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1

Mechanical Models of Fault-Related Folding  

SciTech Connect (OSTI)

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).

Johnson, A. M.

2003-01-09T23:59:59.000Z

2

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

E-Print Network [OSTI]

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

McLain, Christopher Thomas

2001-01-01T23:59:59.000Z

3

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

E-Print Network [OSTI]

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

Hurtado, José Miguel, 1974-

2002-01-01T23:59:59.000Z

4

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

E-Print Network [OSTI]

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

Fossen, Haakon

5

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

E-Print Network [OSTI]

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

Fossen, Haakon

6

Structural analysis of an Inverted half-graben: Implications for fracture distribution and reservior quality in Point Arguello oil field  

SciTech Connect (OSTI)

Analysis of 3-D seismic and well data suggests that the present-day Point Arguello anticline contains part of a northward-elongate Miocene-Pliocene half graben that was compressionally inverted to a northwest-trending double-plunging anticline during the Pliocene-Pleistocene. Upper Sisquoc and Foxen sedimentation postdated the normal faulting event so the shape of the fold at these stratigraphic levels is relatively simple, being the product of only the late, compressional event. Refolding of the earlier rift structure resulted, however, in a relatively complicted saddle-shaped anticline at lower Sisquoc and Monterey reservoir levels. Nevertheless, we observe that several distinct homolinal-dipping panels of rock (kink bands) define the fold shape at reservoir level. We perform a structural analysis using fault-related fold theory and the new technique of Axial Surface Mapping to map kink bands at Monterey reservoir level. Although both folding events produced kink bands, open permeable fractures are associated with the late compression, whereas filled, crenulated fractures likely formed earlier by compaction of syntextensional sediments. Therefore, we predict a greater fracture density within kink bands formed during the late folding event. We also predict better reservoir quality within kink bands within the plunging ends of the structure which show structural thinning and more numerous small faults in seismic profiles than in non-thinned fold limbs. Qualitative predictions of fracture density and reservoir quality based on the fold history and geometry of individual kink bands compare favorably with fracture measurements in core and drill-stem test results.

Genovese, P.G.; Suppe, J. (Princeton Univ., NJ (United States))

1994-04-01T23:59:59.000Z

7

ORIGINAL PAPER The south-western Black Forest and the Upper Rhine Graben  

E-Print Network [OSTI]

ORIGINAL PAPER The south-western Black Forest and the Upper Rhine Graben Main Border Fault: thermal Ă? Springer-Verlag 2008 Abstract The thermal history of the south-westernmost Black Forest (Germany) and microstructural analyses. After intrusion of Palaeozoic granitic plutons in the Black Forest, the thermal regime

Wetzel, Andreas

8

Tectonic and flexural significance of Middle Devonian graben-fill sequence in new Albany shale, central Kentucky  

SciTech Connect (OSTI)

The third tectonic phase of the Acadian orogeny began in the late Middle Devonian, and the sedimentary record of that event is largely restricted to the deeper, more proximal portions of the Appalachian foreland and Illinois intercratonic basins. Much of the intervening area, on and near the Cincinnati arch, was uplifted and subjected to erosion by movement on the peripheral bulge accompanying the initiation of the third tectonic phase. However, bulge movement also reactivated basement fault systems in Kentucky and created a series of grabens that were filled with eroded sediments and debris flows from adjacent horsts. Although rarely preserved, a buried Devonian graben along Carpenter Fork in Boyle County, central Kentucky, reveals such a sequence. The graben is bounded by upthrown blocks of Middle Devonian Boyle Dolomite, which also floors the graben. Within the graben a black-shale unit, apparently absent elsewhere, conformably overlies the Boyle and grades upward into debris-flow deposits represented by the Duffin breccia facies of the New Albany Shale. The Duffin contains clasts of the shale, as well as of chert, silicified fossils, and fine to boulder-size dolostone clasts eroded from the Boyle high on the flanks of the graben. The underlying shale also exhibits evidence of penecontemporaneous soft-sediment deformation related to the debris-flow emplacement of Boyle residue in the graben and due to later loading by the Duffin.

Barnett, S.F.; Ettensohn, F.R.; Mellon, C. (Univ. of Kentucky, Lexington (USA))

1989-08-01T23:59:59.000Z

9

Characterization of the structure of faults in the Eocene Carrizo Formation near Gause, Milam County, Texas  

E-Print Network [OSTI]

-scale graben accommodating NW-SE extension. The Carrizo Fm. consists primarily of friable to weakly lithified quartz sandstones with several horizons with interbedded siltstones and shales. Five faults and fault zones occur in the quarry with displacements...

Yilmaz, Ramazan

2012-06-07T23:59:59.000Z

10

Volcanic rifting at Martian grabens Daniel Me`ge,1  

E-Print Network [OSTI]

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

Mege, Daniel

11

Folding@HomeFolding@Home Vijay Pande  

E-Print Network [OSTI]

Folding@HomeFolding@Home Vijay Pande #12;http://folding.stanford.edu © Vijay S. Pande 1999,000,000 PCs on the internet Folding@Home People donate their idle computer time They visit our website://folding.stanford.edu © Vijay S. Pande 1999-2003 Folding@HomeFolding@Home:: VeryVery powerful & cost effectivepowerful & cost

Dally, William J.

12

Protein folding tames chaos  

E-Print Network [OSTI]

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...

Xia, Kelin

2013-01-01T23:59:59.000Z

13

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

SciTech Connect (OSTI)

The objectives of this study were to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults, (2) The influence of folding and lithostratigraphy on fracture patterns, (3) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics, and (4) The influence of lithostratigraphy and deformation on fluid flow.

Wallace, W.K.; Hanks, C.L.; Whalen, M.T.; Jensen, J.; Atkinson, P.K.; Brinton, J.S.

2001-01-09T23:59:59.000Z

14

Reflection seismic profiling in Wabash Valley fault system in southwestern Indiana  

SciTech Connect (OSTI)

During the summer of 1988 common-depth-point (CDP) reflection seismic profiling was initiated by ARPEX in southwestern Indiana in the Wabash Valley fault system. A 2.2-im (1.4-mi) east-west profile was shot across the Mt. Vernon graben in Posey County. Minihole shooting in 21-m (68.9-ft) patterns using 3.4 kg (7.5 lb) of seismic explosives distributed in five 3-m (10-ft) holes provided the energy source. Most shotholes were made with a reversible air-driven penetrating tool that was effective in dense clays. The 12-geophone array length was 43 m (141 ft), and the nominal far-trace offset was 2.1 km (7,000 ft). A 48-channel recording yielded 24-CDP coverage at 11-m (36-ft) intervals. Data were enhanced by gapped deconvolution, bandpass filtering, and CDP stack. The strongest and most continuous reflections at 0.75 and 1.6 sec are associated with the New Albany Shale (Devonian-Mississippian) and Eau Claire Formation (Cambrian), respectively. Within the Mt. Vernon graben and east of the Spenser Consolidated oil field, the depth to Eau Claire Formation apparently increases by approximately 60 m (197 ft) over a horizontal distance of 1.4 km (0.9 mi). Minor faulting east of the Spencer Consolidated field appears to be synthetic to the Hovey lake fault, which bounds the eastern side of the Mt. Vernon graben. Tentative interpretations of faulting and weak reflections from depths greater than 4.5 km (15,000 ft) may be clarified by additional data processing and by additional seismic profiling planned by ARPEX.

Rene, R.M.; Hester, N.C.; Stanonis, F.L. (Indiana Univ., Bloomington (USA))

1989-08-01T23:59:59.000Z

15

Seismic model study of fault and fold geometries  

E-Print Network [OSTI]

used for both theoretical and enipiri& al factois ivitli tli& latter in italics Most of the reflection events of significant aniplitude in this study (PP. SS. PPPP) are normal inciden&e reflections& oiv&ng t&& thc geometrica] i&stia&tioiis imposed...

Hand, Linda Mimura

2012-06-07T23:59:59.000Z

16

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

SciTech Connect (OSTI)

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

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

1997-02-01T23:59:59.000Z

17

Optimization Approaches to Protein Folding.  

E-Print Network [OSTI]

??This research shows optimization approaches to protein folding. The protein folding problem is to predict the compact three dimensional structure of a protein based on… (more)

Yoon, Hyun-suk

2006-01-01T23:59:59.000Z

18

Simulations of Protein Folding  

E-Print Network [OSTI]

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.

Michael Cahill; Mark Fleharty; Kevin Cahill

1999-09-17T23:59:59.000Z

19

INVERSE PROTEIN FOLDING, HIERARCHICAL OPTIMISATION  

E-Print Network [OSTI]

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

Halligan, Daniel

20

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

SciTech Connect (OSTI)

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

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

2001-07-23T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Protein folding and cosmology  

E-Print Network [OSTI]

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.

González-Diáz, P F

1997-01-01T23:59:59.000Z

22

Protein folding and cosmology  

E-Print Network [OSTI]

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.

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

1997-06-04T23:59:59.000Z

23

Protein folding and heteropolymers  

E-Print Network [OSTI]

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.

T. Garel; H. Orland; E. Pitard

1997-06-12T23:59:59.000Z

24

Petaflop Computing for Protein Folding  

E-Print Network [OSTI]

"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

Izaguirre, JesĂşs A.

25

Computer Simulations of Protein Folding  

E-Print Network [OSTI]

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

Sorin, Eric J.

26

Theoretical Perspectives on Protein Folding  

E-Print Network [OSTI]

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

Thirumalai, Devarajan

27

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

28

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

E-Print Network [OSTI]

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

Temple, Vernon James Jay

1977-01-01T23:59:59.000Z

29

Protein folding in the ER.  

SciTech Connect (OSTI)

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.

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

1999-10-01T23:59:59.000Z

30

Theoretical Perspectives on Protein Folding  

E-Print Network [OSTI]

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.

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

2010-07-18T23:59:59.000Z

31

A Novel Topology for Representing Protein Folds  

E-Print Network [OSTI]

J. (2008). Predicting protein folding rates from geometric1993). Cooperativity in protein-folding kinetics. Proc NatlVoelz VA. (2007). The protein folding problem: when will it

Segal, Mark R

2009-01-01T23:59:59.000Z

32

Uncovering Allostery in a Uniquely Folded Metalloprotein /  

E-Print Network [OSTI]

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

Baxter, Elizabeth Leigh

2013-01-01T23:59:59.000Z

33

Graphene folding on flat substrates  

SciTech Connect (OSTI)

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.

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

2014-10-28T23:59:59.000Z

34

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

SciTech Connect (OSTI)

The Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is detachment folded where it is exposed throughout the northeastern Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study are to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults. (2) The influence of folding and lithostratigraphy on fracture patterns. (3) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics. (4) The influence of lithostratigraphy and deformation on fluid flow. The results of field work during the summer of 1999 offer some preliminary insights: The Lisburne Limestone displays a range of symmetrical detachment fold geometries throughout the northeastern Brooks Range. The variation in fold geometry suggests a generalized progression in fold geometry with increasing shortening: Straight-limbed, narrow-crested folds at low shortening, box folds at intermediate shortening, and folds with a large height-to-width ratio and thickened hinges at high shortening. This sequence is interpreted to represent a progressive change in the dominant shortening mechanism from flexural-slip at low shortening to bulk strain at higher shortening. Structural variations in bed thickness occur throughout this progression. Parasitic folding accommodates structural thickening at low shortening and is gradually succeeded by penetrative strain as shortening increases. The amount of structural thickening at low to intermediate shortening may be inversely related to the local amount of structural thickening of the Kayak Shale, the incompetent unit that underlies the Lisburne. The Lisburne Limestone displays a different structural style in the south, across the boundary between the northeastern Brooks Range and the main axis of the Brooks Range fold-and-thrust belt. The steep forelimbs of angular asymmetrical folds typically have been cut and displaced by thrust faults, resulting in superposition of a fault-bend fold geometry on the truncated folds. Remnant uncut folds within trains of thrust-truncated folds and the predominance of detachment folds to the north suggest that these folds originated as detachment folds. Fold asymmetry and a more uniformly competent Lisburne Limestone may have favored accommodation of a significant proportion of shortening by thrust faulting, in contrast with the dominance of fold shortening to the north. Two dominant sets of fractures are present in the least deformed Lisburne Limestone: Early extension fractures normal to the regional fold trend and late extension and shear fractures parallel to the regional fold trend. These two major fracture sets remain as deformation increases, but they are more variable in orientation, character, and relative age. Compared to fold limbs, the fold hinges display greater density and extent of fractures, more conjugate and shear fractures, and more evidence of penetrative strain. This suggests that hinges remained fixed during fold growth. Late extension fractures normal to the fold axis are common even where penetrative strain is greatest. Fracture density is greater in fine-grained carbonates than in coarse-grained carbonates over the entire spectrum of deformation.

Wesley K. Wallace; Catherine L. Hanks; Michael T. Whalen; Jerry Jensen; Paul K. Atkinson; Joseph S. Brinton

2000-05-01T23:59:59.000Z

35

Solar system fault detection  

DOE Patents [OSTI]

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.

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

1984-05-14T23:59:59.000Z

36

Solar system fault detection  

DOE Patents [OSTI]

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.

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

1986-01-01T23:59:59.000Z

37

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

E-Print Network [OSTI]

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

Avouac, Jean-Philippe

38

Fast events in protein folding  

SciTech Connect (OSTI)

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.

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

1996-04-01T23:59:59.000Z

39

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

SciTech Connect (OSTI)

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

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

1994-04-01T23:59:59.000Z

40

Protein Folding Sculpting Evolutionary Change  

E-Print Network [OSTI]

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, ...

Lindquist, Susan

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

Characterization of protein folding intermediates  

SciTech Connect (OSTI)

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.

Kim, P.S.

1986-01-01T23:59:59.000Z

42

Introduction to Grid computing Protein folding  

E-Print Network [OSTI]

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

Boyar, Joan

43

A motion planning approach to protein folding  

E-Print Network [OSTI]

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

Song, Guang

2004-09-30T23:59:59.000Z

44

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

SciTech Connect (OSTI)

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

Price, E.H.

1982-01-01T23:59:59.000Z

45

Dominant Pathways in Protein Folding  

E-Print Network [OSTI]

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.

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

2006-07-27T23:59:59.000Z

46

Transition-fault test generation  

E-Print Network [OSTI]

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

Cobb, Bradley Douglas

2013-02-22T23:59:59.000Z

47

Optimal fault location  

E-Print Network [OSTI]

for the pre-selected time out to pass and initiate reclosing again. If after selected number of attempts of reclosing, fault is still present, breaker lockout is taking place. There will be no more attempts to reclose automatically the breaker again....2: Trip and reclose sequences on a single breaker In the case of breaker lockout the assumption taken by the operators is that fault is permanent. Special order is issued to the maintenance for the breaker to be closed back in 4 again once...

Knezev, Maja

2009-05-15T23:59:59.000Z

48

Optimal fault location  

E-Print Network [OSTI]

for the pre-selected time out to pass and initiate reclosing again. If after selected number of attempts of reclosing, fault is still present, breaker lockout is taking place. There will be no more attempts to reclose automatically the breaker again....2: Trip and reclose sequences on a single breaker In the case of breaker lockout the assumption taken by the operators is that fault is permanent. Special order is issued to the maintenance for the breaker to be closed back in 4 again once...

Knezev, Maja

2008-10-10T23:59:59.000Z

49

Computer hardware fault administration  

DOE Patents [OSTI]

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.

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

2010-09-14T23:59:59.000Z

50

Disulfide-Linked Protein Folding Pathways  

E-Print Network [OSTI]

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

Bardwell, James

51

Row fault detection system  

DOE Patents [OSTI]

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

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

2012-02-07T23:59:59.000Z

52

Protein folding using contact maps  

E-Print Network [OSTI]

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.

Michele Vendruscolo; Eytan Domany

1999-01-21T23:59:59.000Z

53

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

E-Print Network [OSTI]

. Summary SUMMARY AND CONCLUSIONS REFERENCES . SUPPLEMENTAL SOURCES CONSULTED APPENDIX A VITA 57 58 59 59 60 62 68 70 vn LIST OF TABLES Table II. Ihh Comparison of fault-generated phases during arcing fault test Comparison of fault...-generated phases during arcing fault test Comparison of fault-generated phases during arcing fault test activity on activity on activity on faulted and unfaulted Page 45 faulted and unfaulted 46 faulted and unfaulted 47 vu1 LIST OF FIGURES Figure l...

Benner, Carl Lee

1988-01-01T23:59:59.000Z

54

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

E-Print Network [OSTI]

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

Plotkin, Steven S.

55

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

SciTech Connect (OSTI)

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

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

2002-01-01T23:59:59.000Z

56

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

E-Print Network [OSTI]

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

Croquette, Vincent

57

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

E-Print Network [OSTI]

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-

Horner, Geoffrey Ashworth

2010-01-01T23:59:59.000Z

58

Parametric analysis of RNA folding  

E-Print Network [OSTI]

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

Hower, Valerie

2009-01-01T23:59:59.000Z

59

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

SciTech Connect (OSTI)

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.

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

2004-07-01T23:59:59.000Z

60

Topology to geometry in protein folding: -Lactoglobulin  

E-Print Network [OSTI]

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

Berry, R. Stephen

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

EXPLORING PROTEIN FOLDING TRAJECTORIES USING GEOMETRIC SPANNERS  

E-Print Network [OSTI]

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

Guibas, Leonidas J.

62

Statistical Physics of RNA folding Ralf Bundschuh  

E-Print Network [OSTI]

Statistical Physics of RNA folding Ralf Bundschuh Ohio State University August 15, 2007 Ralf Bundschuh (Ohio State University) Statistical Physics of RNA folding August 15, 2007 1 / 119 #12;Outline University) Statistical Physics of RNA folding August 15, 2007 2 / 119 #12;Part I Introduction to RNA biology

Bundschuh, Ralf

63

UNCORRECTED 3 Protein folding: Then and now  

E-Print Network [OSTI]

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

Dokholyan, Nikolay V.

64

272 Dispatch Protein folding: Chaperones get Hip  

E-Print Network [OSTI]

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

Craig, Elizabeth A

65

Protein folding: not just another optimization  

E-Print Network [OSTI]

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

Karplus, Kevin

66

Atomistic Protein Folding Simulations on the  

E-Print Network [OSTI]

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

Snow, Christopher

67

Thermodynamics of Protein Folding Erik Sandelin  

E-Print Network [OSTI]

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

Sandelin, Erik

68

Approximate Inference and Protein-Folding  

E-Print Network [OSTI]

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

Weiss, Yair

69

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

70

Introducing Protein Folding Using Simple Models  

E-Print Network [OSTI]

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

D. Thirumalai; D. K. Klimov

2001-01-04T23:59:59.000Z

71

Structural and Energetic Heterogeneity in Protein Folding  

E-Print Network [OSTI]

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

Steven S. Plotkin; Jose N. Onuchic

2000-09-27T23:59:59.000Z

72

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

E-Print Network [OSTI]

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

Yang, Hui

73

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

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

74

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

75

Fault current limiter  

DOE Patents [OSTI]

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.

Darmann, Francis Anthony

2013-10-08T23:59:59.000Z

76

Colorado Regional Faults  

SciTech Connect (OSTI)

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

Hussein, Khalid

2012-02-01T23:59:59.000Z

77

Protein-Folding Landscapes in Multi-Chain Systems  

E-Print Network [OSTI]

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

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

2005-01-01T23:59:59.000Z

78

Protein-folding via divide-and-conquer optimization  

E-Print Network [OSTI]

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

Oliva, Ricardo; Crivelli, Silvia; Meza, Juan

2004-01-01T23:59:59.000Z

79

Intermediates and the folding of proteins L and G  

E-Print Network [OSTI]

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

Brown, Scott; Head-Gordon, Teresa

2008-01-01T23:59:59.000Z

80

Folding amphipathic helices into membranes: Amphiphilicity trumps hydrophobicity  

E-Print Network [OSTI]

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

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

2007-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Extending the theoretical framework of protein folding dynamics  

E-Print Network [OSTI]

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

Yang, Sichun

2006-01-01T23:59:59.000Z

82

On the rough folding landscape of green fluorescent protein  

E-Print Network [OSTI]

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

Andrews, Benjamin Thomas

2008-01-01T23:59:59.000Z

83

Observer-based fault detection for nuclear reactors  

E-Print Network [OSTI]

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 ...

Li, Qing, 1972-

2001-01-01T23:59:59.000Z

84

Synchronized sampling improves fault location  

SciTech Connect (OSTI)

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

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

1995-04-01T23:59:59.000Z

85

Protein Vivisection Reveals Elusive Intermediates in Folding  

SciTech Connect (OSTI)

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.

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

2010-05-25T23:59:59.000Z

86

Simulating Temperature Jumps for Protein Folding Studies.  

E-Print Network [OSTI]

??Protein folding is described as a dynamic process of an ensemble of molecules reaching well-defined three dimensional structures to achieve biological activity from linear amino… (more)

Kim, Seonah

2007-01-01T23:59:59.000Z

87

Cotranslational protein folding with L-systems  

E-Print Network [OSTI]

Abstract. A protein molecule adopts a specific 3D structure, necessary for its function in the cell, through a process of folding. Modelling the folding process and predicting the final fold from the unique amino acid sequence remain challenging problems. We have previously described the application of L-systems, parallel rewriting rules, to modelling protein folding using two complementary approaches: a physics-based approach, using calculations of interatomic forces, and a knowledge-based approach, using data from fragments of known protein structures. Here we describe a model combining these two approaches creating an adaptive stochastic open L-systems model of protein folding. L-systems were originally developed to model growth and development. Here we also describe extensions of our L-systems models to investigate cotranslational protein folding, i.e. folding during protein biosynthesis on the ribosome, which is increasingly thought to play an important role. We demonstrate that cotranslational folding fits very naturally into the L-systems framework. Key words: Cotranslational protein folding, L-systems 1

Gemma B. Danks; Susan Stepney; Leo S. D. Caves

88

Arc fault detection system  

DOE Patents [OSTI]

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.

Jha, Kamal N. (Bethel Park, PA)

1999-01-01T23:59:59.000Z

89

Arc fault detection system  

DOE Patents [OSTI]

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.

Jha, K.N.

1999-05-18T23:59:59.000Z

90

Structural Insight into RNA Hairpin Folding Intermediates Gregory R. Bowman,  

E-Print Network [OSTI]

on the Folding@home infrastructure to obtain better sampling and, therefore, greater insight into RNA folding

Guibas, Leonidas J.

91

Hot Pot Detail - Evidence of Quaternary Faulting  

SciTech Connect (OSTI)

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

Lane, Michael

2013-06-27T23:59:59.000Z

92

Hot Pot Detail - Evidence of Quaternary Faulting  

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

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

Lane, Michael

93

STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS  

E-Print Network [OSTI]

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

Dinner, Aaron

94

Fan-fold shielded electrical leads  

DOE Patents [OSTI]

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.

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

1996-06-11T23:59:59.000Z

95

Fan-fold shielded electrical leads  

DOE Patents [OSTI]

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.

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

1996-01-01T23:59:59.000Z

96

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

E-Print Network [OSTI]

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

Pratt, Vaughan

97

Fault-tolerant rotary actuator  

DOE Patents [OSTI]

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

Tesar, Delbert

2006-10-17T23:59:59.000Z

98

Passive fault current limiting device  

DOE Patents [OSTI]

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

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

1999-04-06T23:59:59.000Z

99

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

E-Print Network [OSTI]

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...

Neal, Leslie Ann

2002-01-01T23:59:59.000Z

100

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

E-Print Network [OSTI]

between and oriented oblique to the bounding faults. With increasing displacement on the bounding faults, the system of secondary faults evolves from an Elementary to a Compound, to an Advanced geometry, which includes the formation of secondary... to the primary faults. Synthetic faults form interior to and ahead of the bounding faults, increasing the effective overlap. Displacements on antithetic faults are directly related to changes in displacement on associated bounding faults. Additionally...

Hedgcoxe, Howard Reiffert

2012-06-07T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

Development of Characterization Technology for Fault Zone Hydrology  

E-Print Network [OSTI]

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

Karasaki, Kenzi

2010-01-01T23:59:59.000Z

102

Protein Folding as a Physical Stochastic Process  

E-Print Network [OSTI]

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.

Kerson Huang

2007-07-17T23:59:59.000Z

103

Enhanced sampling and applications in protein folding.  

E-Print Network [OSTI]

??We show that a single-copy tempering method is useful in protein-folding simulations of large scale and high accuracy (explicit solvent, atomic representation, and physics-based potential).… (more)

Zhang, Cheng

2013-01-01T23:59:59.000Z

104

DMBC: Web Planning & Layouts Above the Fold  

E-Print Network [OSTI]

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

Stowell, Michael

105

Mutagenic effects on protein folding and stability  

E-Print Network [OSTI]

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 ...

Anderson, Thomas Anthony, 1973-

2002-01-01T23:59:59.000Z

106

Cooperativity and Contact Order in Protein Folding  

E-Print Network [OSTI]

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

Marek Cieplak

2004-01-11T23:59:59.000Z

107

Self-folding with shape memory composites  

E-Print Network [OSTI]

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

Felton, Samuel M.

108

A phenomenological model of protein folding  

E-Print Network [OSTI]

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.

Danielsson, Ulf H; Niemi, Antti J

2009-01-01T23:59:59.000Z

109

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

E-Print Network [OSTI]

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.

Walter Simmons; Joel L. Weiner

2011-12-28T23:59:59.000Z

110

Protein Folding: A Perspective From Statistical Physics  

E-Print Network [OSTI]

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^{\

Jinzhi Lei; Kerson Huang

2010-02-26T23:59:59.000Z

111

Review Protein Folding and Misfolding on Surfaces  

E-Print Network [OSTI]

Abstract: Protein folding, misfolding and aggregation, as well as the way misfolded and aggregated proteins affects cell viability are emerging as key themes in molecular and structural biology and in molecular medicine. Recent advances in the knowledge of the biophysical basis of protein folding have led to propose the energy landscape theory which provides a consistent framework to better understand how a protein folds rapidly and efficiently to the compact, biologically active structure. The increased knowledge on protein folding has highlighted its strict relation to protein misfolding and aggregation, either process being in close competition with the other, both relying on the same physicochemical basis. The theory has also provided information to better understand the structural and environmental factors affecting protein folding resulting in protein misfolding and aggregation into ordered or disordered polymeric assemblies. Among these, particular importance is given to the effects of surfaces. The latter, in some cases make possible rapid and efficient protein folding but most often recruit proteins/peptides increasing their local concentration thus favouring misfolding and accelerating the rate of nucleation. It is also emerging that surfaces can modify the path of protein misfolding and aggregation generating oligomers and polymers structurally different from those arising in the bulk solution and endowed with different physical properties and cytotoxicities.

Massimo Stefani

2008-01-01T23:59:59.000Z

112

Hierarchical Protein Folding Pathways: A Computational Study of Protein Fragments  

E-Print Network [OSTI]

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

Haspel, Nurit

113

FROM GENETIC CODING TO PROTEIN FOLDING Jean-Luc Jestin  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

114

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

E-Print Network [OSTI]

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

Zaki, Mohammed Javeed

115

DYNAMIC INVARIANTS IN PROTEIN FOLDING PATHWAYS REVEALED BY TENSOR ANALYSIS  

E-Print Network [OSTI]

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

Langmead, Christopher James

116

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

117

Automated Fault Location In Smart Distribution Systems  

E-Print Network [OSTI]

of utilizing a suitable fault location method. As distribution systems are gradually evolving into smart distribution systems, application of more accurate fault location methods based on gathered data from various Intelligent Electronic Devices (IEDs...

Lotfifard, Saeed

2012-10-19T23:59:59.000Z

118

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

E-Print Network [OSTI]

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

Wang, Dajin

119

Protein folding using contact maps Michele Vendruscolo and Eytan Domany  

E-Print Network [OSTI]

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

Domany, Eytan

120

THE UNIVERSITY OF CHICAGO CHARACTERIZATION OF PROTEIN FOLDING INTERMEDIATES  

E-Print Network [OSTI]

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

Sosnick, Tobin R.

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

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

122

Exploring zipping and assembly as a protein folding principle  

E-Print Network [OSTI]

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

Voelz, Vince A; Dill, Ken A

2007-01-01T23:59:59.000Z

123

Protein Folding: A New Geometric Analysis  

E-Print Network [OSTI]

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.

Walter A. Simmons; Joel L. Weiner

2008-09-11T23:59:59.000Z

124

High temperature superconducting fault current limiter  

DOE Patents [OSTI]

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.

Hull, J.R.

1997-02-04T23:59:59.000Z

125

Isolation, folding and structural investigations of the amino...  

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

folding and structural investigations of the amino acid transporter OEP16. Isolation, folding and structural investigations of the amino acid transporter OEP16. Abstract: Membrane...

126

Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios  

E-Print Network [OSTI]

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

Berry, R. Stephen

127

Single-Molecule Dynamics Reveals Cooperative Binding-Folding...  

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

Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition . Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition . Abstract: The...

128

Exploring the mechanisms of protein folding  

E-Print Network [OSTI]

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,...

Xu, Ji; Ren, Ying; Li, Jinghai

2013-01-01T23:59:59.000Z

129

Software Fault Diagnosis Peter Zoeteweij  

E-Print Network [OSTI]

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

Zoeteweij, Peter

130

CSAW: a dynamical model of protein folding  

E-Print Network [OSTI]

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.

Kerson Huang

2006-01-12T23:59:59.000Z

131

Nonlinear conformation of secondary protein folding  

E-Print Network [OSTI]

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.

Januar, M; Handoko, L T

2012-01-01T23:59:59.000Z

132

Energetic Components of Cooperative Protein Folding  

E-Print Network [OSTI]

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

Huseyin Kaya; Hue Sun Chan

2000-10-11T23:59:59.000Z

133

Circular permutant GFP insertion folding reporters  

SciTech Connect (OSTI)

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.

Waldo, Geoffrey S; Cabantous, Stephanie

2013-02-12T23:59:59.000Z

134

Circular permutant GFP insertion folding reporters  

SciTech Connect (OSTI)

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.

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

2008-06-24T23:59:59.000Z

135

Circular permutant GFP insertion folding reporters  

SciTech Connect (OSTI)

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.

Waldo, Geoffrey S.; Cabantous, Stephanie

2013-04-16T23:59:59.000Z

136

Circular permutant GFP insertion folding reporters  

SciTech Connect (OSTI)

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.

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

2011-06-14T23:59:59.000Z

137

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

E-Print Network [OSTI]

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...

Simmons, Walter

2011-01-01T23:59:59.000Z

138

Fast Gravitational Wave Radiometry using Data Folding  

E-Print Network [OSTI]

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

Ain, Anirban; Mitra, Sanjit

2015-01-01T23:59:59.000Z

139

On the Complexity of Protein Folding  

E-Print Network [OSTI]

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

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

140

Simultaneous Alignment and Folding of Protein Sequences  

E-Print Network [OSTI]

is to predict for every input sequence the minimum free-energy non-crossing structure (in O(n3 ) time function. Since the structure of RNA is evolu- tionarily more conserved than its sequence, predicting a folding with minimal free energy [5, 6, 7, 8, 9]. Albeit this so-named thermodynamic approach is a success

Gifford, David K.

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

Heuristics for PLA folding: an analytical approach  

SciTech Connect (OSTI)

A practical problem that arises in the automatic design and layout of Programmable Logic Arrays (PLA's) is examined. Folding is a technique used to reduce the area of PLA's. The problem of folding a PLA to its smallest possible area is known to be NP-Complete. The practical importance of this problem motivates the study of heuristics. So far, much of the work on heuristics for this problem has been of an experimental nature. Here an analytical study of heuristic algorithms for this problem is carried out. The performance measure used to evaluate a heuristic (referred to as the folding ratio of the heuristic) is the worst case ratio of the optimal value to the value produced by the heuristic. The results indicate very strongly that no polynomial time approximation algorithm can guarantee a constant worst case ratio for an arbitrary PLA. However, for restricted classes of PLA's, it is shown that constant ratios can be obtained in polynomial time. A variant of the folding problem (the orderability problem) is addressed, and some new results are presented.

Ravi, S.S.

1984-01-01T23:59:59.000Z

142

Folded-path optical analysis gas cell  

DOE Patents [OSTI]

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.

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

1995-08-08T23:59:59.000Z

143

Folded-path optical analysis gas cell  

DOE Patents [OSTI]

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.

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

1995-01-01T23:59:59.000Z

144

Critical aspects of hierarchical protein folding  

E-Print Network [OSTI]

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.

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

1998-01-13T23:59:59.000Z

145

Solvent-induced forces in protein folding  

SciTech Connect (OSTI)

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.

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

1990-08-23T23:59:59.000Z

146

Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics  

E-Print Network [OSTI]

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

Santiago, Juan G.

147

COMMUNICATION First Principles Prediction of Protein Folding Rates  

E-Print Network [OSTI]

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

Goddard III, William A.

148

Cellular mechanisms of membrane protein folding William R Skach  

E-Print Network [OSTI]

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

Cai, Long

149

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

150

Protein folding by zipping and assembly S. Banu Ozkan*  

E-Print Network [OSTI]

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

Southern California, University of

151

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

152

Early Events in Protein Folding Explored by Rapid Mixing Methods  

E-Print Network [OSTI]

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

Roder, Heinrich

153

Automated Discovery of Structural Signatures of Protein Fold and Function  

E-Print Network [OSTI]

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

Muggleton, Stephen H.

154

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

E-Print Network [OSTI]

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

Roma "La Sapienza", UniversitĂ  di

155

Planning to fold multiple objects from a single self-folding sheet  

E-Print Network [OSTI]

This paper considers planning and control algorithms that enable a programmable sheet to realize different shapes by autonomous folding. Prior work on self-reconfiguring machines has considered modular systems in which ...

An, Byoung Kwon

156

Simple Models of the Protein Folding Problem  

E-Print Network [OSTI]

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

Chao Tang

1999-12-26T23:59:59.000Z

157

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

E-Print Network [OSTI]

measured at feeder substations and the fault distance algorithm was tested using data obtained by staging faults on a model of an overhead feeder using EMTP/ATP simulation. The results obtained from the tests were promising. A simple illustration...

Andoh, Kwame Sarpong

2000-01-01T23:59:59.000Z

158

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

E-Print Network [OSTI]

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

Savage, Heather M.; Brodsky, Emily E.

2011-01-01T23:59:59.000Z

159

The detection of high impedance faults using random fault behavior  

E-Print Network [OSTI]

the energy 120 100 80 O& 60 C Lu 40 20 100 200 300 400 500 600 700 800 900 1000 1100 Cycle Number Figure 1. Typical lugh frequency energy per cycle for an arcing fault. 23 . 055 . 050 . 025 Ol . 020 . 01 5 . 010 . 005 25 50 75 100 125... 150 175 200 225 250 275 500 Cycle Number Figure 2. Typical high frequency energy per cycle for a normal system. 24 3 Vl c uj 2 100 200 300 400 500 600 700 800 900 '1000 1100 Cycle Number Figure 3. Typical high frequency energy per cycle for a...

Carswell, Patrick Wayne

1988-01-01T23:59:59.000Z

160

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

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

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

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

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

E-Print Network [OSTI]

presents research works in the topics of fault analysis and fault tolerant control of an electric vehicle mechanism (transition strategy) at sensor fault occurrence. Index Terms--Electric vehicle, induction motor-tolerant AC motor drives in industrial applications [9-10- 41]. II. ELECTRIC VEHICLE POWERTRAIN COMPONENTS

Brest, Université de

162

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

E-Print Network [OSTI]

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

Chakrabarty, Krishnendu

163

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

E-Print Network [OSTI]

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

Sandiford, Mike

164

Earthquake behavior and structure of oceanic transform faults  

E-Print Network [OSTI]

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 ...

Roland, Emily Carlson

2012-01-01T23:59:59.000Z

165

Low-cost motor drive embedded fault diagnosis systems  

E-Print Network [OSTI]

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

Akin, Bilal

2009-05-15T23:59:59.000Z

166

Structural traps I, tectonic fold traps  

SciTech Connect (OSTI)

This book contains studies of fields that exist because of the presence of an anticline; without the anticline there would be no trap. The fields described in this volume illustrate the complex nature of a trap type that some explorationists mistakenly regard as simple and therefore not worthy of close scrutiny. Anticlinal traps are like all other fields - each has its own peculiar personality. Many of the fields in this volume are sourced from continentally derived organic matter. All have sandstone reservoirs. Most have shale seals, but one, Sarir, has an evaporite seal. Many are faulted anticlines. Some of the anticlines formed in a compressional tectonic setting, whereas others formed in a tensional tectonic setting.

Beaumont, E.A.; Foster, N.H.

1990-01-01T23:59:59.000Z

167

Why are MD simulated protein folding times wrong? Dmitry Nerukh  

E-Print Network [OSTI]

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

Nerukh, Dmitry

168

Protein Folding Simulation in CCP Luca Bortolussi1  

E-Print Network [OSTI]

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

Bortolussi, Luca

169

New Crystal Structures Lift Fog around Protein Folding  

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

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

170

Computational and experimental investigations of forces in protein folding  

E-Print Network [OSTI]

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

Schell, David Andrew

2005-02-17T23:59:59.000Z

171

Experimental and Computational Studies on Protein Folding, Misfolding and Stability  

E-Print Network [OSTI]

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...

Wei, Yun

2010-07-14T23:59:59.000Z

172

active fault segments: Topics by E-print Network  

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

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

173

Modeling and Measurement Constraints in Fault Diagnostics for HVAC Systems  

E-Print Network [OSTI]

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

Najafi, Massieh

2010-01-01T23:59:59.000Z

174

Sensor Fault Diagnosis Using Principal Component Analysis  

E-Print Network [OSTI]

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...

Sharifi, Mahmoudreza

2010-07-14T23:59:59.000Z

175

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

SciTech Connect (OSTI)

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.

Boles, James [Professor

2013-05-24T23:59:59.000Z

176

Introduction to protein folding for physicists  

E-Print Network [OSTI]

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.

Pablo Echenique

2007-05-13T23:59:59.000Z

177

Combinatorial Problems on Strings with Applications to Protein Folding  

E-Print Network [OSTI]

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

Newman, Alantha

178

Protein Folding Simulation by Two-Stage Optimization  

E-Print Network [OSTI]

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

Will, Sebastian

179

Protein folding with stochastic L-systems Gemma Danks1  

E-Print Network [OSTI]

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

Stepney, Susan

180

Protein Folding Challenge and Theoretical Computer Science Somenath Biswas  

E-Print Network [OSTI]

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

Biswas, Somenath

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

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 to protein kinases, -propellers and TIM-barrels. The observed diversity of protein folds in different

182

Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding  

E-Print Network [OSTI]

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

Michalet, Xavier

183

Polymer Collapse, Protein Folding, and the Percolation Threshold  

E-Print Network [OSTI]

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

Meirovitch, Hagai

184

Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives  

E-Print Network [OSTI]

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

Janke, Wolfhard

185

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

E-Print Network [OSTI]

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

Weston, Ken

186

John von Neumann Institute for Computing Monte Carlo Protein Folding  

E-Print Network [OSTI]

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

Hsu, Hsiao-Ping

187

Protein folding: Then and now Yiwen Chen 1  

E-Print Network [OSTI]

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

Dokholyan, Nikolay V.

188

Author's personal copy Protein folding: Then and now  

E-Print Network [OSTI]

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

Dokholyan, Nikolay V.

189

COMMUNICATION Are Residues in a Protein Folding Nucleus  

E-Print Network [OSTI]

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

Dai, Yang

190

MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix  

E-Print Network [OSTI]

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

Dix, Daniel B.

191

Evolutionary Monte Carlo for protein folding simulations Faming Lianga)  

E-Print Network [OSTI]

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

Liang, Faming

192

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

E-Print Network [OSTI]

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

Smith, J. MacGregor

193

Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao  

E-Print Network [OSTI]

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

Bystroff, Chris

194

Folding simulations of small proteins Seung-Yeon Kima  

E-Print Network [OSTI]

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

Lee, Jooyoung

195

Self-triggering superconducting fault current limiter  

DOE Patents [OSTI]

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.

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

2008-10-21T23:59:59.000Z

196

The Quirky Collider Signals of Folded Supersymmetry  

SciTech Connect (OSTI)

We investigate the collider signals associated with scalar quirks ('squirks') in folded supersymmetric models. As opposed to regular superpartners in supersymmetric models these particles are uncolored, but are instead charged under a new confining group, leading to radically different collider signals. Due to the new strong dynamics, squirks that are pair produced do not hadronize separately, but rather form a highly excited bound state. The excited 'squirkonium' loses energy to radiation before annihilating back into Standard Model particles. We calculate the branching fractions into various channels for this process, which is prompt on collider time-scales. The most promising annihilation channel for discovery is W+photon which dominates for squirkonium near its ground state. We demonstrate the feasibility of the LHC search, showing that the mass peak is visible above the SM continuum background and estimate the discovery reach.

Burdman, Gustavo; Chacko, Z.; Goh, Hock-Seng; Harnik, Roni; Krenke, Christopher A.

2008-08-01T23:59:59.000Z

197

Neural net application to transmission line fault detection and classification  

E-Print Network [OSTI]

, is to perform fault analysis by expert operators using their knowledge about the power systems and experience with past faults. Because of the time required to deal with complex fault situations, detailed fault analysis can not be performed by human operators...

Rikalo, Igor

1994-01-01T23:59:59.000Z

198

Development of Hydrologic Characterization Technology of Fault Zones  

E-Print Network [OSTI]

rock interaction, fracture interconnectivity, fault-rockvalues, given the interconnectivity of fractures that are

Karasaki, Kenzi

2009-01-01T23:59:59.000Z

199

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

E-Print Network [OSTI]

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

Weinkam, Patrick

2009-01-01T23:59:59.000Z

200

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

E-Print Network [OSTI]

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

Capraro, Dominique T.

2008-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

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

E-Print Network [OSTI]

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

Sagle, Laura B.

2006-01-01T23:59:59.000Z

202

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

E-Print Network [OSTI]

L. & Englander, S. W. (1995). Protein folding intermediates:Unifying features in protein- folding mechanisms. Proc Natlintermediate state in protein folding by a hydrophobic

Connell, Katelyn Blair

2010-01-01T23:59:59.000Z

203

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

E-Print Network [OSTI]

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

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

2014-01-01T23:59:59.000Z

204

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

E-Print Network [OSTI]

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

Polinkovsky, Mark E.; Polinkovsky, Mark E.

2012-01-01T23:59:59.000Z

205

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

E-Print Network [OSTI]

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

Cho, Samuel Sung-Il

2007-01-01T23:59:59.000Z

206

Fault Tolerant Control using Cartesian Genetic Programming  

E-Print Network [OSTI]

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

Fernandez, Thomas

207

A dynamical approach to protein folding  

E-Print Network [OSTI]

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.

Alessandro Torcini; Roberto Livi; Antonio Politi

2001-03-13T23:59:59.000Z

208

Accordian-folded boot shield for flexible swivel connection  

SciTech Connect (OSTI)

This patent describes an apparatus for connecting a first boot section to a second boot section, the first and second boots having openings therethrough, the second boot having at least two adjacent accordion folds at the end having the opening. The second boot is positioned through the opening of the first boot such that a first of the accordion folds is within the first boot and a second of the accordion folds is outside of the first boot comprising: first and second annular discs, the first disc being positioned within and across the first accordion fold, the second disc being positioned within and across the second accordion fold such that the first boot is moveably and rigidly connected between the first and second accordion folds.

Hoh, J.C.

1986-08-26T23:59:59.000Z

209

Inferring the Rate-Length Law of Protein Folding  

E-Print Network [OSTI]

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.

Lane, Thomas J

2013-01-01T23:59:59.000Z

210

An energy landscape theory for cotranslational protein folding  

E-Print Network [OSTI]

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...

Tourigny, David S

2013-01-01T23:59:59.000Z

211

Microscopic feather fractures in the faulting process  

E-Print Network [OSTI]

assumptions. Although the problem was not solved in this study, the expected ol trajectories for such a solution are shown in Figure 5 (page 20). Both of these concepts indicate a tendency for the local ol to make an angle with the fault greater than 6..., maximum compressive stress, trajectories to a two dimensional during sliding along (dashed lines) in a cylindrical specimen reduced elastic problem. (b) Expected ol trajectories a fault. crack by shear along the crack surfaces (Bieniawski, 1967...

Conrad, Robert Eugene

1974-01-01T23:59:59.000Z

212

arrestin fold variations: Topics by E-print Network  

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

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

213

Protein folding and diffusion: from in vitro to live cells.  

E-Print Network [OSTI]

??Protein folding landscapes and protein-protein interaction landscapes are subject to modulation by many factors inside living cells: crowding, electrostatics, hydrophobic interactions, and even hydrodynamic phenomena.… (more)

Guo, Minghao

2014-01-01T23:59:59.000Z

214

Biophysical Studies of Protein Folding and Binding Stability.  

E-Print Network [OSTI]

?? Interactions between charged residues are known to have significant effects on protein folding stability and binding properties. The contributions of different types of non-covalent… (more)

Batra, Jyotica

2009-01-01T23:59:59.000Z

215

A Computational Genome-wide Study of Protein Folding Rate.  

E-Print Network [OSTI]

??Proteins should be able to ‘fold’ to a native three-dimensional structure in a biologically relevant time to be functional. In our current study, we tried… (more)

Gorla, Sandeep C.

2012-01-01T23:59:59.000Z

216

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...

217

Variational theory for site resolved protein folding free energy surfaces  

E-Print Network [OSTI]

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

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

1999-01-18T23:59:59.000Z

218

Protein folding: A complex potential for the driving force  

E-Print Network [OSTI]

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.

Chekmarev, Sergei F

2013-01-01T23:59:59.000Z

219

Thermodynamics of protein folding: a random matrix formulation  

E-Print Network [OSTI]

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.

Pragya Shukla

2010-10-16T23:59:59.000Z

220

Topological complexity, contact order and protein folding rates  

E-Print Network [OSTI]

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

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

2002-05-29T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

E-Print Network 3.0 - andreas fault zone Sample Search Results  

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

Chester Summary: accommodated along large plate-boundary faults like the San Andreas transform fault in California. These faults... depend in part on the structure of the tabular...

222

E-Print Network 3.0 - active fault zone Sample Search Results  

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

Earth Structure (2nd Edition), 2004 Summary: 292010 Oceanic Transform Faults and Fracture Zones Transform Fault: Active displacement. Fracture Zone: Fossil... fault, no active...

223

Development of a Hydrologic Characterization Technology for Fault Zones Final Report  

E-Print Network [OSTI]

Hydrologic Characterization Technology of Fault Zones, Phaseof Characterization Technology for Fault Zones, LBNL-1635E,Characterization on Technology of Fault Zones – Phase II

Karasaki, Kenzi

2014-01-01T23:59:59.000Z

224

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

SciTech Connect (OSTI)

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.

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

2011-05-15T23:59:59.000Z

225

Fault Locating, Prediction and Protection (FLPPS)  

SciTech Connect (OSTI)

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

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

2010-09-30T23:59:59.000Z

226

Statistical Analysis of Protein Folding Kinetics Aaron R. Dinner  

E-Print Network [OSTI]

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

Dinner, Aaron

227

Multi-Agent Simulation of Protein Folding Luca Bortolussi1  

E-Print Network [OSTI]

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

Bortolussi, Luca

228

Thermodynamic control and dynamical regimes in protein folding  

E-Print Network [OSTI]

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

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

2001-10-07T23:59:59.000Z

229

Method for fabricating fan-fold shielded electrical leads  

DOE Patents [OSTI]

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.

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

1994-12-27T23:59:59.000Z

230

Method for fabricating fan-fold shielded electrical leads  

DOE Patents [OSTI]

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.

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

1994-01-01T23:59:59.000Z

231

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

E-Print Network [OSTI]

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...

Mohazab, Ali R

2012-01-01T23:59:59.000Z

232

VCSEL fault location apparatus and method  

DOE Patents [OSTI]

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.

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

2007-05-15T23:59:59.000Z

233

Physics of Caustics and Protein Folding: Mathematical Parallels  

E-Print Network [OSTI]

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.

Walter Simmons; Joel L. Weiner

2011-08-13T23:59:59.000Z

234

Criterion based Two Dimensional Protein Folding Using Extended GA  

E-Print Network [OSTI]

Abstract — In the dynamite field of biological and protein research, the protein fold recognition for long pattern protein sequences is a great confrontation for many years. With that consideration, this paper contributes to the protein folding research field and presents a novel procedure for mapping appropriate protein structure to its correct 2D fold by a concrete model using swarm intelligence. Moreover, the model incorporates Extended Genetic Algorithm (EGA) with concealed Markov model (CMM) for effectively folding the protein sequences that are having long chain lengths. The protein sequences are preprocessed, classified and then, analyzed with some parameters (criterion) such as fitness, similarity and sequence gaps for optimal formation of protein structures. Fitness correlation is evaluated for the determination of bonding strength of molecules, thereby involves in efficient fold recognition task. Experimental results have shown that the proposed method is more adept in 2D protein folding and outperforms the existing algorithms. Index Terms — classification, CMM, criterion analysis, EGA, protein folding, sequence gaps I.

T. Kalai Chelvi; P. Rangarajan

235

Synthesis and evaluation of fault-tolerant quantum computer architectures  

E-Print Network [OSTI]

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 ...

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

2005-01-01T23:59:59.000Z

236

Observations on the capability of the Criner fault, southern Oklahoma  

E-Print Network [OSTI]

Results of previous investigations have indicated the possibility that recent deformation has occurred on the Criner fault of southern Oklahoma. The Criner fault is located in Carter and Love Counties, Oklahoma, approximately 100 kilometers...

Williamson, Shawn Collin

2012-06-07T23:59:59.000Z

237

Scalable, Fault-tolerant Management in a Service Oriented Architecture  

E-Print Network [OSTI]

Scalable, Fault-tolerant Management in a Service Oriented Architecture Harshawardhan Gadgil: Scalable, Fault-tolerance, Service Oriented Management, Architecture 1. Introduction With the explosion. The service-oriented architecture provides a simple and flexible framework for building sophisticated

238

FEATURE BASED HANDLING OF SURFACE FAULTS IN COMPACT DISC PLAYERS  

E-Print Network [OSTI]

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

Wickerhauser, M. Victor

239

New approach to the fault location problem using synchronized sampling  

E-Print Network [OSTI]

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

Mrkic, Jasna

2012-06-07T23:59:59.000Z

240

Frictional properties of faults: from observation on the  

E-Print Network [OSTI]

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

Winfree, Erik

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Robust model-based fault diagnosis for chemical process systems  

E-Print Network [OSTI]

diagnosis systems, which use limited information about the process model to robustly detect, discriminate, and reconstruct instrumentation faults. Broadly, the proposed method consists of a novel nonlinear state and parameter estimator coupled with a fault...

Rajaraman, Srinivasan

2006-08-16T23:59:59.000Z

242

Development of a bridge fault extractor tool  

E-Print Network [OSTI]

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...

Bhat, Nandan D.

2005-02-17T23:59:59.000Z

243

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

E-Print Network [OSTI]

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.

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

2013-01-01T23:59:59.000Z

244

Modeling two-state cooperativity in protein folding  

E-Print Network [OSTI]

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

K. Fan; J. Wang; W. Wang

2001-03-19T23:59:59.000Z

245

Water dynamics clue to key residues in protein folding  

SciTech Connect (OSTI)

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.

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

2010-01-29T23:59:59.000Z

246

Understanding Fault Characteristics of Inverter-Based Distributed Energy Resources  

SciTech Connect (OSTI)

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

Keller, J.; Kroposki, B.

2010-01-01T23:59:59.000Z

247

Statistical estimation of multiple faults in aircraft gas turbine engines  

E-Print Network [OSTI]

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

Ray, Asok

248

A Parametric Spectral Estimator for Faults Detection in Induction Machines  

E-Print Network [OSTI]

for fault diagnosis in electrical machines. Current spectral estimation is usually performed using classical and productivity of electrical drives. For electrical motors and generators, fault detection is usually performedA Parametric Spectral Estimator for Faults Detection in Induction Machines El Houssin El Bouchikhi

Boyer, Edmond

249

UNSUPERVISED CLUSTERING FOR FAULT DIAGNOSIS IN NUCLEAR POWER PLANT COMPONENTS  

E-Print Network [OSTI]

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

Boyer, Edmond

250

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

E-Print Network [OSTI]

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

Sharkey, Amanda

251

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

E-Print Network [OSTI]

STRUCTURE OF THE EASTERN RED ROCKS AND WIND RIDGE THRUST FAULTS, WYOMING: HOW A THRUST FAULT GAINS DISPLACEMENT ALONG STRIKE A Thesis by BRENT STANLEY HUNTSMAN Submitted to the Graduate College of Texas A&M University in partial fulfillment... of the requirements for the degree of MASTER OF SCIENCE December 1983 Major Subject: Geology STRUCTURE OF THE EASTERN RED ROCKS AND WIND RIDGE THRUST FAULTS, WYOMING: HOW A THRUST FAULT GAINS DISPLACEMENT ALONG STRIKE A Thesis by BRENT STANLEY HUNTSMAN...

Huntsman, Brent Stanley

1983-01-01T23:59:59.000Z

252

PCB origami : folding circuit boards into electronic products  

E-Print Network [OSTI]

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 ...

Sterman, Yoav

2013-01-01T23:59:59.000Z

253

UFO (UnFold Operator) computer program abstract  

SciTech Connect (OSTI)

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.

Kissel, L.; Biggs, F.

1982-11-01T23:59:59.000Z

254

INTRODUCTION Lateral propagation of folds is a process in  

E-Print Network [OSTI]

; (2) decrease in elevation of wind gaps; (3) decrease in relief of the topographic profile along in rotation and inclination of the forelimb. As a result of style of folding and variable geomorphic response

Keller, Ed

255

Low energy pathways for reproducible in vivo protein folding  

E-Print Network [OSTI]

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.

Leonor Cruzeiro

2011-01-03T23:59:59.000Z

256

Physics of Caustics and Protein Folding: Mathematical Parallels  

E-Print Network [OSTI]

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 ...

Simmons, Walter

2011-01-01T23:59:59.000Z

257

Determining the role of hydration forces in protein folding  

SciTech Connect (OSTI)

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.

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

1999-07-01T23:59:59.000Z

258

Characterization of the vocal fold lamina propria towards voice restoration  

E-Print Network [OSTI]

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

Hahn, Mariah S

2004-01-01T23:59:59.000Z

259

Seismoelectric Imaging of a Shallow Fault System Employing Fault Guided Waves  

E-Print Network [OSTI]

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

Cohrs, Frelynn Joseph Reese

2012-07-16T23:59:59.000Z

260

Fault Tolerant CORBASpecification, OMG document: ptc/20000404  

E-Print Network [OSTI]

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

Roma "La Sapienza", Universitŕ di

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Global Trajectory Planning for Fault Tolerant Manipulators  

E-Print Network [OSTI]

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

262

Fault-tolerant, Universal Adiabatic Quantum Computation  

E-Print Network [OSTI]

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

Ari Mizel

2014-03-30T23:59:59.000Z

263

All row, planar fault detection system  

DOE Patents [OSTI]

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.

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

2013-07-23T23:59:59.000Z

264

FPGA Interconnect Delay Fault Testing Erik Chmelar  

E-Print Network [OSTI]

A satisfactory FPGA testing method meets several crite- ria. First, the routing resources must be explicitlyFPGA Interconnect Delay Fault Testing Erik Chmelar Center for Reliable Computing Stanford is a scalable manufactur- ing test method for all SRAM-based FPGAs, able to detect multiple interconnect delay

Stanford University

265

Master equation approach to protein folding and kinetic traps  

E-Print Network [OSTI]

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.

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

1998-04-21T23:59:59.000Z

266

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]

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

Mochrie, Simon

267

Coordinated Fault Tolerance for High-Performance Computing  

SciTech Connect (OSTI)

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.

Dongarra, Jack; Bosilca, George; et al.

2013-04-08T23:59:59.000Z

268

Probabilistic model of fault detection in quantum circuits  

E-Print Network [OSTI]

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

Anindita Banerjee; Anirban Pathak

2009-05-12T23:59:59.000Z

269

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

E-Print Network [OSTI]

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

Mukamel, Shaul

270

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

E-Print Network [OSTI]

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

Langmead, Christopher James

271

RoadmapMethodsforProteinFolding MarkMoll, DavidSchwarz, LydiaE.Kavraki  

E-Print Network [OSTI]

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

Kavraki, Lydia E.

272

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

E-Print Network [OSTI]

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

Carbonell, Jaime

273

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

274

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

SciTech Connect (OSTI)

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.

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

2012-08-01T23:59:59.000Z

275

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

E-Print Network [OSTI]

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

California at Irvine, University of

276

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

E-Print Network [OSTI]

can accelerate protein folding. Proc Natl Acad Sci U S A 96(coupling between protein folding and prolyl isomerization.The speed limit for protein folding measured by triplet-

Bernstein, Rachel Simma

2011-01-01T23:59:59.000Z

277

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

E-Print Network [OSTI]

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

Cecconi, Fabio

278

Parallel ContinuationBased Global Optimization for Molecular Conformation and Protein Folding  

E-Print Network [OSTI]

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

Neumaier, Arnold

279

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

E-Print Network [OSTI]

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

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

2006-01-01T23:59:59.000Z

280

Intermediates and the folding of proteins L and G  

SciTech Connect (OSTI)

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.

Brown, Scott; Head-Gordon, Teresa

2003-07-01T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Completing fault models for abductive diagnosis  

SciTech Connect (OSTI)

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

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

1992-11-05T23:59:59.000Z

282

Calculating the probability of injected carbon dioxide plumes encountering faults  

SciTech Connect (OSTI)

One of the main concerns of storage in saline aquifers is leakage via faults. In the early stages of site selection, site-specific fault coverages are often not available for these aquifers. This necessitates a method using available fault data to estimate the probability of injected carbon dioxide encountering and migrating up a fault. The probability of encounter can be calculated from areal fault density statistics from available data, and carbon dioxide plume dimensions from numerical simulation. Given a number of assumptions, the dimension of the plume perpendicular to a fault times the areal density of faults with offsets greater than some threshold of interest provides probability of the plume encountering such a fault. Application of this result to a previously planned large-scale pilot injection in the southern portion of the San Joaquin Basin yielded a 3% and 7% chance of the plume encountering a fully and half seal offsetting fault, respectively. Subsequently available data indicated a half seal-offsetting fault at a distance from the injection well that implied a 20% probability of encounter for a plume sufficiently large to reach it.

Jordan, P.D.

2011-04-01T23:59:59.000Z

283

Directed Evolution Designed to Optimize the in vivo Protein Folding Environment.  

E-Print Network [OSTI]

??Protein folding is assisted by molecular chaperones and folding catalysts in vivo. Understanding how chaperones are regulated and how they function in vivo may provide… (more)

Quan, Shu

2010-01-01T23:59:59.000Z

284

Folding of a DNA Hairpin Loop Structure in Explicit SolventUsingRepli...  

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

Folding of a DNA Hairpin Loop Structure in Explicit Solvent UsingReplica-Exchange Molecular Dynamics Simulations. Folding of a DNA Hairpin Loop Structure in Explicit Solvent...

285

E-Print Network 3.0 - assisted protein folding Sample Search...  

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

protein folding Search Powered by Explorit Topic List Advanced Search Sample search results for: assisted protein folding Page: << < 1 2 3 4 5 > >> 1 BIOLOGICAL FRAMEWORKS FOR...

286

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

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

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

287

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

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

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

288

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

E-Print Network [OSTI]

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

Bigelow, Stephen

289

E-Print Network 3.0 - affecting protein folding Sample Search...  

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

protein folding Search Powered by Explorit Topic List Advanced Search Sample search results for: affecting protein folding Page: << < 1 2 3 4 5 > >> 1 Current status of membrane...

290

E-Print Network 3.0 - abakaliki fold belt Sample Search Results  

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

exploration province located in deep waters... as detachment folds cored by autochthonous Middle Jurassic Louann Salt. The fold belt overlies rifted... Blickwede and Tom Queffelec...

291

Stuck-at-fault test set compaction  

E-Print Network [OSTI]

. Test set size under pattern score based dynamic compaction . . . 13 . . . 17 Figure 7. Pattern Score distribution v:ith pattern metric dynamic compaction. . . . . . . . . . . . . . I g LIST OF TABLES Page Table l. l. nuit Target Sclcction Methods.... Fault Target Selection Methods Random Minimum Detection Count Circuit Name c432 c499 c880 c1355 c1908 G2670 Excitation Balance 0. 136296 0. 191652 0. 170293 0. 173310 0. 187486 0. 190484 Pattern Count 1152 873 2693 1394 1708 5148...

Vanfickell, Jason Michael

2013-02-22T23:59:59.000Z

292

Folded Compact Range Development and Coherent Change Detection Measurement Project  

SciTech Connect (OSTI)

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

Sorensen, K.W.

1995-03-01T23:59:59.000Z

293

Concentration-Temperature Superposition of Helix Folding Rates in Gelatin  

E-Print Network [OSTI]

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.

J. L. Gornall; E. M. Terentjev

2006-03-05T23:59:59.000Z

294

Heteropolymer freezing and design: Towards physical models of protein folding  

SciTech Connect (OSTI)

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.

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

2000-01-01T23:59:59.000Z

295

Collective aspects of protein folding illustrated by a toy model  

SciTech Connect (OSTI)

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.

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

1995-09-01T23:59:59.000Z

296

Undulator Hall Air Temperature Fault Scenarios  

SciTech Connect (OSTI)

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.

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

2010-11-17T23:59:59.000Z

297

Characterization of Protein Folding by Dominant Reaction Pathways  

E-Print Network [OSTI]

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.

Pietro Faccioli

2008-06-23T23:59:59.000Z

298

The role of the energy gap in protein folding dynamics  

E-Print Network [OSTI]

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

Estelle Pitard; Henri Orland

1998-11-17T23:59:59.000Z

299

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

E-Print Network [OSTI]

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

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

2012-01-01T23:59:59.000Z

300

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

E-Print Network [OSTI]

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

DeVries, Ingrid L.

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

Similarity Matching Techniques for Fault Diagnosis in Automotive Infotainment Electronics  

E-Print Network [OSTI]

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...

Kabir, Mashud

2009-01-01T23:59:59.000Z

302

Pressure test data reveal reservoir barriers/faults  

SciTech Connect (OSTI)

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

Hurd, J.D.

1984-07-30T23:59:59.000Z

303

A Turing Machine Resisting Isolated Bursts Of Faults  

E-Print Network [OSTI]

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

Capuni, Ilir

2012-01-01T23:59:59.000Z

304

Fault Detection and Diagnosis Method for VAV Terminal Units  

E-Print Network [OSTI]

: Air density [kg/m3] NOMENCLATURE REFERENCES 1) IEA Annex 25, Building Optimization and Fault Diagnosis Source Book, Eds. J. Hyvarinen and S. Karki, Technical Research Center of Finland, 1996 2) Harunori Yoshida: Typical Faults of Air Conditioning..., IEA Annex 34 ?Detection and Diagnosis Methods in Real Building?, Eds. A. Dexter and J. Pakanen, Section C.2, pp.143-148, 2001 6) Harunori Yoshida, Sanjay Kumar, Yasunori Morita: Online Fault Detection and Diagnosis in VAV Air Handling Unit by RARX...

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

2004-01-01T23:59:59.000Z

305

Folding model description of reactions with exotic nuclei  

SciTech Connect (OSTI)

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

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

2012-08-15T23:59:59.000Z

306

Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives  

E-Print Network [OSTI]

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.

Michael Bachmann; Wolfhard Janke

2007-10-25T23:59:59.000Z

307

PHOTOVOLTAIC DC ARC FAULT DETECTOR TESTING AT SANDIA NATIONAL  

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

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

308

automatic fault management: Topics by E-print Network  

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

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

309

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...

310

Controls on Fault-Hosted Fluid Flow: Preliminary Results from...  

Open Energy Info (EERE)

Results from the Coso Geothermal Field, CA Abstract cap rock, permeability, fault, fracture, clay, Coso Authors Davatzes, N.C.; Hickman and S.H. Published Geothermal Resource...

311

Fault-tolerant distributed transactions for partitioned OLTP databases  

E-Print Network [OSTI]

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 ...

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

2012-01-01T23:59:59.000Z

312

Active Fault Segments As Potential Earthquake Sources- Inferences...  

Open Energy Info (EERE)

have not been investigated to determine their subsurface geometry, faulting intensity and constituents (fluids, sediments) for proper characterization of tectonic rift...

313

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

Open Energy Info (EERE)

eastern California Jump to: navigation, search OpenEI Reference LibraryAdd to library Conference Proceedings: Upper crustal faulting in an obliquely extending orogen,...

314

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

E-Print Network [OSTI]

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

Levitt, Michael

315

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

E-Print Network [OSTI]

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

Istrail, Sorin

316

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

E-Print Network [OSTI]

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

Fidanova, Stefka

317

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

E-Print Network [OSTI]

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

Pal, Debnath

318

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

E-Print Network [OSTI]

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

Emmerich, Michael

319

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

E-Print Network [OSTI]

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

Hagen, Stephen J.

320

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

DOE Patents [OSTI]

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.

Waldo, Geoffrey S. (Santa Fe, NM)

2007-09-18T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

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

E-Print Network [OSTI]

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

Stanley, H. Eugene

322

The energy landscape for protein folding and possible connections to function  

E-Print Network [OSTI]

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

Onuchic, José

323

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

E-Print Network [OSTI]

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

Dai, Yang

324

BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum  

E-Print Network [OSTI]

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

Petzold, Linda R.

325

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

E-Print Network [OSTI]

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

Domany, Eytan

326

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

E-Print Network [OSTI]

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

Bachmann, Michael

327

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

328

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

E-Print Network [OSTI]

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

Hebert, Daniel N.

329

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

E-Print Network [OSTI]

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

Janke, Wolfhard

330

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

E-Print Network [OSTI]

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

Lebendiker, Mario

331

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

E-Print Network [OSTI]

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

Mirny, Leonid

332

Predicting Experimental Quantities in Protein Folding Kinetics using Stochastic Roadmap Simulation  

E-Print Network [OSTI]

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

Pratt, Vaughan

333

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

E-Print Network [OSTI]

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

Istrail, Sorin

334

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

E-Print Network [OSTI]

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

Istrail, Sorin

335

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

E-Print Network [OSTI]

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

Clark, Patricia L.

336

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

E-Print Network [OSTI]

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

Kavraki, Lydia E.

337

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

E-Print Network [OSTI]

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

Neary, Tiffany Jonean

2008-01-01T23:59:59.000Z

338

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

E-Print Network [OSTI]

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

Yang, Hui

339

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

E-Print Network [OSTI]

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

Zhou, Yaoqi

340

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

E-Print Network [OSTI]

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

Firenze, UniversitĂ  degli Studi di

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

The structure and evolution of small-displacement strike-slip faults in porous sandstone  

E-Print Network [OSTI]

relationship between the progressive addition of subsidiary fault segments (deformation bands) and earlier-formed linkage structures. The along-strike variability and distribution of fault structure are documented and used to assess the role of early fault...

Schafer, Kirk Wyatt

2002-01-01T23:59:59.000Z

342

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

E-Print Network [OSTI]

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

Klinger, Yann

343

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

E-Print Network [OSTI]

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 catastrophic...

Zhang, Xujia

2006-08-16T23:59:59.000Z

344

Fewer Faults for Faster Computing | EMSL  

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

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation ProposedUsing ZirconiaPolicyFeasibility ofSmall15.000TechnologyTuneFewer Faults for Faster

345

Sandia National Laboratories: parallel arc-fault  

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

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1developmentturbine bladelifetime ismobileparallel arc-fault Sandia Research on PV

346

Sandia National Laboratories: arc-fault detector  

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

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1development Sandia, NREL Release Wavearc-fault circuit interrupter Sandia Research

347

Sandia National Laboratories: Arc-Fault Detection  

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

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -the Mid-Infrared0Energy Advanced Nuclear EnergyCouncilSandia's Work withArc-Fault

348

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

E-Print Network [OSTI]

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.

Stefan Schnabel; Michael Bachmann; Wolfhard Janke

2009-02-16T23:59:59.000Z

349

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

Office of Scientific and Technical Information (OSTI)

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

350

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

SciTech Connect (OSTI)

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

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

2008-07-01T23:59:59.000Z

351

Strong Nernst-Ettingshausen effect in folded graphene  

E-Print Network [OSTI]

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.

Friedemann Queisser; Ralf Schützhold

2013-01-17T23:59:59.000Z

352

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

E-Print Network [OSTI]

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

Pierpaolo Bruscolini

1997-07-24T23:59:59.000Z

353

Invariant patterns in crystal lattices: Implications for protein folding algorithms  

SciTech Connect (OSTI)

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.

HART,WILLIAM E.; ISTRAIL,SORIN

2000-06-01T23:59:59.000Z

354

The faults that move during earthquakes do not always come  

E-Print Network [OSTI]

often live near active faults, because where there is a fault there is usually a water supply. And that means these places become part of major trade routes, like the Silk Roads across Asia from Xi urban building. What is even more frighten- ing is that in many parts of the world poor

Cipolla, Roberto

355

Fault Detection, Identification and Accommodation for an Electro-hydraulic  

E-Print Network [OSTI]

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

Yao, Bin

356

Fuzzy Pattern Recognition Based Fault Diagnosis Rafik Bensaadi1  

E-Print Network [OSTI]

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

Boyer, Edmond

357

Arcing fault in sub-distribution branch circuits  

SciTech Connect (OSTI)

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

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

1993-04-01T23:59:59.000Z

358

Symbolic identification for fault detection in aircraft gas turbine engines  

E-Print Network [OSTI]

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

Ray, Asok

359

Fault detection and diagnosis capabilities of test sequence selection  

E-Print Network [OSTI]

Review Fault detection and diagnosis capabilities of test sequence selection methods based on the FSM model T Ramalingam*, Anindya Dast and K ThuIasiraman* Different test sequence selection methods resolution in diagnosing the fault. The test sequence selection methods are then compared based on the length

Thulsiraman, Krishnaiyan

360

SEISMIC INVESTIGATION OF WRENCH FAULTING AND FRACTURING AT RULISON  

E-Print Network [OSTI]

to gas production at Rulison. Fracture zones are associated with fault trends and areas of deformation networks that help determine gas migration and accumulation. This thesis presents the characterization of the complex wrench fault network at Rulison Field, and its linkage to enhanced natural fracture zones. Rulison

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

All-to-all sequenced fault detection system  

DOE Patents [OSTI]

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

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

2010-11-02T23:59:59.000Z

362

Automatic Fault Characterization via Abnormality-Enhanced Classification  

SciTech Connect (OSTI)

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.

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

2010-12-20T23:59:59.000Z

363

Fault Tolerant Oxygen Control of a Diesel Engine Air System  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

364

Online Fault Detection and Tolerance for Photovoltaic Energy Harvesting Systems  

E-Print Network [OSTI]

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

Pedram, Massoud

365

Using Reinforcement Learning for Proactive Network Fault Management  

E-Print Network [OSTI]

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

Shayman, Mark A.

366

When pigs fly: a study of computer generated paper folding  

E-Print Network [OSTI]

&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Approved by: Chair of Committee, Carol LaFayette Committee Members, Frederic I. Parke Michael Greenwald Head of Department, Tim McLaughlin December 2008... Major Subject: Visualization Sciences iii ABSTRACT When Pigs Fly: A Study of Computer Generated Paper Folding. (December 2008) Elizabeth Jeanette Nitsch, B.E.D., Texas A&M University Chair of Advisory Committee: Prof. Carol LaFayette...

Nitsch, Elizabeth Jeanette

2009-05-15T23:59:59.000Z

367

Elastic energy of proteins and the stages of protein folding  

E-Print Network [OSTI]

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^{\

Lei, Jinzhi

2010-01-01T23:59:59.000Z

368

Combined approach to the inverse protein folding problem. Final report  

SciTech Connect (OSTI)

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).

Ruben A. Abagyan

2000-06-01T23:59:59.000Z

369

Invariant patterns in crystal lattices: Implications for protein folding algorithms  

SciTech Connect (OSTI)

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.

Hart, W.E.; Istrail, S.

1995-12-11T23:59:59.000Z

370

Development of Hydrologic Characterization Technology of Fault Zones  

SciTech Connect (OSTI)

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.

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

2008-03-31T23:59:59.000Z

371

Test generation and fault detection for VLSI PPL circuits  

SciTech Connect (OSTI)

The problem of design for testability of PPL logic circuits is addressed. A test-generation package was developed which utilizes the special features of PPL logic to generate high fault coverage test vectors at a reduced computational cost. The test strategy assumes that one of the scan design techniques is used. A new methodology for test-vectors compaction without compromising the fault coverage is also proposed. A fault-oriented test-generation algorithm combined with a heuristic test-generation algorithm are the essential ingredients of this package. The fault-oriented algorithm uses a modified D-algorithm which includes look-ahead features and a new seven-valued logic to improve the average speed of the test-generation process. Fault coverages in the 90% range were obtained using the test sequences generated by this package.

Amin, A.A.M.

1987-01-01T23:59:59.000Z

372

Acceleration and evolution of faults: An example from the Hunter MountainPanamint Valley fault zone, Eastern California  

E-Print Network [OSTI]

: R.D. van der Hilst Keywords: geodesy fault evolution InSAR rock mechanics Western United States assumes a monotonic increase in slip rate with time as the fault matures and straightens. The rate. However, before this can be realized, we need to better understand the various sources for discrepancies

Amelung, Falk

373

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

E-Print Network [OSTI]

drilling through the Nojima and 1 Chelungpu faults 2 3 Anne-Marie Boullier 4-Marie.Boullier@obs.ujf-grenoble.fr 8 9 Abstract 10 Several drilling projects have been conducted through significant topics 32 for future research, one of which was "fault zone drilling

Paris-Sud XI, Université de

374

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

E-Print Network [OSTI]

drilling through the Nojima and 1 Chelungpu faults 2 3 Anne-Marie Boullier 4-Marie.Boullier@obs.ujf-grenoble.fr 8 9 Abstract 10 Several drilling projects have been conducted through was "fault zone drilling combined with surface-based 33 geophysical and geological

Boyer, Edmond

375

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

E-Print Network [OSTI]

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

Engelmann, Christian

376

Review Protein folding: Then and now www.elsevier.com/locate/yabbi  

E-Print Network [OSTI]

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 in understanding diseases and our abilities to rationally manipulate cellular life by engineering protein folding pathways. We review and contrast past and recent developments in the protein folding field. Specifically, we discuss the progress in our understanding of protein folding thermodynamics and kinetics, the properties of evasive intermediates, and unfolded states. We also discuss how some abnormalities in protein folding lead to protein aggregation and human diseases.

Yiwen Chen; Feng Ding; Huifen Nie; Adrian W. Serohijos; Shantanu Sharma; Kyle C. Wilcox; Shuangye Yin; Nikolay V. Dokholyan

2007-01-01T23:59:59.000Z

377

Steps toward fault-tolerant quantum chemistry.  

SciTech Connect (OSTI)

Developing quantum chemistry programs on the coming generation of exascale computers will be a difficult task. The programs will need to be fault-tolerant and minimize the use of global operations. This work explores the use a task-based model that uses a data-centric approach to allocate work to different processes as it applies to quantum chemistry. After introducing the key problems that appear when trying to parallelize a complicated quantum chemistry method such as coupled-cluster theory, we discuss the implications of that model as it pertains to the computational kernel of a coupled-cluster program - matrix multiplication. Also, we discuss the extensions that would required to build a full coupled-cluster program using the task-based model. Current programming models for high-performance computing are fault-intolerant and use global operations. Those properties are unsustainable as computers scale to millions of CPUs; instead one must recognize that these systems will be hierarchical in structure, prone to constant faults, and global operations will be infeasible. The FAST-OS HARE project is introducing a scale-free computing model to address these issues. This model is hierarchical and fault-tolerant by design, allows for the clean overlap of computation and communication, reducing the network load, does not require checkpointing, and avoids the complexity of many HPC runtimes. Development of an algorithm within this model requires a change in focus from imperative programming to a data-centric approach. Quantum chemistry (QC) algorithms, in particular electronic structure methods, are an ideal test bed for this computing model. These methods describe the distribution of electrons in a molecule, which determine the properties of the molecule. The computational cost of these methods is high, scaling quartically or higher in the size of the molecule, which is why QC applications are major users of HPC resources. The complexity of these algorithms means that MPI alone is insufficient to achieve parallel scaling; QC developers have been forced to use alternative approaches to achieve scalability and would be receptive to radical shifts in the programming paradigm. Initial work in adapting the simplest QC method, Hartree-Fock, to this the new programming model indicates that the approach is beneficial for QC applications. However, the advantages to being able to scale to exascale computers are greatest for the computationally most expensive algorithms; within QC these are the high-accuracy coupled-cluster (CC) methods. Parallel coupledcluster programs are available, however they are based on the conventional MPI paradigm. Much of the effort is spent handling the complicated data dependencies between the various processors, especially as the size of the problem becomes large. The current paradigm will not survive the move to exascale computers. Here we discuss the initial steps toward designing and implementing a CC method within this model. First, we introduce the general concepts behind a CC method, focusing on the aspects that make these methods difficult to parallelize with conventional techniques. Then we outline what is the computational core of the CC method - a matrix multiply - within the task-based approach that the FAST-OS project is designed to take advantage of. Finally we outline the general setup to implement the simplest CC method in this model, linearized CC doubles (LinCC).

Taube, Andrew Garvin

2010-05-01T23:59:59.000Z

378

Self field triggered superconducting fault current limiter  

DOE Patents [OSTI]

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.

Tekletsadik, Kasegn D. (Rexford, NY)

2008-02-19T23:59:59.000Z

379

Locating hardware faults in a parallel computer  

DOE Patents [OSTI]

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.

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

2010-04-13T23:59:59.000Z

380

Development of Characterization Technology for Fault Zone Hydrology  

SciTech Connect (OSTI)

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.

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

2010-08-06T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

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

E-Print Network [OSTI]

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.

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

2011-01-01T23:59:59.000Z

382

Directed transport as a mechanism for protein folding in vivo  

E-Print Network [OSTI]

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.

Ernesto Gonzalez-Candela; Victor Romero-Rochin

2009-09-23T23:59:59.000Z

383

Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics  

SciTech Connect (OSTI)

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.

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

2003-06-25T23:59:59.000Z

384

Visualization of stacking faults in fcc crystals in plastic deformations  

E-Print Network [OSTI]

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.

Takeshi Kawasaki; Akira Onuki

2011-11-27T23:59:59.000Z

385

Fault-tree construction and calculations on a microcomputer  

E-Print Network [OSTI]

Figure 17 - Program Overview Screen Figure 18 ? Main Menu Screen Figure 19 ? Invalid Command Screen Figure 20 - First Usage of Disk Screen Figure 21 ? Fault-tree Name Screen Figure 22 - Invalid Fault-tree Name Screen Fi gure 23 ? TOP EVENT Label... to do? Fi gure 19. Inval i d Command Screen 53 CREATE - This command allows the user to build a new fault tree. After a CREATE command is entered, the system wi 1 1 display the screen in Figure 20. This question is asked in order to determine...

Beckmann, Jeffery Linn

1985-01-01T23:59:59.000Z

386

Experimental characterization of faults on low-voltage systems  

E-Print Network [OSTI]

arcing ground faults '10'. The first scheme is very similar to the Ground Sensor Protection scheme described in i8j. The second scheme employs the fact that the voltage waveshape at the 1'suit point is flat topped. Harmonic analysis shows that... value when an arcing fault takes place. Continued presence of a, relatively high third- harmonic component in the bus voltage is a definite sign that there is an arcing fault in the system, Kusko and Peeran recommended the use of a, third harmonic...

Ahmed, Jubayer

1992-01-01T23:59:59.000Z

387

On-Line Fault Detection and Compensation of Hydraulic Driven Machines Using Modelling Techniques  

E-Print Network [OSTI]

On-Line Fault Detection and Compensation of Hydraulic Driven Machines Using Modelling Techniques C purpose of hydraulic driven machines as well as for the compensation of incipient faults where applicable: Modelling, Simulation, Hydraulic motors, Fault detection, Fault Compensation 1. Introduction Model

Thawonmas, Ruck

388

Thermal anomalies indicate preferential flow along faults in unconsolidated sedimentary aquifers  

E-Print Network [OSTI]

Thermal anomalies indicate preferential flow along faults in unconsolidated sedimentary aquifers V in unconsolidated siliciclastic aquifers off-set by normal-faults in the Lower Rhine Embayment, Germany. High plane. Most current models of fault hydrology in unconsolidated sedimentary sequences assume faults

Bense, Victor

389

Geometry and scaling relations of a population of very small rift-related normal faults  

E-Print Network [OSTI]

normal faults within the Solite Quarry of the Dan River rift basin range in length from a few millimetres AND SCALING RELATIONS The small normal faults are present in quarries of the Virginia Solite Corporation outcrops and quarried boulders (Fig. 2). The fault traces are typically straight, although the fault tips

390

Analysis of the growth of strike-slip faults using effective medium theory  

SciTech Connect (OSTI)

Increases in the dimensions of strike-slip faults including fault length, thickness of fault rock and the surrounding damage zone collectively provide quantitative definition of fault growth and are commonly measured in terms of the maximum fault slip. The field observations indicate that a common mechanism for fault growth in the brittle upper crust is fault lengthening by linkage and coalescence of neighboring fault segments or strands, and fault rock-zone widening into highly fractured inner damage zone via cataclastic deformation. The most important underlying mechanical reason in both cases is prior weakening of the rocks surrounding a fault's core and between neighboring fault segments by faulting-related fractures. In this paper, using field observations together with effective medium models, we analyze the reduction in the effective elastic properties of rock in terms of density of the fault-related brittle fractures and fracture intersection angles controlled primarily by the splay angles. Fracture densities or equivalent fracture spacing values corresponding to the vanishing Young's, shear, and quasi-pure shear moduli were obtained by extrapolation from the calculated range of these parameters. The fracture densities or the equivalent spacing values obtained using this method compare well with the field data measured along scan lines across the faults in the study area. These findings should be helpful for a better understanding of the fracture density/spacing distribution around faults and the transition from discrete fracturing to cataclastic deformation associated with fault growth and the related instabilities.

Aydin, A.; Berryman, J.G.

2009-10-15T23:59:59.000Z

391

Protein folding and macromolecular dynamics : fundamental limits of length and time scales.  

E-Print Network [OSTI]

??In this thesis, physics-based models of protein folding at the secondary and tertiary level are developed to resolve long-standing issues of protein folding kinetics. As… (more)

Lin, Milo M.

2012-01-01T23:59:59.000Z

392

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

E-Print Network [OSTI]

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

Berry, R. Stephen

393

Protein folding and phylogenetic tree reconstruction using stochastic approximation Monte Carlo  

E-Print Network [OSTI]

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

Cheon, Sooyoung

2007-09-17T23:59:59.000Z

394

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models  

E-Print Network [OSTI]

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models SOLOMON SHENKER,1 introduce a complete methodology to

Gifford, David K.

395

The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations  

E-Print Network [OSTI]

, ) 91 ps-1). The Folding@Home distributed computing project was used to generate an aggregate simulation

Snow, Christopher

396

Controlling protein molecular dynamics: How to accelerate folding while preserving the native state  

E-Print Network [OSTI]

pioneered, in particular, in the Folding@Home project and taken to the extent where hundred of thousands

Nerukh, Dmitry

397

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

E-Print Network [OSTI]

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.

Stefan Schnabel; Michael Bachmann; Wolfhard Janke

2007-10-25T23:59:59.000Z

398

Folding and Function of Proteorhodopsins in Photoenergy Transducing Membranes  

SciTech Connect (OSTI)

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

Spudich, John L

2012-08-10T23:59:59.000Z

399

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

E-Print Network [OSTI]

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

Sali, Andrej

400

Kinetics of Folding of Proteins and RNA D. THIRUMALAI* AND S. A. WOODSON  

E-Print Network [OSTI]

protein folding is a self-assembly process; i.e., the information needed for obtaining the three of protein folding came from Levinthal6 who wondered how a protein molecule searches the astronomically large to general kinetic scenarios for protein folding which are just beginning to be con- firmed experimentally

Thirumalai, Devarajan

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401

BarMap: RNA Folding on Dynamics Energy Landscapes Ivo L. Hofacker,a  

E-Print Network [OSTI]

of pulling polymers through a pore. Key words: RNA folding kinetics, barrier tree, dynamic energy landscapeBarMap: RNA Folding on Dynamics Energy Landscapes Ivo L. Hofacker,a , Christoph Flamma , Christian required to analyse the folding energy landscapes to a one-time preprocessing step. The basic idea

Flamm, Christoph

402

Cooperativity, Smooth Energy Landscapes and the Origins of Topology-dependent Protein Folding Rates  

E-Print Network [OSTI]

folding of simple proteins. We demonstrate that tra- ditional GoŻ polymers lack the extreme cooperativityCooperativity, Smooth Energy Landscapes and the Origins of Topology-dependent Protein Folding Rates Barbara Santa Barbara, CA 93106-9510 USA The relative folding rates of simple, single-domain proteins

Levine, Alex J.

403

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

E-Print Network [OSTI]

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

Stepney, Susan

404

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

E-Print Network [OSTI]

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

Hoos, Holger H.

405

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

E-Print Network [OSTI]

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

LaValle, Steven M.

406

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

E-Print Network [OSTI]

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

Hoos, Holger H.

407

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

Fraenkel, Aviezri

408

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

E-Print Network [OSTI]

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

Newman, Alantha

409

Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines  

E-Print Network [OSTI]

Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support, Columbia, Missouri * Corresponding author: chengji@missouri.edu Abstract Predicting protein folding rate is useful for understanding protein folding process and guiding protein design. Here we developed a method

Cheng, Jianlin Jack

410

PROTEIN FOLD RECOGNITION USING RESIDUE-BASED ALIGNMENTS OF SEQUENCE AND SECONDARY STRUCTURE  

E-Print Network [OSTI]

PROTEIN FOLD RECOGNITION USING RESIDUE-BASED ALIGNMENTS OF SEQUENCE AND SECONDARY STRUCTURE Zafer methods [3,4]. Index Terms- protein fold recognition, secondary structure alignment, amino acid alignment &sabanciuniv.edu culated for each sequence-structure alignment. Protein fold recog- nition problem can

Erdogan, Hakan

411

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

E-Print Network [OSTI]

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

Bigelow, Stephen

412

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

E-Print Network [OSTI]

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

Istrail, Sorin

413

Single-molecule spectroscopy of protein folding in a chaperonin cage  

E-Print Network [OSTI]

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

Lipman, Everett A.

414

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

E-Print Network [OSTI]

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

Berne, Bruce J.

415

Lattice Protein Folding With Two and Four-Body Statistical Hin Hark Gan,1  

E-Print Network [OSTI]

Lattice Protein Folding With Two and Four-Body Statistical Potentials Hin Hark Gan,1 Alexander/sequence compatibility of proteins,5,6 homology modeling,7 and protein folding simulations.8 ­10 Currently, most structures. Multibody potentials may help improve our understanding of the cooperativity of protein folding

Schlick, Tamar

416

Reliable Protein Folding on Complex Energy Landscapes: The Free Energy Reaction Path  

E-Print Network [OSTI]

Reliable Protein Folding on Complex Energy Landscapes: The Free Energy Reaction Path Gregg Lois the dynamics of protein folding. The key insight is that the search for the native protein conformation. In the ``new view'' of protein folding (3,7), statistical fluctuations on an energy landscape give rise

O'Hern, Corey S.

417

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

E-Print Network [OSTI]

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

Levine, Alex J.

418

A new approach to multi-modal diffusions with applications to protein folding  

E-Print Network [OSTI]

A new approach to multi-modal diffusions with applications to protein folding Julie Lyng Forman1 rates are estimated. The new models provide a better fit to this type of protein folding data than time; measurement error; martingale estimating func- tion; multi-modality; protein folding; stochastic

Sørensen, Michael

419

Is Protein Unfolding the Reverse of Protein Folding? A Lattice Simulation Analysis  

E-Print Network [OSTI]

Is Protein Unfolding the Reverse of Protein Folding? A Lattice Simulation Analysis Aaron R. Dinner1- turing conditions are commonly employed to study the mechanism by which a protein folds to its native of determining the mechanism by which a protein folds would be to use an accurate high-resolution model

Dinner, Aaron

420

Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability  

E-Print Network [OSTI]

Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how on the effects of macro- molecular crowding on protein folding and binding stability has been reached. Crowders

Weston, Ken

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to obtain the most current and comprehensive results.


421

Predicting protein folding rates from geometric contact and amino acid sequence  

E-Print Network [OSTI]

Predicting protein folding rates from geometric contact and amino acid sequence ZHENG OUYANG structural properties. Keywords: protein folding; geometric contact number; zippers model; folding rate, USA (RECEIVED January 22, 2008; FINAL REVISION April 4, 2008; ACCEPTED April 7, 2008) Abstract Protein

Dai, Yang

422

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

E-Print Network [OSTI]

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

Croquette, Vincent

423

AN ANALYSIS OF PROTEIN FOLDING BY DECODING THE HIERARCHY OF NATIVE-STATE STRUCTURAL INTERACTIONS  

E-Print Network [OSTI]

AN ANALYSIS OF PROTEIN FOLDING BY DECODING THE HIERARCHY OF NATIVE-STATE STRUCTURAL INTERACTIONS and Department of Physics and Astronomy 2002 #12;ABSTRACT AN ANALYSIS OF PROTEIN FOLDING BY DECODING by which proteins fold is one of the most intensely studied prob- lems in science. Here, an analysis

Thorpe, Michael

424

Signatures of the Protein Folding Pathway in Two-Dimensional Ultraviolet Spectroscopy  

E-Print Network [OSTI]

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

Mukamel, Shaul

425

Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level  

E-Print Network [OSTI]

Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level coupled to the process of protein folding in vivo. While previous studies have provided invaluable insight about how crowding affects protein folding dynamics at the secondary structure level. In this study, we

Shorter, James

426

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

E-Print Network [OSTI]

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

Santiago, Juan G.

427

Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics  

E-Print Network [OSTI]

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

Morozov, Alexandre V.

428

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

E-Print Network [OSTI]

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

Harries, Daniel

429

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

E-Print Network [OSTI]

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

Neumaier, Arnold

430

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

E-Print Network [OSTI]

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

Istrail, Sorin

431

Pathways for protein folding: is a "new view" needed? Vijay S Pande1  

E-Print Network [OSTI]

Pathways for protein folding: is a "new view" needed? Vijay S Pande1 , Alexander Yu Grosberg2 energy MG Molten globule Introduction How do proteins fold? While the thirty five years since Anfinsen has demonstrated the complexity of protein folding, the search continues for the general principles

Croquette, Vincent

432

A minimum-reaction-flux solution to master-equation models of protein folding  

E-Print Network [OSTI]

A minimum-reaction-flux solution to master-equation models of protein folding Huan-Xiang Zhoua; published online 20 May 2008 Master equations are widely used for modeling protein folding. Here- ceptual and quantitative models for protein folding.1­15 In such models, the conformational space

Weston, Ken

433

Relationship between protein folding thermodynamics and the energy landscape Jaegil Kim,* Thomas Keyes,  

E-Print Network [OSTI]

Relationship between protein folding thermodynamics and the energy landscape Jaegil Kim,* Thomas Received 23 September 2008; published 4 March 2009 The origin of protein folding thermodynamics is examined.15.Cc, 05.70. a, 87.15.A Protein folding--i.e., how a polypeptide chain reaches a unique native state

Straub, John E.

434

From residue matching patterns to protein folding topographies: General model and bovine  

E-Print Network [OSTI]

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

Berry, R. Stephen

435

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

E-Print Network [OSTI]

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

Chen, Kuang-Yu

436

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity  

E-Print Network [OSTI]

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity¨lich, 52425 Ju¨lich, Germany Received June 14, 2010; E-mail: deserno@andrew.cmu.edu Abstract: Protein folding be difficult to measure. Therefore, protein folding cooperativity is often probed using the calorimetric

Bachmann, Michael

437

[25] Identifying Importance of Amino Acids for Protein Folding from Crystal Structures  

E-Print Network [OSTI]

[25] Identifying Importance of Amino Acids for Protein Folding from Crystal Structures By Nikolay V their unique three-dimensional structure. This ques- tion, known as the protein-folding problem,1­25 is of great importance because understanding protein-folding mechanisms is a key to success- ful manipulation

Dokholyan, Nikolay V.

438

Combining Task-and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform  

E-Print Network [OSTI]

Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform Is efficient protein folding possible with CHARMM on the United Devices MetaProcessor? B. Uk1 , M. Taufer1 parallelism and might not fit the needs for protein folding simulations with explicit water molecules. A short

Taufer, Michela

439

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

E-Print Network [OSTI]

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. In this study Beta3s was folded by molecular dynamics (MD) simulation and intermediate conformational ensembles

Mukamel, Shaul

440

3D finite amplitude folding: Implications for stress evolution during crustal and lithospheric deformation  

E-Print Network [OSTI]

3D finite amplitude folding: Implications for stress evolution during crustal and lithospheric-layer folding to study this instability in 3D. It is demonstrated that linear theories correctly describe insensitive to the applied background shortening directions. Furthermore, the 3D folding instability reduces

Kaus, Boris

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to obtain the most current and comprehensive results.


441

Techniques for modeling and analyzing RNA and protein folding energy landscapes  

E-Print Network [OSTI]

techniques can be used to study RNA and protein fold- ing kinetics such as population kinetics, folding rates, and the folding of particular subsequences. In particular, a map-based Master Equation (MME) method can be used to analyze the population kinetics...

Tang, Xinyu

2009-05-15T23:59:59.000Z

442

Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics  

E-Print Network [OSTI]

Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics John involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the preceding

Takada, Shoji

443

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

E-Print Network [OSTI]

­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

Fleming, Patrick

444

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

E-Print Network [OSTI]

Late Cenozoic partitioning of oblique plate convergence in the Zagros fold-and-thrust belt (Iran of oblique plate convergence in the Zagros fold-and-thrust belt (Iran), Tectonics, 25, TC3002, doi:10.1029/2005TC001860. 1. Introduction [2] The Zagros fold-and-thrust belt of southern Iran, the longest

Paris-Sud XI, Université de

445

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

E-Print Network [OSTI]

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

Chakraborty, Debrup

446

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

E-Print Network [OSTI]

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

Gräter, Frauke

447

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

E-Print Network [OSTI]

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

Unger, Ron

448

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

E-Print Network [OSTI]

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

Chan, Hue Sun

449

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

E-Print Network [OSTI]

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

Moll, Mark

450

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

E-Print Network [OSTI]

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

Lindquist, Susan

451

Implementation and Characterization of Protein Folding on a Desktop Computational Grid  

E-Print Network [OSTI]

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

Taufer, Michela

452

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

E-Print Network [OSTI]

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

453

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

E-Print Network [OSTI]

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

Di Mauro, Nicola

454

Task-parallel global optimization with application to protein folding C. Voglis, P. E. Hadjidoukas,  

E-Print Network [OSTI]

Task-parallel global optimization with application to protein folding C. Voglis, P. E. Hadjidoukas parallelization of a real application case that concerns the protein folding problem. The experimental evaluation, cluster programming, numerical differentiation, global optimization, protein folding. 1. INTRODUCTION Many

Dimakopoulos, Vassilios

455

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

E-Print Network [OSTI]

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

456

Predicting Protein Folds with Structural Repeats Using a Chain Graph Model  

E-Print Network [OSTI]

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

Xing, Eric P.

457

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

E-Print Network [OSTI]

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

Istrail, Sorin

458

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

459

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

E-Print Network [OSTI]

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

Palczewski, Krzysztof

460

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

E-Print Network [OSTI]

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

Muggleton, Stephen H.

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461

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 Home5b9fcbce19 No revision hasInformation Earth's Heat Jump to:PhotonHolyName HousingIII Wind Farm Facility Horse HollowHorst

462

Automated transmission line fault analysis using synchronized sampling at two ends  

SciTech Connect (OSTI)

This paper introduces a new approach to fault analysis using synchronized sampling. A digital fault recorder with Global Positioning System (GPS) satellite receiver is the source of data for this approach. Fault analysis functions, such as fault detection, classification and location are implemented for a transmission line using synchronized samples from two ends of a line. This technique can be extremely fast, selective and accurate, providing fault analysis performance that can not easily be matched by other known techniques.

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

1996-02-01T23:59:59.000Z

463

Automated transmission line fault analysis using synchronized sampling at two ends  

SciTech Connect (OSTI)

This paper introduces a new approach to fault analysis using synchronized sampling. A digital fault recorder with Global Positioning System (GPS) satellite receiver is the source of data for this approach. Fault analysis functions, such as fault detection, classification and location are implemented for a transmission line using synchronized samples from two ends of a line. This technique can be extremely fast, selective and accurate, providing fault analysis performance that can not easily be matched by other known techniques.

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

1995-12-31T23:59:59.000Z

464

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

E-Print Network [OSTI]

), evaporator fouling (Evapfoul), liquid-line restriction (Llrestr), low refrigerant charge (Reflow), and refrigerant high charge (Refhigh). Except for refrigerant charge and compressor leakage faults for which five fault levels were introduced, four fault... for these tests. The method could detect low refrigerant charge and loss of compressor performance at the lowest levels introduced and all other faults at the second level. All of the faults could be reliably diagnosed before a 5% degradation in capacity...

Li, H.; Braun, J.

2006-01-01T23:59:59.000Z

465

arcing fault fires: Topics by E-print Network  

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

stacking faults at a production-rate of few gmin. A guideline for controlling the number of layers of such FLG has also been suggested. Karmakar, Soumen; Lalla, Niranjan P;...

466

assembly line fault: Topics by E-print Network  

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

of fault data to verify that all elements of the protection system Siegel, Mel 190 Bucket brigades on in-tree assembly networks John J. Bartholdi III a,*, Donald D. Eisenstein...

467

Microgrid Fault Protection Based on Symmetrical and Differential Current Components  

E-Print Network [OSTI]

Microgrid Fault Protection Based on Symmetrical and Differential Current Components Prepared.........................................................................................8 2. AEP CERTS MICROGRID .........................................................................9 ........................................................................67 #12;3 Index of Figures Figure 1: Schematic representation of the AEP CERTS microgrid

468

Characteristics of Wind Turbines Under Normal and Fault Conditions: Preprint  

SciTech Connect (OSTI)

This paper investigates the characteristics of a variable-speed wind turbine connected to a stiff or weak grid under normal and fault conditions and the role of reactive power compensation.

Muljadi, E.; Butterfield, C. P.; Parsons, B.; Ellis, A.

2007-02-01T23:59:59.000Z

469

Faults as potential hydrocarbon barriers, Arroyo Grande, California  

E-Print Network [OSTI]

Faulting in a sandstone introduces properties which are different from the country rock. Previous work has shown that these new properties can significantly impede the flow of hydrocarbons through the country rock. This thesis seeks to analyze...

Switek, Daniel Paul

1994-01-01T23:59:59.000Z

470

An information model for inter-organizational fault Patricia Marcu  

E-Print Network [OSTI]

in the IT Infrastructure Library (ITIL) [2] and related frameworks in the area of IT service management (ITSM). But since ITIL and the related ITSM frameworks do not consider specific aspects of inter- organizational (fault

471

Understanding Fault Characteristics And Sediment Depth For Geothermal...  

Open Energy Info (EERE)

Fault Characteristics And Sediment Depth For Geothermal Exploration Using 3D Gravity Inversion In Walker Valley, Nevada Jump to: navigation, search OpenEI Reference LibraryAdd to...

472

Non-intrusive fault detection in reciprocating compressors  

E-Print Network [OSTI]

This thesis presents a set of techniques for non-intrusive sensing and fault detection in reciprocating compressors driven by induction motors. The procedures developed here are "non-intrusive" because they rely only on ...

Schantz, Christopher James

2011-01-01T23:59:59.000Z

473

CAPRI : a common architecture for distributed probabilistic Internet fault diagnosis  

E-Print Network [OSTI]

This thesis presents a new approach to root cause localization and fault diagnosis in the Internet based on a Common Architecture for Probabilistic Reasoning in the Internet (CAPRI) in which distributed, heterogeneous ...

Lee, George J. (George Janbing), 1979-

2007-01-01T23:59:59.000Z

474

CAPRI: A Common Architecture for Distributed Probabilistic Internet Fault Diagnosis  

E-Print Network [OSTI]

This thesis presents a new approach to root cause localization and fault diagnosis in the Internet based on a Common Architecture for Probabilistic Reasoning in the Internet (CAPRI) in which distributed, heterogeneous ...

Lee, George J.

2007-06-04T23:59:59.000Z

475

Lossless fault-tolerant data structures with additive overhead  

E-Print Network [OSTI]

We develop the first dynamic data structures that tolerate ? memory faults, lose no data, and incur only an O(? ) additive overhead in overall space and time per operation. We obtain such data structures for arrays, linked ...

Christiano, Paul F.

476

anatolian fault zone: Topics by E-print Network  

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

across the Mudurnu segment of the North Anatolian Fault Zone (NAFZ) in northwestern Turkey Ben-Zion, Yehuda 2 Velocity contrast across the 1944 rupture zone of the North...

477

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

Open Energy Info (EERE)

FLANK AND COSO WASH Jump to: navigation, search OpenEI Reference LibraryAdd to library Conference Proceedings: STRESS AND FAULTING IN THE COSO GEOTHERMAL FIELD: UPDATE AND...

478

Identifying Efficiency Degrading Faults in Split Air Conditioning Systems  

E-Print Network [OSTI]

Studies estimate that as much as 50% of packaged air conditioning systems operate in faulty conditions that degrade system efficiency. Common faults include: under- and over-charged systems (too much or too little refrigerant), faulty expansions...

Terrill, T. J.; Brown, M. L.; Cheyne, R. W. Jr.; Cousins, A. J.; Daniels, B. P.; Erb, K. L.; Garcia, P. A.; Leutermann, M. J.; Nel, A. J.; Robert, C. L.; Widger, S. B.; Williams, A. G.; Rasmussen, B. P.

2013-01-01T23:59:59.000Z

479

The northwest extension of the Meers Fault in southwestern Oklahoma  

E-Print Network [OSTI]

THE NORTHWEST EXTENSION OF THE MEERS FAULT IN SOUTIRVESTERN OKLAHOMA A Thesis by HASAN CETIN Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE... May 1991 Major Subject: Geology THE NORTHWEST EXTENSION OF THE MEERS FAULT IN SOUTHWESTERN OKLAHOMA A Thesis by HASAN CETIN Approved as to style and content by: Norman R. ford (Chair of ommittee) Chr stopher C. Mathewson (Member) ne A...

Cetin, Hasan

1991-01-01T23:59:59.000Z

480

Two Similarity Measure Approaches to Whole Building Fault Diagnosis  

E-Print Network [OSTI]

consumption in buildings using similarity measures. The method is referred to as the cosine similarity method if cosine similarity is adopted and is referred to as the Euclidean distance similarity method if Euclidean distance similarity is implemented.... Fig. 1 Block diagram for diagnosing abnormal energy consumption Step 1: Reference Control Change Library Determination Whole building fault diagnosis is different from component level fault diagnosis. It can only give a general clue, for example...

Lin, G.; Claridge, D.

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "faults folds grabens" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


481

The application of satellite time references to HVDC fault location  

SciTech Connect (OSTI)

An HVdc fault location scheme is described which relies on very precise detection of the time of arrival of fault created surges at both ends of the line. Such detection is achieved by a very accurate data acquisition and processing system combined with the time reference signals provided by a global positioning system receiver. Extensive digital simulation is carried out to determine the voltage and current waveforms, to identify the main sources of error and suggest possible compensation techniques.

Dewe, M.B.; Sankar, S.; Arrillaga, J. (Univ. of Canterbury, Christchurch (New Zealand))

1993-07-01T23:59:59.000Z

482

Occupancy Based Fault Detection on Building Level - a Feasibility Study  

E-Print Network [OSTI]

-going commissioning and fault detection and diagnostics (FDD) has been performed to improve the current situation of building problems by comparing measured building performance with design predictions [Portland 2003]. For fault detection, different methods... conference on building commissioning, Portland Energy Conservation. Portland. 2003. Methods for automated and continuous commissioning of building systems. US department of commerce, Portland energy conservation inc. Schijndel, A.W.M. van, 2008...

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

2010-01-01T23:59:59.000Z

483

Microcomputer applications of, and modifications to, the modular fault trees  

SciTech Connect (OSTI)

The LaSalle Probabilistic Risk Assessment was the first major application of the modular logic fault trees after the IREP program. In the process of performing the analysis, many errors were discovered in the fault tree modules that led to difficulties in combining the modules to form the final system fault trees. These errors are corrected in the revised modules listed in this report. In addition, the application of the modules in terms of editing them and forming them into the system fault trees was inefficient. Originally, the editing had to be done line by line and no error checking was performed by the computer. This led to many typos and other logic errors in the construction of the modular fault tree files. Two programs were written to help alleviate this problem: (1) MODEDIT - This program allows an operator to retrieve a file for editing, edit the file for the plant specific application, perform some general error checking while the file is being modified, and store the file for later use, and (2) INDEX - This program checks that the modules that are supposed to form one fault tree all link up appropriately before the files are,loaded onto the mainframe computer. Lastly, the modules were not designed for relay type logic common in BWR designs but for solid state type logic. Some additional modules were defined for modeling relay logic, and an explanation and example of their use are included in this report.

Zimmerman, T.L.; Graves, N.L.; Payne, A.C. Jr.; Whitehead, D.W. [Sandia National Labs., Albuquerque, NM (United States)] [Sandia National Labs., Albuquerque, NM (United States)

1994-10-01T23:59:59.000Z

484

The San Andreas Fault System Paul Withers Wallace RE, The San Andreas Fault System, California, USGS Professional Paper 1515,  

E-Print Network [OSTI]

mainland Mexico. The San Andreas fault is commonly referred to as the boundary between the Pacific is correlated with the local geological setting. CO2 lubrication, #12;increased pore pressure, and decreased

Withers, Paul

485

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

E-Print Network [OSTI]

This dissertation investigates the interaction of model II in-plane dynamic rupture with a geometrical discontinuity along the fault strike: stepover. One goal is to understand how large the stepover width must be to stop the dynamic rupture...

Liu, Zaifeng

2014-05-05T23:59:59.000Z

486

Realistic fault modeling and quality test generation of combined delay faults  

E-Print Network [OSTI]

. Summary . . Page . . Vi . Vii . 1X . I 2 . 5 . 5 . 6 . 6 . . . 14 . 14 . 16 . 17 . 18 . 18 . 20 . 20 23 , 33 . 34 36 36 38 . . 44 53 53 2. Future Work . . . . . REFERENCES . VITA Page 54 55 LIST OF FIGURES Fig. 1. Fault... 24 Fig. 10. Fig. 11. Fig. 12. Fig. 13. Fig. 14. Fig. 15. Fig. 16. Fig. 17. Fig. 18. Fig. 19. Fig. 20. Fig. 21. Fig. 22. Fig. 23. Fig. 24. Fig. 25. Path generation algorithm. Example for graph theory . Propagation along longest path...

Thadhlani, Ajaykumar A

2001-01-01T23:59:59.000Z

487

Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding  

SciTech Connect (OSTI)

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

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

1996-12-01T23:59:59.000Z

488

Topological crossovers in the forced folding of self-avoiding matter  

E-Print Network [OSTI]

We study the scaling properties of forced folding of thin materials of different geometry. The scaling relations implying the topological crossovers from the folding of threedimensional plates to the folding of two-dimensional sheets, and further to the packing of one-dimensional strings, are derived for elastic and plastic manifolds. These topological crossovers in the folding of plastic manifolds were observed in experiments with predominantly plastic aluminum strips of different geometry. Elasto-plastic materials, such as paper sheets during the (fast) folding under increasing confinement force, are expected to obey the scaling force-diameter relation derived for elastic manifolds. However, in experiments with paper strips of different geometry, we observed the crossover from packing of one-dimensional strings to folding two dimensional sheets only, because the fractal dimension of the set of folded elasto-plastic sheets is the thickness dependent due to the strain relaxation after a confinement force is withdrawn.

Alexander S. Balankin; Daniel Morales Matamoros; Ernesto Pineda Leon; Antonio Horta Rangel; Miguel Angel Martinez Cruz; Didier Samayoa Ochoa

2009-07-25T23:59:59.000Z

489

Abstract--A method for fault detection and isolation is proposed and applied to inverter faults in multi-phase drives. An  

E-Print Network [OSTI]

energy source, a five- leg inverter and a five-phase star-connected PMSM. It has to be noticed that all-magnet synchronous machine (PMSM) drive. The faults under consideration are: open-phase faults and open-switch faults

Boyer, Edmond

490

Ultraviolet resonance Raman and fluorescence studies of folded and unfolded conformations of the membrane protein OmpA  

E-Print Network [OSTI]

Thermodynamics of Membrane Protein Folding: Lessons from theA Model for Membrane Protein Folding”, H. S. Shafaat, K. M.goals of membrane protein folding studies is to ascertain

Sanchez, Katheryn Marie

2010-01-01T23:59:59.000Z

491

YidC protein, a molecular chaperone for LacY protein folding via the SecYEG protein machinery  

E-Print Network [OSTI]

GroEL-GroES- mediated protein folding. Chem. Rev. 106, 1917–of chaperone-mediated protein folding in the cytosol. Nat.that impair membrane protein folding and generate a membrane

Zhu, L; Kaback, HR; Dalbey, RE

2013-01-01T23:59:59.000Z

492

Exploring the protein folding dynamics of beta3s with two-dimensional ultraviolet (2DUV) spectroscopy  

E-Print Network [OSTI]

Wang* Exploring the Protein Folding Dynamics of Beta3s withExploring the Protein Folding Dynamics of Beta3s with Two-echo signals to monitor the protein folding pro- cess of the

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

2014-01-01T23:59:59.000Z

493

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

E-Print Network [OSTI]

the westernmost exposed thrusts in this area (Figs. 3 and 4). The Chukou fault terminates to the north at the Chuchi uunsverse fault, and to the south is inferred to merge, and transfer displacement with, the Lunhou fault (Lin, 1996) just east of the Nanliao... surveys were then conducted in early 1996 and 1997 across the island using both these new monuments and pre-existing ones. These surveys were conducted with survey-grade GPS receivers on 4 to 12 sites simultaneously, with an average site occupation time...

Hickman, John Bibb

2012-06-07T23:59:59.000Z

494

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

SciTech Connect (OSTI)

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

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

2003-05-28T23:59:59.000Z

495

Development and application of all-atom structure-based models for studying the role of geometry in biomolecular folding and function  

E-Print Network [OSTI]

in Protein Folding . . . . . . . . . . . . . . . . . . . . .P. G. (2004) Theory of protein folding. Curr. Opin. Struct.statistical mechanics of protein folding. Proc. Nat. Acad.

Noel, Jeffrey Kenneth

2012-01-01T23:59:59.000Z

496

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]

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

Lambert, George Randall

1993-01-01T23:59:59.000Z

497

Accident Fault Trees for Defense Waste Processing Facility  

SciTech Connect (OSTI)

The purpose of this report is to document fault tree analyses which have been completed for the Defense Waste Processing Facility (DWPF) safety analysis. Logic models for equipment failures and human error combinations that could lead to flammable gas explosions in various process tanks, or failure of critical support systems were developed for internal initiating events and for earthquakes. These fault trees provide frequency estimates for support systems failures and accidents that could lead to radioactive and hazardous chemical releases both on-site and off-site. Top event frequency results from these fault trees will be used in further APET analyses to calculate accident risk associated with DWPF facility operations. This report lists and explains important underlying assumptions, provides references for failure data sources, and briefly describes the fault tree method used. Specific commitments from DWPF to provide new procedural/administrative controls or system design changes are listed in the ''Facility Commitments'' section. The purpose of the ''Assumptions'' section is to clarify the basis for fault tree modeling, and is not necessarily a list of items required to be protected by Technical Safety Requirements (TSRs).

Sarrack, A.G.

1999-06-22T23:59:59.000Z

498

Theory and practice of microlensing lightcurves around fold singularities  

E-Print Network [OSTI]

Among all galactic microlensing events, those involving a passage of the observed source star over the caustic created by a binary lens are particularly useful in providing information about stellar atmospheres, the dynamics of stellar populations in our own and neighbouring galaxies, and the statistical properties of stellar and sub-stellar binaries. This paper presents a comprehensive guide for modelling and interpreting the lightcurves obtained in events involving fold-caustic crossings. A new general, consistent, and optimal choice of parameters provides a deep understanding of the involved features, avoids numerical difficulties and minimizes correlations between model parameters. While the photometric data of a microlensing event around a caustic crossing itself do not provide constraints on the characteristics of the underlying binary lens and does not allow predictions of the behaviour of other regions of the lightcurve, vital constraints can be obtained in an efficient way if these are combined with a few simple characteristics of data outside the caustic crossings. A corresponding algorithm containing some improvements over an earlier approach which takes into account multi-site observations is presented and discussed in detail together with the arising parameter constraints paying special attention to the role of source and background fluxes.

M. Dominik

2004-06-23T23:59:59.000Z

499

Power law scaling of lateral deformations with universal Poissons index for randomly folded thin sheets  

E-Print Network [OSTI]

We study the lateral deformations of randomly folded elastoplastic and predominantly plastic thin sheets under the uniaxial and radial compressions. We found that the lateral deformations of cylinders folded from elastoplastic sheets of paper obey a power law behavior with the universal Poissons index nu = 0.17 pm 0.01, which does not depend neither the paper kind and sheet sizes, nor the folding confinement ratio. In contrast to this, the lateral deformations of randomly folded predominantly plastic aluminum foils display the linear dependence on the axial compression with the universal Poissons ratio nu_e = 0.33 pm 0.01. This difference is consistent with the difference in fractal topology of randomly folded elastoplastic and predominantly plastic sheets, which is found to belong to different universality classes. The general form of constitutive stress-deformation relations for randomly folded elastoplastic sheets is suggested.

Alexander S. Balankin; Didier Samayoa Ochoa; Ernesto Pineda Leon; Rolando Cortes Montes de Oca; Antonio Horta Rangel; Miguel Angel Martinez Cruz

2008-08-24T23:59:59.000Z

500

Transferable coarse-grained potential for $\\textit{de novo}$ protein folding and design  

E-Print Network [OSTI]

Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and folding is introduced. With computer simulations it is shown that, for a large set of real protein structures, the model produces designed sequences with similar physical properties to the corresponding natural occurring sequences. The designed sequences are not yet fully realistic and require further experimental testing. For an independent set of proteins, notoriously difficult to fold, the correct folding of both the designed and the natural sequences is also demonstrated. The folding properties are characterized by free energy calculations. which not only are consistent among natural and designed proteins, but we also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, this novel coarse-grained protein model ...

Coluzza, Ivan

2014-01-01T23:59:59.000Z