National Library of Energy BETA

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

    2013-07-01

    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.

    2003-01-09

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

  3. Can flat-ramp-flat fault geometry be inferred from fold shape?: A comparison of kinematic and mechanical folds

    E-Print Network [OSTI]

    Savage, Heather M.

    in the suprajacent fold shapes. Differences between the kinematic and mechanical fault-fold relationships highlight rights reserved. Keywords: Fault-bend folding; Mechanical models; Kinematic models; Fault geometry and mechanical models have been used to analyze fault-cored folds. Kinematic models, which balance the geometry

  4. Interplay between faulting and base level in the development of Himalayan frontal fold topography

    E-Print Network [OSTI]

    Interplay between faulting and base level in the development of Himalayan frontal fold topography] Fold topography preserves a potentially accessible record of the structure and evolution of an underlying thrust fault system, provided we understand the factors that shape that topography. Here we

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

    E-Print Network [OSTI]

    McLain, Christopher Thomas

    2001-01-01

    with a weak brittle layer that deforms by faulting and fracturing (dried pottery clay simulates an interbedded siliciclastic unit). The models were deformed in a triaxial deformation rig at confining pressure of 50 Mpa at room temperature. Each model...

  6. Folds above angular fault bends: mechanical constraints for backlimb trishear kinematic models 

    E-Print Network [OSTI]

    Zhang, Li

    2004-11-15

    for the degree of MASTER OF SCIENCE Approved as to style and content by: Judith S. Chester (Chair of Committee) Frederick M. Chester (Member) Charles P. Aubeny (Member) Andrew Hajash Jr. (Head of Department) August 2003 Major Subject: Geology iii ABSTRACT Folds... above Angular Fault Bends: Mechanical Constraints for Backlimb Trishear Kinematic Models. (August 2003) Li Zhang, B.E.; M.S., Southwest Petroleum Institute, P.R.China Chair of Advisory Committee: Dr. Judith S. Chester The backlimb trishear velocity eld...

  7. Kinematics of fault-related folding derived from a sandbox experiment Sylvain Bernard,1,2

    E-Print Network [OSTI]

    Avouac, Jean-Philippe

    be used to determine incremental defor- mation associated with active folds [e.g., Rockwell et al., 1988

  8. 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

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

    SciTech Connect (OSTI)

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

    1986-05-01

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

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

    E-Print Network [OSTI]

    Lambert, George Randall

    1993-01-01

    Results. . Isotope Thermometry . FRACTURE MECHANICS . Analysis Procedure and Results DISCUSSION . Thrust Faulting and Overburden Temperatures. Geothermal Gradient Constraints. Twtn Creek Formation Fluid Flow? Closed system. Open System. . tv vt...C. The lithostatic and hydrostatic thermobartc gradients were calculated using a 26 MPa/km hthostatic gradient, a 10 MPa/km hydrostatic gradient and a 25oC/km geothermal gradient. The present mean surface temperature in this portion of the Idaho-Wyoming-Utah fold...

  11. 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 on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QA J-E-1 SECTION J APPENDIXsource History View NewGuam: Energyarea,Magazine Jump to:II Wind FarmHorst and Graben

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

    SciTech Connect (OSTI)

    Bruno, Michael

    2014-12-08

    Geomechanics Technologies has completed a detailed characterization study of the Wilmington Graben offshore Southern California area for large-scale CO? 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 CO? 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 CO? storage in the area would represent higher risk than other similar size projects in the US and overseas.

  13. Folding Photons

    SciTech Connect (OSTI)

    Gregg, B. A.; van de Lagemaat, J.

    2012-05-01

    Scientists have shown that wrinkles and folds can be used to maximize the absorption of low-energy photons by efficiently redirecting them into a thin absorbing film. This inexpensive technique for structuring photonic substrates could be used to increase the efficiency of many organic photovoltaic cells.

  14. 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))

    1992-01-01

    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.

  15. Fault finder

    DOE Patents [OSTI]

    Bunch, Richard H. (1614 NW. 106th St., Vancouver, WA 98665)

    1986-01-01

    A fault finder for locating faults along a high voltage electrical transmission line. Real time monitoring of background noise and improved filtering of input signals is used to identify the occurrence of a fault. A fault is detected at both a master and remote unit spaced along the line. A master clock synchronizes operation of a similar clock at the remote unit. Both units include modulator and demodulator circuits for transmission of clock signals and data. All data is received at the master unit for processing to determine an accurate fault distance calculation.

  16. 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))

    1993-03-01

    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.

  17. Late Cenozoic partitioning of oblique plate convergence in the Zagros fold-and-thrust belt (Iran)

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Late Cenozoic partitioning of oblique plate convergence in the Zagros fold-and-thrust belt (Iran 2 May 2006. [1] The NW trending Zagros fold-and-thrust belt is affected by two major dextral faults operating at the rear of the belt has become partitioned along the newly formed Main Recent Fault

  18. Origami DNA model Mountain fold

    E-Print Network [OSTI]

    Csürös, Miklós

    Origami DNA model Mountain fold Solid lines are "mountains" and are to be folded away from you with the peak pointing towards you. 1. Fold all solid lines going lengthwise down the page into "mountain folds fold 2. Fold all dashed lines going lengthwise down the page into "valley folds". Mountain folds along

  19. Protein folding tames chaos

    E-Print Network [OSTI]

    Xia, Kelin

    2013-01-01

    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...

  20. Paleotectonics of a complex Miocene half graben formed above a detachment fault: The Diligencia basin, Orocopia Mountains, Southern California

    E-Print Network [OSTI]

    2014-01-01

    California: stratigraphy, petrology, sedimentology andthe age, stratigraphy, sedimentology, petrol- ogy, andstructure, stratigraphy, and sedimentology of a rapidly

  1. Paleotectonics of a complex Miocene half graben formed above a detachment fault: The Diligencia basin, Orocopia Mountains, Southern California

    E-Print Network [OSTI]

    2014-01-01

    eds. , Marine clastic sedimentology: London, Graham andstratigraphy, and sedimentology of a rapidly extendedStratigraphy and sedimentology of the type San Francisquito

  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.

    1997-08-01

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

  3. Algorithmic folding complexity

    E-Print Network [OSTI]

    Cardinal, Jean

    2009-01-01

    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. Fold and thrust partitioning in a contracting fold belt: Insights from the 1931 Mach earthquake in Baluchistan

    E-Print Network [OSTI]

    Bilham, Roger

    models of the earthquake cycle in this fold and thrust belt suggest that slip on the frontal thrust fault is $5 mm/yr. Hence the minimum renewal time between earthquakes with 1.2-m mean displacement should is taken into account the minimum renewal time may exceed 2000 years. Citation: Szeliga, W., R. Bilham, D

  5. Bulletin of the Seismological Society of America, Vol. 94, No. 2, pp. 747752, April 2004 Activity of the Offshore NewportInglewood Rose Canyon Fault Zone,

    E-Print Network [OSTI]

    Shearer, Peter

    Activity of the Offshore Newport­Inglewood Rose Canyon Fault Zone, Coastal Southern California, from Relocated Microseismicity by Lisa B. Grant and Peter M. Shearer Abstract An offshore zone of faulting faults and Quaternary folds have been imaged by seismic reflection profiling along the offshore fault

  6. Simulations of Protein Folding

    E-Print Network [OSTI]

    Michael Cahill; Mark Fleharty; Kevin Cahill

    1999-09-17

    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.

  7. 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

  8. Protein folding and cosmology

    E-Print Network [OSTI]

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

    1997-06-04

    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.

  9. Protein folding and heteropolymers

    E-Print Network [OSTI]

    T. Garel; H. Orland; E. Pitard

    1997-06-12

    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.

  10. Effects of burial history, rock ductility and recovery magnitude on inversion of normal faulted strata 

    E-Print Network [OSTI]

    Kuhle, Nathan John

    2001-01-01

    , and distributed fracturing and folding. The relative contribution of these mechanisms depends on the relative ductility of the rock and magnitude of inversion. Reverse slip on the normal fault and distributed fracturing occur during early stages of inversion...

  11. Optimal fault location 

    E-Print Network [OSTI]

    Knezev, Maja

    2008-10-10

    sequence of events newly obtained recording belongs. Software prototype of the proposed automated fault location analysis is developed using Java programming language. Fault location analysis is automatically triggered by appearance of new event files in a...

  12. Heavy oil reservoirs in the Tulare Fold Belt, Cymric-McKittrick fields, Kern County, California

    SciTech Connect (OSTI)

    Farley, T. (Chevron U.S.A., Bakersfield, CA (USA))

    1990-05-01

    The Tulare fold belt is a series of asymmetric, generally northeast-verging anticlines and synclines in the Pliocene-Pleistocene Tulare Formation that trend northwestward through the Cymric-McKittrick fields. Anticlines within the deformed belt generally originated as fault propagation folds above decollements, the most important of which is the regional decollement on top of the Amnicola sand, the basal Tulare unit. The Amnicola decollement is the northeast subsurface extension of the McKittrick thrust, a low-angle fault that has displaced the Miocene Antelope shale over the Pliocene San Joaquin Formation and locally over the Tulare Formation. The Amnicola decollement is itself deformed by folding related to a younger, deeper decollement near the base of the San Joaquin Formation that merges westward with the Amnicola decollement and defines a zone of faulting associated with the McKittrick thrust Heavy oil reservoirs in the Tulare Formation are currently undergoing active development by thermal recovery techniques. In general, the geometry of heavy oil reservoirs is determined by location within the Tulare fold belt combined with the position of a subhorizontal fluid level trap that forms the updip limit of fluid-saturated rock Reservoir geometry is complicated by complex local structure, discontinuous stratigraphy, and partial depletion of heavy oil reservoirs by fluid withdrawal due to gravity drainage. Proper resolution of fold geometry, fault geometry, and position of the fluid level trap is crucial to the design and monitoring of thermal recovery projects within the Tulare fold belt.

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

    SciTech Connect (OSTI)

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

    1991-06-01

    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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. Protein folding in the ER.

    SciTech Connect (OSTI)

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

    1999-10-01

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

  19. Theoretical Perspectives on Protein Folding

    E-Print Network [OSTI]

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

    2010-07-18

    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.

  20. Scale dependencies in structural analysis as illustrated by chevron folds along the Beartooth Front, Wyoming 

    E-Print Network [OSTI]

    Cook, Robert Annan

    1972-01-01

    of fracture sets found in folded layered rocks and their relationship with fold axis (modified from Stearns, 1968) ~ . 30 Kinking of laminae structures along set 4, fractures in shale . . . . . . . . . . . 31 lla, b, and c. Photographs of typical arcuate... are also under this category. The ductility is assessed by the intensity of layer descrip- tion from fractures and faults. The materials previously mentioned are nearly free of such structures. This ab- sence is not only true for the center...

  1. 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)

    2014-10-28

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

  2. Fault simulation and test generation for small delay faults 

    E-Print Network [OSTI]

    Qiu, Wangqi

    2007-04-25

    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...

  3. Compact intermediates in RNA folding

    SciTech Connect (OSTI)

    Woodson, S.A. (JHU)

    2011-12-14

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

  4. Solar system fault detection

    DOE Patents [OSTI]

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

    1984-05-14

    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.

  5. Solar system fault detection

    DOE Patents [OSTI]

    Farrington, Robert B. (Wheatridge, CO); Pruett, Jr., James C. (Lakewood, CO)

    1986-01-01

    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.

  6. Fast events in protein folding

    SciTech Connect (OSTI)

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

    1996-04-01

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

  7. Transient fault modeling and fault injection simulation 

    E-Print Network [OSTI]

    Yuan, Xuejun

    1996-01-01

    An accurate transient fault model is presented in this thesis. A 7-term exponential current upset model is derived from the results of a device-level, 3-dimensional, single-event-upset simulation. A curve-fitting algorithm is used to extract...

  8. The Wallula fault and tectonic framework of south-central Washington, as interpreted from magnetic and gravity anomalies

    SciTech Connect (OSTI)

    Blakely, Richard J.; Sherrod, Brian; Weaver, Craig; Wells, Ray E.; Rohay, Alan C.

    2014-06-11

    Magnetic and gravity data, collected in south-central Washington near the Yakima Fold and Thrust Belt (YFTB) are used to model upper crustal structure, the extent of the late Columbia River Basalt flow named the Ice Harbor member, the vertical conduits (dikes) that the Ice Harbor erupted from, and whether the dikes are offset or affected by faulting on the Wallula Fault zone.

  9. Effective potentials for Folding Proteins

    E-Print Network [OSTI]

    Nan-yow Chen; Zheng-Yao Su; Chung-Yu Mou

    2006-01-28

    A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of the wild-type sequence of protein G and may have provided important hints to the study of protein folding.

  10. Protein Folding Sculpting Evolutionary Change

    E-Print Network [OSTI]

    Lindquist, Susan

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

  11. 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. Characterization of protein folding intermediates

    SciTech Connect (OSTI)

    Kim, P.S.

    1986-01-01

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

  13. A motion planning approach to protein folding 

    E-Print Network [OSTI]

    Song, Guang

    2004-09-30

    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 ...

  14. A Novel Topology for Representing Protein Folds

    E-Print Network [OSTI]

    Segal, Mark R

    2009-01-01

    1993). Cooperativity in protein-folding kinetics. Proc NatlVoelz VA. (2007). The protein folding problem: when will itMS, Weikl TR. (2008). The protein folding problem. Annu Rev

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

    Office of Scientific and Technical Information (OSTI)

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

  16. SciTech Connect: "protein folding"

    Office of Scientific and Technical Information (OSTI)

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

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

    E-Print Network [OSTI]

    Carswell, Patrick Wayne

    1988-01-01

    and cleared by conventional overcurrent devices. Examples of high impedance fault scenarios include broken conductors and grounded conductors as is the case with tree faults. Most high impedance fault situations occur on the power distribution system due... of the most promising proposals are presented and commented upon as to their weaknesses and limitations if implemented on an actual power distribution system. A new algorithm is developed which attempts to detect the presence of a high impedance fault...

  18. Dominant Pathways in Protein Folding

    E-Print Network [OSTI]

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

    2006-07-27

    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.

  19. Simultaneous Alignment and Folding of Protein Sequences

    E-Print Network [OSTI]

    Devadas, Srinivas

    Simultaneous Alignment and Folding of Protein Sequences J´er^ome Waldisp¨uhl1,2 , Charles W. O techniques are widely applicable to many more protein families. partiFold-Align is available at http://partiFold.csail.mit.edu. 1 Introduction The consensus fold of two proteins is their common minimum energy structure, given

  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. ACCEPTED MANUSCRIPT Fold interaction and wavelength selection

    E-Print Network [OSTI]

    Kaus, Boris

    with the Fars region of the Zagros fold-and-thrust belt including a large range of fold aspect ratio, such as the Makran, appear to be dominated by thrusting, whereas others such as the Simply Folded Belt at Zagros is active which amplifies sufficiently fast. In the Zagros Simply Folded Belt, they argued that weak

  2. Fault tolerant linear actuator

    DOE Patents [OSTI]

    Tesar, Delbert

    2004-09-14

    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.

  3. 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)

    2010-09-14

    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.

  4. 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

  5. Protein folding using contact maps

    E-Print Network [OSTI]

    Michele Vendruscolo; Eytan Domany

    1999-01-21

    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.

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

    E-Print Network [OSTI]

    Horner, Geoffrey Ashworth

    2010-01-01

    Are there pathways for protein folding. J Chim Phys, 1968.p. Dobson, C.M. , Protein folding and misfolding. Nature,Bai, Y. , et al. , Protein folding intermediates: native-

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

    E-Print Network [OSTI]

    Horner, Geoffrey Ashworth

    2010-01-01

    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.

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

    SciTech Connect (OSTI)

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

    2004-07-01

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

  10. Simultaneous alignment and folding of protein sequences

    E-Print Network [OSTI]

    Waldispuhl, Jerome

    Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We presentpartiFold-Align, the first ...

  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. Introduzione alle Proteine e al Protein Folding

    E-Print Network [OSTI]

    Giannozzi, Paolo

    Chapter 4 Introduzione alle Proteine e al Protein Folding 4.1 Proteine: propriet`a strutturali Le protein folding `e il cosiddetto modello HP, nel quale a ogni amino acido `e assegnata l'etichetta di

  13. Shallow structure from a seismic reflection profile across the Borah Peak, Idaho, fault scarp

    E-Print Network [OSTI]

    Miller, Richard D.; Steeples, Don W.

    1986-09-01

    A short 12-fold CDP seismic-reflection survey was performed along the road to Doublespring Pass across the fault scarp formed by the October 28, 1983, magnitude-7.3, Idaho earthquake. This high-resolution reflection survey was conducted to determine...

  14. 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

  15. Simultaneous Alignment and Folding of Protein Sequences

    E-Print Network [OSTI]

    Will, Sebastian

    Simultaneous Alignment and Folding of Protein Sequences J´er^ome Waldisp¨uhl1,2 , Charles W. O-homology proteins. In this work, we present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is poly- nomial in time

  16. 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

  17. 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

  18. 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

  19. Atomistic Protein Folding Simulations on the

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    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

  20. 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

  1. 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

  2. Protein-Folding Dynamics: Overview of Molecular

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Protein-Folding Dynamics: Overview of Molecular Simulation Techniques Harold A. Scheraga, Mey folding in silico. Although just a few years ago the dynamic be- havior of a protein molecule could models of proteins now make it possible to study protein- folding pathways from completely unfolded

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

    Open Energy Info (EERE)

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

  4. Fault interaction near Hollister, California

    SciTech Connect (OSTI)

    Mavko, G.M.

    1982-09-10

    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.

  5. Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures*

    E-Print Network [OSTI]

    Istrail, Sorin

    Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known technique to study protein folding pathways of several small proteins and obtained encouraging results. In this pa- per, we describe how our motion planning framework can be used to study protein folding kinetics

  6. 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

  7. 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

  8. 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

  9. Topological Solitons and Folded Proteins

    E-Print Network [OSTI]

    M. N. Chernodub; Shuangwei Hu; Antti J. Niemi

    2010-03-23

    We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by assembling the solitons together, one after another. We present a simple theoretical model that realizes our proposal and apply it to a number of biologically active proteins including 1VII, 2RB8, 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to construct solitons that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 0.7 Angstrom or less for the central alpha-carbons, i.e. within the limits of current experimental accuracy.

  10. Fault current limiter

    DOE Patents [OSTI]

    Darmann, Francis Anthony

    2013-10-08

    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.

  11. Fault Current Limiters

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious Rank EERE:FinancingPetroleum12, 2015Executive Order14, 20111,FYDepartment of5 NovemberFarms to FuelFault

  12. Protein-Folding Landscapes in Multi-Chain Systems

    E-Print Network [OSTI]

    Cellmer, Troy; Bratko, Dusan; Prausnitz, John M.; Blanch, Harvey

    2005-01-01

    a common approach to studying protein folding in isolationto investigate protein folding in the presence of multipleProtein-Folding Landscapes in Multi-Chain Systems Major

  13. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01

    W. A. (2004). The protein folding 'speed limit'. CurrentG. (1997). Theory of protein folding: the energy landscapeenergy landscape of protein folding: a synthesis. Proteins

  14. Protein-folding via divide-and-conquer optimization

    E-Print Network [OSTI]

    Oliva, Ricardo; Crivelli, Silvia; Meza, Juan

    2004-01-01

    Protein-folding vianumerical optimization Protein folding via divide-and-premise brings the protein-folding problem into the realm of

  15. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01

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

  16. Elucidating amyloid ?-protein folding and assembly: A multidisciplinary approach

    E-Print Network [OSTI]

    2006-01-01

    dynamics approach to protein folding and aggregation.study of amyloid ?-protein folding and oligomerization.nucleation of amyloid ?-protein folding. Proc. Natl. Acad.

  17. Folding amphipathic helices into membranes: Amphiphilicity trumps hydrophobicity

    E-Print Network [OSTI]

    Fernández-Vidal, Mónica; Jayasinghe, Sajith; Ladokhin, Alexey S; White, Stephen H

    2007-01-01

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

  18. On the rough folding landscape of green fluorescent protein

    E-Print Network [OSTI]

    Andrews, Benjamin Thomas

    2008-01-01

    H. (2008). Understanding protein folding: small proteins inmultiple pathways of protein folding. Chem Biol 2, 255-60.Polymer principles and protein folding. Protein Sci 8, 1166-

  19. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01

    unifying mechanism for protein folding? [Review]. Trends incoordinate for protein folding. Journal of Chemical PhysicsIntermediates can accelerate protein folding. Proceedings of

  20. Extending the theoretical framework of protein folding dynamics

    E-Print Network [OSTI]

    Yang, Sichun

    2006-01-01

    Stochastic Dynamics on a Protein Folding Energy Landscape .and J. N. Onuchic. Protein folding funnels: kinetic pathwaysand T. Head-Gordon. Protein folding by distributed computing

  1. Colorado Regional Faults

    SciTech Connect (OSTI)

    Hussein, Khalid

    2012-02-01

    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

  2. Optimized Fault Location Final Project Report

    E-Print Network [OSTI]

    Optimized Fault Location Final Project Report Power Systems Engineering Research Center A National Engineering Research Center Optimized Fault Location Concurrent Technologies Corporation Final Project Report

  3. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect (OSTI)

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

    2010-05-25

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

  4. Observer-based fault detection for nuclear reactors

    E-Print Network [OSTI]

    Li, Qing, 1972-

    2001-01-01

    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 ...

  5. DMBC: Web Planning & Layouts Above the Fold

    E-Print Network [OSTI]

    Stowell, Michael

    DMBC: Web Planning & Layouts Above the Fold · Website width · Website Height · Important content · From an Image Web Layouts Photoshop · Canvas Size · Guide Lines · Shapes #12;· Text (Lorem Ipsum

  6. Arc fault detection system

    DOE Patents [OSTI]

    Jha, Kamal N. (Bethel Park, PA)

    1999-01-01

    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.

  7. Arc fault detection system

    DOE Patents [OSTI]

    Jha, K.N.

    1999-05-18

    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.

  8. Insights into fold growth using fold-related joint patterns and mechanical stratigraphy

    E-Print Network [OSTI]

    Savage, Heather M.

    Insights into fold growth using fold-related joint patterns and mechanical stratigraphy Heather M Available online 17 September 2010 Keywords: Sheep Mountain Anticline Joint pattern Mechanical stratigraphy, we integrate mechanical stratigraphy with joint pattern analysis to determine relative timing

  9. Hot Pot Detail - Evidence of Quaternary Faulting

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

    Lane, Michael

    2013-06-27

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

  10. 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.

  11. STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS

    E-Print Network [OSTI]

    Dinner, Aaron

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

  12. 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 sequence-independent local interactions which are found to strongly influence the thermodynamics

  13. Control of folding by gravity and matrix thickness: Implications for large-scale folding

    E-Print Network [OSTI]

    Podladchikov, Yuri

    and the Zagros Mountains but does control folding in central Asia. Applicability conditions of viscous and thin

  14. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1996-06-11

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

  15. Cooperative Tertiary Interaction Network Guides RNA Folding

    SciTech Connect (OSTI)

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

    2013-04-08

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

  16. Fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1996-01-01

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

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

    E-Print Network [OSTI]

    Latombe, Jean-Claude

    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

  18. Fault-tolerant TCP mechanisms 

    E-Print Network [OSTI]

    Satapati, Suresh Kumar

    2000-01-01

    While fault-tolerance is supported by a variety of critical services that can be accessed over the Internet, they are not robust in that they are oblivious of the impact of their tolerant mechanisms on the service they ...

  19. A fluvial record of active fault-propagation folding, Salsomaggiore anticline, northern Apennines, Italy

    E-Print Network [OSTI]

    Pazzaglia, Frank J.

    terraces [e.g., Rockwell et al., 1988; Molnar et al., 1994; Benedetti et al., 2000; Lave´ and Avouac, 2000

  20. Modeling the shortening history of a fault tip fold using structural and geomorphic records of deformation

    E-Print Network [OSTI]

    Avouac, Jean-Philippe

    [Rockwell et al., 1988; Lave´ and Avouac, 2000; Benedetti et al., 2000; Thompson et al., 2002]. At deeper

  1. 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

  2. Multiple folding pathways of proteins with shallow knots and co-translational folding

    E-Print Network [OSTI]

    Chwastyk, Mateusz

    2015-01-01

    We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding.

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

    E-Print Network [OSTI]

    Neal, Leslie Ann

    2002-01-01

    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...

  4. Protein Folding as a Physical Stochastic Process

    E-Print Network [OSTI]

    Kerson Huang

    2007-07-17

    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.

  5. Sandia Energy - PV Arc-Fault and Ground Fault Detection and Mitigation...

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

    Program Home Stationary Power Energy Conversion Efficiency Solar Energy Photovoltaics PV Systems Reliability PV Arc-Fault and Ground Fault Detection and Mitigation Program PV...

  6. Cotranslational folding of deeply knotted proteins

    E-Print Network [OSTI]

    Chwastyk, Mateusz

    2015-01-01

    Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.

  7. Inverse Folding of RNA Pseudoknot Structures

    E-Print Network [OSTI]

    Gao, James Z M; Reidys, Christian M

    2010-01-01

    Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \\pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, {\\tt RNAinverse}, {\\tt RNA-SSD} as well as {\\tt INFO-RNA} are limited to RNA secondary structures, we present in this paper the inverse folding algorithm {\\tt Inv} which can deal with 3-noncrossing, canonical pseudoknot structures. Results: In this paper we present the inverse folding algorithm {\\tt Inv}. We give a detailed analysis of {\\tt Inv}, including pseudocodes. We show that {\\tt Inv} allows to...

  8. Mutagenic effects on protein folding and stability

    E-Print Network [OSTI]

    Anderson, Thomas Anthony, 1973-

    2002-01-01

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

  9. 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

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

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-12-28

    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.

  11. A phenomenological model of protein folding

    E-Print Network [OSTI]

    Danielsson, Ulf H; Niemi, Antti J

    2009-01-01

    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.

  12. 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

  13. 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

  14. 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

  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. 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

  17. Protein Folding: A Perspective From Statistical Physics

    E-Print Network [OSTI]

    Jinzhi Lei; Kerson Huang

    2010-02-26

    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^{\

  18. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01

    and the mechanism of protein folding. Ann Rev Biochem 1982;Baldwin RL. How does protein folding get started? TRENDS inNucleation mechanisms in protein folding. Current Opinion in

  19. Increasing Stability Reduces Conformational Heterogeneity in a Protein Folding

    E-Print Network [OSTI]

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

  20. Exploring zipping and assembly as a protein folding principle

    E-Print Network [OSTI]

    Voelz, Vince A; Dill, Ken A

    2007-01-01

    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

  1. 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

  2. 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

  3. Predicting Protein Folding Kinetics via Temporal Logic Model Checking: Extended

    E-Print Network [OSTI]

    Langmead, Christopher James

    Predicting Protein Folding Kinetics via Temporal Logic Model Checking: Extended Abstract Abstract. We present a novel approach for predicting protein folding kinetics using techniques from checking. We tested our method on 19 test proteins. The quantitative predictions regarding folding rates

  4. Sensor Fault Detection and Isolation System 

    E-Print Network [OSTI]

    Yang, Cheng-Ken

    2014-08-01

    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 ...

  5. Boullier The fault zone geology 1 Fault zone geology: lessons from drilling through the Nojima and 1

    E-Print Network [OSTI]

    Boyer, Edmond

    Boullier The fault zone geology 1 Fault zone geology: lessons from active faults with the aim of 11 learning about the geology of the fault all 18 their objectives, have still contributed to a better geological

  6. Fault Models for Quantum Mechanical Switching Networks

    E-Print Network [OSTI]

    Jacob Biamonte; Jeff S. Allen; Marek A. Perkowski

    2010-01-19

    The difference between faults and errors is that, unlike faults, errors can be corrected using control codes. In classical test and verification one develops a test set separating a correct circuit from a circuit containing any considered fault. Classical faults are modelled at the logical level by fault models that act on classical states. The stuck fault model, thought of as a lead connected to a power rail or to a ground, is most typically considered. A classical test set complete for the stuck fault model propagates both binary basis states, 0 and 1, through all nodes in a network and is known to detect many physical faults. A classical test set complete for the stuck fault model allows all circuit nodes to be completely tested and verifies the function of many gates. It is natural to ask if one may adapt any of the known classical methods to test quantum circuits. Of course, classical fault models do not capture all the logical failures found in quantum circuits. The first obstacle faced when using methods from classical test is developing a set of realistic quantum-logical fault models. Developing fault models to abstract the test problem away from the device level motivated our study. Several results are established. First, we describe typical modes of failure present in the physical design of quantum circuits. From this we develop fault models for quantum binary circuits that enable testing at the logical level. The application of these fault models is shown by adapting the classical test set generation technique known as constructing a fault table to generate quantum test sets. A test set developed using this method is shown to detect each of the considered faults.

  7. 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

  8. Protein Folding: A New Geometric Analysis

    E-Print Network [OSTI]

    Walter A. Simmons; Joel L. Weiner

    2008-09-11

    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.

  9. High temperature superconducting fault current limiter

    DOE Patents [OSTI]

    Hull, J.R.

    1997-02-04

    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.

  10. High temperature superconducting fault current limiter

    DOE Patents [OSTI]

    Hull, John R. (Hinsdale, IL)

    1997-01-01

    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).

  11. Exploring the mechanisms of protein folding

    E-Print Network [OSTI]

    Xu, Ji; Ren, Ying; Li, Jinghai

    2013-01-01

    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,...

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

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01

    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...

  13. CSAW: a dynamical model of protein folding

    E-Print Network [OSTI]

    Kerson Huang

    2006-01-12

    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.

  14. Nonlinear conformation of secondary protein folding

    E-Print Network [OSTI]

    Januar, M; Handoko, L T

    2012-01-01

    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.

  15. Resistance proof, folding-inhibitor drugs

    E-Print Network [OSTI]

    R. Broglia; G. Tiana; R. Berera

    2002-10-09

    Conventional drugs work, as a rule, by inhibiting the enzymatic activity of specific proteins, capping their active site. In this paper we present a model of non- conventional drug design based on the inhibiting effects small peptides obtained from segments of the protein itself have on the folding ability of the system. Such peptides attach to the newly expressed (unfolded) protein and inhibit its folding, inhibition which cannot be avoided but through mutations which in any case denaturate the enzyme. These peptides, or their mimetic molecules, can be used as effective alternative drugs to those already available, displaying the advantage of not suffering from the upraise of resistence.

  16. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

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

    2011-06-14

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

  17. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

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

    2008-06-24

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

  18. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12

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

  19. Circular permutant GFP insertion folding reporters

    DOE Patents [OSTI]

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16

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

  20. DNA Nanomechanical Switches under Folding Kinetics Control

    E-Print Network [OSTI]

    Meller, Amit

    DNA Nanomechanical Switches under Folding Kinetics Control Virgile Viasnoff,, Amit Meller operate at equilibrium under changes in solution composition. We propose an alternative DNA switch design after heat denaturation drives the switch to its lowest energy conformation, while rapid cooling (>100

  1. Solvent-induced forces in protein folding

    SciTech Connect (OSTI)

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

    1990-08-23

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

  2. Critical aspects of hierarchical protein folding

    E-Print Network [OSTI]

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

    1998-01-13

    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.

  3. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

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

    1995-08-08

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

  4. Folded-path optical analysis gas cell

    DOE Patents [OSTI]

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

    1995-01-01

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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. A simple theory of protein folding kinetics

    E-Print Network [OSTI]

    Pande, Vijay S

    2010-01-01

    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.

  14. Inverse folding of RNA pseudoknot structures

    E-Print Network [OSTI]

    Gao, James Z M; Reidys, Christian M

    2009-01-01

    Results: In this paper we present the inverse folding algorithm {\\tt inv} as well as two applications. We give a detailed analysis of {\\tt inv}, including pseudocodes. The algorithm is freely available at \\url{http://www.combinatorics.cn/cbpc/inv.html}. We show, using 3-noncrossing nonplanar RNA pseudoknot structures as an example, that {\\tt inv} allows to design specific 3-noncrossing RNA structures. Furthermore we use {\\tt inv} for estimating the distance of the neutral networks. Conclusions: The algorithm {\\tt inv} extends inverse folding capabilities to RNA pseudoknot structures. In comparison with {\\tt RNAinverse} it uses new ideas, for instance by taking sets of competing structures into consideration. As a result, {\\tt inv} is able to find novel sequences even for RNA secondary structures.

  15. The coarsening of folds in hanging drapes

    E-Print Network [OSTI]

    Peter Bella; Robert V. Kohn

    2015-07-29

    We consider the elastic energy of a hanging drape -- a thin elastic sheet, pulled down by the force of gravity, with fine-scale folding at the top that achieves approximately uniform confinement. This example of energy-driven pattern formation in a thin elastic sheet is of particular interest because the length scale of folding varies with height. We focus on how the minimum elastic energy depends on the physical parameters. As the sheet thickness vanishes, the limiting energy is due to the gravitational force and is relatively easy to understand. Our main accomplishment is to identify the "scaling law" of the correction due to positive thickness. We do this by (i) proving an upper bound, by considering the energies of several constructions and taking the best; (ii) proving an ansatz-free lower bound, which agrees with the upper bound up to a parameter-independent prefactor. The coarsening of folds in hanging drapes has also been considered in the recent physics literature, using a self-similar construction whose basic cell has been called a "wrinklon." Our results complement and extend that work, by showing that self-similar coarsening achieves the optimal scaling law in a certain parameter regime, and by showing that other constructions (involving lateral spreading of the sheet) do better in other regions of parameter space. Our analysis uses a geometrically linear F\\"{o}ppl-von K\\'{a}rm\\'{a}n model for the elastic energy, and is restricted to the case when Poisson's ratio is zero.

  16. Fault-tolerant dynamic task graph scheduling

    SciTech Connect (OSTI)

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

    2014-11-16

    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.

  17. 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.

    2011-01-01

    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

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

    E-Print Network [OSTI]

    Andoh, Kwame Sarpong

    2000-01-01

    Locating the faulted section of a distribution system is a difficult task because of lack of accurate system models and the presence of uncertainty in the data used for estimating the fault section. Many of the methods used to account...

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

    E-Print Network [OSTI]

    Cohrs, Frelynn Joseph Reese

    2012-07-16

    . The seismic data revealed dispersive energy packets, indicative of guided waves, within the fault zone and absent in the surrounding lithologies. The seismoelectric data was able to produce comparable signals in the fault zone showing guided waves....

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

    E-Print Network [OSTI]

    Thadhlani, Ajaykumar A

    2001-01-01

    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 model and does not account...

  1. Earthquake Nucleation on Geometrically Complex Faults

    E-Print Network [OSTI]

    Fang, Zijun

    2009-01-01

    Preseismic fault slip and earthquake prediction, J. Geophys.Day, The 1999 Izmit, Turkey, earthquake: A 3D dynamic stresstransfer model of intra-earthquake triggering, Bull.

  2. Earthquake Nucleation on Geometrically Complex Faults

    E-Print Network [OSTI]

    Fang, Zijun

    2009-01-01

    fault slip and earthquake prediction, J. Geophys. Res. , [implications for an earthquake prediction field monitoringpredictions of hypocenter location and occurrence time of earthquakes,

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

    E-Print Network [OSTI]

    Sar-Dessai, Vijay Ramesh

    1999-01-01

    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 ...

  4. Earthquake behavior and structure of oceanic transform faults

    E-Print Network [OSTI]

    Roland, Emily Carlson

    2012-01-01

    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 ...

  5. Fault Intersection | 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 on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QA J-E-1 SECTIONRobertsdale, AlabamaETEC GmbHFarinello Geothermal Power Station JumpFaroeFaulk County,Fault

  6. Fault Mapping | 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 on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QA J-E-1 SECTIONRobertsdale, AlabamaETEC GmbHFarinello Geothermal Power Station JumpFaroeFaulk County,FaultMapping

  7. Intermediates and the folding of proteins L and G

    E-Print Network [OSTI]

    Brown, Scott; Head-Gordon, Teresa

    2008-01-01

    a unifying mechanism for protein folding? [Review]. TrendsOn the transition coordinate for protein folding. Journal ofMonoclonal Antibodies. Protein Science 6(1), 99-108. Strang,

  8. 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

  9. On the Kinematics of Protein Folding SEAN CAHILL,1

    E-Print Network [OSTI]

    Cahill, Kevin

    On the Kinematics of Protein Folding SEAN CAHILL,1 MICHAEL CAHILL,2 KEVIN CAHILL3 1 Department words: protein folding; homology modeling; loops; Monte Carlo; kinematics; wriggling Three Kinematic

  10. 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

  11. New Crystal Structures Lift Fog around Protein Folding

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

    may have found a new way to modify protein-folding activities. For example, engineering the nucleotide-sensing loop so that it promotes the desired rate of protein folding...

  12. Computational and experimental investigations of forces in protein folding 

    E-Print Network [OSTI]

    Schell, David Andrew

    2005-02-17

    Properly folded proteins are necessary for all living organisms. Incorrectly folded proteins can lead to a variety of diseases such as Alzheimer?s Disease or Bovine Spongiform Encephalitis (Mad Cow Disease). Understanding ...

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

    E-Print Network [OSTI]

    Wei, Yun

    2010-07-14

    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...

  14. How paper folds: bending with local constraints

    E-Print Network [OSTI]

    Jemal Guven; Martin Michael Mueller

    2007-12-06

    A variational framework is introduced to describe how a surface bends when it is subject to local constraints on its geometry. This framework is applied to describe the patterns of a folded sheet of paper. The unstretchability of paper implies a constraint on the surface metric; bending is penalized by an energy quadratic in mean curvature. The local Lagrange multipliers enforcing the constraint are identified with a conserved tangential stress that couples to the extrinsic curvature of the sheet. The framework is illustrated by examining the deformation of a flat sheet into a generalized cone.

  15. A Fault Oblivious Extreme-Scale Execution Environment

    SciTech Connect (OSTI)

    McKie, Jim

    2014-11-20

    The FOX project, funded under the ASCR X-stack I program, developed systems software and runtime libraries for a new approach to the data and work distribution for massively parallel, fault oblivious application execution. Our work was motivated by the premise that exascale computing systems will provide a thousand-fold increase in parallelism and a proportional increase in failure rate relative to today’s machines. To deliver the capability of exascale hardware, the systems software must provide the infrastructure to support existing applications while simultaneously enabling efficient execution of new programming models that naturally express dynamic, adaptive, irregular computation; coupled simulations; and massive data analysis in a highly unreliable hardware environment with billions of threads of execution. Our OS research has prototyped new methods to provide efficient resource sharing, synchronization, and protection in a many-core compute node. We have experimented with alternative task/dataflow programming models and shown scalability in some cases to hundreds of thousands of cores. Much of our software is in active development through open source projects. Concepts from FOX are being pursued in next generation exascale operating systems. Our OS work focused on adaptive, application tailored OS services optimized for multi ? many core processors. We developed a new operating system NIX that supports role-based allocation of cores to processes which was released to open source. We contributed to the IBM FusedOS project, which promoted the concept of latency-optimized and throughput-optimized cores. We built a task queue library based on distributed, fault tolerant key-value store and identified scaling issues. A second fault tolerant task parallel library was developed, based on the Linda tuple space model, that used low level interconnect primitives for optimized communication. We designed fault tolerance mechanisms for task parallel computations employing work stealing for load balancing that scaled to the largest existing supercomputers. Finally, we implemented the Elastic Building Blocks runtime, a library to manage object-oriented distributed software components. To support the research, we won two INCITE awards for time on Intrepid (BG/P) and Mira (BG/Q). Much of our work has had impact in the OS and runtime community through the ASCR Exascale OS/R workshop and report, leading to the research agenda of the Exascale OS/R program. Our project was, however, also affected by attrition of multiple PIs. While the PIs continued to participate and offer guidance as time permitted, losing these key individuals was unfortunate both for the project and for the DOE HPC community.

  16. Investigation of active faulting at the Emigrant Peak fault in Nevada using shallow seismic reflection and ground penetrating radar

    E-Print Network [OSTI]

    Christie, Michael Wayne

    2007-12-18

    The objective of this study was to assess fault displacement, off-fault deformation, and alluvial fan stratigraphy at the Emigrant Peak fault zone (EPFZ) in Fish Lake Valley, Nevada utilizing shallow seismic reflection (SSR) and ground penetrating...

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

    E-Print Network [OSTI]

    Burrell, Richard Dennis

    1997-01-01

    being cited as responsible for the Meers Fault scarp. Earthquakes of magnitude 7 to 8 occurring in conjunction with recent reactivation of the fault have been calculated. However, evidence found within the Wichita Mountains just south of the fault...

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

    E-Print Network [OSTI]

    Dong, Yimai

    2013-11-07

    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...

  19. 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

  20. 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

  1. Predicting Protein Folding Kinetics via Temporal Logic Model Checking

    E-Print Network [OSTI]

    Predicting Protein Folding Kinetics via Temporal Logic Model Checking Christopher James Langmead award from the U.S. Department of Energy. #12;Keywords: protein folding, model checking, temporal logic #12;Abstract We present a novel approach for predicting protein folding kinetics using techniques from

  2. 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

  3. Protein Folding Simulation by Two-Stage Optimization

    E-Print Network [OSTI]

    Will, Sebastian

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

  4. 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

  5. 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

  6. 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

  7. A Complete and Effective Move Set for Simplified Protein Folding

    E-Print Network [OSTI]

    Whitesides, Sue

    A Complete and Effective Move Set for Simplified Protein Folding Neal Lesh Mitsubishi Electric­13, 2003, Berlin, Germany. Copyright 2003 ACM 1-58113-635-8/03/0004 ...$5.00. Keywords protein folding, it captures the main features of the protein folding prob- lem. This problem is NP-complete, and hence

  8. 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

  9. 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

  10. 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

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

    E-Print Network [OSTI]

    Janke, Wolfhard

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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. Self-folding miniature elastic electric devices Shuhei Miyashita1

    E-Print Network [OSTI]

    Wood, Robert

    , inspired by Origami art work and protein folding, have been exploited for the con- struction of various folds using global heating [9]. Whitney et al developed m-scale robots based on pop- up methods [10], and Abel et al presented a theoretical fra- mework for designing pop-up parallel folds [11]. Techniques

  18. Protein Folding in Contact Map Space Eytan Domany

    E-Print Network [OSTI]

    Domany, Eytan

    Protein Folding in Contact Map Space Eytan Domany Department of Physics of Complex Systems to the free energy is unable to stabilize the native fold of a single protein against a set of carefully dimensional structure determines the biological function of a protein. The pro­ tein folding problem, i

  19. Distribution of Protein Folds in the Three Superkingdoms of Life

    E-Print Network [OSTI]

    Distribution of Protein Folds in the Three Superkingdoms of Life Yuri I. Wolf,1,4 Steven E. Brenner Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois 60611 USA A sensitive protein-fold. In the completely sequenced genomes, folds could be automatically identified for 20%­30% of the proteins, with 3

  20. Folding simulations of small proteins Seung-Yeon Kima

    E-Print Network [OSTI]

    Lee, Jooyoung

    Folding simulations of small proteins Seung-Yeon Kima , Julian Leeb , Jooyoung Leea,* a School Abstract Understanding how a protein folds is a long-standing challenge in modern science. We have used an optimized atomistic model (united- residue force field) to simulate folding of small proteins of various

  1. Folding energy landscape and network dynamics of small globular proteins

    E-Print Network [OSTI]

    Berry, R. Stephen

    Folding energy landscape and network dynamics of small globular proteins Naoto Horia , George for review September 17, 2008) The folding energy landscape of proteins has been suggested to be funnel coordinates Proteins fold on large-dimensional energy landscapes through myriads of conformations. One energy

  2. Protein Folding in the Endoplasmic Reticulum Ineke Braakman1

    E-Print Network [OSTI]

    Hebert, Daniel N.

    Protein Folding in the Endoplasmic Reticulum Ineke Braakman1 and Daniel N. Hebert2 1 Cellular Correspondence: i.braakman@uu.nl; dhebert@biochem.umass.edu In this article, wewill cover the folding of proteins­trans isomerase families. We will conclude with the perspective of the folding protein: a comparison

  3. Structure Learning for Generative Models of Protein Fold Families

    E-Print Network [OSTI]

    Structure Learning for Generative Models of Protein Fold Families Sivaraman Balakrishnan composition of the proteins within a fold family are widely used in science and engineering. Existing composition of the proteins within a fold family provide insights into the constraints that govern structure

  4. Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble

    E-Print Network [OSTI]

    Stanley, H. Eugene

    Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble Feng Ding for the interpretation of experimental results and understanding of protein folding mechanics, which has at- tracted, 1999; Guerois and Serrano, 2000) have been proposed to predict the transition states in protein folding

  5. Folding simulations of a three-stranded antiparallel -sheet peptide

    E-Print Network [OSTI]

    Caflisch, Amedeo

    for review May 11, 2000) Protein folding is a grand challenge of the postgenomic era. In this paper, 58 in general for antiparallel -sheets with short turns. protein folding energy landscape implicit solvation model Theoretical and experimental studies have provided insights into the protein folding process (1

  6. PeriodicitiesinSequenceResidueHydropathyandtheImplicationsonProteinFolds Nancy Zhang

    E-Print Network [OSTI]

    Brutlag, Doug

    1 PeriodicitiesinSequenceResidueHydropathyandtheImplicationsonProteinFolds Nancy Zhang March, 2000 algorithms is that there are hidden variables effecting the protein folding mechanism and explain why it is crucial to a protein's fold. In section III, I will explain how the Fourier transform

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

    E-Print Network [OSTI]

    Ali R. Mohazab; Steven S. Plotkin

    2012-11-30

    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-dominated folding mechanisms for sufficiently long chains. We further quantify the minimal folding pathways by collecting the sequence of uncrossing moves, which generally involve leg, loop, and elbow-like uncrossing moves, and rendering the collection of these moves over the unfolded ensemble as a multiple-transformation "alignment". The consensus minimal pathway is constructed and shown schematically for representative cases of an $\\alpha$, $\\beta$, and knotted protein. An overlap parameter is defined between pathways; we find that $\\alpha$ proteins have minimal overlap indicating diverse folding pathways, knotted proteins are highly constrained to follow a dominant pathway, and $\\beta$ proteins are somewhere in between. Thus we have shown how topological chain constraints can induce dominant pathway mechanisms in protein folding.

  8. PERSPECTIVES Deep Earthquakes: A Fault Too Big?

    E-Print Network [OSTI]

    Stein, Seth

    PERSPECTIVES Deep Earthquakes: A Fault Too Big? Seth Stein Because deep Earth processes are inacces. Recent results for the mys- terious deep earthquakes that occur to depths greater than 600 km is that large deep earthquakes (1-3) seem to have occurred on faults larger than ex- pected from the competing

  9. 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

  10. Sensor Fault Diagnosis Using Principal Component Analysis 

    E-Print Network [OSTI]

    Sharifi, Mahmoudreza

    2010-07-14

    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...

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

    SciTech Connect (OSTI)

    Boles, James [Professor

    2013-05-24

    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.

  12. Introduction to protein folding for physicists

    E-Print Network [OSTI]

    Pablo Echenique

    2007-05-13

    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.

  13. Self-triggering superconducting fault current limiter

    DOE Patents [OSTI]

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

    2008-10-21

    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.

  14. Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins

    E-Print Network [OSTI]

    Janke, Wolfhard

    parts of the sequence. Moreover, for most proteins, the folding process is relatively slow (microsecTwo-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins Stefan Schnabel,* Michael Bachmann, and Wolfhard Janke Institut fu¨r Theoretische

  15. Effects of Familial Alzheimer's Disease Mutations on the Folding Nucleation of the Amyloid ?-Protein

    E-Print Network [OSTI]

    2008-01-01

    nucleation of amyloid ?-protein folding. Proc. Natl Acad.dynamics method for protein folding. Chem. Phys. Lett. 314,Atomic simulations of protein folding using the replica

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

    E-Print Network [OSTI]

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

    2014-01-01

    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

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

    E-Print Network [OSTI]

    Cho, Samuel Sung-Il

    2007-01-01

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

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

    E-Print Network [OSTI]

    Capraro, Dominique T.

    2008-01-01

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

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

    E-Print Network [OSTI]

    Polinkovsky, Mark E.; Polinkovsky, Mark E.

    2012-01-01

    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.

    2006-01-01

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

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

    E-Print Network [OSTI]

    Connell, Katelyn Blair

    2010-01-01

    Unifying features in protein- folding mechanisms. Proc NatlDramatic acceleration of protein folding by stabilization ofL. & Englander, S. W. (1995). Protein folding intermediates:

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

    E-Print Network [OSTI]

    Weinkam, Patrick

    2009-01-01

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

  3. A biochemical analysis of the complex protein folding machinery in algal chloroplasts

    E-Print Network [OSTI]

    Tran, Miller

    2012-01-01

    1992). "Hsp90 chaperones protein folding in vitro." NatureMolecular chaperones in protein folding and proteostasis."analysis of the complex protein folding machinery in algal

  4. Amyloid ?-Protein Monomer Folding: Free-Energy Surfaces Reveal Alloform-Specific Differences

    E-Print Network [OSTI]

    Yang, M; Teplow, DB

    2008-01-01

    study of amyloid ?-protein folding and oligomerization.Elucidating amyloid ?-protein folding and assembly: A multi-of Alzheimer's amyloid ?-protein folding and assembly. Curr.

  5. Fault-Tolerant Exact State Transmission

    E-Print Network [OSTI]

    Zhao-Ming Wang; Lian-Ao Wu; Michele Modugno; Wang Yao; Bin Shao

    2012-05-02

    We show that a category of one-dimensional XY-type models may enable high-fidelity quantum state transmissions, regardless of details of coupling configurations. This observation leads to a fault- tolerant design of a state transmission setup. The setup is fault-tolerant, with specified thresholds, against engineering failures of coupling configurations, fabrication imperfections or defects, and even time-dependent noises. We propose the implementation of the fault-tolerant scheme using hard-core bosons in one-dimensional optical lattices.

  6. Cooperative application/OS DRAM fault recovery.

    SciTech Connect (OSTI)

    Ferreira, Kurt Brian; Bridges, Patrick G. (University of New Mexico, Albuquerque, NM); Heroux, Michael Allen; Hoemmen, Mark; Brightwell, Ronald Brian

    2012-05-01

    Exascale systems will present considerable fault-tolerance challenges to applications and system software. These systems are expected to suffer several hard and soft errors per day. Unfortunately, many fault-tolerance methods in use, such as rollback recovery, are unsuitable for many expected errors, for example DRAM failures. As a result, applications will need to address these resilience challenges to more effectively utilize future systems. In this paper, we describe work on a cross-layer application/OS framework to handle uncorrected memory errors. We illustrate the use of this framework through its integration with a new fault-tolerant iterative solver within the Trilinos library, and present initial convergence results.

  7. Fault Detection and Diagnosis in Building HVAC Systems

    E-Print Network [OSTI]

    Najafi, Massieh

    2010-01-01

    of outside air condition, occupant behavior, and buildingair condition and occupant behavior) and fault condition (

  8. Initiation of the San Jacinto Fault and its Interaction with the San Andreas Fault: Insights from Geodynamic Modeling

    E-Print Network [OSTI]

    Liu, Mian

    Initiation of the San Jacinto Fault and its Interaction with the San Andreas Fault: Insights from Geodynamic Modeling QINGSONG LI 1,2 and MIAN LIU 1 Abstract--The San Andreas Fault (SAF) is the Pacific is accommodated by the San Jacinto Fault (SJF). Here we investigate the initiation of the SJF and its interaction

  9. 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

  10. The propagation and linkage of normal faults: Insights from the Strathspey-Brent-Statfjord fault array, northern North Sea

    E-Print Network [OSTI]

    McLeod, Aileen E.

    2001-01-01

    Through examination of the scaling relations of faults and the use of seismic stratigraphic techniques,

  11. Inferring the Rate-Length Law of Protein Folding

    E-Print Network [OSTI]

    Lane, Thomas J

    2013-01-01

    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.

  12. An energy landscape theory for cotranslational protein folding

    E-Print Network [OSTI]

    Tourigny, David S

    2013-01-01

    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...

  13. Dodging the crisis of folding proteins with knots

    E-Print Network [OSTI]

    Joanna I. Su?kowska; Piotr Su?kowski; José N. Onuchic

    2009-12-30

    Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, which involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in around 1-2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies.

  14. Accordian-folded boot shield for flexible swivel connection

    DOE Patents [OSTI]

    Hoh, Joseph C. (Naperville, IL)

    1986-01-01

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

  15. 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

    1983-01-01

    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...

  16. When pigs fly: a study of computer generated paper folding 

    E-Print Network [OSTI]

    Nitsch, Elizabeth Jeanette

    2009-05-15

    of folds form bases, or starting shapes, which are common to the construction of more than one figure. The classic, or best-known bases, are the kite base, fish base, bird base, and frog base [5] (Fig. 5). 4 Fig. 4. Basic origami folds... suitable for everything from clothing and architecture to lanterns, kites, and, of course, origami [11]. 6 HISTORY OF ORIGAMI Given that paper originated in China, many historians trace the development of artistic paper folding to that country...

  17. A connecting network with fault tolerance capabilities

    SciTech Connect (OSTI)

    Ciminiera, L.; Serra, A.

    1986-06-01

    A new multistage interconnection network is presented in this paper. It is able to handle the communications between the connected devices correctly, even in the presence of fault(s) in the network. This goal is achieved by using redundant paths with a fast procedure able to dynamically reroute the message. It is also shown that the rerouting properties are still valid when broadcasting transmission is used.

  18. A dynamical approach to protein folding

    E-Print Network [OSTI]

    Alessandro Torcini; Roberto Livi; Antonio Politi

    2001-03-13

    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.

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

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

    for parallel readwrite processes. (Click image to view larger.) VERIFI code optimization yields three-fold increase in engine simulation speed By Greg Cunningham * May 7,...

  20. New Crystal Structures Lift Fog around Protein Folding

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

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

  1. Hundred-Fold Improvement in Temperature Mapping Reveals the Stresses...

    Office of Science (SC) Website

    Hundred-Fold Improvement in Temperature Mapping Reveals the Stresses Inside Tiny Transistors Basic Energy Sciences (BES) BES Home About Research Facilities Science Highlights...

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

    E-Print Network [OSTI]

    Chekmarev, Sergei F

    2013-01-01

    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.

  3. Thermodynamics of protein folding: a random matrix formulation

    E-Print Network [OSTI]

    Pragya Shukla

    2010-10-16

    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.

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

  6. Folded inflatable protective device and method for making same

    DOE Patents [OSTI]

    Behr, V.L.; Nelsen, J.M.; Gwinn, K.W.

    1998-10-20

    An apparatus and method are disclosed for making an inflatable protective device made of lightweight material that can withstand the initial stress from inflation and enhance radial inflation. The device includes a cushion and an inflator port. The invention further includes several stacks of folded cushion material including a combination of full-width stacks and half-width stacks: a first full-width stack defined by one or more fan folds in a first lateral half of the cushion wherein the folds are substantially centered above a first center line and are substantially over the inflator port; a second full-width stack defined by one or more fan folds in a second lateral half of the cushion wherein the folds are substantially centered above the first center line and substantially over the inflator port in the first full-width stack; a first half-width stack defined by a plurality of fan folds in the bottom of the cushion where neither edge of each fold extends substantially over the second center line; and a second half-width stack defined by a plurality of fan folds in the top of the cushion wherein neither edge of each fold extends substantially over the second center line. 22 figs.

  7. Folded inflatable protective device and method for making same

    DOE Patents [OSTI]

    Behr, Vance L. (Albuquerque, NM); Nelsen, James M. (Albuquerque, NM); Gwinn, Kenneth W. (Cedar Crest, NM)

    1998-01-01

    An apparatus and method for making an inflatable protective device made of lightweight material that can withstand the initial stress from inflation and enhance radial inflation. The device includes a cushion and an inflator port. The invention further includes several stacks of folded cushion material including a combination of full-width stacks and half-width stacks: a first full-width stack defined by one or more fan folds in a first lateral half of the cushion wherein the folds are substantially centered above a first center line and are substantially over the inflator port; a second full-width stack defined by one or more fan folds in a second lateral half of the cushion wherein the folds are substantially centered above the first center line and substantially over the inflator port in the first full-width stack; a first half-width stack defined by a plurality of fan folds in the bottom of the cushion where neither edge of each fold extends substantially over the second center line; and a second half-width stack defined by a plurality of fan folds in the top of the cushion wherein neither edge of each fold extends substantially over the second center line.

  8. Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2007-10-24

    Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are permutations of each other. Despite the simplicity of the model, the knowledge of the free-energy landscape in dependence of a suitable system order parameter enables us to reveal complex folding characteristics known from real bioproteins and synthetic peptides, such as two-state folding, folding through weakly stable intermediates, and glassy metastability.

  9. Aerial photographic interpretation of lineaments and faults in late cenozoic deposits in the Eastern part of the Benton Range 1:100,000 quadrangle and the Goldfield, Last Chance Range, Beatty, and Death Valley Junction 1:100,000 quadrangles, Nevada and California

    SciTech Connect (OSTI)

    Reheis, M.C.; Noller, J.S.

    1991-09-01

    Lineaments and faults in Quaternary and late Tertiary deposits in the southern part of the Walker Lane are potentially active and form patterns that are anomalous with respect to the typical fault patterns in most of the Great Basin. Little work has been done to identify and characterize these faults, with the exception of those in the Death Valley-Furnace Creek (DVFCFZ) fault system and those in and near the Nevada Test Site. Four maps at a scale of 1:100,000 summarize the existing knowledge about these lineaments and faults based on extensive aerial-photo interpretation, limited field investigations, and published geologic maps. The lineaments and faults in all four maps can be divided geographically into two groups. The first group includes west- to north-trending lineaments and faults associated with the DVFCFZ and with the Pahrump fault zone in the Death Valley Junction quadrangle. The second group consists of north- to east-northeast-trending lineaments and faults in a broad area that lies east of the DVFCFZ and north of the Pahrump fault zone. Preliminary observations of the orientations and sense of slip of the lineaments and faults suggest that the least principle stress direction is west-east in the area of the first group and northwest-southeast in the area of the second group. The DVFCFZ appears to be part of a regional right-lateral strike-slip system. The DVFCFZ steps right, accompanied by normal faulting in an extensional zone, to the northern part of the Walker Lane a the northern end of Fish Lake Valley (Goldfield quadrangle), and appears to step left, accompanied by faulting and folding in a compressional zone, to the Pahrump fault zone in the area of Ash Meadows (Death Valley Junction quadrangle). 25 refs.

  10. Coseismic fault-related fold model, growth structure, and the historic multisegment blind thrust earthquake on the

    E-Print Network [OSTI]

    Mueller, Karl

    [Philip and Meghraoui, 1983; Rockwell et al., 1984, 1988; Bullard and Lettis, 1993; Molnar et al., 1994

  11. 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

  12. Realization of User Level Fault Tolerant Policy Management through a Holistic Approach for Fault Correlation

    SciTech Connect (OSTI)

    Park, Byung H [ORNL; Naughton, III, Thomas J [ORNL; Agarwal, Pratul K [ORNL; Bernholdt, David E [ORNL; Geist, Al [ORNL; Tippens, Jennifer L [ORNL

    2011-01-01

    Many modern scientific applications, which are designed to utilize high performance parallel com- puters, occupy hundreds of thousands of computational cores running for days or even weeks. Since many scien- tists compete for resources, most supercomputing centers practice strict scheduling policies and perform meticulous accounting on their usage. Thus computing resources and time assigned to a user is considered invaluable. However, most applications are not well prepared for un- foreseeable faults, still relying on primitive fault tolerance techniques. Considering that ever-plunging mean time to interrupt (MTTI) is making scientific applications more vulnerable to faults, it is increasingly important to provide users not only an improved fault tolerant environment, but also a framework to support their own fault tolerance policies so that their allocation times can be best utilized. This paper addresses a user level fault tolerance policy management based on a holistic approach to digest and correlate fault related information. It introduces simple semantics with which users express their policies on faults, and illustrates how event correlation techniques can be applied to manage and determine the most preferable user policies. The paper also discusses an implementation of the framework using open source software, and demonstrates, as an example, how a molecular dynamics simulation application running on the institutional cluster at Oak Ridge National Laboratory benefits from it.

  13. 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

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

    SciTech Connect (OSTI)

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

    2011-05-15

    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.

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

    SciTech Connect (OSTI)

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

    2014-08-24

    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.

  16. Folding Mechanisms Earth Structure (2nd Edition), 2003

    E-Print Network [OSTI]

    Maryland Appalachians Swiss Alps #12;© EarthStructure (2nd ed) 311/7/2010 Bending and Buckling CompressionFolding Mechanisms Earth Structure (2nd Edition), 2003 W.W. Norton & Co, New York Slide show by Ben van der Pluijm © WW Norton; unless noted otherwise #12;© EarthStructure (2nd ed) 211/7/2010 Folds

  17. Counting Mountain-Valley Assignments for Flat Folds

    E-Print Network [OSTI]

    Hull, Thomas C.

    Counting Mountain-Valley Assignments for Flat Folds Thomas Hull Department of Mathematics Merrimack), a mountain-valley (MV) assignment is a function f : E {M,V} which indicates which crease lines are con- vex can be thought of as a structural blueprint of the fold.) Creases come in two types: mountain creases

  18. Coarsely resolved topography along protein folding pathways Ariel Fernandez

    E-Print Network [OSTI]

    Berry, R. Stephen

    Coarsely resolved topography along protein folding pathways Ariel Ferna´ndez Instituto de Matema . The topography is represented as a sequence of minima and effective saddle points. The dominant folding pathway. Initially misfolded states form and dismantle revealing no definite pattern in the topography and exhibiting

  19. 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

  20. 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

  1. A Gauge Field Theory of Chirally Folded Homopolymers with Applications to Folded Proteins

    E-Print Network [OSTI]

    Ulf H. Danielsson; Martin Lundgren; Antti J. Niemi

    2010-08-26

    We combine the principle of gauge invariance with extrinsic string geometry to develop a lattice model that can be employed to theoretically describe properties of chiral, unbranched homopolymers. We find that in its low temperature phase the model is in the same universality class with proteins that are deposited in the Protein Data Bank, in the sense of the compactness index. We apply the model to analyze various statistical aspects of folded proteins. Curiously we find that it can produce results that are a very good good match to the data in the Protein Data Bank.

  2. Fault Locating, Prediction and Protection (FLPPS)

    SciTech Connect (OSTI)

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

    2010-09-30

    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

  3. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1994-12-27

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

  4. Method for fabricating fan-fold shielded electrical leads

    DOE Patents [OSTI]

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

    1994-01-01

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

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

    E-Print Network [OSTI]

    Mohazab, Ali R

    2012-01-01

    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...

  6. 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

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

    E-Print Network [OSTI]

    Lin, Chen-Han

    2014-11-21

    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...

  8. VCSEL fault location apparatus and method

    DOE Patents [OSTI]

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

    2007-05-15

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

    E-Print Network [OSTI]

    AhYoung, AP; Koehl, A; Cascio, D; Egea, PF

    2015-01-01

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

  10. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Walter Simmons; Joel L. Weiner

    2011-08-13

    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.

  11. Fault-tolerant three-level inverter

    DOE Patents [OSTI]

    Edwards, John; Xu, Longya; Bhargava, Brij B.

    2006-12-05

    A method for driving a neutral point clamped three-level inverter is provided. In one exemplary embodiment, DC current is received at a neutral point-clamped three-level inverter. The inverter has a plurality of nodes including first, second and third output nodes. The inverter also has a plurality of switches. Faults are checked for in the inverter and predetermined switches are automatically activated responsive to a detected fault such that three-phase electrical power is provided at the output nodes.

  12. Development of a bridge fault extractor tool 

    E-Print Network [OSTI]

    Bhat, Nandan D.

    2005-02-17

    are tools that analyze chip layouts and produce a realistic list of bridging faults within that chip. FedEx, previously developed at Texas A&M University, extracts all two-node intralayer bridges of any given chip layout and optionally extracts all two...) for this tool which aids in more effectively visualizing the bridge faults across the chip. The final aim of this thesis was to perform FedEx output analysis to understand the nature of the defects, such as variation of critical area (the area where...

  13. Motivation Methodology Conclusions A Fault Tolerance Bisimulation Proof for

    E-Print Network [OSTI]

    Francalanza, Adrian

    Motivation Methodology Conclusions A Fault Tolerance Bisimulation Proof for Consensus Adrian of Somewhere and Elsewhere A Fault Tolerance Bisimulation Proof for Consensus #12;Motivation Methodology Conclusions Outline 1 Motivation 2 Methodology 3 Conclusions Adrian Francalanza, Matthew Hennessy Universities

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

    Open Energy Info (EERE)

    field in the central Coso Range, eastern California, image brittle faults and other structures in a zone of localized crustal extension between two major strike-slip faults. The...

  15. Occupancy Based Fault Detection on Building Level - a Feasibility Study 

    E-Print Network [OSTI]

    Tuip, B.; Houten, M.; Trcka, M.; Hensen, M.

    2010-01-01

    -line, self learning fault detection tool on building level. Taking passive user behavior into account, the tool aims to distinguish real faults from unexpected user behavior. An artificial neural network model is used to predict building energy consumption...

  16. Two Similarity Measure Approaches to Whole Building Fault Diagnosis 

    E-Print Network [OSTI]

    Lin, G.; Claridge, D.

    2012-01-01

    similarity are defined and the methodology for implementing the proposed whole building fault diagnosis approaches is presented. Cosine similarity and Euclidean distance similarity are applied to two field observed fault test cases, and both the cosine...

  17. Dining philosophers with masking tolerance to crash faults 

    E-Print Network [OSTI]

    Idimadakala, Vijaya K.

    2009-05-15

    We examine the tolerance of dining philosopher algorithms subject to process crash faults in arbitrary conflict graphs. This classic problem is unsolvable in asynchronous message-passing systems subject to even a single crash fault. By contrast...

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

    E-Print Network [OSTI]

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

    2005-01-01

    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 ...

  19. Development of a Hydrologic Characterization Technology for Fault Zones Final Report

    E-Print Network [OSTI]

    Karasaki, Kenzi

    2014-01-01

    times by triggering a GFCI (Ground Fault Circuit Interrupt).time, rain caused a GFCI (ground fault circuit interrupt),

  20. Water dynamics clue to key residues in protein folding

    SciTech Connect (OSTI)

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

    2010-01-29

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

  1. Fault-Tolerant Non-interference Extended Version

    E-Print Network [OSTI]

    Russo, Alejandro

    a fault (induced by holding a light-bulb near the processor!) triggers a single bit flip in a malicious

  2. Adjustable direct current and pulsed circuit fault current limiter

    DOE Patents [OSTI]

    Boenig, Heinrich J.; Schillig, Josef B.

    2003-09-23

    A fault current limiting system for direct current circuits and for pulsed power circuit. In the circuits, a current source biases a diode that is in series with the circuits' transmission line. If fault current in a circuit exceeds current from the current source biasing the diode open, the diode will cease conducting and route the fault current through the current source and an inductor. This limits the rate of rise and the peak value of the fault current.

  3. Deep drilling phase of the Pen Brand Fault Program

    SciTech Connect (OSTI)

    Stieve, A.

    1991-05-15

    This deep drilling activity is one element of the Pen Branch Fault Program at Savannah River Site (SRS). The effort will consist of three tasks: the extension of wells PBF-7 and PBF-8 into crystalline basement, geologic and drilling oversight during drilling operations, and the lithologic description and analysis of the recovered core. The drilling program addresses the association of the Pen Branch fault with order fault systems such as the fault that formed the Bunbarton basin in the Triassic.

  4. 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.

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

    E-Print Network [OSTI]

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

    2013-01-01

    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.

  6. ELECTROMAGNETIC IMAGES OF THE TINTINA FAULT (NORTHERN CANADIAN CORDILLERA)

    E-Print Network [OSTI]

    Jones, Alan G.

    ELECTROMAGNETIC IMAGES OF THE TINTINA FAULT (NORTHERN CANADIAN CORDILLERA) Juanjo Ledo1 , Alan G to obtain a crustal scale electromagnetic image of the fault. A short, higher station density profile-dimensional (2- D) electromagnetic behavior of the fault. Distortion decomposition of the responses corroborated

  7. NASA Technical Memorandum 89098 The Fault-Tree Compiler

    E-Print Network [OSTI]

    Butler, Ricky W.

    L - NASA Technical Memorandum 89098 The Fault-Tree Compiler Anna L. Martensen Ricky W. Butler in preliminary design analysis. The goal of the Fault Tree Compiler (m)program is to provide the user with a tool also be performed, providing the user The motivation for the development of the Fault Tree Compiler

  8. Development of the Global Earthquake Model's neotectonic fault database

    E-Print Network [OSTI]

    New Hampshire, University of

    Development of the Global Earthquake Model's neotectonic fault database Annemarie Christophersen1 database and a unique graphical interface for the compilation of new fault data. A key design principle is that of an electronic field notebook for capturing observations a geologist would make about a fault. The database

  9. Synthesizing Round Based FaultTolerant Programs using Genetic Programming

    E-Print Network [OSTI]

    Fernandez, Thomas

    Synthesizing Round Based Fault­Tolerant Programs using Genetic Programming Ling Zhu and Sandeep based distributed fault­tolerant programs using stack based genetic pro­ gramming. Our approach evolves a fault­tolerant program based on a round based structure and the program specification. To permit

  10. 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

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

    E-Print Network [OSTI]

    Pedram, Massoud

    Online Fault Detection and Tolerance for Photovoltaic Energy Harvesting Systems Xue Lin 1 , Yanzhi, yanzhiwa, dizhu, pedram}@usc.edu, 2 naehyuck@elpl.snu.ac.kr ABSTRACT Photovoltaic energy harvesting systems, Performance, Reliability. Keywords Photovoltaic System, Fault Detection, Fault Tolerance, Photovoltaic Panel

  12. Symbolic Dynamic Analysis of Transient Time Series for Fault

    E-Print Network [OSTI]

    Ray, Asok

    Symbolic Dynamic Analysis of Transient Time Series for Fault Detection in Gas Turbine Engines paper presents a symbolic dynamics-based method for detection of incipient faults in gas turbine engines dynamics, fault detection, aircraft gas turbine engines 1 Introduction Performance monitoring of aircraft

  13. PCB origami : folding circuit boards into electronic products

    E-Print Network [OSTI]

    Sterman, Yoav

    2013-01-01

    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 ...

  14. UFO (UnFold Operator) computer program abstract

    SciTech Connect (OSTI)

    Kissel, L.; Biggs, F.

    1982-11-01

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

  15. Physics of Caustics and Protein Folding: Mathematical Parallels

    E-Print Network [OSTI]

    Simmons, Walter

    2011-01-01

    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 ...

  16. Determining the role of hydration forces in protein folding

    SciTech Connect (OSTI)

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

    1999-07-01

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

  17. Low energy pathways for reproducible in vivo protein folding

    E-Print Network [OSTI]

    Leonor Cruzeiro

    2011-01-03

    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.

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

    E-Print Network [OSTI]

    Roder, Heinrich

    of unfolded or partially folded states, (V7 10/11 12:16) VCH/G J-1079 Buchner I PMU: WSL(W) 19/08/04 AC1: WSL

  19. Investigation of Peptide Folding by Nuclear Magnetic Resonance Spectroscopy 

    E-Print Network [OSTI]

    Hwang, SoYoun

    2012-07-16

    . Solution-state nuclear magnetic resonance (NMR) is a powerful technique to investigate protein structure, dynamics, and folding mechanisms, since it provides residue-specific information. One of the major contributions that govern protein structure appears...

  20. Mechanisms of protein-folding diseases at a glance

    E-Print Network [OSTI]

    Valastyan, Julie Suzanne

    For a protein to function appropriately, it must first achieve its proper conformation and location within the crowded environment inside the cell. Multiple chaperone systems are required to fold proteins correctly. In ...

  1. SOFTWARE Open Access RNAexinv: An extended inverse RNA folding from

    E-Print Network [OSTI]

    Barash, Danny

    SOFTWARE Open Access RNAexinv: An extended inverse RNA folding from shape and physical attributes problem that aims to predict the secondary structure of a given RNA sequence. Software packages are nowa

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

    E-Print Network [OSTI]

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

    2014-12-02

    of its biological functions, are poorly understood. In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic...

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

    E-Print Network [OSTI]

    Regan, Lynne

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

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

    E-Print Network [OSTI]

    Benner, Carl Lee

    1988-01-01

    . 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...

  5. Master equation approach to protein folding and kinetic traps

    E-Print Network [OSTI]

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

    1998-04-21

    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.

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

    E-Print Network [OSTI]

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

  7. 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

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

    E-Print Network [OSTI]

    Mukamel, Shaul

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

  9. RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki

    E-Print Network [OSTI]

    Moll, Mark

    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

  10. Unifying sensor fault detection with energy conservation

    E-Print Network [OSTI]

    Dobson, Simon

    Unifying sensor fault detection with energy conservation Lei Fang and Simon Dobson School energy usage. Section 2 presents our framework, which is evaluated in section 3 by means of some reliability. Sensors are often energy-hungry and cannot operate over the long term, and the data they gather

  11. Symmetrical Fault Analysis 1.0 Definition

    E-Print Network [OSTI]

    McCalley, James D.

    , shunt admittances, and -Y phase shifts are neglected. Synchronous machines (generators and motors-286]. We begin with the simplest of examples. 3.0 Example Consider a single generator supplying an R that will be faulted). Eg: steady-state internal gen voltage Xd: synchronous (steady-state) reactance IL: load

  12. All row, planar fault detection system

    DOE Patents [OSTI]

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

    2013-07-23

    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.

  13. Safety Requirements and Fault Trees using Retrenchment

    E-Print Network [OSTI]

    Banach, Richard

    this initial model has been created, the elicitation of safety requirements yields a fresh set of criteria are applied, the information linking the design and the safety assessment phases is often carried outSafety Requirements and Fault Trees using Retrenchment R. Banach and R. Cross Computer Science

  14. Coordinated Fault Tolerance for High-Performance Computing

    SciTech Connect (OSTI)

    Dongarra, Jack; Bosilca, George; et al.

    2013-04-08

    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.

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

    SciTech Connect (OSTI)

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

    2012-08-01

    This document is one in a series of topical reports compiled by the Pacific Northwest National Laboratory to summarize technical information on selected topics important to the performance of a probabilistic seismic hazard analysis of the Hanford Site. The purpose of this report is to summarize available data and analyses relevant to fault recurrence and strain rates within the Yakima Fold Belt. Strain rates have met with contention in the expert community and may have a significant potential for impact on the seismic hazard estimate at the Hanford Site. This report identifies the alternative conceptual models relevant to this technical issue and the arguments and data that support those models. It provides a brief description of the technical issue and principal uncertainties; a general overview on the nature of the technical issue, along with alternative conceptual models, supporting arguments and information, and uncertainties; and finally, suggests some prospective approaches to reducing uncertainties about earthquake recurrence rates for the Yakima Fold Belt.

  16. 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

  17. 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

    2006-01-01

    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

  18. 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

  19. 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

  20. 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

  1. 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

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

    E-Print Network [OSTI]

    Bernstein, Rachel Simma

    2011-01-01

    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

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

    E-Print Network [OSTI]

    Sagle, Laura B.

    2006-01-01

    for Mechanisms of Protein Folding. Proc. Natl. Acad. Sci. U.Ptitsyn, O. B. , Protein Folding: Hypothesis andEvidenc for Barrier-Limited Protein Folding Kinetics on the

  4. Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping

    E-Print Network [OSTI]

    Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping distances between proteins. This method shows significant improvement in protein fold recognition. Overall March 2014 Keywords: Protein sequence Fold recognition Alignment method Feature extraction

  5. Intermediates and the folding of proteins L and G

    SciTech Connect (OSTI)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

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

  6. On the use of finite fault solution for tsunami generation problems

    E-Print Network [OSTI]

    Dutykh, Denys; Gardeil, Xavier

    2010-01-01

    The present study is devoted to the tsunami wave generation problem. The main goal of this work is two-fold. First of all, we propose a simple and computationally inexpensive model for the description of the sea bed displacement during an underwater earthquake, based on the finite fault solution for the slip distribution under some assumptions on the rupturing process dynamics. Once the bottom motion is reconstructed, we study waves induced on the free surface of the ocean. For this purpose we consider three different models approximating the Euler equations of the water wave theory. Namely, we deal with linearized Euler equations (also known as Cauchy-Poisson problem), a Boussinesq system and a weakly nonlinear model. An intercomparison of these approaches is performed. All developments in this study are illustrated on the real world example of the July 17, 2006 Java event.

  7. SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm

    E-Print Network [OSTI]

    Lobstein, Julie; Emrich, Charlie A; Jeans, Chris; Faulkner, Melinda; Riggs, Paul; Berkmen, Mehmet

    2012-01-01

    Schein CH: Optimizing protein folding to the native state inJ, Terwilliger TC: Rapid protein-folding assay using greenbuilding bridges in protein folding. Trends Biochem Sci

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

    E-Print Network [OSTI]

    DeVries, Ingrid L.

    2011-01-01

    in the transition state of protein folding: alternativeet al. (2008). "Protein folding and stability usingto enzyme catalysis and protein folding. New York, W.H.

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

    E-Print Network [OSTI]

    J. L. Gornall; E. M. Terentjev

    2006-03-05

    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.

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

    SciTech Connect (OSTI)

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

    1995-09-01

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

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

    SciTech Connect (OSTI)

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

    2000-01-01

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

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

    E-Print Network [OSTI]

    Zhang, Cheng

    2010-01-01

    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.

  13. Undulator Hall Air Temperature Fault Scenarios

    SciTech Connect (OSTI)

    Sevilla, J.; Welch, J.; ,

    2010-11-17

    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.

  14. Minimal models for proteins and RNA: From folding to function

    E-Print Network [OSTI]

    D. L. Pincus; S. S. Cho; C. Hyeon; D. Thirumalai

    2008-08-22

    We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key applications ranging from folding of proteins with disulfide bonds to functions of molecular machines. After presenting the theoretical basis that justifies the use of CG models, we explore the biophysical basis for the emergence of a finite number of folds from lattice models. The lattice model simulations of approach to the folded state show that non-native interactions are relevant only early in the folding process - a finding that rationalizes the success of structure-based models that emphasize native interactions. Applications of off-lattice $C_{\\alpha}$ and models that explicitly consider side chains ($C_{\\alpha}$-SCM) to folding of $\\beta$-hairpin and effects of macromolecular crowding are briefly discussed. Successful application of a new class of off-lattice model, referred to as the Self-Organized Polymer (SOP), is shown by describing the response of Green Fluorescent Protein (GFP) to mechanical force. The utility of the SOP model is further illustrated by applications that clarify the functions of the chaperonin GroEL and motion of the molecular motor kinesin. We also present two distinct models for RNA, namely, the Three Site Interaction (TIS) model and the SOP model, that probe forced unfolding and force quench refolding of a simple hairpin and {\\it Azoarcus} ribozyme. The predictions based on the SOP model show that force-induced unfolding pathways of the ribozyme can be dramatically changed by varying the loading rate. We conclude with a discussion of future prospects for the use of coarse-grained models in addressing problems of outstanding interest in biology.

  15. Characterization of Protein Folding by Dominant Reaction Pathways

    E-Print Network [OSTI]

    Pietro Faccioli

    2008-06-23

    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.

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

    E-Print Network [OSTI]

    Simmons, Walter

    2015-01-01

    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.

  17. Development of Integrated Meso/Microscale Traffic Simulation Software for Testing Fault Detection and Handling in AHS

    E-Print Network [OSTI]

    Horowitz, Roberto

    2004-01-01

    Traffic Simulation Software for Testing Fault Detection andTraf?c Simulation Software for Testing Fault Detection andTraf?c Simulation Software for Testing Fault Detection and

  18. Features and Dimensions of the Hayward fault zone in the Strawberry and Blackberry Creek Area Berkeley, California

    E-Print Network [OSTI]

    Williams, P.L.

    2011-01-01

    Hayward Fault Zone in the Strawberry and Blackberry Creekward Fault Zone in the Strawberry and Blackberry Creek Area,Hayward fault zone in the Strawberry and Blackberry Creek

  19. 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

    2008-01-01

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

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

    E-Print Network [OSTI]

    Kabir, Mashud

    2009-01-01

    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...

  1. Neurobiology of Disease Cortical Folding Abnormalities in Autism Revealed by

    E-Print Network [OSTI]

    Van Essen, David

    Neurobiology of Disease Cortical Folding Abnormalities in Autism Revealed by Surface-based morphometry across a range of autism spectrum disorders (7.5­18 years of age). We generated sulcal depth maps autism spectrum disorder subgroups: low-functioning autism, high-functioning autism, and Asperger

  2. Modeling Learningless Vulnerability Discovery using a Folded Distribution

    E-Print Network [OSTI]

    Malaiya, Yashwant K.

    model is logistic, and thus the increase and decrease in the discovery process is assumedModeling Learningless Vulnerability Discovery using a Folded Distribution Awad A. Younis1 , Hyun, CO 80523, USA Abstract ­ A vulnerability discovery model describes the vulnerability discovery rate

  3. Folded-Light-Path Colloidal Quantum Dot Solar Cells

    E-Print Network [OSTI]

    Sargent, Edward H. "Ted"

    Folded-Light-Path Colloidal Quantum Dot Solar Cells Ghada I. Koleilat*, Illan J. Kramer*, Chris T-processed solar cells offer the promise of low cost, large-area processing, and, prospectively, high solar power solar cell performance20,21 . Results In the present work, we sought to increase the interaction

  4. Thermal and Kinematic Evolution of the Eastern Cordillera Fold and

    E-Print Network [OSTI]

    Toro, Jaime

    Thermal and Kinematic Evolution of the Eastern Cordillera Fold and Thrust Belt, Colombia Jaime Toro and then calculated the conductive thermal state of key steps of the kinematic history using ThrustpackR 4.0. The models were constrained by well, seismic, apatite fission-track, and thermal-maturity data. The main

  5. NICMOS OPTICS OffAxis Conicoids Fold Mirrors

    E-Print Network [OSTI]

    Schneider, Glenn

    NICMOS OPTICS Off­Axis Conicoids Fold Mirrors Cameras 3, 1, 2 Pupil Al ignment Mirror Reimaging Optics (and Witness Samples) Before Installation The integrated NICMOS optical system is comprised of the fifteen NICMOS mirrors are mounted to a graphite epoxy truss, called the Fore­Optics Bracket (FOB

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

    E-Print Network [OSTI]

    Michael Bachmann; Wolfhard Janke

    2007-10-25

    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.

  7. The Mathematics of Wrinkles and Folds Robert V. Kohn

    E-Print Network [OSTI]

    and Folds #12;Paper, deformed smoothly Essential mechanics of paper: it resists bending. If midline") prefers isometry. It is nonconvex (for paper: many smooth minimizers). Second term ("bending energy inextensible sheets (like paper) extensible sheets (rubber or cloth) thin crystalline films on substrates

  8. POLYMER PROGRAM SEMINAR Folding gels and shells: Designing reconfigurable

    E-Print Network [OSTI]

    Alpay, S. Pamir

    POLYMER PROGRAM SEMINAR Folding gels and shells: Designing reconfigurable 3D shapes and `mechanical and reconfigurable 3D shapes and properties. In particular, we have studied the use of photo-crosslinkable polymer films to prepare polymer sheets and multilayers containing stimuli-responsive hydrogel elements

  9. 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

  10. 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

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

    E-Print Network [OSTI]

    Mukamel, Shaul

    RESEARCH ARTICLE Open Access Probing the folding of mini-protein Beta3s by two-dimensional infrared-dimensional correlation spectroscopy (2DCS) to characterize the folding mechanism of the mini-protein Beta3s with experimental 2DCS to study the folding mechanism of proteins. In addition to exploring the folding mechanism

  12. 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

  13. 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

  14. 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

  15. 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

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

    E-Print Network [OSTI]

    Bachmann, Michael

    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

  17. 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

  18. 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

  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. 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

  1. 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

  2. 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

  3. 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

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

    E-Print Network [OSTI]

    Latombe, Jean-Claude

    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

  5. Membrane protein folding on the example of outer membrane protein A of Escherichia coli

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

    Membrane protein folding on the example of outer membrane protein A of Escherichia coli J. H and mechanisms by which membrane proteins insert and fold into a biomem- brane have mostly been studiedA that involves at least three struc- turally distinct folding intermediates. Key words. Membrane protein folding

  6. Protein Fold Class Prediction using Neural Networks with Tailored Early-Stopping

    E-Print Network [OSTI]

    Igel, Christian

    Protein Fold Class Prediction using Neural Networks with Tailored Early-Stopping Thomas fold class given the primary sequence of a protein. Different feature spaces for primary sequences the fold class of proteins [8], [9], [10], [11], [12], [13], [14], [15], [16], [17]. A fold class contains

  7. The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity

    E-Print Network [OSTI]

    Berry, R. Stephen

    The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity links protein fold and biological function: the conservation of the fold across distant homol- ogous hydrogen bond (3­9), recently termed dehydron (7), which is encoded in the 3D structure of protein folded

  8. Origami-like Folded MEMS for Realization of TIMU: Fabrication Technology and Initial

    E-Print Network [OSTI]

    Chen, Zhongping

    single-axis sensors and then folding them into a 3-D Fig. 1. Commercial MEMS IMUs Performance Fig. 2 for assembly of the integrated MEMS sensor cluster in a 3-D configuration, or folding in a 3-D shape. FoldedOrigami-like Folded MEMS for Realization of TIMU: Fabrication Technology and Initial Demonstration

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

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM)

    2007-09-18

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

  10. RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki

    E-Print Network [OSTI]

    Kavraki, Lydia E.

    RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki Abstract--Protein folding reviews a class of methods for studying the folding process called roadmap methods. e goal. It is assumed that the folded state is known. Roadmap methods build a graph representation of sampled

  11. The effects of nonnative interactions on protein folding rates: Theory and simulation

    E-Print Network [OSTI]

    Plotkin, Steven S.

    The effects of nonnative interactions on protein folding rates: Theory and simulation CECILIA interaction energy can actually assist the folding to the native structure. Keywords: protein folding: see www.proteinscience.org The mechanism of protein folding is of central importance to structural

  12. 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

  13. 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

  14. 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

  15. Fault-induced delayed voltage recovery in a long inhomogeneous...

    Office of Scientific and Technical Information (OSTI)

    Article: Fault-induced delayed voltage recovery in a long inhomogeneous power-distribution feeder Citation Details In-Document Search This content will become publicly...

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

    E-Print Network [OSTI]

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

    2009-01-01

    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

  17. STRESS AND FAULTING IN THE COSO GEOTHERMAL FIELD: UPDATE AND...

    Open Energy Info (EERE)

    108 24 in a transitional strike-slip to normal faulting stress regime. These structures bound regions of intense micro-seismicity and are complexly associated with surface...

  18. 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...

  19. MODELING AND SIMULATION OF HVAC FAULTS IN ENERGYPLUS

    E-Print Network [OSTI]

    Basarkar, Mangesh

    2013-01-01

    and simulated building energy performance, Norford et al. (faults on whole building performance – energy consumption,and simulated energy performance of buildings is that most

  20. Recency of Faulting and Neotectonic Framework in the Dixie Valley...

    Open Energy Info (EERE)

    by active geothermal springs. More specifically, our investigation shows that induced stress concentrations at the endpoints of normal fault ruptures appear to promote favorable...

  1. Recency Of Faulting And Neotechtonic Framework In The Dixie Valley...

    Open Energy Info (EERE)

    by active geothermal springs. More specifically, our investigation shows that induced stress concentrations at the endpoints of normal fault ruptures appear to promote favorable...

  2. 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...

  3. Fault-tolerant distributed transactions for partitioned OLTP databases

    E-Print Network [OSTI]

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

    2012-01-01

    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 ...

  4. Arc-Fault Detector Algorithm Evaluation Method Utilizing Prerecorded...

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

    Electrical Code Article 690.11 requires photovoltaic systems on or penetrating a building to include a DC arc-fault protection device. In order to satisfy this...

  5. Checksum-Based Fault Tolerance for LU Factorization

    E-Print Network [OSTI]

    Davies, Teresa

    2014-01-01

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

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

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

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

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

    Open Energy Info (EERE)

    LibraryAdd to library Conference Proceedings: MICRO-SEISMICITY, FAULT STRUCTURE AND HYDRAULIC COMPARTMENTALIZATION WITHIN THE COSO GETHERMAL FIELD, CALIFORNIA Abstract High...

  8. 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...

  9. 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

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

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2009-02-16

    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.

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

    E-Print Network [OSTI]

    Janecke, Alex Karl

    2012-10-19

    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. Neural Network-Based Classification of Single-Phase Distribution Transformer Fault Data 

    E-Print Network [OSTI]

    Zhang, Xujia

    2006-08-16

    The ultimate goal of this research is to develop an online, non-destructive, incipient fault detection system that is able to detect incipient faults in transformers and other electric equipment before the faults become ...

  14. Fluids migration and dynamics of a blocks-and-faults system

    E-Print Network [OSTI]

    1910-70-11

    Keywords: earthquake catalog, block model, fault, tectonic structure, fluid, fil- ...... nal vertical fault near upper vertices of adjacent internal blocks, and formation of ... acts near the right external vertical fault: fractures filled in with water emerge ...

  15. Evaluation of a Decoupling-Based Fault Detection and Diagnostic Technique - Part I: Field Emulation Evaluation 

    E-Print Network [OSTI]

    Li, H.; Braun, J.

    2006-01-01

    Existing methods addressing automated fault detection and diagnosis (FDD) for vapor compression air conditioning system have good performance for faults that occur individually, but they have difficulty in handling multiple-simultaneous faults...

  16. ALLIANCE: An Architecture for Fault Tolerant, Cooperative Control of Heterogeneous Mobile Robots

    E-Print Network [OSTI]

    Parker, Lynne E.

    ALLIANCE: An Architecture for Fault Tolerant, Cooperative Control of Heterogeneous Mobile Robots ALLIANCE, that utilizes adaptive action selection to achieve fault toler- ant cooperative control in robot demonstration. These experiments illustrate the ability of ALLIANCE to achieve adaptive, fault

  17. Fault Tolerant Arithmetic with Applications in Nanotechnology based Systems

    E-Print Network [OSTI]

    Rao, Wenjing

    Fault Tolerant Arithmetic with Applications in Nanotechnology based Systems Wenjing Rao UC San nanotechnologies have been displaying the Neg- ative Differential Resistance (NDR) characteristic, which makes them fault-tolerant arithmetic in NDR nanotechnologies. Specifically, we show how linear block codes can

  18. Automatic Fault Characterization via Abnormality-Enhanced Classification

    SciTech Connect (OSTI)

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

    2010-12-20

    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.

  19. Fault current limiter with shield and adjacent cores

    DOE Patents [OSTI]

    Darmann, Francis Anthony; Moriconi, Franco; Hodge, Eoin Patrick

    2013-10-22

    In a fault current limiter (FCL) of a saturated core type having at least one coil wound around a high permeability material, a method of suppressing the time derivative of the fault current at the zero current point includes the following step: utilizing an electromagnetic screen or shield around the AC coil to suppress the time derivative current levels during zero current conditions.

  20. 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

  1. 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

  2. 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

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

    E-Print Network [OSTI]

    Dong, Ming

    --Distributed event detection, fault tolerance, sensor fusion, energy-efficiency, wireless sensor networks. æ 1 to choose a proper neighborhood size n for a sensor node in fault correction such that the energy could to achieve better detection and better balance between detection accuracy and energy usage. Our work makes

  4. Common Trends in Software Fault and Failure Data

    E-Print Network [OSTI]

    Goseva-Popstojanova, Katerina

    Common Trends in Software Fault and Failure Data Maggie Hamill, Member, IEEE, and Katerina Goseva with the findings from related studies. The consistency of several main trends across software systems in this paper-Popstojanova, Senior Member, IEEE Abstract--The benefits of the analysis of software faults and failures have been

  5. Fault Reporting Processes in Business-Critical Systems

    E-Print Network [OSTI]

    and reporting7 Quantitative and qualitativeHazard analysis vs. fault report analysis - DAIM 6 Qualitative projects4 Quantitative, explorativeFault report study of four projects3 Qualitative, descriptive and Information Science (IDI) University of Science and Technology (NTNU) Trondheim, Norway PhD thesis

  6. Fault Detection and Diagnosis Method for VAV Terminal Units 

    E-Print Network [OSTI]

    Miyata, M.; Yoshida, H.; Asada, M.; Wang, F.; Hashiguchi, S.

    2004-01-01

    This paper proposes two fault detection and diagnosis methods for VAV units without a sensor of supply air volume, and the results of applying these methods to a real building are presented. One method detects faults by applying a statistical method...

  7. SHIELD: A Fault-Tolerant MPI for an Infiniband Cluster

    E-Print Network [OSTI]

    Yeom, Heon Young

    SHIELD: A Fault-Tolerant MPI for an Infiniband Cluster Hyuck Han, Hyungsoo Jung, Jai Wug Kim, a successful solution has yet to be delivered to commercial vendors. This paper presents SHIELD, a prac- tical and easily-deployable fault-tolerant MPI and management system of MPI for an Infiniband cluster. SHIELD

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

    E-Print Network [OSTI]

    Lehman, Brad

    . The models must be modified due to different PV capacity, solar cell technology, or installation locationOutlier Detection Rules for Fault Detection in Solar Photovoltaic Arrays Ye Zhao, Brad Lehman Abstract-- Solar photovoltaic (PV) arrays are unique power sources that may have uncleared fault current

  9. Original Article Multi-sensor information fusion for fault

    E-Print Network [OSTI]

    Ray, Asok

    The article addresses data-driven fault detection in commercial aircraft gas turbine engines in the framework is validated on the NASA C-MAPSS simulation test bed of aircraft gas turbine engines; both single is also addressed. Keywords Gas turbine engines, fault detection, information fusion Date received: 15 May

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

    E-Print Network [OSTI]

    Yao, Bin

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

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

    SciTech Connect (OSTI)

    HART,WILLIAM E.; ISTRAIL,SORIN

    2000-06-01

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

  12. Strong Nernst-Ettingshausen effect in folded graphene

    E-Print Network [OSTI]

    Friedemann Queisser; Ralf Schützhold

    2013-01-17

    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.

  13. Multi-sensor Wireless System for Fault Detection in Induction Motors

    E-Print Network [OSTI]

    Tarkesh Esfahani, Ehsan

    2012-01-01

    2 Faults in Motors 2.1 Bearing Faultcombined faults in induction motors,” IEEE Transactions onV. Climente-Alarcon, “Induction motor diagnosis based on a

  14. Development of Integrated Meso/Microscale Traffic Simulation Software for Testing Fault Detection and Handling Algorithms in AHS: Final Report

    E-Print Network [OSTI]

    Horowitz, Roberto

    2003-01-01

    Traffic Simulation Software for Testing Fault Detection andTra?c Simulation Software for Testing Fault Detection and

  15. Experimental continuation of periodic orbits through a fold

    E-Print Network [OSTI]

    J. Sieber; A. Gonzalez-Buelga; S. A. Neild; D. J. Wagg; B. Krauskopf

    2008-06-12

    We present a continuation method that enables one to track or continue branches of periodic orbits directly in an experiment when a parameter is changed. A control-based setup in combination with Newton iterations ensures that the periodic orbit can be continued even when it is unstable. This is demonstrated with the continuation of initially stable rotations of a vertically forced pendulum experiment through a fold bifurcation to find the unstable part of the branch.

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

    SciTech Connect (OSTI)

    Hart, W.E.; Istrail, S.

    1995-12-11

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

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

    SciTech Connect (OSTI)

    Ruben A. Abagyan

    2000-06-01

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

  18. Living With Radical Uncertainty. The Exemplary case of Folding Protein

    E-Print Network [OSTI]

    Ignazio Licata

    2010-04-21

    Laplace's demon still makes strong impact on contemporary science, in spite of the fact that Logical Mathematics outcomes, Quantum Physics advent and more recently Complexity Science have pointed out the crucial role of uncertainty in the World's descriptions. We focus here on the typical problem of folding protein as an example of uncertainty, radical emergence and a guide to the "simple" principles for studying complex systems.

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

    E-Print Network [OSTI]

    Lei, Jinzhi

    2010-01-01

    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^{\

  20. Development of Hydrologic Characterization Technology of Fault Zones

    SciTech Connect (OSTI)

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

    2008-03-31

    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.

  1. Application-Specific Fault Tolerance via Data Access Characterization

    SciTech Connect (OSTI)

    Ali, Nawab; Krishnamoorthy, Sriram; Govind, Niranjan; Kowalski, Karol; Sadayappan, Ponnuswamy

    2011-08-30

    Recent trends in semiconductor technology and supercomputer design predict an increasing probability of faults during an application's execution. Designing an application that is resilient to system failures requires careful evaluation of the impact of various approaches on preserving key application state. In this paper, we present our experiences in an ongoing effort to make a large computational chemistry application fault tolerant. We construct the data access signatures of key application modules to evaluate alternative fault tolerance approaches. We present the instrumentation methodology, characterization of the application modules, and evaluation of fault tolerance techniques using the information collected. The application signatures developed capture application characteristics not traditionally revealed by performance tools. We believe these can be used in the design and evaluation of runtimes beyond fault tolerance.

  2. Feb. 11, 2008 Advanced Fault Tolerance Solutions for High Performance Computing 1/47 Advanced Fault Tolerance Solutions

    E-Print Network [OSTI]

    Engelmann, Christian

    Feb. 11, 2008 Advanced Fault Tolerance Solutions for High Performance Computing 1/47 RAS RAS Advanced Fault Tolerance Solutions for High Performance Computing Christian Engelmann Oak Ridge National Solutions for High Performance Computing 2/47 · Nation's largest energy laboratory · Nation's largest

  3. Rupture Dynamics of Strike-Slip Faults with Stepovers: From Conceptually Simplified to Realistically Complex Fault Systems 

    E-Print Network [OSTI]

    Liu, Zaifeng

    2014-05-05

    . The coupling effect of those two effects has also been studied. The possible correlation between the slip gradient nearby the first fault end and the ability of the rupture to jump over the structure stepover in the strike-slip fault system has been verified...

  4. Locating hardware faults in a parallel computer

    DOE Patents [OSTI]

    Archer, Charles J.; Megerian, Mark G.; Ratterman, Joseph D.; Smith, Brian E.

    2010-04-13

    Locating hardware faults in a parallel computer, including defining within a tree network of the parallel computer two or more sets of non-overlapping test levels of compute nodes of the network that together include all the data communications links of the network, each non-overlapping test level comprising two or more adjacent tiers of the tree; defining test cells within each non-overlapping test level, each test cell comprising a subtree of the tree including a subtree root compute node and all descendant compute nodes of the subtree root compute node within a non-overlapping test level; performing, separately on each set of non-overlapping test levels, an uplink test on all test cells in a set of non-overlapping test levels; and performing, separately from the uplink tests and separately on each set of non-overlapping test levels, a downlink test on all test cells in a set of non-overlapping test levels.

  5. Self field triggered superconducting fault current limiter

    DOE Patents [OSTI]

    Tekletsadik, Kasegn D. (Rexford, NY)

    2008-02-19

    A superconducting fault current limiter array with a plurality of superconductor elements arranged in a meanding array having an even number of supconductors parallel to each other and arranged in a plane that is parallel to an odd number of the plurality of superconductors, where the odd number of supconductors are parallel to each other and arranged in a plane that is parallel to the even number of the plurality of superconductors, when viewed from a top view. The even number of superconductors are coupled at the upper end to the upper end of the odd number of superconductors. A plurality of lower shunt coils each coupled to the lower end of each of the even number of superconductors and a plurality of upper shunt coils each coupled to the upper end of each of the odd number of superconductors so as to generate a generally orthoganal uniform magnetic field during quenching using only the magenetic field generated by the superconductors.

  6. Online Monitoring System for Performance Fault Detection

    SciTech Connect (OSTI)

    Gioiosa, Roberto; Kestor, Gokcen; Kerbyson, Darren J.

    2014-05-19

    To achieve the exaFLOPS performance within a contain power budget, next supercomputers will feature hundreds of millions of components operating at low- and near-threshold voltage. As the probability that at least one of these components fails during the execution of an application approaches certainty, it seems unrealistic to expect that any run of a scientific application will not experience some performance faults. We believe that there is need of a new generation of light-weight performance and debugging tools that can be used online even during production runs of parallel applications and that can identify performance anomalies during the application execution. In this work we propose the design and implementation of a monitoring system that continuously inspects the evolution of run

  7. Development of Characterization Technology for Fault Zone Hydrology

    SciTech Connect (OSTI)

    Karasaki, Kenzi; Onishi, Tiemi; Gasperikova, Erika; Goto, Junichi; Tsuchi, Hiroyuki; Miwa, Tadashi; Ueta, Keiichi; Kiho, Kenzo; MIyakawa, Kimio

    2010-08-06

    Several deep trenches were cut, and a number of geophysical surveys were conducted across the Wildcat Fault in the hills east of Berkeley, California. The Wildcat Fault is believed to be a strike-slip fault and a member of the Hayward Fault System, with over 10 km of displacement. So far, three boreholes of ~;; 150m deep have been core-drilled and borehole geophysical logs were conducted. The rocks are extensively sheared and fractured; gouges were observed at several depths and a thick cataclasitic zone was also observed. While confirming some earlier, published conclusions from shallow observations about Wildcat, some unexpected findings were encountered. Preliminary analysis indicates that Wildcat near the field site consists of multiple faults. The hydraulic test data suggest the dual properties of the hydrologic structure of the fault zone. A fourth borehole is planned to penetrate the main fault believed to lie in-between the holes. The main philosophy behind our approach for the hydrologic characterization of such a complex fractured system is to let the system take its own average and monitor a long term behavior instead of collecting a multitude of data at small length and time scales, or at a discrete fracture scale and to ?up-scale,? which is extremely tenuous.

  8. Creases and folds : applying geometry to a pop-up fashion pavilion

    E-Print Network [OSTI]

    Li, Yujing, S.B. Massachusetts Institute of Technology

    2010-01-01

    This thesis explores the architectural opportunities embedded in geometric folding by studying the limitations and possibilities of a variety of patterns. In particular; the thesis focuses on the Yoshimura or diamond folding ...

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

    E-Print Network [OSTI]

    Tang, Xinyu

    2009-05-15

    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 ...

  10. 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 ...

  11. An 8-bit current mode ripple folding analog to digital converter 

    E-Print Network [OSTI]

    Dinc, Huseyin

    2002-01-01

    Design of an 8-bit current mode, ripple-folding analog to digital (A/D) converter is discussed. The ripple folding technique and the possible implementations in different process technologies are summarized. To have an A/D ...

  12. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect (OSTI)

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

    2005-02-10

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

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

    E-Print Network [OSTI]

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

    2011-01-01

    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.

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

    E-Print Network [OSTI]

    Ernesto Gonzalez-Candela; Victor Romero-Rochin

    2009-09-23

    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.

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

    E-Print Network [OSTI]

    Gonzalez-Candela, Ernesto

    2009-01-01

    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.

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

    E-Print Network [OSTI]

    Stefan Schnabel; Michael Bachmann; Wolfhard Janke

    2007-10-25

    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.

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

    Office of Scientific and Technical Information (OSTI)

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

  18. Visualization of stacking faults in fcc crystals in plastic deformations

    E-Print Network [OSTI]

    Takeshi Kawasaki; Akira Onuki

    2011-11-27

    Using molecular dynamics simulation, we investigate the dynamics of stacking faults in fcc crystals in uniaxial stretching in a Lennard-Jones binary mixture composed of 4096 particles in three dimensions. We visualize stacking faults using a disorder variable $D_j(t)$ for each particle $j$ constructed from local bond order parameters based on spherical harmonics (Steinhardt order parameters). Also introducing a method of bond breakage, we examine how stacking faults are formed and removed by collective particle motions. These processes are relevant in plasticity of fcc crystals.

  19. Static Fault Attack on Hardware DES Registers Philippe Loubet-Moundi, Francis Olivier, and David Vigilant

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    Static Fault Attack on Hardware DES Registers Philippe Loubet-Moundi, Francis Olivier, and David deals with static faults which lie in between. A static fault modifies a value loaded in a volatile], quickly became a privileged target for DFA. #12;2 Static Fault Attacks on Hardware DES Registers Indeed

  20. Can Fault Prediction Models and Metrics be Used for Vulnerability Prediction? Yonghee Shin and Laurie Williams

    E-Print Network [OSTI]

    Young, R. Michael

    are built with traditional metrics of complexity, code churn, and fault history. We have performed to the code [17]. Hence, complexity metrics and code churn metrics have been used for fault prediction [5, 17 fault prediction metrics ­ complexity, code churn, and fault history metrics for vulnerability

  1. Seismic behaviour of the Dead Sea fault along Araba valley, Y. Klinger,1,

    E-Print Network [OSTI]

    Avouac, Jean-Philippe

    rue Lafayette, F-75480 Paris cedex 10, France 4 Department of Geology, University of Jordan, Amman-lateral strike-slip fault. South of the Dead Sea basin, the Wadi Araba fault extends over 160 km to the Gulf the fault except around the Dead Sea and Gulf of Aqaba, where the fault splays into complex pull-apart basin

  2. 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

  3. Structural genomics of minimal organisms and protein fold space Sung-Hou Kim1,2,

    E-Print Network [OSTI]

    Structural genomics of minimal organisms and protein fold space Sung-Hou Kim1,2, *, Dong Hae Shin2: Berkeley Structural Genomics Center, minimal organisms, molecular function, protein fold space, structural determination. The results from the pipeline substantially increased the coverage of the protein fold space of M

  4. Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-

    E-Print Network [OSTI]

    Snow, Christopher

    Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide protein-folding theory. q 2002 Elsevier Science Ltd. All rights reserved Keywords: molecular dynamics; protein folding; villin headpiece; ensemble averaging; distributed computing*Corresponding author

  5. Outer membrane protein A of E. coli folds into detergent micelles, but not in the

    E-Print Network [OSTI]

    Kleinschmidt, Jörg H.

    Outer membrane protein A of E. coli folds into detergent micelles, but not in the presence-barrel membrane proteins, folding of OmpA was studied as a function of the hydrophobic chain length, the chemical; membrane protein folding; outer membrane protein A; porin; protein­detergent interaction; protein

  6. Parallel Folding Pathways in the SH3 Domain Protein , J. M. Borreguero2

    E-Print Network [OSTI]

    Buldyrev, Sergey

    Parallel Folding Pathways in the SH3 Domain Protein A. R. Lam1 , J. M. Borreguero2 , F. Ding3 , N of protein conformations with an equal probability to fold or unfold. Its characterization is crucial for an understanding of the folding process. We determined the TSE of the src-SH3 domain protein by using extensive

  7. Discrete molecular dynamics studies of the folding of a protein-like model

    E-Print Network [OSTI]

    Buldyrev, Sergey

    Discrete molecular dynamics studies of the folding of a protein-like model Nikolay V Dokholyan1 to resolve in time the folding of model proteins in computer simulations. Different computational approaches). Results: We used the recently proposed approach of Zhou and Karplus to study the folding of a protein

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

    E-Print Network [OSTI]

    Unger, Ron

    1996-01-01

    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

  10. Protein Folding and Misfolding in Disease Instructors: Jean Baum and Ron Levy

    E-Print Network [OSTI]

    Chen, Kuang-Yu

    Protein Folding and Misfolding in Disease Instructors: Jean Baum and Ron Levy Tuesday 2:30-5:00 PDB Training Room Syllabus Part I: Protein Folding 9/4: Introduction to Protein Architecture 9/11: Cooperative Transitions in Protein Molecules 9/16: Kinetics of Protein Folding and the Energy Landscape Model 9

  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. Nano Res. 2011, 4(12): 124212471242 Chemical Versus Thermal Folding of Graphene Edges

    E-Print Network [OSTI]

    Simons, Jack

    Nano Res. 2011, 4(12): 1242­12471242 Chemical Versus Thermal Folding of Graphene Edges Ninghai Su dynamics (MD) simulations, we have investigated the kinetics of the graphene edge folding processV/Å (or about 120 meV per edge atom) for folding the edges of intrinsic clean single-layer graphene (SLG

  13. 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

  14. Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms

    E-Print Network [OSTI]

    Okamoto, Yuko

    Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms Yuji Sugita1 uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two simulation algorithms have been intro- duced to the protein folding problem (for reviews see, e.g., Refs. [1

  15. Using Motion Planning to Study Protein Folding Pathways Department of Computer Science

    E-Print Network [OSTI]

    LaValle, Steven M.

    Using Motion Planning to Study Protein Folding Pathways #3; Guang Song Department of Computer a framework for studying protein folding path- ways and potential landscapes which is based on techniques and study with other methods. Our focus in this work is to study the protein folding mech- anism assuming we

  16. Semi-deterministic and genetic algorithms for global optimization of microfluidic protein folding

    E-Print Network [OSTI]

    Santiago, Juan G.

    Semi-deterministic and genetic algorithms for global optimization of microfluidic protein folding of a fast microfluidic protein folding device. The aim of the latter design is to reduce mixing times protein folding devices design. Section 3 presents three global optimization algorithms with associated

  17. Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study

    E-Print Network [OSTI]

    Levine, Alex J.

    Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study Re October 1998 In the framework of a lattice-model study of protein folding, we investigate the interplay model. Lattice models have been widely used in the study of protein folding dynamics.2­8 The main

  18. Protein Folding in Contact Map Space M. Vendruscolo, R. Najmanovich and E. Domany

    E-Print Network [OSTI]

    Domany, Eytan

    Protein Folding in Contact Map Space M. Vendruscolo, R. Najmanovich and E. Domany Department the contact map representation for protein folding. We devel­ oped an efficient search procedure in the space­ tational physics, chemistry and biology is that of protein folding; e.g. to predict the conformation

  19. Protein Folding, Spin Glass and Computational Complexity 1 Aviezri S. Fraenkel

    E-Print Network [OSTI]

    Protein Folding, Spin Glass and Computational Complexity 1 Aviezri S. Fraenkel Abstract of protein folding to solve computationally intractable problems. One way of investigating this idea is to encode known NP­complete problems in terms of protein folding. The main content of this paper is to do

  20. Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent

    E-Print Network [OSTI]

    Berne, Bruce J.

    Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent protein folding in explicit solvent. This method is based on exaggerating the hydrophobic effect understanding of protein folding and misfolding is critical to many problems in computational biology.1 Many

  1. 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

  2. Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence and theoretical studies have revealed that protein folding kinetics can be quite complex and diverse depending theoretical understanding of the kinetics of protein folding [1­8]. The general scenarios that have emerged

  3. Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks Gregg Lois,1,2

    E-Print Network [OSTI]

    O'Hern, Corey S.

    Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks Gregg a protein fold reliably to its native conforma- tion even though a large number of metastable states exist the funneled energy landscape may explain how some proteins fold reliably 7 , a different picture, i.e., rugged

  4. Single-molecule spectroscopy of protein folding in a chaperonin cage

    E-Print Network [OSTI]

    Lipman, Everett A.

    Single-molecule spectroscopy of protein folding in a chaperonin cage Hagen Hofmanna , Frank for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms In the recent past, a large number of components have been identified that control and modulate protein folding

  5. Cotranslational protein folding with L-systems Gemma B. Danks1,2

    E-Print Network [OSTI]

    Stepney, Susan

    Cotranslational protein folding with L-systems Gemma B. Danks1,2 , Susan Stepney2 , and Leo S. D-systems, parallel rewriting rules, to modelling protein folding using two complementary approaches: a physics an adaptive stochas- tic open L-systems model of protein folding. L-systems were originally developed to model

  6. Fast tree search for enumeration of a lattice model of protein folding Henry Cejtin,a)

    E-Print Network [OSTI]

    Li, Hao

    Fast tree search for enumeration of a lattice model of protein folding Henry Cejtin,a) Jan Edler conformations structures for a protein folding model on a cubic lattice of size 4 3 3. We used two types. © 2002 American Institute of Physics. DOI: 10.1063/1.1423324 I. INTRODUCTION The protein folding problem1

  7. An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem

    E-Print Network [OSTI]

    Hoos, Holger H.

    An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem Alena hydrophobic-polar (2D HP) protein folding problem. We present an improved version of our recently proposed Ant search. Overall, the results presented here establish our new ACO algorithm for 2D HP protein folding

  8. An Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem

    E-Print Network [OSTI]

    Hoos, Holger H.

    An Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem Alena Shmygelska, Rosal, the two dimensional hydrophobic-polar (2D HP) protein folding problem. We introduce an ant colony algorithm closely approaches that of specialised, state-of-the methods for 2D HP protein folding. 1

  9. Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results

    E-Print Network [OSTI]

    Istrail, Sorin

    Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results a comprehensive survey of combinatorial algorithms and theorems about lattice protein folding models obtained in the almost 15 years since the publication in 1995 of the first protein folding approximation algorithm

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

    E-Print Network [OSTI]

    Newman, Alantha

    A New Algorithm for Protein Folding in the HP Model Alantha Newman #3; Abstract We consider the problem of protein folding in the HP model on the two-dimensional square lattice. This problem but not in the string) are present. The protein folding problem in the hydrophobic-hydrophilic (HP) model on the 2D

  11. Gibbs Adsorption Isotherm Combined with Monte Carlo Sampling to See Action of Cosolutes on Protein Folding

    E-Print Network [OSTI]

    Harries, Daniel

    Driven by conditions set by smaller solutes, proteins fold and unfold. Experimentally, these conditions stability. Proteins 2004;57:311­321. © 2004 Wiley-Liss, Inc. INTRODUCTION Inside cells, proteins fold poten- tials, to follow the process of protein folding or unfolding in response to its environment

  12. Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics

    E-Print Network [OSTI]

    Morozov, Alexandre V.

    Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics Eric Alm1 underlying the protein-folding problem can be tested by developing and characterizing simple models that make prefactor for protein folding. Finally, we discuss the limitations of simple native-state-based models

  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. Modulation of the Maladaptive Stress Response to Manage Diseases of Protein Folding

    E-Print Network [OSTI]

    Morimoto, Richard

    Modulation of the Maladaptive Stress Response to Manage Diseases of Protein Folding Daniela Martino homeostasis components that direct protein folding and function. To identify global principles of misfolding. In diseased cells, maladaptation alters protein structure­function relationships, impacts protein folding

  15. Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies

    E-Print Network [OSTI]

    Croquette, Vincent

    Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies for protein folding studies and has been extensively stud- ied, both experimentally (at the ensemble level concentration. It is shown that new infor- mation about different aspects of the protein folding reaction can

  16. Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete

    E-Print Network [OSTI]

    Istrail, Sorin

    Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete Bonnie Berger* Tom Leightont Abstract One of the simplest and most popular biophysical mod- els of protein folding is the hydrophobic-hydrophilic (HP) model. The HP model abstracts the hydrophobic in- teraction in protein folding

  17. A New Constraint Solver for 3D Lattices and its Application to the Protein Folding Problem

    E-Print Network [OSTI]

    Dal Palù, Alessandro

    A New Constraint Solver for 3D Lattices and its Application to the Protein Folding Problem protein folding) problem can be defined as the problem of determining, given the molecular composition of a protein. The predominant strategy in solving #12;the protein folding problem has been to determine a state

  18. The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding

    E-Print Network [OSTI]

    Fleming, Patrick

    ­coil theories and protein folding. Contrary to the hypothesis, we find that systematic local steric effects can). The central thermodynamic question in protein folding is: How can a polypeptide chain overcome conformational­6) and protein-folding theories (7). It follows from the hypothesis that local structural transitions are ruled

  19. Identification of the protein folding transition state from molecular dynamics trajectories

    E-Print Network [OSTI]

    Caflisch, Amedeo

    Identification of the protein folding transition state from molecular dynamics trajectories S. Muff The rate of protein folding is governed by the transition state so that a detailed characterization of its. INTRODUCTION Proteins fold from the heterogeneous set of denatured conformations to the structurally well

  20. Protein folding: from theory to practice D Thirumalai1,2

    E-Print Network [OSTI]

    Thirumalai, Devarajan

    Protein folding: from theory to practice D Thirumalai1,2 , Zhenxing Liu3 , Edward P O'Brien4 and Govardhan Reddy1 A quantitative theory of protein folding should make testable predictions using theoretical globules represent major advances in the proteins folding field. Addresses 1 Biophysics Program, Institute