING SMALL FAULT DISPLACEMENT USING FAULT GOUGE THICKNESS AND PROTOLITH TEXTURE??????????... 4.1 Previous Work... is proportional to mean?????????????????????. 26 Combined scatterplot of faults with known gouge thickness versus known displacement and faults with known gouge thickness versus estimated displacement????????????????????. Page 37 38 39 40 43 45 47 48...

  18. Fault Analysis at a Wind Power Plant for One Year of Observation: Preprint

    SciTech Connect (OSTI)

    Muljadi, E.; Mills, Z.; Foster, R.; Conto, J.; Ellis, A.

    2008-07-01T23:59:59.000Z

    This paper analyzes the fault characteristics observed at a wind power plant, and the behavior of the wind power plant under fault events.

  19. SciTech Connect: Development of Asset Fault Signatures for Prognostic...

    Office of Scientific and Technical Information (OSTI)

    Development of Asset Fault Signatures for Prognostic and Health Management in the Nuclear Industry Citation Details In-Document Search Title: Development of Asset Fault Signatures...

  20. 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

  1. 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 ...

  2. 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 ...

  3. 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...

  4. 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.

  5. Automatic Fault Characterization via Abnormality-Enhanced Classification

    SciTech Connect (OSTI)

    Bronevetsky, G; Laguna, I; de Supinski, B R

    2010-12-20T23:59:59.000Z

    Enterprise and high-performance computing systems are growing extremely large and complex, employing hundreds to hundreds of thousands of processors and software/hardware stacks built by many people across many organizations. As the growing scale of these machines increases the frequency of faults, system complexity makes these faults difficult to detect and to diagnose. Current system management techniques, which focus primarily on efficient data access and query mechanisms, require system administrators to examine the behavior of various system services manually. Growing system complexity is making this manual process unmanageable: administrators require more effective management tools that can detect faults and help to identify their root causes. System administrators need timely notification when a fault is manifested that includes the type of fault, the time period in which it occurred and the processor on which it originated. Statistical modeling approaches can accurately characterize system behavior. However, the complex effects of system faults make these tools difficult to apply effectively. This paper investigates the application of classification and clustering algorithms to fault detection and characterization. We show experimentally that naively applying these methods achieves poor accuracy. Further, we design novel techniques that combine classification algorithms with information on the abnormality of application behavior to improve detection and characterization accuracy. Our experiments demonstrate that these techniques can detect and characterize faults with 65% accuracy, compared to just 5% accuracy for naive approaches.

  6. The northwest extension of the Meers Fault in southwestern Oklahoma

    E-Print Network [OSTI]

    Cetin, Hasan

    1991-01-01T23:59:59.000Z

    + t '+ + + ~et t 30 mt ~ 39 ~ 40 mt ~ 49 a 50 mt 59 060 m& 69 O20 mts29 26 26 ASZ ? ANNA SEISMIC ZONE ES ? ENOLA SWARM KRF ? KENTUCKY RIVER FAULT MF ? MEERS FAULT MU ? MONROE UPLIFT NM ? NEW MADRID NU ? NEMAHA UPLIFT PSD ? PIERRE, SOUTH DAKOTA WVF...

  7. An Information Flow Model of Fault Detection Margaret C. Thompson ?

    E-Print Network [OSTI]

    Massachusetts at Amherst, University of

    not be practical. Nonethe­ less, Relay provides insight into testing and fault de­ tection and suggests an approach and Computer Science Amherst, MA 01003 University of California Irvine, CA 92717 Abstract Relay is a model of how a fault causes a failure on execution of some test datum. This process begins with introduction

  8. Fault Tolerant Oxygen Control of a Diesel Engine Air System

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Fault Tolerant Oxygen Control of a Diesel Engine Air System Rainer Nitsche Matthias Bitzer control problem of a Diesel engine air system having a jammed Exhaust Gas Recirculation (EGR) valve of the air system. Keywords: Fault tolerant control, Diesel engine, Air system, Model-based trajectory

  9. All-to-all sequenced fault detection system

    DOE Patents [OSTI]

    Archer, Charles Jens (Rochester, MN); Pinnow, Kurt Walter (Rochester, MN); Ratterman, Joseph D. (Rochester, MN); Smith, Brian Edward (Rochester, MN)

    2010-11-02T23:59:59.000Z

    An apparatus, program product and method enable nodal fault detection by sequencing communications between all system nodes. A master node may coordinate communications between two slave nodes before sequencing to and initiating communications between a new pair of slave nodes. The communications may be analyzed to determine the nodal fault.

  10. Fault Detection, Identification and Accommodation for an Electro-hydraulic

    E-Print Network [OSTI]

    Yao, Bin

    Fault Detection, Identification and Accommodation for an Electro-hydraulic System: An Adaptive in electro-hydraulic systems. It is well known fact that any realistic model of a hydraulic system suffers, such a scheme becomes a natural choice for designing robust fault detection algorithms for electro-hydraulic

  11. Arcing fault in sub-distribution branch circuits

    SciTech Connect (OSTI)

    Parise, G.; Grasseli, U.; Luozzo, V. Di (Univ. di Roma, Rome (Italy). Dept. di Ingegneria Elettrica)

    1993-04-01T23:59:59.000Z

    It's well known the importance of short-circuit current evaluation for the design of any power system. Every system is subject to faults, moreover short-circuits and ground faults can be expected in any point. Even if the maximum and minimum values are generally defined with reference at a bolted-fault, bolted short-circuits are rare and the fault usually involves arcing and burning; particularly the limit value of minimum short-circuit depends really on arcing-fault. In earlier experimental investigations into the functional simulation of insulation loss, in branch circuit conductors, the authors chose to normalize the arcing-fault simulation to be used in laboratory tests. This conventional simulation allows characterization of this intrinsically random phenomenon by means of a probabilistic approach, in order to define in statistical terms the expected short circuit value. The authors examine more closely the arcing-fault in the design of sub distribution branch-circuits as weak points of the installation. In fact, what they propose are straightforward criteria, whether in the structure of the system or in the coordination of protection, which afford a more rational control on arcing-fault.

  12. Stator current demodulation for induction machine rotor faults diagnosis

    E-Print Network [OSTI]

    Boyer, Edmond

    with emphasis on stator current processing [1], [2]. It has been proven that mechanical and electrical faultsStator current demodulation for induction machine rotor faults diagnosis El Houssin El Bouchikhi of the stator currents. Hence, demodulation of the stator currents is of high interest for induction machines

  13. Fuzzy Pattern Recognition Based Fault Diagnosis Rafik Bensaadi1

    E-Print Network [OSTI]

    Boyer, Edmond

    Fuzzy Pattern Recognition Based Fault Diagnosis Rafik Bensaadi1 , Leïla H. Mouss1 , Mohamed D in this paper the design of a Fuzzy Pattern Recognition System (FPRS) that solves, in real time, the main. Keywords: Diagnosis, fault detection, pattern recognition, fuzzy control, conjugate gradients, complex

  14. Symbolic identification for fault detection in aircraft gas turbine engines

    E-Print Network [OSTI]

    Ray, Asok

    Symbolic identification for fault detection in aircraft gas turbine engines S Chakraborty, S Sarkar and computationally inexpensive technique of component-level fault detection in aircraft gas-turbine engines identification, gas turbine engines, language-theoretic analysis 1 INTRODUCTION The propulsion system of modern

  15. Online Fault Detection and Tolerance for Photovoltaic Energy Harvesting Systems

    E-Print Network [OSTI]

    Pedram, Massoud

    and weather conditions (e.g., clouds), and the output power of PV systems is directly dependent on solar and mitigate the output power shortage under low levels of solar irradiance. Moreover, PV panels exhibit highly fault detection and tolerance. Our fault detection and tolerance technique reduces output power

  16. Using Reinforcement Learning for Proactive Network Fault Management

    E-Print Network [OSTI]

    Shayman, Mark A.

    fault management demands intelligent man­ agement actions be taken by central manager or remote agents.g., alarms) which appear sequentially. For example, on the manager's side, polling devices randomly (orUsing Reinforcement Learning for Proactive Network Fault Management Qiming He, Mark A. Shayman

  17. Development of Hydrologic Characterization Technology of Fault Zones

    SciTech Connect (OSTI)

    Karasaki, Kenzi; Onishi, Tiemi; Wu, Yu-Shu

    2008-03-31T23:59:59.000Z

    Through an extensive literature survey we find that there is very limited amount of work on fault zone hydrology, particularly in the field using borehole testing. The common elements of a fault include a core, and damage zones. The core usually acts as a barrier to the flow across it, whereas the damage zone controls the flow either parallel to the strike or dip of a fault. In most of cases the damage zone isthe one that is controlling the flow in the fault zone and the surroundings. The permeability of damage zone is in the range of two to three orders of magnitude higher than the protolith. The fault core can have permeability up to seven orders of magnitude lower than the damage zone. The fault types (normal, reverse, and strike-slip) by themselves do not appear to be a clear classifier of the hydrology of fault zones. However, there still remains a possibility that other additional geologic attributes and scaling relationships can be used to predict or bracket the range of hydrologic behavior of fault zones. AMT (Audio frequency Magneto Telluric) and seismic reflection techniques are often used to locate faults. Geochemical signatures and temperature distributions are often used to identify flow domains and/or directions. ALSM (Airborne Laser Swath Mapping) or LIDAR (Light Detection and Ranging) method may prove to be a powerful tool for identifying lineaments in place of the traditional photogrammetry. Nonetheless not much work has been done to characterize the hydrologic properties of faults by directly testing them using pump tests. There are some uncertainties involved in analyzing pressure transients of pump tests: both low permeability and high permeability faults exhibit similar pressure responses. A physically based conceptual and numerical model is presented for simulating fluid and heat flow and solute transport through fractured fault zones using a multiple-continuum medium approach. Data from the Horonobe URL site are analyzed to demonstrate the proposed approach and to examine the flow direction and magnitude on both sides of a suspected fault. We describe a strategy for effective characterization of fault zone hydrology. We recommend conducting a long term pump test followed by a long term buildup test. We do not recommend isolating the borehole into too many intervals. We do recommend ensuring durability and redundancy for long term monitoring.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

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

    E-Print Network [OSTI]

    Gräter, 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. [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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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-ðCNÞ2 are compared to that of the guanidine to differentiate the peptide dynamic contributions to the observables from those of the water solvent. Because

  17. 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

  18. 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

  19. 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

  20. 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