Science.gov

Sample records for folded compact range

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

    SciTech Connect

    Sorensen, K.W.

    1995-03-01

    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.

  2. Coherent change detection and interferometric ISAR measurements in the folded compact range

    SciTech Connect

    Sorensen, K.W.

    1996-08-01

    A folded compact range configuration has been developed ant the Sandia National Laboratories` compact range antenna and radar-cross- section measurement facility as a means of performing indoor, environmentally-controlled, far-field simulations of synthetic aperture radar (SAR) measurements of distributed target samples (i.e. gravel, sand, etc.). The folded compact range configuration has previously been used to perform coherent-change-detection (CCD) measurements, which allow disturbances to distributed targets on the order of fractions of a wavelength to be detected. This report describes follow-on CCD measurements of other distributed target samples, and also investigates the sensitivity of the CCD measurement process to changes in the relative spatial location of the SAR sensor between observations of the target. Additionally, this report describes the theoretical and practical aspects of performing interferometric inverse-synthetic-aperture-radar (IFISAR) measurements in the folded compact range environment. IFISAR measurements provide resolution of the relative heights of targets with accuracies on the order of a wavelength. Several examples are given of digital height maps that have been generated from measurements performed at the folded compact range facility.

  3. Development of a folded compact range and its application in performing coherent change detection and interferometric ISAR measurement

    SciTech Connect

    Sorensen, K.W.; Zittel, D.H.; Littlejohn, J.H.

    1996-09-01

    A folded compact range configuration has been developed at the Sandia National Laboratories` compact range antenna and radar cross section measurement facility as a means of performing indoor, environmentally controlled far-field simulations of synthetic aperture radar (SAR) measurements of distributed target samples (i.e. gravel, sand, etc.). In particular, the folded compact range configuration has been used to perform both highly sensitive coherent change detection (CCD) measurements and interferometric inverse synthetic aperture radar (IFSAR) measurements, which, in addition to the two-dimensional spatial resolution afforded by typical interferometric SAR (ISAR) processing, provides resolution of the relative height of targets with accuracies on the order of a wavelength. This paper describes the development of the folded compact range, as well as the coherent change detection and interferometric measurements that have been made with the system. The measurement have been very successful, and have demonstrated not only the viability of the folded compact range concept in simulating SAR CCD and IFSAR measurements, but also its usefulness as a tool in the research and development of SAR CCD and IFSAR image generation and measurement methodologies.

  4. Compact intermediates in RNA folding

    SciTech Connect

    Woodson, S.A.

    2011-12-14

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

  5. Development of an optimized compact test range

    NASA Astrophysics Data System (ADS)

    Dudok, Evert; Fasold, Dietmar; Steiner, Hans-Juergen

    A method of measuring the electromagnetic far field characteristics of microwave antennas is introduced by means of compact test ranges. The performances of the front-fed Cassegrain system, which avoids the usually weak cross-polarization performance of the compact range geometries, are established. The chosen manufacturing process, milling of cast-iron reflectors, guaranteed highest achievable surface accuracies, even for very large reflectors. The structural analysis showed that extremely high surface accuracies require well regulated temperature conditions of the experiment.

  6. Compact range for variable-zone measurements

    DOEpatents

    Burnside, Walter D.; Rudduck, Roger C.; Yu, Jiunn S.

    1988-01-01

    A compact range for testing antennas or radar targets includes a source for directing energy along a feedline toward a parabolic reflector. The reflected wave is a spherical wave with a radius dependent on the distance of the source from the focal point of the reflector.

  7. Compact range for variable-zone measurements

    DOEpatents

    Burnside, Walter D.; Rudduck, Roger C.; Yu, Jiunn S.

    1988-08-02

    A compact range for testing antennas or radar targets includes a source for directing energy along a feedline toward a parabolic reflector. The reflected wave is a spherical wave with a radius dependent on the distance of the source from the focal point of the reflector.

  8. Compact range for variable-zone measurements

    DOEpatents

    Burnside, W.D.; Rudduck, R.C.; Yu, J.S.

    1987-02-27

    A compact range for testing antennas or radar targets includes a source for directing energy along a feedline toward a parabolic reflector. The reflected wave is a spherical wave with a radius dependent on the distance of the source from the focal point of the reflector. 2 figs.

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

    SciTech Connect

    Guth, P.L.

    1985-01-01

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

  10. Fault-related folding during extension: Plunging basement-cored folds in the Basin and Range

    USGS Publications Warehouse

    Howard, K.A.; John, Barbara E.

    1997-01-01

    Folds are able to form in highly extended areas where stratified cover rocks respond to basement fault offsets. The response of cover rocks to basement faulting can be studied especially well in plunging structures that expose large structural relief. The southern Basin and Range province contains plunging folds kilometres in amplitude at the corners of domino-like tilt blocks of basement rocks, where initially steep transverse and normal faults propagated upward toward the layered cover rocks. Exposed tilted cross sections, as much as 8 km thick, display transitions from faulted basement to folded cover that validate laboratory models of forced folds. The folded cover masks a deeper extensional style of brittle segmentation and uniform steep tilting.

  11. The complex kinetics of protein folding in wide temperature ranges.

    PubMed

    Wang, Jin

    2004-10-01

    The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T0 is found to be smaller than the folding transition temperature Tf. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal behavior, from high-temperature exponential Poissonian kinetics to the relatively low-temperature highly non-exponential kinetics. The transition temperature is at Tk and T0 < Tk < Tf. In certain low-temperature regimes, a power law behavior at long time emerges. At very low temperatures (lower than trapping transition temperature T < T0/(4 approximately 6)), the kinetics is an exponential Poissonian process again.

  12. Methodology Investigation. Phase 1. Compact Range Test Applications

    DTIC Science & Technology

    1991-08-01

    incorporate a dual-axis hydraulic positioner into the existing protocol used by commercial antenna positioner controllers. The USAEPG Compact Range could not...o :0.0/ 4.,V - -$’\\ 5.3 Elevation Increments: Sin Off 0.01 deg. (𔃻v VbAi No CoAP 0.05 deg. 0.1 deg. " " 0.2 deg. < 1" .* M1At, ’ /A ., , 0,01 5.4

  13. Compact-range coordinate system established using a laser tracker.

    SciTech Connect

    Gallegos, Floyd H.; Bryce, Edwin Anthony

    2006-12-01

    Establishing a Cartesian coordinate reference system for an existing Compact Antenna Range using the parabolic reflector is presented. A SMX (Spatial Metrix Corporation) M/N 4000 laser-based coordinate measuring system established absolute coordinates for the facility. Electric field characteristics with positional movement correction are evaluated. Feed Horn relocation for alignment with the reflector axis is also described. Reference points are established for follow-on non-laser alignments utilizing a theodolite.

  14. Offset dual-shaped reflectors for dual chamber compact ranges

    NASA Technical Reports Server (NTRS)

    Galindo-Israel, Victor; Imbriale, William A.; Rengarajan, Sembiam R.; Mittra, Raj

    1991-01-01

    The application of the theory of the synthesis of offset dual-shaped reflectors to the design of compact ranges is examined. The object of the compact range is to provide a uniform plane wave with minimum amplitude and phase ripple over as large a volume as possible for a given size reflector. Ripple can be lowered by reducing the edge diffraction from the reflector producing the plane wave. This has been done either by serrating or rolling the edge. An alternative approach is to use dual offset-shaped reflector synthesis techniques to produce a reflector aperture distribution that is uniform over most of the aperture, but with a Gaussian taper near the edge. This approach can be used together with rolling and/or serration if desirable. The amount of phase and amplitude ripple obtained with two different dual-shaped reflector designs is studied as a function of position in the plane wave zone and reflector size in wavelengths. The amount of both transverse and longitudinal (z-component) cross polarization is studied.

  15. Osmolytes stabilize ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states.

    PubMed

    Ratnaparkhi, G S; Varadarajan, R

    2001-08-03

    Osmolytes stabilize proteins to thermal and chemical denaturation. We have studied the effects of the osmolytes sarcosine, betaine, trimethylamine-N-oxide, and taurine on the structure and stability of the protein.peptide complex RNase S using x-ray crystallography and titration calorimetry, respectively. The largest degree of stabilization is achieved with 6 m sarcosine, which increases the denaturation temperatures of RNase S and S pro by 24.6 and 17.4 degrees C, respectively, at pH 5 and protects both proteins against tryptic cleavage. Four crystal structures of RNase S in the presence of different osmolytes do not offer any evidence for osmolyte binding to the folded state of the protein or any perturbation in the water structure surrounding the protein. The degree of stabilization in 6 m sarcosine increases with temperature, ranging from -0.52 kcal mol(-1) at 20 degrees C to -5.4 kcal mol(-1) at 60 degrees C. The data support the thesis that osmolytes that stabilize proteins, do so by perturbing unfolded states, which change conformation to a compact, folding competent state in the presence of osmolyte. The increased stabilization thus results from a decrease in conformational entropy of the unfolded state.

  16. A Cassegrain reflector system for compact range applications

    NASA Technical Reports Server (NTRS)

    Rader, Mark D.; Burnside, Walter D.

    1986-01-01

    An integral part of a compact range is the means of providing a uniform plane wave. A Cassegrain reflector system is one alternative for achieving this goal. Theoretically, this system offers better performance than a simple reflector system. The longer pathlengths in the Cassegrain system lead to a more uniform field in the plane of interest. The addition of the subreflector creates several problems, though. System complexity is increased both in terms of construction and performance analysis. The subreflector also leads to aperture blockage and the orientation of the feed now results in spillover illuminating the target areas as well as the rest of the range. Finally, the addition of the subreflector leads to interaction between the two reflectors resulting in undesired field variations in the plane of interest. These difficulties are addressed and through the concept of blending the surfaces, a Cassegrain reflector system is developed that will provide a uniform plane wave that offers superior performance over large target areas for a given size reflector system. Design and analysis is implemented by considering the main reflector and subreflector separately. Then the system may be put together and the final design and system analysis completed.

  17. Achieving large dynamic range control of gene expression with a compact RNA transcription-translation regulator.

    PubMed

    Westbrook, Alexandra M; Lucks, Julius B

    2017-04-06

    RNA transcriptional regulators are emerging as versatile components for genetic network construction. However, these regulators suffer from incomplete repression in their OFF state, making their dynamic range less than that of their protein counterparts. This incomplete repression causes expression leak, which impedes the construction of larger synthetic regulatory networks as leak propagation can interfere with desired network function. To address this, we demonstrate how naturally derived antisense RNA-mediated transcriptional regulators can be configured to regulate both transcription and translation in a single compact RNA mechanism that functions in Escherichia coli. Using in vivo gene expression assays, we show that a combination of transcriptional termination and ribosome binding site sequestration increases repression from 85% to 98%, or activation from 10-fold to over 900-fold, in response to cognate antisense RNAs. We also show that orthogonal repressive versions of this mechanism can be created through engineering minimal antisense RNAs. Finally, to demonstrate the utility of this mechanism, we use it to reduce network leak in an RNA-only cascade. We anticipate these regulators will find broad use as synthetic biology moves beyond parts engineering to the design and construction of more sophisticated regulatory networks.

  18. A 240 GHZ Polarimetric Compact Range for Scale Model RCS Measurements

    DTIC Science & Technology

    2010-10-01

    an ISAR measurement example. Keywords: Compact Range, Instrumentation, Millimeter- Wave, RCS Measurements, Scale Modeling, Terahertz. 1...including sample range profiles, and an overview of the calibration approach used. An ISAR image of a complex target is presented as sample data...side to produce a clean 27? FWHM quiet zone. In this paper a description of this 240 GHz compact range is provided along with an ISAR measurement example

  19. Strategies to stabilize compact folding and minimize aggregation of antibody-based fragments

    PubMed Central

    Schrum, Adam G.

    2015-01-01

    Monoclonal antibodies (mAbs) have proven to be useful for development of new therapeutic drugs and diagnostic techniques. To overcome the difficulties posed by their complex structure and folding, reduce undesired immunogenicity, and improve pharmacokinetic properties, a plethora of different Ab fragments have been developed. These include recombinant Fab and Fv segments that can display improved properties over those of the original mAbs upon which they are based. Antibody (Ab) fragments such as Fabs, scFvs, diabodies, and nanobodies, all contain the variable Ig domains responsible for binding to specific antigenic epitopes, allowing for specific targeting of pathological cells and/or molecules. These fragments can be easier to produce, purify and refold than a full Ab, and due to their smaller size they can be well absorbed and distributed into target tissues. However, the physicochemical and structural properties of the immunoglobulin (Ig) domain, upon which the folding and conformation of all these Ab fragments is based, can limit the stability of Ab-based drugs. The Ig domain is fairly sensitive to unfolding and aggregation when produced out of the structural context of an intact Ab molecule. When unfolded, Ab fragments may lose their specificity as well as establish non-native interactions leading to protein aggregation. Aggregated antibody fragments display altered pharmacokinetic and immunogenic properties that can augment their toxicity. Therefore, much effort has been placed in understanding the factors impacting the stability of Ig folding at two different levels: 1) intrinsically, by studying the effects of the amino acid sequence on Ig folding; 2) extrinsically, by determining the environmental conditions that may influence the stability of Ig folding. In this review we will describe the structure of the Ig domain, and the factors that impact its stability, to set the context for the different approaches currently used to achieve stable recombinant Ig

  20. Optical design and development of near-range compact lidar

    NASA Astrophysics Data System (ADS)

    Shiina, Tatsuo

    2011-12-01

    There are large demands to monitor the atmosphere in the closed space (hall, factory and so on), to check vegetation remotely and to detect hazardous gases such as explosive gas and bio terror from explosion-proof distance. On the contrary, traditional lidars have blind area, it is hard to monitor the atmosphere and the gas in the near range. In this study, optical designs and concrete developments for the atmosphere monitoring and the certain gas detection in near range were accomplished. Unique optical designs are introduced and their practical setups are explained.

  1. Range-Gated Metrology with Compact Optical Head

    NASA Technical Reports Server (NTRS)

    Dubovitsky, Serge; Shaddock, Daniel; Ware, Brent; Lay, Oliver

    2008-01-01

    This work represents a radical simplification in the design of the optical head needed for high-precision laser ranging applications. The optical head is now a single fiber-optic collimator with dimensions of order of 1 1 2 cm, which can be easily integrated into the system being measured with minimal footprint.

  2. Design and implementation of the ESL compact range underhung bridge crane

    NASA Technical Reports Server (NTRS)

    Shamansky, H. T.; Dominek, A. K.; Burnside, W. D.

    1987-01-01

    As the indoor compact range technology has continued to increase, the need to handle larger and heavier targets has also increased. This need for target lifting and handling prompted the feasibility study of the use of an underhung bridge crane to be installed in the ESL (ElectroScience Laboratory, Ohio State University) compact range. This report documents both the design of the underhung bridge crane that was installed and the implementation of the design in the actual installation of the crane.

  3. A compact and high flow-rate piezoelectric micropump with a folded vibrator

    NASA Astrophysics Data System (ADS)

    Wang, Xue Yan; Ma, Yu Ting; Yan, Gang Yi; Feng, Zhi Hua

    2014-11-01

    This paper presents the design, fabrication, dynamic analysis, and experimental results of an efficient resonantly-driven piezoelectric micropump. The micropump consists of a folded vibrator, two polydimethylsiloxane (PDMS) check valves and compressible spaces. A newly developed folded vibrator with piezoelectric sheets serves as the resonantly-driven actuator. The vibrator provides uniform strain distribution in piezoelectric sheets surfaces to improve their utilizing efficiency. The PDMS check valves used in this design increase pump’s working stability and largely reduce the leakage rate. In addition, the performance of the micropump is significantly improved by two compressible spaces near the check valves. Experimental results on a prototype with dimensions of 20 mm × 20 mm × 28 mm demonstrate that the maximum flow rate of 118 ml min-1 and maximum back pressure of 22.5 kPa are obtained when the micropump is driven by a sinusoidal voltage of 120 Vpp at 361 Hz. A stable minimum flow rate of 160 μl min-1 can be obtained with driving voltage of 4 Vpp. The maximum power consumption of the micropump is approximately 62 mW for 118 ml min-1 at zero backpressure.

  4. Moho topography, ranges and folds of Tibet by analysis of global gravity models and GOCE data

    PubMed Central

    Shin, Young Hong; Shum, C.K.; Braitenberg, Carla; Lee, Sang Mook; Na, Sung -Ho; Choi, Kwang Sun; Hsu, Houtse; Park, Young-Sue; Lim, Mutaek

    2015-01-01

    The determination of the crustal structure is essential in geophysics, as it gives insight into the geohistory, tectonic environment, geohazard mitigation, etc. Here we present the latest advance on three-dimensional modeling representing the Tibetan Mohorovičić discontinuity (topography and ranges) and its deformation (fold), revealed by analyzing gravity data from GOCE mission. Our study shows noticeable advances in estimated Tibetan Moho model which is superior to the results using the earlier gravity models prior to GOCE. The higher quality gravity field of GOCE is reflected in the Moho solution: we find that the Moho is deeper than 65 km, which is twice the normal continental crust beneath most of the Qinghai-Tibetan plateau, while the deepest Moho, up to 82 km, is located in western Tibet. The amplitude of the Moho fold is estimated to be ranging from −9 km to 9 km with a standard deviation of ~2 km. The improved GOCE gravity derived Moho signals reveal a clear directionality of the Moho ranges and Moho fold structure, orthogonal to deformation rates observed by GPS. This geophysical feature, clearly more evident than the ones estimated using earlier gravity models, reveals that it is the result of the large compressional tectonic process. PMID:26114224

  5. Relevance of structural segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model.

    PubMed

    Barbosa, Marco Aurélio A; de Araújo, Antônio F Pereira

    2003-05-01

    The relevance of inside-outside segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model is probed by complete enumeration of two-dimensional chains of up to 18 monomers in the square lattice. The exact computation of Z scores for uniquely designed sequences confirms that Z tends to decrease linearly with sigma square root of N, as previously suggested by theoretical analysis and Monte Carlo simulations, where sigma, the standard deviation of the number of contacts made by different monomers in the target structure, is a measure of structural segregation and N is the chain length. The probability that the target conformation is indeed the unique global energy minimum of the designed sequence is found to increase dramatically with sigma, approaching unity at maximal segregation. However, due to the huge number of conformations with sub-maximal values of sigma, which correspond to intermediate, only mildly discriminative, values of Z, in addition to significant oscillations of Z around its estimated value, the probability that a correctly designed sequence corresponds to a maximally segregated conformation is small. This behavior of Z also explains the observed relation between sigma and different measures of folding cooperativity of correctly designed sequences.

  6. The Cenozoic structural evolution of a fold-and-thrust belt, northeastern Brooks Range, Alaska

    SciTech Connect

    Hanks, C.L. )

    1993-03-01

    A Cenozoic fold-and-thrust belt in the eastern structural province of the northeastern Brooks Range exposes polydeformed low-grade metasedimentary and metavolcanic rocks of the pre-Mississippian basement and its sedimentary cover immediately adjacent to much younger foredeep deposits. Analysis of mesoscopic and map-scale structures in the range-front region suggests that at least one pre-Mississippian deformational event was recorded into the basement sequence by north-vergent fold-and-thrust structures and associated penetrative structures. Most of later Cenozoic shortening of the pre-Mississippian rocks was accommodated by thrust duplication, with little development of penetrative mesoscopic structures. Although separated from the underlying basement rocks by a major regional decollement horizon, Cenozoic deformation in the overlying Mississippian through Lower Cretaceous cover sequence also was primarily by thrust duplication. Although local and regional structural trends within the cover sequence suggest that Cenozoic deformation was north-northwest directed, east-west Cenozoic structural trends within the pre-Mississippian rocks may reflect an inherited pre-Mississippian structural grain and/or pre-Mississippian-age structures reactivated during Cenozoic deformation. A regional balanced cross section of the eastern structural province was constructed. 29 refs., 14 figs.

  7. Strike-slip faulting in a foreland fold-thrust belt, western Salt Range, central Pakistan

    SciTech Connect

    McDougall, J.W.

    1985-01-01

    The N15W-trending Kalabagh fault zone (KFZ) is part of the Himalayan frontal fault (HFF) and is nearly orthogonal to active ENE-trending folds and thrust faults associated with Himalayan convergence. The KFZ extends 20 km north of Kalabagh village on the Indus River (NW Salt Range) before bending to the west along several north-dipping reverse faults. Quaternary low-angle thrust displacement appears to be concentrated at the HFF, especially the Salt Range frontal thrust. Siwalik conglomerate and sandstone cut by the KFZ north of the HFF may be as young as Quaternary, however, late Quaternary faulting has not been documented north of the HFF near Kalabagh village. Evidence of right-lateral strike-slip offset along the KFZ is seen in the field along the NNW-trending western edge of the Salt Range and from there north to Shakardarra village. Focal mechanism solutions of earthquakes show right-slip faulting in basement extending from the southernmost surface trace of the KFZ over 150 km farther south in the Punjab plain. Residual gravity anomalies and the strike of an abrupt change in Bouguer gravity values follow the KFZ along the western Salt Range and farther south. The sedimentary sequence exposed east of the KFZ is thought to be decoupled from basement along a detachment surface underlying much of the Potwar Plateau. West of the KFZ, a similar sedimentary sequence may be more strongly coupled to basement. Detachment surfaces involving major displacement probably ramp upsection, creating relatively complex fold and fault geometry on the west side of the KFZ.

  8. Folding mechanism of a polymer chain with short-range attractions

    NASA Astrophysics Data System (ADS)

    Leitold, Christian; Dellago, Christoph

    2014-10-01

    We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling. The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are coupled via harmonic springs, the non-neighboring monomers interact via a hard core and a short-ranged attractive potential. For a sufficiently small interaction range λ, the system undergoes a first-order freezing transition from an expanded, disordered phase to a compact crystalline state. Using a new shooting move tailored to polymers combined with a committor analysis, we study the transition state ensemble of an N = 128 chain and search for possible reaction coordinates based on likelihood maximization. We find that typical transition states consist of a crystalline nucleus with one or more chain fragments attached to it. Furthermore, we show that the number of particles in the crystalline core is not well suited as a reaction coordinate. We then present an improved reaction coordinate, which includes information from the potential energy and the overall crystallinity of the polymer.

  9. Compact silicon photonic wavelength-tunable laser diode with ultra-wide wavelength tuning range

    SciTech Connect

    Kita, Tomohiro Tang, Rui; Yamada, Hirohito

    2015-03-16

    We present a wavelength-tunable laser diode with a 99-nm-wide wavelength tuning range. It has a compact wavelength-tunable filter with high wavelength selectivity fabricated using silicon photonics technology. The silicon photonic wavelength-tunable filter with wide wavelength tuning range was realized using two ring resonators and an asymmetric Mach-Zehnder interferometer. The wavelength-tunable laser diode fabricated by butt-joining a silicon photonic filter and semiconductor optical amplifier shows stable single-mode operation over a wide wavelength range.

  10. Compact silicon photonic wavelength-tunable laser diode with ultra-wide wavelength tuning range

    NASA Astrophysics Data System (ADS)

    Kita, Tomohiro; Tang, Rui; Yamada, Hirohito

    2015-03-01

    We present a wavelength-tunable laser diode with a 99-nm-wide wavelength tuning range. It has a compact wavelength-tunable filter with high wavelength selectivity fabricated using silicon photonics technology. The silicon photonic wavelength-tunable filter with wide wavelength tuning range was realized using two ring resonators and an asymmetric Mach-Zehnder interferometer. The wavelength-tunable laser diode fabricated by butt-joining a silicon photonic filter and semiconductor optical amplifier shows stable single-mode operation over a wide wavelength range.

  11. Miocene extension and fault-related folding in the Highland Range, southern Nevada: A three-dimensional perspective

    USGS Publications Warehouse

    Faulds, J.E.; Olson, E.L.; Harlan, S.S.; McIntosh, W.C.

    2002-01-01

    The Highland Range of southern Nevada contains a major anticline and syncline that constitute the westernmost segments of the Black Mountains accommodation zone in the highly extended Colorado River extensional corridor. The folds are defined by thick tilted sections of Miocene volcanic and sedimentary strata that accumulated immediately prior to and during regional extension. The folds are generally symmetrical, with interlimb angles that exceed 90??, subhorizontal hingelines, and steeply inclined axial surfaces. East- and west-dipping normal faults dominate the west- and east-tilted limbs of the folds, respectively. The limbs of the folds are parts of major half grabens. Tilt fanning within these half grabens and 15 new 40Ar/39Ar dates bracket major extension between about 16.5 and 11 Ma. Tilting of the opposing fold limbs occurred simultaneously and was contemporaneous with extension. The anticline and syncline are therefore interpreted as fault-related extensional folds produced by the partial, along-strike overlap of oppositely dipping normal-fault systems and attendant tilt-block domains. The anticline developed between overlapping listric normal faults that dip toward one another, including the east-dipping McCullough Range and west-dipping Keyhole Canyon faults. Each limb of the anticline is a rollover fold developed in the hanging wall of the inwardly dipping listric normal faults. The syncline formed between overlapping outwardly dipping listric faults, as adjacent fault blocks were tilted toward one another. The dominant folding style was fault-bend folding, with drag-folding and displacement-gradient folding playing subsidiary roles. The anticline and syncline significantly affected depositional patterns, with synextensional units, including two major ash-flow tuffs, thinning toward the anticlinal hinge and thickening toward the synclinal hinge. The Black Mountains accommodation zone is largely composed of intersecting northwest-trending anticlines and

  12. A method to design blended rolled edges for compact range reflectors

    NASA Technical Reports Server (NTRS)

    Gupta, Inder J.; Burnside, Walter D.

    1989-01-01

    A method to design blended rolled edges for arbitrary rim shape compact range reflectors is presented. The reflectors may be center-fed or offset-fed. The method leads to rolled edges with minimal surface discontinuities. It is shown that the reflectors designed using the prescribed method can be defined analytically using simple expressions. A procedure to obtain optimum rolled edges parameter is also presented. The procedure leads to blended rolled edges that minimize the diffracted fields emanating from the junction between the paraboloid and the rolled edge surface while satisfying certain constraints regarding the reflector size and the minimum operating frequency of the system.

  13. Range-Gated Metrology: An Ultra-Compact Sensor for Dimensional Stabilization

    NASA Technical Reports Server (NTRS)

    Lay, Oliver P.; Dubovitsky, Serge; Shaddock, Daniel A.; Ware, Brent; Woodruff, Christopher S.

    2008-01-01

    Point-to-point laser metrology systems can be used to stabilize large structures at the nanometer levels required for precision optical systems. Existing sensors are large and intrusive, however, with optical heads that consist of several optical elements and require multiple optical fiber connections. The use of point-to-point laser metrology has therefore been limited to applications where only a few gauges are needed and there is sufficient space to accommodate them. Range-Gated Metrology is a signal processing technique that preserves nanometer-level or better performance while enabling: (1) a greatly simplified optical head - a single fiber optic collimator - that can be made very compact, and (2) a single optical fiber connection that is readily multiplexed. This combination of features means that it will be straightforward and cost-effective to embed tens or hundreds of compact metrology gauges to stabilize a large structure. In this paper we describe the concept behind Range-Gated Metrology, demonstrate the performance in a laboratory environment, and give examples of how such a sensor system might be deployed.

  14. Uniform GTD solution for the diffraction by metallic tapes on panelled compact-range reflectors

    NASA Technical Reports Server (NTRS)

    Somers, G. A.; Pathak, P. H.

    1992-01-01

    Metallic tape is commonly used to cover the interpanel gaps which occur in paneled compact-range reflectors. It is therefore of interest to study the effect of the scattering by the tape on the field in the target zone of the range. An analytical solution is presented for the target zone fields scattered by 2D metallic tapes. It is formulated by the generalized scattering matrix technique in conjunction with the Wiener-Hopf procedure. An extension to treat 3D tapes can be accomplished using the 2D solution via the equivalent current concept. The analytical solution is compared with a reference moment method solution to confirm the accuracy of the former.

  15. Compact MEMS mirror based Q-switch module for pulse-on-demand laser range finders

    NASA Astrophysics Data System (ADS)

    Milanović, Veljko; Kasturi, Abhishek; Atwood, Bryan; Su, Yu; Limkrailassiri, Kevin; Nettleton, John E.; Goldberg, Lew; Cole, Brian J.; Hough, Nathaniel

    2015-02-01

    A highly compact and low power consuming Q-switch module was developed based on a fast single-axis MEMS mirror, for use in eye-safe battery-powered laser range finders The module's 1.6mm x 1.6mm mirror has <99% reflectance at 1535nm wavelength and can achieve mechanical angle slew rates of over 500 rad/sec when switching the Er/Yb:Glass lasing cavity from pumping to lasing state. The design targeted higher efficiency, smaller size, and lower cost than the traditional Electro-Optical Q-Switch. Because pulse-on-demand capability is required, resonant mirrors cannot be used to achieve the needed performance. Instead, a fast point-to-point analog single-axis tilt actuator was designed with a custom-coated high reflectance (HR) mirror to withstand the high intra-cavity laser fluence levels. The mirror is bonded on top of the MEMS actuator in final assembly. A compact MEMS controller was further implemented with the capability of autonomous on-demand operation based on user-provided digital trigger. The controller is designed to receive an external 3V power supply and a digital trigger and it consumes ~90mW during the short switching cycle and ~10mW in standby mode. Module prototypes were tested in a laser cavity and demonstrated high quality laser pulses with duration of ~20ns and energy of over 3mJ.

  16. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

    PubMed

    Lieberman-Aiden, Erez; van Berkum, Nynke L; Williams, Louise; Imakaev, Maxim; Ragoczy, Tobias; Telling, Agnes; Amit, Ido; Lajoie, Bryan R; Sabo, Peter J; Dorschner, Michael O; Sandstrom, Richard; Bernstein, Bradley; Bender, M A; Groudine, Mark; Gnirke, Andreas; Stamatoyannopoulos, John; Mirny, Leonid A; Lander, Eric S; Dekker, Job

    2009-10-09

    We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  17. User manual for semi-circular compact range reflector code: Version 2

    NASA Technical Reports Server (NTRS)

    Gupta, Inder J.; Burnside, Walter D.

    1987-01-01

    A computer code has been developed at the Ohio State University ElectroScience Laboratory to analyze a semi-circular paraboloidal reflector with or without a rolled edge at the top and a skirt at the bottom. The code can be used to compute the total near field of the reflector or its individual components at a given distance from the center of the paraboloid. The code computes the fields along a radial, horizontal, vertical or axial cut at that distance. Thus, it is very effective in computing the size of the sweet spot for a semi-circular compact range reflector. This report describes the operation of the code. Various input and output statements are explained. Some results obtained using the computer code are presented to illustrate the code's capability as well as being samples of input/output sets.

  18. Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins.

    PubMed

    Selvaraj, S; Gromiha, M Michael

    2004-06-01

    Understanding the folding pathways of proteins is a challenging task. The Phi value approach provides a detailed understanding of transition-state structures of folded proteins. In this work, we have computed the hydrophobicity associated with each residue in the folded state of 16 two-state proteins and compared the Phi values of each mutant residue. We found that most of the residues with high Phi value coincide with local maximum in surrounding hydrophobicity, or have nearby residues that show such maximum in hydrophobicity, indicating the importance of hydrophobic interactions in the transition state. We have tested our approach to different structural classes of proteins, such as alpha-helical, SH3 domains of all-beta proteins, beta-sandwich, and alpha/beta proteins, and we observed a good agreement with experimental results. Further, we have proposed a hydrophobic contact network pattern to relate the Phi values with long-range contacts, which will be helpful to understand the transition-state structures of folded proteins. The present approach could be used to identify potential hydrophobic clusters that may form through long-range contacts during the transition state.

  19. Tectonic insight based on anisotropy of magnetic susceptibility and compaction studies in the Sierras Australes thrust and fold belt (southwest Gondwana boundary, Argentina)

    NASA Astrophysics Data System (ADS)

    Arzadún, Guadalupe; Tomezzoli, Renata N.; Cesaretti, Nora N.

    2016-04-01

    The Sierras Australes fold and thrust belt (Buenos Aires Province, Argentina) was in the southwestern Gondwanaland margin during the Paleozoic. The Tunas Formation (Permian) is exposed along the eastern part of it and continues eastward beneath the Claromecó Basin. Anisotropy of magnetic susceptibility (AMS) and compaction studies are described and compared with previous paleomagnetic studies with the aim of determining direction and magnitude of the main stresses acting during the sedimentation of the Tunas Formation. The anisotropy ellipsoids are triaxial with oblate or prolate shapes, reflecting different stages of layer parallel shortening during the evolution of the basin. Kmax axes trend NW-SE, parallel to the fold axes, while Kmin move from a horizontal (base) to a vertical orientation at the top of the succession, showing a change from a tectonic to almost a sedimentary fabric. The magnitude of anisotropy and compaction degree decreases toward the top of the succession. The AMS results are consistent with the outcrop structural observations and the compaction and paleomagnetic data. Regional pattern indicates a compression from the SW along this part of Gondwana, with a migration of the orogenic front and attenuation toward the NE in the foreland basin during the Upper Paleozoic. This deformation, locally assigned to the San Rafael noncollisional orogenic phase, is the result of the latitudinal movements toward the Equator of Gondwana (southern plates) and Laurentia (northern plates) during the Permian. This movement is the result of a rearrangement of the microplates that collided with Gondwana during the Late Devonian, to configure Pangea during the Triassic.

  20. Nucleosomes, Linker DNA, and Linker Histone form a Unique Structural Motif that Directs the Higher-Order Folding and Compaction of Chromatin

    NASA Astrophysics Data System (ADS)

    Bednar, Jan; Horowitz, Rachel A.; Grigoryev, Sergei A.; Carruthers, Lenny M.; Hansen, Jeffrey C.; Koster, Abraham J.; Woodcock, Christopher L.

    1998-11-01

    The compaction level of arrays of nucleosomes may be understood in terms of the balance between the self-repulsion of DNA (principally linker DNA) and countering factors including the ionic strength and composition of the medium, the highly basic N termini of the core histones, and linker histones. However, the structural principles that come into play during the transition from a loose chain of nucleosomes to a compact 30-nm chromatin fiber have been difficult to establish, and the arrangement of nucleosomes and linker DNA in condensed chromatin fibers has never been fully resolved. Based on images of the solution conformation of native chromatin and fully defined chromatin arrays obtained by electron cryomicroscopy, we report a linker histone-dependent architectural motif beyond the level of the nucleosome core particle that takes the form of a stem-like organization of the entering and exiting linker DNA segments. DNA completes ≈ 1.7 turns on the histone octamer in the presence and absence of linker histone. When linker histone is present, the two linker DNA segments become juxtaposed ≈ 8 nm from the nucleosome center and remain apposed for 3-5 nm before diverging. We propose that this stem motif directs the arrangement of nucleosomes and linker DNA within the chromatin fiber, establishing a unique three-dimensional zigzag folding pattern that is conserved during compaction. Such an arrangement with peripherally arranged nucleosomes and internal linker DNA segments is fully consistent with observations in intact nuclei and also allows dramatic changes in compaction level to occur without a concomitant change in topology.

  1. Evaluation of thrusting and folding of the Deadman Creek Thrust Fault, Sangre de Cristo range, Saguache County, Colorado

    NASA Astrophysics Data System (ADS)

    Weigel, Jacob F., II

    The Deadman Creek Thrust Fault was mapped in a structural window on the west side of the Sangre de Cristo Range. The study area, located in southern Colorado, is a two square mile area halfway between the town of Crestone and the Great Sand Dunes National Park. The Deadman Creek Thrust Fault is the center of this study because it delineates the fold structure in the structural window. The fault is a northeast-directed low-angle thrust folded by subsequent additional compression. This study was directed at understanding the motion of the Deadman Creek Thrust Fault as affected by subsequent folding, and the driving mechanism behind the folding of the Pole Creek Anticline as part of a broader study of Laramide thrust faulting in the range. This study aids in the interpretation of the geologic structure of the San Luis Valley, which is being studied by staff of the United States Geological Survey (USGS), to understand Rio Grande Rift basin evolution by focusing on rift and pre-rift tectonic activity. It also provides a geologic interpretation for the Saguache County Forest Service, Great Sand Dunes National Park, and its visitors. The Sangre de Cristo Mountain Range has undergone tectonic events in the Proterozoic, Pennsylvanian (Ancestral Rocky Mountains), Cretaceous-Tertiary (Laramide Orogeny) and mid-Tertiary (Rio Grande Rift). During the Laramide Orogeny the Deadman Creek Thrust Fault emplaced Proterozoic gneiss over Paleozoic sedimentary rocks and Proterozoic granodiorite in the area. Continued deformation resulted in folding of the fault to form the Pole Creek Anticline. The direction of motion of both the fault and fold is northeastward. A self-consistent net of cross-sections and stereonet plots generated from existing and new field data show that the anticline is an overturned isoclinal fold in Pole Creek Canyon, which shows an increasing inter-limb angle and a more vertical axial surface northwestward toward Deadman Creek Canyon. Southwest-directed apparent

  2. A compact, short-pulse laser for near-field, range-gated imaging

    SciTech Connect

    Zutavern, F.J.; Helgeson, W.D.; Loubriel, G.M.; Yates, G.J.; Gallegos, R.A.; McDonald, T.E.

    1996-12-31

    This paper describes a compact laser, which produces high power, wide-angle emission for a near-field, range-gated, imaging system. The optical pulses are produced by a 100 element laser diode array (LDA) which is pulsed with a GaAs, photoconductive semiconductor switch (PCSS). The LDA generates 100 ps long, gain-switched, optical pulses at 904 nm when it is driven with 3 ns, 400 A, electrical pulses from a high gain PCSS. Gain switching is facilitated with this many lasers by using a low impedance circuit to drive an array of lasers, which are connected electrically in series. The total optical energy produced per pulse is 10 microjoules corresponding to a total peak power of 100 kW. The entire laser system, including prime power (a nine volt battery), pulse charging, PCSS, and LDA, is the size of a small, hand-held flashlight. System lifetime, which is presently limited by the high gain PCSS, is an active area of research and development. Present limitations and potential improvements will be discussed. The complete range-gated imaging system is based on complementary technologies: high speed optical gating with intensified charge coupled devices (ICCD) developed at Los Alamos National Laboratory (LANL) and high gain, PCSS-driven LDAs developed at Sandia National Laboratories (SNL). The system is designed for use in highly scattering media such as turbid water or extremely dense fog or smoke. The short optical pulses from the laser and high speed gating of the ICCD are synchronized to eliminate the back-scattered light from outside the depth of the field of view (FOV) which may be as short as a few centimeters. A high speed photodiode can be used to trigger the intensifier gate and set the range-gated FOV precisely on the target. The ICCD and other aspects of the imaging system are discussed in a separate paper.

  3. Planar near-field scanning for compact range bistatic radar cross-section measurement. Thesis Final Report

    NASA Technical Reports Server (NTRS)

    Tuhela-Reuning, S. R.; Walton, E. K.

    1991-01-01

    The design, construction, and testing of a low cost, planar scanning system to be used in a compact range environment for bistatic radar cross-section (bistatic RCS) measurement data are discussed. This scanning system is similar to structures used for measuring near-field antenna patterns. A synthetic aperture technique is used for plane wave reception. System testing entailed comparison of measured and theoretical bistatic RCS of a sphere and a right circular cylinder. Bistatic scattering analysis of the ogival target support, target and pedestal interactions, and compact range room was necessary to determine measurement validity.

  4. Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif.

    PubMed

    Guzzo, Cristiane R; Nagem, Ronaldo A P; Barbosa, João A R G; Farah, Chuck S

    2007-11-15

    The YaeQ family of proteins are found in many Gram-negative and a few Gram-positive bacteria. We have determined the first structure of a member of the YaeQ family by X-ray crystallography. Comparisons with other structures indicate that YaeQ represents a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif found in type II endonucleases and enzymes involved in DNA replication, repair, and recombination. We show that catalytically important residues in the PD-(D/E)XK nuclease superfamily are spatially conserved in YaeQ and other highly conserved YaeQ residues may be poised to interact with nucleic acid structures.

  5. Extreme Folding

    NASA Astrophysics Data System (ADS)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  6. Mechanics of the Salt Range-Potwar Plateau, Pakistan: A fold-and-thrust belt underlain by evaporites

    NASA Astrophysics Data System (ADS)

    Jaumé, Steven C.; Lillie, Robert J.

    1988-02-01

    The Salt Range and Potwar Plateau are part of the active foreland fold-and-thrust belt of the Himalaya in northern Pakistan. In this region the distance from the Main Boundary Thrust (MBT) to the front of the fold-and-thrust belt is very wide (100-150 km) because a thick evaporite sequence forms the zone of décollement. Recent studies have combined seismic reflection profiles, petroleum exploration wells, Bouguer gravity anomalies, and surface geology to construct cross sections in the eastern, central, and western Salt Range-Potwar Plateau areas. In this study the sections are compared with a model that considers the mechanics of a fold-and-thrust belt to be analogous to that of a wedge of snow or soil pushed in front of a bulldozer (Chapple, 1978; Davis et al., 1983; Dahlen et al., 1984; Dahlen, 1984). Models which include the effects of evaporites at the base (Chapple, 1978; Davis and Engelder, 1985) suggest that these thrust belts will have (1) narrow (< 1°) cross-sectional tapers, (2) larger widths than areas not underlain by evaporites, (3) symmetrical structures, and (4) changes in deformational style at the edge of the evaporite basin. The section across the eastern Potwar Plateau most closely resembles this latter model, having (1) a taper of 0.8° ± 0.1°, (2) a width of 100-150 km, (3) thrust faults that verge both to the north and south, and (4) structures rotated 30° counterclockwise with respect to the Salt Range. From the observed taper and pore fluid pressures of the eastern Potwar Plateau, estimates of the values for the yield strength of the evaporites (τo) and the coefficient of internal friction of the overlying wedge (μ) are calculated as τo = 1.33-1.50 MPa and μ = 0.95-1.04, which are then applied to the other cross sections. In the central and western sections a basement uplift, the Sargodha High, interferes with the front of the fold-and-thrust belt. This feature causes the ramping of the Salt Range Thrust and produces a relatively

  7. Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes.

    PubMed

    Ferreira, Diogo C; van der Linden, Marx G; de Oliveira, Leandro C; Onuchic, José N; de Araújo, Antônio F Pereira

    2016-04-01

    Recent ab initio folding simulations for a limited number of small proteins have corroborated a previous suggestion that atomic burial information obtainable from sequence could be sufficient for tertiary structure determination when combined to sequence-independent geometrical constraints. Here, we use simulations parameterized by native burials to investigate the required amount of information in a diverse set of globular proteins comprising different structural classes and a wide size range. Burial information is provided by a potential term pushing each atom towards one among a small number L of equiprobable concentric layers. An upper bound for the required information is provided by the minimal number of layers L(min) still compatible with correct folding behavior. We obtain L(min) between 3 and 5 for seven small to medium proteins with 50 ≤ Nr ≤ 110 residues while for a larger protein with Nr = 141 we find that L ≥ 6 is required to maintain native stability. We additionally estimate the usable redundancy for a given L ≥ L(min) from the burial entropy associated to the largest folding-compatible fraction of "superfluous" atoms, for which the burial term can be turned off or target layers can be chosen randomly. The estimated redundancy for small proteins with L = 4 is close to 0.8. Our results are consistent with the above-average quality of burial predictions used in previous simulations and indicate that the fraction of approachable proteins could increase significantly with even a mild, plausible, improvement on sequence-dependent burial prediction or on sequence-independent constraints that augment the detectable redundancy during simulations.

  8. Strike-slip faulting in a foreland fold-thrust belt: The Kalabaugh fault and western Salt range, Pakistan

    NASA Astrophysics Data System (ADS)

    McDougall, James W.; Khan, Shahid Hasan

    1990-10-01

    The 120-km-long Kalabagh fault zone is formed by transpressive right-lateral strike-slip along the western Salt Range-Potwar Plateau allochthon in northern Pakistan. Lateral ramping from a decollement thrust along an Eocambrian evaporite layer produced NNW- to NW-trending folds and NE- to N-dipping thrust faults in a topographically emergent zone up to 10 km wide. Piercing points along the main Kalabagh fault indicate 12-14 km of middle to late Quaternary right-lateral offset. The older right-lateral Surghar fault displaced axes of frontal folds of the eastern Surghar Range by 4-5 km. Total displacement is reduced northward in the Kalabagh fault zone where north-dipping thrust faults splay to the west. Cumulative right-slip offset in the Kalabagh fault zone is comparable to displacement along the Salt Range frontal thrust, at a minimum average displacement rate of 7-10 mm/year near the Indus River since 2 Ma. In the basement, which dips 2-3° north along the Kalabagh fault, a NNW-trending discontinuous ridge beneath the lateral ramp is interpreted from residual gravity anomalies. The eastern flank of this basement ridge probably ramped allochthonous strata upward from a depth of over 5 km in the Kalabagh fault zone. Kalabagh faulting displaced and uplifted Holocene terrace deposits and shifted the course of the Indus River eastward. A high slip rate and associated seismicity indicate that the Kalabagh fault zone should be considered active and capable of earthquakes.

  9. Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques

    NASA Astrophysics Data System (ADS)

    Bystricky, Kerstin; Heun, Patrick; Gehlen, Lutz; Langowski, Jörg; Gasser, Susan M.

    2004-11-01

    Little is known about how chromatin folds in its native state. Using optimized in situ hybridization and live imaging techniques have determined compaction ratios and fiber flexibility for interphase chromatin in budding yeast. Unlike previous studies, ours examines nonrepetitive chromatin at intervals short enough to be meaningful for yeast chromosomes and functional domains in higher eukaryotes. We reconcile high-resolution fluorescence in situ hybridization data from intervals of 14-100 kb along single chromatids with measurements of whole chromosome arms (122-623 kb in length), monitored in intact cells through the targeted binding of bacterial repressors fused to GFP derivatives. The results are interpreted with a flexible polymer model and suggest that interphase chromatin exists in a compact higher-order conformation with a persistence length of 170-220 nm and a mass density of 110-150 bp/nm. These values are equivalent to 7-10 nucleosomes per 11-nm turn within a 30-nm-like fiber structure. Comparison of long and short chromatid arm measurements demonstrates that chromatin fiber extension is also influenced by nuclear geometry. The observation of this surprisingly compact chromatin structure for transcriptionally competent chromatin in living yeast cells suggests that the passage of RNA polymerase II requires a very transient unfolding of higher-order chromatin structure. higher-order structure | 30-nm fiber | nucleosomes

  10. The Gogebic Iron Range - A Sample of the Northern Margin of the Penokean Fold and Thrust Belt

    USGS Publications Warehouse

    Cannon, William F.; LaBerge, Gene L.; Klasner, John S.; Schulz, Klaus J.

    2008-01-01

    The Gogebic iron range is an elongate belt of Paleoproterozoic strata extending from the west shore of Lake Gogebic in the upper peninsula of Michigan for about 125 km westward into northern Wisconsin. It is one of six major informally named iron ranges in the Lake Superior region and produced about 325 million tons of direct-shipping ore between 1887 and 1967. A significant resource of concentrating-grade ore remains in the western and eastern parts of the range. The iron range forms a broad, gently southward-opening arc where the central part of the range exposes rocks that were deposited somewhat north of the eastern and western parts. A fundamental boundary marking both the tectonic setting of deposition and the later deformation within the Penokean orogen lies fortuitously in an east-west direction along the range so that the central part of the range preserves sediments deposited north of that boundary, whereas the eastern and western parts of the range were deposited south of the boundary. Thus, the central part of the range provides a record of sedimentation and very mild deformation in a part of the Penokean orogen farthest from the interior of the orogen to the south. The eastern and western parts of the range, in contrast, exhibit a depositional and deformational style typical of parts closer to the interior of the orogen. A second fortuitous feature of the iron range is that the entire area was tilted from 40° to 90° northward by Mesoproterozoic deformation so that the map view offers an oblique cross section of the Paleoproterozoic sedimentary sequence and structures. Together, these features make the Gogebic iron range a unique area in which to observe (1) the lateral transition from deposition on a stable platform to deposition in a tectonically and volcanically active region, and (2) the transition from essentially undeformed Paleoproterozoic strata to their folded and faulted equivalents.Paleoproterozoic strata in the Gogebic iron range are part

  11. Seismic images of the Brooks Range fold and thrust belt, Arctic Alaska, from an integrated seismic reflection/refraction experiment

    USGS Publications Warehouse

    Levander, A.; Fuis, G.S.; Wissinger, E.S.; Lutter, W.J.; Oldow, J.S.; Moore, T.E.

    1994-01-01

    We describe results of an integrated seismic reflection/refraction experiment across the Brooks Range and flanking geologic provinces in Arctic Alaska. The seismic acquisition was unusual in that reflection and refraction data were collected simultaneously with a 700 channel seismograph system deployed numerous times along a 315 km profile. Shot records show continuous Moho reflections from 0-180 km offset, as well as numerous upper- and mid-crustal wide-angle events. Single and low-fold near-vertical incidence common midpoint (CMP) reflection images show complex upper- and middle-crustal structure across the range from the unmetamorphosed Endicott Mountains allochthon (EMA) in the north, to the metamorphic belts in the south. Lower-crustal and Moho reflections are visible across the entire reflection profile. Travel-time inversion of PmP arrivals shows that the Moho, at 33 km depth beneath the North Slope foothills, deepens abruptly beneath the EMA to a maximum of 46 km, and then shallows southward to 35 km at the southern edge of the range. Two zones of upper- and middle-crustal reflections underlie the northern Brooks Range above ~ 12-15 km depth. The upper zone, interpreted as the base of the EMA, lies at a maximum depth of 6 km and extends over 50 km from the range front to the north central Brooks Range where the base of the EMA outcrops above the metasedimentary rocks exposed in the Doonerak window. We interpret the base of the lower zone, at ~ 12 km depth, to be from carbonate rocks above the master detachment upon which the Brooks Range formed. The seismic data suggest that the master detachment is connected to the faults in the EMA by several ramps. In the highly metamorphosed terranes south of the Doonerak window, the CMP section shows numerous south-dipping events which we interpret as a crustal scale duplex involving the Doonerak window rocks. The basal detachment reflections can be traced approximately 100 km, and dip southward from about 10-12 km

  12. Long range Trp-Trp interaction initiates the folding pathway of a pro-angiogenic β-hairpin peptide

    NASA Astrophysics Data System (ADS)

    Diana, Donatella; De Rosa, Lucia; Palmieri, Maddalena; Russomanno, Anna; Russo, Luigi; La Rosa, Carmelo; Milardi, Danilo; Colombo, Giorgio; D'Andrea, Luca D.; Fattorusso, Roberto

    2015-11-01

    HPLW, a designed VEGF (Vascular Endothelium Growth Factor) receptor-binding peptide, assumes a well folded β-hairpin conformation in water and is able to induce angiogenesis in vivo. In this study, we investigated at atomic resolution the thermal folding/unfolding pathway of HPLW by means of an original multi-technique approach combining DSC, NMR, MD and mutagenesis analyses. In particular, careful NMR investigation of the single proton melting temperatures together with DSC analysis accurately delineate the peptide folding mechanism, which is corroborated by computational folding/unfolding simulations. The HPLW folding process consists of two main events, which are successive but do not superimpose. The first folding step initiates at 320 K upon the hydrophobic collapse of the Trp5 and Trp13 side-chains which stabilizes the concurrent β-turn formation, whose COi-HNi + 3 hydrogen bond (Asp10 → Arg7) appears particularly stable. At 316 K, once the β-turn is completely formed, the two β-strands pair, very likely starting by Trp5 and Trp13, which thus play a key role also in the final step of the β-hairpin folding. Overall, here we describe a multi-state hierarchical folding pathway of a highly structured β-hairpin, which can be classified as a broken-zipper mechanism.

  13. Long range Trp-Trp interaction initiates the folding pathway of a pro-angiogenic β-hairpin peptide

    PubMed Central

    Diana, Donatella; De Rosa, Lucia; Palmieri, Maddalena; Russomanno, Anna; Russo, Luigi; La Rosa, Carmelo; Milardi, Danilo; Colombo, Giorgio; D’Andrea, Luca D.; Fattorusso, Roberto

    2015-01-01

    HPLW, a designed VEGF (Vascular Endothelium Growth Factor) receptor-binding peptide, assumes a well folded β-hairpin conformation in water and is able to induce angiogenesis in vivo. In this study, we investigated at atomic resolution the thermal folding/unfolding pathway of HPLW by means of an original multi-technique approach combining DSC, NMR, MD and mutagenesis analyses. In particular, careful NMR investigation of the single proton melting temperatures together with DSC analysis accurately delineate the peptide folding mechanism, which is corroborated by computational folding/unfolding simulations. The HPLW folding process consists of two main events, which are successive but do not superimpose. The first folding step initiates at 320 K upon the hydrophobic collapse of the Trp5 and Trp13 side-chains which stabilizes the concurrent β-turn formation, whose COi-HNi + 3 hydrogen bond (Asp10 → Arg7) appears particularly stable. At 316 K, once the β-turn is completely formed, the two β-strands pair, very likely starting by Trp5 and Trp13, which thus play a key role also in the final step of the β-hairpin folding. Overall, here we describe a multi-state hierarchical folding pathway of a highly structured β-hairpin, which can be classified as a broken-zipper mechanism. PMID:26602442

  14. The influence of age, anthropometrics and range of motion on the morphometry of the synovial folds of the lateral atlanto-axial joints: a pilot study.

    PubMed

    Webb, Alexandra; Darekar, Angela; Rassoulian, Hamid

    2011-04-01

    The purpose of this study was to investigate the effect of age, anthropometrics and cervical range of motion upon synovial fold volume. Ten healthy female subjects aged 20-40 years were included in the study. Age, height, body mass, dimensions of the head and neck and cervical range of motion of each subject were measured. Magnetic resonance (MR) images of the cervical spine were acquired; the volume of the ventral and dorsal synovial folds of the right and the left lateral atlanto-axial joints was measured using seed growing and thresholding methods. Using Spearman's correlation coefficient, it was determined that there was no correlation between synovial fold volume and age. Synovial fold volume was positively correlated with subject height and neck length but negatively correlated with body mass, body mass index and the circumference of the head and neck. The relationship between synovial fold volume and range of cervical motion varied with the plane of movement. The ability to image the synovial folds of the lateral atlanto-axial joints using MR imaging to determine their normal morphology provides the basis for investigating synovial fold pathology in patients with neck pain and headache.

  15. Association of deformation and fluid events in the central Brooks Range fold-and-thrust belt, Northern Alaska

    USGS Publications Warehouse

    Moore, Thomas E.; Potter, Christopher J.; O'Sullivan, Paul B.; Shelton, Kevin L.; Underwood, Michael B.

    2003-01-01

    Ocentral Brooks Range consists of two superposed north-directed contractional orogens, one formed between 140-120 Ma and the other at ~60-45 Ma. The older orogen was an arc-continent collisional zone characterized by far-traveled allochthons and relatively low structural relief. The younger orogen is a retroarc thrust belt with relatively low amounts of shortening and high structural relief. Folding and thrusting of the younger episode is superimposed on the thin-skinned deformational wedge of the earlier orogen and also produced a frontal triangle zone in a thick sequence of mid-Cretaceous foreland basin sediments to the north. Stable isotope compositions of calcite and quartz veins indicate two fluid events including: (1) an earlier, higher-temperature (~250-300° C) event that produced veins in deformed Devonian clastic rocks, and (2) a younger, lower-temperature (~150° C) event that deposited veins in deformed Mississippian through Albian strata. The fluids in the first event had variable d18O values, but nearly constant d13C values buffered by limestone lithologies. The vein-forming fluids in the second event had similarly variable d18O values, but with distinctly lower d13C values as a result of oxidation of organic matter and/or methane. Zircon fission track ages demonstrate cooling to temperatures below 200° C between 140-120 Ma for the Devonian rocks, whereas zircon and apatite fission track ages show that Mississippian to Albian rocks were never heated above 200° C and cooled below 110-90° C at ~60-45 Ma. These data are interpreted as indicating that the older, high-temperature fluid event was active during thrusting at 120-140 Ma, and the younger fluid event during deformation at ~60-45 Ma. The data and results presented in this poster will be published in early 2004 in Moore and others (in press).

  16. Geometrical optics design of a compact range Gregorian subreflector system by the principle of the central ray

    NASA Technical Reports Server (NTRS)

    Clerici, Giancarlo; Burnside, Walter D.

    1989-01-01

    In recent years, the compact range has become very popular for measuring Radar Cross Section (RCS) and antenna patterns. The compact range, in fact, offers several advantages due to reduced size, a controlled environment, and privacy. On the other hand, it has some problems of its own, which must be solved properly in order to achieve high quality measurement results. For example, diffraction from the edges of the main reflector corrupts the plane wave in the target zone and creates spurious scattering centers in RCS measurements. While diffraction can be minimized by using rolled edges, the field of an offset single reflector compact range is corrupted by three other errors: the taper of the reflected field, the cross polarization introduced by the tilt of the feed and the aperture blockage introduced by the feed itself. These three errors can be eliminated by the use of a subreflector system. A properly designed subreflector system offers very little aperture blockage, no cross-polarization introduced and a minimization of the taper of the reflected field. A Gregorian configuration has been adopted in order to enclose the feed and the ellipsoidal subreflector in a lower chamber, which is isolated by absorbers from the upper chamber, where the main parabolic reflector and the target zone are enclosed. The coupling between the two rooms is performed through a coupling aperture. The first cut design for such a subreflector system is performed through Geometrical Optics ray tracing techniques (GO), and is greatly simplified by the use of the concept of the central ray introduced by Dragone. The purpose of the GO design is to establish the basic dimensions of the main reflector and subreflector, the size of the primary and secondary illuminating surfaces, the tilt angles of the subreflector and feed, and estimate the feed beamwidth. At the same time, the shape of the coupling aperture is initially determined.

  17. PBL dynamic measurements with new compact long range wind Lidar WINDCUBE WLS70

    NASA Astrophysics Data System (ADS)

    Cariou, J.; Sauvage, L.; Lolli, S.; Parmentier, R.; Boquet, M.; Loaec, S.

    2008-12-01

    The WindCube WLS70 is a new generation wind Lidar developed by LEOSPHERE for meteorological applications. The Lidar is derived from the commercial WindCube widely used for autonomous and very accurate short range measurements by the wind industry. It has been modified increasing the range up to 4 km and can even detect cirrus at 8km. First results of the measurement campaign which took place in Orsay, France in August 2008 put in evidence both vertical wind speed and atmosphere structure (PBL height , clouds top and base) derived from Lidar data with good time resolution (30s per profile), good range resolution (50m from 100m to 4000m), and good velocity resolution (0.2m/s). These measurement data play a key role in many meteorological applications, and can be used as input for forecast mathematical models.

  18. A Compact 3D Omnidirectional Range Sensor of High Resolution for Robust Reconstruction of Environments

    PubMed Central

    Marani, Roberto; Renò, Vito; Nitti, Massimiliano; D'Orazio, Tiziana; Stella, Ettore

    2015-01-01

    In this paper, an accurate range sensor for the three-dimensional reconstruction of environments is designed and developed. Following the principles of laser profilometry, the device exploits a set of optical transmitters able to project a laser line on the environment. A high-resolution and high-frame-rate camera assisted by a telecentric lens collects the laser light reflected by a parabolic mirror, whose shape is designed ad hoc to achieve a maximum measurement error of 10 mm when the target is placed 3 m away from the laser source. Measurements are derived by means of an analytical model, whose parameters are estimated during a preliminary calibration phase. Geometrical parameters, analytical modeling and image processing steps are validated through several experiments, which indicate the capability of the proposed device to recover the shape of a target with high accuracy. Experimental measurements show Gaussian statistics, having standard deviation of 1.74 mm within the measurable range. Results prove that the presented range sensor is a good candidate for environmental inspections and measurements. PMID:25621605

  19. The role of Precambrian rock compositions and fabrics on the structural development of a large foreland fold, southern Front Range, Colorado

    SciTech Connect

    Clarey, T.L.; Chase, R.B. . Dept. of Geology)

    1994-04-01

    Royal Gorge arch is a south-plunging, eastward asymmetrical, broad foreland fold. Precambrian lithologies occupy more than 50 km[sup 2] of the fold core and vary considerably from amphibolite-grade quartzofeldspathic, migmatitic gneiss on the south to poorly foliated to massive granodioritic gneiss on the north. The boundary between these two lithologies is marked by abundant and fairly concordant granitic pegmatites, and a change in fold style from broad folding in the northern sector to tighter folding to the south. Cover rocks are broadly arched carbonates, arenites, and lutites ranging in age from Ordovician to Late Cretaceous. Based on foliation patterns, basement rocks can be divided into seven homogeneous, cylindrical domains. Jointing appears strongly controlled by the foliation patterns. Joints and foliations in each domain show rotation in the same direction and magnitude with respect to other domains. The pattern of jointing in three sedimentary domains changes from flank to flank and does not match jointing in the Precambrian core, except in the unfoliated sectors. The sedimentary domains do not show the same sense of rotation as basement domains and basement joint clusters. These differences in deformation of the sedimentary cover reflect heterogeneous folding in response to fabric differences in the adjacent basement rocks. Analysis of slickenlines indicates that a non-uniform stress field developed within the Precambrian basement. Stresses apparently refracted through the core of the uplift, with refraction directions traceable across domain boundaries.

  20. Curved fold-and-thrust accretion during the extrusion of a synorogenic viscous allochthonous sheet: The Estepa Range (External Zones, Western Betic Cordillera, Spain)

    NASA Astrophysics Data System (ADS)

    Pedrera, Antonio; MaríN-Lechado, Carlos; Martos-Rosillo, Sergio; RoldáN, Francisco Javier

    2012-08-01

    New structural, borehole, and time domain electromagnetic data allow us to reconstruct the 3-D geometry of the Estepa range (External Zones of the Western Betic Cordillera), which constitutes an isolated curved fold-and-thrust range made up of Jurassic shallow marine carbonates and Cretaceous to Paleocene marls and marly limestones. Contraction and rising load linked to the accretion of the Subbetic nappe enhanced the expulsion of Triassic evaporites and overpressured clays during the early and middle Miocene, finally forming part of a highly deformed mélange unit. This plastic extrusion favored the disconnection of External and Middle Subbetic blocks, including the Sierra de Estepa Range. There, deformation is characterized by northwest-vergent curved folds-and-thrusts associated with NE-SW frontal ramps and NW-SE lateral transfer faults that segmented the folds active between 18 and 12 Ma. At a local scale, curvature was achieved under a nearly uniform NW/WNW transport direction suggesting a primary arc type. Friction variation across the heterogeneous detached plastic basal Triassic unit mainly controlled the curvature and segmentation of the fold systems. Transport direction is consistent with previously published slip data from the Internal Subbetic and the Campo de Gibraltar units. After the Late Serravallian, accretion slowed down and a shallow marine unit deposited unconformably placed over the main thrust and folds. The sequence of deformation and emplacement of these ranges is interpreted as a continuous process linked to the early Miocene E continental collision of the Iberian margin thin continental crust and subduction of the Flysch trough oceanic crust beneath the Alboran continental domain.

  1. Evolution of fold-thrust belts and Cenozoic uplifting of the South Tianshan Mountain range in the Kuqa region, Northwest China

    NASA Astrophysics Data System (ADS)

    Wen, Lei; Li, Yue-Jun; Zhang, Guang-Ya; Tian, Zuo-Ji; Peng, Geng-Xin; Qiu, Bin; Huang, Zhi-Bin; Luo, Jun-Cheng; Zhang, Qiang

    2017-03-01

    The evolution of the Kuqa fold-thrust belt is accompanied with the Cenozoic uplifting of South Tianshan Mountain range. The critical Coubomb wedge theory can be well applied to the structural evolution of the Kuqa fold-thrust belt where the décollement structures are well developed. Following the initial hypotheses of this theory, with the base of the taper wedge (not the sea level) as the reference level, we propose a geometric relationship between the evolution of fold-thrust belt and tectonic uplifting of orogen, and deduce a calculation formula between orogen tectonic uplifting amount (very different from the topographic uplifting) (∂H), fold-thrust belt extending distance (∂S) and crustal shortening amount (∂L): ∂H = (∂S - ∂L) ∗ tan(α + ∂α) + [tan(α + ∂α)/tanα - 1] ∗ H0. In this paper we select two representative seismic profiles across the Kuqa fold-thrust belt to reconstruct the structural evolution, and use the calculation formula to get the uplifting amount of the South Tianshan Mountain range in Kuqa region during two geological periods. The results showed: during the end of Miocene to the end of Pliocene, the uplifting amount of the South Tianshan Mountain range in the middle segment of Kuqa (∂HM1) is 4.1 km; during the end of Pliocene to the present, the uplifting amount of the South Tianshan Mountain range in the middle segment of Kuqa (∂HM2) is 4.7 km, and in the east segment of Kuqa (∂HE) is 5.0 km.

  2. First observation of SASE radiation using the compact wide-spectral-range XUV spectrometer at FLASH2

    NASA Astrophysics Data System (ADS)

    Tanikawa, T.; Hage, A.; Kuhlmann, M.; Gonschior, J.; Grunewald, S.; Plönjes, E.; Düsterer, S.; Brenner, G.; Dziarzhytski, S.; Braune, M.; Brachmanski, M.; Yin, Z.; Siewert, F.; Dzelzainis, T.; Dromey, B.; Prandolini, M. J.; Tavella, F.; Zepf, M.; Faatz, B.

    2016-09-01

    The Free-electron LASer in Hamburg (FLASH) has been extended with a new undulator line FLASH2 in 2014. A compact grazing-incident wide-spectral-range spectrometer based on spherical-variable-line-spacing (SVLS) gratings in the extreme ultraviolet (XUV) region was constructed to optimize and characterize the free-electron laser (FEL) performance at FLASH2. The spectrometer is equipped with three different concave SVLS gratings covering a spectral range from 1 to 62 nm to analyze the spectral characteristics of the XUV radiation. Wavelength calibration and evaluation of the spectral resolution were performed at the plane grating monochromator beamline PG2 at FLASH1 before the installation at FLASH2, and compared with analytical simulations. The first light using self-amplified spontaneous emission from FLASH2 was observed by the spectrometer during a simultaneous operation of both undulator lines-FLASH1 and FLASH2. In addition, the spectral resolution of the spectrometer was evaluated by comparing the measured spectrum from FLASH2 with FEL simulations.

  3. Ultra-compact and wide-spectrum-range thermo-optic switch based on silicon coupled photonic crystal microcavities

    SciTech Connect

    Zhang, Xingyu E-mail: swapnajit.chakravarty@omegaoptics.com Chung, Chi-Jui; Pan, Zeyu; Yan, Hai; Chakravarty, Swapnajit E-mail: swapnajit.chakravarty@omegaoptics.com; Chen, Ray T. E-mail: swapnajit.chakravarty@omegaoptics.com

    2015-11-30

    We design, fabricate, and experimentally demonstrate a compact thermo-optic gate switch comprising a 3.78 μm-long coupled L0-type photonic crystal microcavities on a silicon-on-insulator substrate. A nanohole is inserted in the center of each individual L0 photonic crystal microcavity. Coupling between identical microcavities gives rise to bonding and anti-bonding states of the coupled photonic molecules. The coupled photonic crystal microcavities are numerically simulated and experimentally verified with a 6 nm-wide flat-bottom resonance in its transmission spectrum, which enables wider operational spectrum range than microring resonators. An integrated micro-heater is in direct contact with the silicon core to efficiently drive the device. The thermo-optic switch is measured with an optical extinction ratio of 20 dB, an on-off switching power of 18.2 mW, a thermo-optic tuning efficiency of 0.63 nm/mW, a rise time of 14.8 μs, and a fall time of 18.5 μs. The measured on-chip loss on the transmission band is as low as 1 dB.

  4. Fault propagation folds induced by gravitational failure and slumping of the Central Costa Rica volcanic range - Implications for large terrestrial and Martian volcanic edifices

    NASA Technical Reports Server (NTRS)

    Borgia, Andrea; Burr, Jeremiah; Montero, Walter; Morales, Luis Diego; Alvarado, Guillermo E.

    1990-01-01

    Maps are presented that describe the compressional tectonic structures found at the base of the Central Costa Rica volcanic range (CCRVR), which comprise thrust faults and related fault propagation folds, only partly covered by syntectonic and posttectonic volcanoclastic deposits. Evidence is presented that these structures formed by gravitational failure and lumping of the flanks of the volcanic range. It is suggested that similar structures may be found at the toe of the southern flank of Kilauea volcano, Hawaii, and along the perimeter scarp of the Olympus Mons volcano on Mars.

  5. Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome

    PubMed Central

    Dejardin, Stephanie; Allemand, Frederic; Gamot, Adrien; Labesse, Gilles; Cuvier, Olivier; Nègre, Nicolas; Cohen-Gonsaud, Martin; Margeat, Emmanuel; Nöllmann, Marcelo

    2014-01-01

    Chromatin insulators are genetic elements implicated in the organization of chromatin and the regulation of transcription. In Drosophila, different insulator types were characterized by their locus-specific composition of insulator proteins and co-factors. Insulators mediate specific long-range DNA contacts required for the three dimensional organization of the interphase nucleus and for transcription regulation, but the mechanisms underlying the formation of these contacts is currently unknown. Here, we investigate the molecular associations between different components of insulator complexes (BEAF32, CP190 and Chromator) by biochemical and biophysical means, and develop a novel single-molecule assay to determine what factors are necessary and essential for the formation of long-range DNA interactions. We show that BEAF32 is able to bind DNA specifically and with high affinity, but not to bridge long-range interactions (LRI). In contrast, we show that CP190 and Chromator are able to mediate LRI between specifically-bound BEAF32 nucleoprotein complexes in vitro. This ability of CP190 and Chromator to establish LRI requires specific contacts between BEAF32 and their C-terminal domains, and dimerization through their N-terminal domains. In particular, the BTB/POZ domains of CP190 form a strict homodimer, and its C-terminal domain interacts with several insulator binding proteins. We propose a general model for insulator function in which BEAF32/dCTCF/Su(HW) provide DNA specificity (first layer proteins) whereas CP190/Chromator are responsible for the physical interactions required for long-range contacts (second layer). This network of organized, multi-layer interactions could explain the different activities of insulators as chromatin barriers, enhancer blockers, and transcriptional regulators, and suggest a general mechanism for how insulators may shape the organization of higher-order chromatin during cell division. PMID:25165871

  6. The Long-Range P3 Helix of the Tetrahymena Ribozyme Is Disrupted During Folding Between the Native and Misfolded Conformations

    PubMed Central

    Mitchell, David; Jarmoskaite, Inga; Seval, Nikhil; Seifert, Soenke; Russell, Rick

    2013-01-01

    RNAs are prone to misfolding, but how misfolded structures are formed and resolved remains incompletely understood. The Tetrahymena group I intron ribozyme folds in vitro to a long-lived misfolded conformation (M) that includes extensive native structure but is proposed to differ in topology from the native state (N). A leading model predicts that exchange of the topologies requires unwinding of the long-range, core helix P3, despite the presence of P3 in both conformations. To test this model, we constructed sixteen mutations to strengthen or weaken P3. Catalytic activity and in-line probing showed that nearly all of the mutants form the M state before folding to N. The P3-weakening mutations accelerated refolding from M (3–30-fold) and the P3-strengthening mutations slowed refolding (6–1400-fold), suggesting that P3 indeed unwinds transiently. Upon depletion of Mg2+, the mutations had analogous effects on unfolding from N to intermediates that subsequently fold to M. The magnitudes for the P3-weakening mutations were larger than in refolding from M, and small angle X-ray scattering showed that the ribozyme expands rapidly to intermediates from which P3 is disrupted subsequently. These results are consistent with previous results indicating unfolding of native peripheral structure during refolding from M, which probably permits rearrangement of the core. Together, our results demonstrate that exchange of the native and misfolded conformations requires loss of a core helix in addition to peripheral structure. Further, the results strongly suggest that misfolding arises from a topological error within the ribozyme core, and a specific topology is proposed. PMID:23702292

  7. The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations.

    PubMed

    Mitchell, David; Jarmoskaite, Inga; Seval, Nikhil; Seifert, Soenke; Russell, Rick

    2013-08-09

    RNAs are prone to misfolding, but how misfolded structures are formed and resolved remains incompletely understood. The Tetrahymena group I intron ribozyme folds in vitro to a long-lived misfolded conformation (M) that includes extensive native structure but is proposed to differ in topology from the native state (N). A leading model predicts that exchange of the topologies requires unwinding of the long-range, core helix P3, despite the presence of P3 in both conformations. To test this model, we constructed 16 mutations to strengthen or weaken P3. Catalytic activity and in-line probing showed that nearly all of the mutants form the M state before folding to N. The P3-weakening mutations accelerated refolding from M (3- to 30-fold) and the P3-strengthening mutations slowed refolding (6- to 1400-fold), suggesting that P3 indeed unwinds transiently. Upon depletion of Mg(2+), the mutations had analogous effects on unfolding from N to intermediates that subsequently fold to M. The magnitudes for the P3-weakening mutations were larger than in refolding from M, and small-angle X-ray scattering showed that the ribozyme expands rapidly to intermediates from which P3 is disrupted subsequently. These results are consistent with previous results indicating unfolding of native peripheral structure during refolding from M, which probably permits rearrangement of the core. Together, our results demonstrate that exchange of the native and misfolded conformations requires loss of a core helix in addition to peripheral structure. Further, the results strongly suggest that misfolding arises from a topological error within the ribozyme core, and a specific topology is proposed.

  8. Cenozoic thrust emplacement of a Devonian batholith, northeastern Brooks Range: Involvement of crystalline rocks in a foreland fold-and-thrust belt

    NASA Astrophysics Data System (ADS)

    Hanks, Catherine L.; Wallace, Wesley K.

    1990-05-01

    Involvement of crystalline rocks in thrusting near the foreland basin of a fold-and-thrust belt is relatively uncommon. In the northeastern Brooks Range, the Devonian Okpilak batholith was thrust northward and structurally elevated above adjacent foreland basin deposits during Cenozoic fold-and-thrust deformation. The batholith may have acted initially as a regional structural buttress, but a drop in the basal detachment surface to greater depth south of the batholith resulted in northward transport of the batholith. Shortening within the batholith was accommodated by (1) the development of discrete thrust slices bounded by ductile shear zones, (2) simple shear and development of penetrative mesoscopic and microscopic fabrics throughout the batholith, or both. The Mississippian Kayak Shale, a regional detachment horizon at the base of the overlying cover sequence, is depositionally thin or absent adjacent to the batholith. Thus, most of the cover sequence remained structurally coupled to the batholith during thrusting and was shortened by the development of penetrative structures.

  9. Microsecond subdomain folding in dihydrofolate reductase.

    PubMed

    Arai, Munehito; Iwakura, Masahiro; Matthews, C Robert; Bilsel, Osman

    2011-07-08

    The characterization of microsecond dynamics in the folding of multisubdomain proteins has been a major challenge in understanding their often complex folding mechanisms. Using a continuous-flow mixing device coupled with fluorescence lifetime detection, we report the microsecond folding dynamics of dihydrofolate reductase (DHFR), a two-subdomain α/β/α sandwich protein known to begin folding in this time range. The global dimensions of early intermediates were monitored by Förster resonance energy transfer, and the dynamic properties of the local Trp environments were monitored by fluorescence lifetime detection. We found that substantial collapse occurs in both the locally connected adenosine binding subdomain and the discontinuous loop subdomain within 35 μs of initiation of folding from the urea unfolded state. During the fastest observable ∼550 μs phase, the discontinuous loop subdomain further contracts, concomitant with the burial of Trp residue(s), as both subdomains achieve a similar degree of compactness. Taken together with previous studies in the millisecond time range, a hierarchical assembly of DHFR--in which each subdomain independently folds, subsequently docks, and then anneals into the native conformation after an initial heterogeneous global collapse--emerges. The progressive acquisition of structure, beginning with a continuously connected subdomain and spreading to distal regions, shows that chain entropy is a significant organizing principle in the folding of multisubdomain proteins and single-domain proteins. Subdomain folding also provides a rationale for the complex kinetics often observed.

  10. Quantitation of Teriflunomide in Human Serum/Plasma Across a 40,000-Fold Concentration Range by LC/MS/MS.

    PubMed

    Rule, Geoffrey S; Rockwood, Alan L; Johnson-Davis, Kamisha L

    2016-01-01

    Leflunomide is a prodrug used primarily for treatment of rheumatoid arthritis. The active metabolite, teriflunomide (A77 1726), inhibits the enzyme dihydroorotate dehydrogenase and thereby reduces the synthesis of pyrimidine ribonucleotides. Teriflunomide is also administered directly and finds use in treating multiple sclerosis. Therapeutic concentrations are generally in the tens of μg/mL serum or plasma and, due to adverse effects and the time required to reach steady state, therapeutic drug monitoring is beneficial. The drug is also a potential teratogen. A method was developed and validated to quantify the drug teriflunomide over a 40,000-fold concentration range of 5 ng/mL to 200 μg/mL in serum or plasma. This is accomplished by dividing the quantitative range into two separate but overlapping regions; a high curve and a low curve range. Samples are evaluated first against the high curve after a 100-fold dilution of the sample extract. Samples falling below the upper curve region are evaluated again without dilution and quantified, if possible, against the low curve calibration standards. Appropriate choice of a concentration for the deuterated internal standard (D4-teriflunomide) allows for a single, identical, extraction procedure to be performed for both curve regions but with the dilution performed for high curve samples. The method is rugged and reliable with good accuracy and precision statistics.

  11. Bistatic image processing for a 32 x 19 inch model aircraft using scattered fields obtained in the OSU-ESL compact range

    NASA Technical Reports Server (NTRS)

    Lee, T-H.; Burnside, W. D.

    1992-01-01

    Inverse Synthetic Aperture Radar (ISAR) images for a 32 in long and 19 in wide model aircraft are documented. Both backscattered and bistatic scattered fields of this model aircraft were measured in the OSU-ESL compact range to obtain these images. The scattered fields of the target were measured for frequencies from 2 to 18 GHz with a 10 MHz increment and for full 360 deg azimuth rotation angles with a 0.2 deg step. For the bistatic scattering measurement, the compact range was used as the transmitting antenna; while, a broad band AEL double ridge horn was used as the receiving antenna. Bistatic angles of 90 deg and 135 deg were measured. Due to the size of the chamber and target, the receiving antenna was in the near field of the target; nevertheless, the image processing algorithm was valid for this case.

  12. Folding Beauties

    ERIC Educational Resources Information Center

    Berman, Leah Wrenn

    2006-01-01

    This article has its genesis in an MAA mini-course on origami, where a way to get a parabola by folding paper was presented. This article discusses the methods and mathematics of other curves obtained by paper-folding.

  13. Evaluation of microdosing strategies for studies in preclinical drug development: demonstration of linear pharmacokinetics in dogs of a nucleoside analog over a 50-fold dose range.

    PubMed

    Sandhu, Punam; Vogel, John S; Rose, Mark J; Ubick, Esther A; Brunner, Janice E; Wallace, Michael A; Adelsberger, Jennifer K; Baker, Maribeth P; Henderson, Paul T; Pearson, Paul G; Baillie, Thomas A

    2004-11-01

    The technique of accelerator mass spectrometry (AMS) was validated successfully and used to study the pharmacokinetics and disposition in dogs of a preclinical drug candidate (7-deaza-2'-C-methyl-adenosine; Compound A), after oral and intravenous administration. The primary objective of this study was to examine whether Compound A displayed linear kinetics across subpharmacological (microdose) and pharmacological dose ranges in an animal model, before initiation of a human microdose study. The AMS-derived disposition properties of Compound A were comparable to data obtained via conventional techniques such as liquid chromatography-tandem mass spectrometry and liquid scintillation counting analyses. Compound A displayed multiphasic kinetics and exhibited low plasma clearance (5.8 ml/min/kg), a long terminal elimination half-life (17.5 h), and high oral bioavailability (103%). Currently, there are no published comparisons of the kinetics of a pharmaceutical compound at pharmacological versus subpharmacological doses using microdosing strategies. The present study thus provides the first description of the full pharmacokinetic profile of a drug candidate assessed under these two dosing regimens. The data demonstrated that the pharmacokinetic properties of Compound A following dosing at 0.02 mg/kg were similar to those at 1 mg/kg, indicating that in the case of Compound A, the pharmacokinetics in the dog appear to be linear across this 50-fold dose range. Moreover, the exceptional sensitivity of AMS provided a pharmacokinetic profile of Compound A, even after a microdose, which revealed aspects of the disposition of this agent that were inaccessible by conventional techniques.

  14. Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.

    PubMed

    Welty, Robb; Hall, Kathleen B

    2016-11-06

    The tertiary structure of the GTPase center (GAC) of 23S ribosomal RNA (rRNA) as seen in cocrystals is extremely compact. It is stabilized by long-range hydrogen bonds and nucleobase stacking and by a triloop that forms within its three-way junction. Its folding pathway from secondary structure to tertiary structure has not been previously observed, but it was shown to require Mg(2+) ions in equilibrium experiments. The fluorescent nucleotide 2-aminopurine was substituted at selected sites within the 60-nt GAC. Fluorescence intensity changes upon addition of MgCl2 were monitored over a time-course from 1ms to 100s as the RNA folds. The folding pathway is revealed here to be hierarchical through several intermediates. Observation of the nucleobases during folding provides a new perspective on the process and the pathway, revealing the dynamics of nucleobase conformational exchange during the folding transitions.

  15. Folding of apominimyoglobin.

    PubMed Central

    De Sanctis, G; Ascoli, F; Brunori, M

    1994-01-01

    The acid unfolding pathway of apominimyoglobin (apo-mini-Mb), a 108-aa fragment (aa 32-139) of horse heart apomyoglobin has been studied by means of circular dichroism, in comparison with the native apoprotein. Similar to sperm whale apomyoglobin [Hughson, F. M., Wright, P. E. & Baldwin, R. L. (1990) Science 249, 1544-1548], a partly folded intermediate (alpha-helical content approximately 35%) is populated at pH 4.2 for horse heart apomyoglobin. For this intermediate, Hughson et al. proposed a structural model with a compact subdomain involving tertiary interactions between the folded A, G, and H helices, with the remainder of the protein essentially unfolded. As described in this paper, a folding intermediate with an alpha-helical content of approximately 33% is populated at pH 4.3-5.0 also in apo-mini-Mb. The acid unfolding pathway is similarly affected in both the native and the mini apoprotein by 15% trifluoroethanol, a helix-stabilizing compound. Thus, the folding of the apo-mini-Mb intermediate is similar to that observed for the native apoprotein, in spite of the absence in the miniprotein of the A helix and of a large part of the H helix, which are crucial for the stability of apo-Mb intermediate. Our results suggest that acquisition of a folded state in apo-mini-Mb occurs through an alternative pathway, which may or may not be shared also by apo-Mb. PMID:7972092

  16. Compact field programmable gate array (FPGA)-based multi-axial interferometer for simultaneous tilt and distance measurement in the sub-nanometre range

    NASA Astrophysics Data System (ADS)

    Strube, Sebastian; Molnar, Gabor; Danzebrink, Hans-Ulrich

    2011-09-01

    Quantitative determination of microstructure and nanostructure properties is essential in research, development and in control of the production process. In instruments for dimensional nanometrology the positioning stage is the key component, since the characteristics of the position acquisition and control determine directly the achievable precision of the complete system. Compact commercial positioning systems usually employ capacitive or inductive position sensors. Both technologies not only offer a resolution in the nanometre range, but also require a (periodic) calibration. To achieve traceable measurements, interferometric sensors need to be implemented into the metrology system. However, currently available commercial interferometers turned out to be too large to be installed in miniature positioning stages easily. Therefore, a new highly compact interferometer to allow for traceability and an uncertainty in the Ångstrom range was developed. One of its first applications will be the new metrological low-noise atomic force microscope at the Physikalisch-Technische Bundesanstalt. The new interferometer is based on a modified homodyne Twyman-Green interferometer concept. It uses a novel signal processing approach based on a field programmable gate array, whereby a spatial interferogram is acquired by a high-speed CMOS line sensor and transformed into its frequency spectrum through a discrete Fourier transform. The spectral representation is analyzed for its major components; the phase information bears a direct connection to the displacement of the positioning unit. Furthermore, a possible stage tilt during the scan gives rise to a shift of the peak magnitude in the frequency spectrum. In addition, the developed system proved to be easily extendable to multiple axes by superimposing multiple interferograms on a single line sensor.

  17. Evaluation Of Microdosing Strategies For Studies In Preclinical Drug Development: Demonstration Of Linear Pharmacokinetics In Dogs Of A Nucleoside Analogue Over A 50-Fold Dose Range

    SciTech Connect

    Sandhu, P; Vogel, J S; Rose, M J; Ubick, E A; Brunner, J E; Wallace, M A; Adelsberger, J K; Baker, M P; Henderson, P T; Pearson, P G; Baillie, T A

    2004-04-22

    The technique of accelerator mass spectrometry (AMS) was validated successfully and utilized to study the pharmacokinetics and disposition in dogs of a preclinical drug candidate (Compound A), after oral and intravenous administration. The primary objective of this study was to examine whether Compound A displayed linear kinetics across sub-pharmacological (microdose) and pharmacological dose ranges in an animal model, prior to initiation of a human microdose study. The AMS-derived disposition properties of Compound A were comparable to data obtained via conventional techniques such as LC-MS/MS and liquid scintillation counting analyses. Thus, Compound A displayed multiphasic kinetics and possessed low plasma clearance (4.4 mL/min/kg), a long terminal elimination half-life (19.4 hr) and high oral bioavailability (82%). Currently there are no published comparisons of the kinetics of a pharmaceutical compound at pharmacological versus sub-pharmacological doses employing microdosing strategies. The present study thus provides the first description of the pharmacokinetics of a drug candidate assessed under these two dosing regimens. The data demonstrated that the pharmacokinetic properties of Compound A were similar following dosing at 0.02 mg/kg as at 1 mg/kg, indicating that in the case of Compound A, the kinetics of absorption, distribution and elimination in the dog appear to be linear across this 50-fold dose range. Moreover, the exceptional sensitivity of AMS provided a pharmacokinetic profile of Compound A, even following a microdose, which revealed aspects of the disposition of this agent that were inaccessible by conventional techniques. The applications of accelerator mass spectrometry (AMS) are broad ranging and vary from studying environmental and ecological issues such as the isotopic composition of the atmosphere, soil and water (Hughen et al., 2000; Beck et al., 2001; Keith-Roach et al., 2001; Mironov et al., 2002), to archaeology and volcanology

  18. Dynamics and function of compact nucleosome arrays.

    PubMed

    Poirier, Michael G; Oh, Eugene; Tims, Hannah S; Widom, Jonathan

    2009-09-01

    The packaging of eukaryotic DNA into chromatin sterically occludes polymerases, recombinases and repair enzymes. How chromatin structure changes to allow their actions is unknown. We constructed defined fluorescently labeled trinucleosome arrays, allowing analysis of chromatin conformational dynamics via fluorescence resonance energy transfer (FRET). The arrays undergo reversible Mg2+-dependent folding similar to that of longer arrays studied previously. We define two intermediate conformational states in the reversible folding of the nucleosome arrays and characterize the microscopic rate constants. Nucleosome arrays are highly dynamic even when compact, undergoing conformational fluctuations on timescales in the second to microsecond range. Compact states of the arrays allow binding to DNA within the central nucleosome via site exposure. Protein binding can also drive decompaction of the arrays. Thus, our results reveal multiple modes by which spontaneous chromatin fiber dynamics allow for the invasion and action of DNA-processing protein complexes.

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

    PubMed

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

    2014-12-31

    RNA hairpins play a pivotal role in a diverse range of cellular functions, and are integral components of ribozymes, mRNA, and riboswitches. However, the mechanistic and kinetic details of RNA hairpin folding, which are key determinants of most of its biological functions, are poorly understood. In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic detail. Our results show that the potential energy landscapes have a distinct funnel-like bias toward the folded hairpin state, consistent with efficient structure-seeking properties. Mechanistic and kinetic information is analyzed in terms of kinetic transition networks. We find microsecond folding times, consistent with temperature jump experiments, for hairpin folding initiated from relatively compact unfolded states. This process is essentially driven by an initial collapse, followed by rapid zippering of the helix stem in the final phase. Much lower folding rates are predicted when the folding is initiated from extended chains, which undergo longer excursions on the energy landscape before nucleation events can occur. Our work therefore explains recent experiments and coarse-grained simulations, where the folding kinetics exhibit precisely this dependency on the initial conditions.

  20. A repeated-measures analysis of the effects of soft tissues on wrist range of motion in the extant phylogenetic bracket of dinosaurs: Implications for the functional origins of an automatic wrist folding mechanism in Crocodilia.

    PubMed

    Hutson, Joel David; Hutson, Kelda Nadine

    2014-07-01

    A recent study hypothesized that avian-like wrist folding in quadrupedal dinosaurs could have aided their distinctive style of locomotion with semi-pronated and therefore medially facing palms. However, soft tissues that automatically guide avian wrist folding rarely fossilize, and automatic wrist folding of unknown function in extant crocodilians has not been used to test this hypothesis. Therefore, an investigation of the relative contributions of soft tissues to wrist range of motion (ROM) in the extant phylogenetic bracket of dinosaurs, and the quadrupedal function of crocodilian wrist folding, could inform these questions. Here, we repeatedly measured wrist ROM in degrees through fully fleshed, skinned, minus muscles/tendons, minus ligaments, and skeletonized stages in the American alligator Alligator mississippiensis and the ostrich Struthio camelus. The effects of dissection treatment and observer were statistically significant for alligator wrist folding and ostrich wrist flexion, but not ostrich wrist folding. Final skeletonized wrist folding ROM was higher than (ostrich) or equivalent to (alligator) initial fully fleshed ROM, while final ROM was lower than initial ROM for ostrich wrist flexion. These findings suggest that, unlike the hinge/ball and socket-type elbow and shoulder joints in these archosaurs, ROM within gliding/planar diarthrotic joints is more restricted to the extent of articular surfaces. The alligator data indicate that the crocodilian wrist mechanism functions to automatically lock their semi-pronated palms into a rigid column, which supports the hypothesis that this palmar orientation necessitated soft tissue stiffening mechanisms in certain dinosaurs, although ROM-restricted articulations argue against the presence of an extensive automatic mechanism. Anat Rec, 297:1228-1249, 2014. © 2014 Wiley Periodicals, Inc.

  1. A compact laser target designator

    NASA Astrophysics Data System (ADS)

    Lee, S. T.; Silver, M.; Barron, A.; Borthwick, A.; Morton, G.; McRae, I.; Coghill, M.; Smith, C.; Scouler, C.; Gardiner, G.; Imlach, N.; McNeill, C.; McSporran, D.; Rodgers, D.; Kerr, D.; Alexander, W.

    2016-05-01

    Lasers intended for application to man-portable and hand-held laser target designators are subject to significant constraints on size, weight, power consumption and cost. These constraints must be met while maintaining adequate performance across a challenging environmental specification. One of the challenges of operating a Nd3+:YAG laser over a broad ambient temperature range is that of diode-pump-tuning. This system is specified to operate over an ambient temperature range of -46°C to +71°C, and the system electrical power consumption requirements preclude active temperature control. As a result the laser must tolerate a 32.8nm pump wavelength range. The optical absorption of Nd3+:YAG varies dramatically over this wavelength range. This paper presents a laser that minimizes the effect of this change on laser output. A folded U-shaped geometry laser resonator is presented, made up of a corner cube at one end and a plane mirror substrate at the other. The action of the corner cube coupled with this configuration of end mirrors results in a resonator that is significantly less sensitive to misalignment of the end mirror and/or the corner cube. This Ushaped resonator is then further folded to fit the laser into a smaller volume. Insensitivity of this compact folded resonator to mirror misalignments was analyzed in Zemax via a Monte-Carlo analysis and the results of this analysis are presented. The resulting laser output energy, pulse duration and beam quality of this athermally pumped, misalignment insensitive folded laser resonator are presented over an ambient temperature range of -46°C to +71°C.

  2. Folding above faults, Rocky Mountains

    SciTech Connect

    McConnell, D.A. . Dept. of Geology)

    1992-01-01

    Asymmetric folds formed above basement faults can be observed throughout the Rocky Mountains. Several previous interpretations of the folding process made the implicit assumption that one or both fold hinges migrated or rolled'' through the steep forelimb of the fold as the structure evolved (rolling hinge model). Results of mapping in the Bighorn and Seminoe Mountains, WY, and Sangre de Cristo Range, CO, do not support this hypothesis. An alternative interpretation is presented in which fold hinges remained fixed in position during folding (fixed hinge model). Mapped folds share common characteristics: (1) axial traces of the folds intersect faults at or near the basement/cover interface, and diverge from faults upsection; (2) fold hinges are narrow and interlimb angles cluster around 80--100[degree] regardless of fold location; (3) fold shape is typically angular, despite published cross sections that show concentric folds; and, (4) beds within the folds show thickening and/or thinning, most commonly adjacent to fold hinges. The rolling hinge model requires that rocks in the fold forelimbs bend through narrow fold hinges as deformation progressed. Examination of massive, competent rock units such as the Ord. Bighorn Dolomite, Miss. Madison Limestone, and, Penn. Tensleep Sandstone reveals no evidence of the extensive internal deformation that would be expected if hinges rolled through rocks of the forelimb. The hinges of some folds (e.g. Golf Creek anticline, Bighorn Mountains) are offset by secondary faults, effectively preventing the passage of rocks from backlimb to forelimb. The fixed hinge model proposes that the fold hinges were defined early in fold evolution, and beds were progressively rotated and steepened as the structure grew.

  3. A compact representation for the auditory full-range response and its fast denoising using an image filter based on the Radon transform.

    PubMed

    Kohl, Manuel C; Strauss, Daniel J; Kohl, Manuel C; Strauss, Daniel J; Strauss, Daniel J; Kohl, Manuel C

    2016-08-01

    The Auditory Brainstem, Middle-Latency and Late Responses, a class of event-related potentials (ERPs), are of considerable interest in neuroscience research as robust neural correlates of different processing stages along the auditory pathway. While most research to date centers around one of the responses at a time for practical reasons, recent efforts indicate a paradigm shift towards acquiring them together, enabling the simultaneous monitoring of all auditory processing stages from the brainstem to the cortex. In this paper, we introduce a compact representation for this Auditory Full-Range Response (AFRR) as an ERP map with adaptive sampling rate, making it suitable for computationally inexpencive image filtering. Furthermore, we propose a novel algorithm for the fast denoising of such ERP maps based on the Radon Transform and its inversion by filtered backprojection. Its performance is compared qualitatively to a Gaussian means filter using a real-world chirp-evoked AFRR recording. The algorithm exhibits good noise suppression as well as high preservance of the single-response structure, making it a promising denoising tool for future ERP studies.

  4. An initial measurement of a fast neutral spectrum for ion cyclotron range of frequency heated plasma using two-channel compact neutral particle analyzers in KSTAR

    NASA Astrophysics Data System (ADS)

    Kim, S. H.; Wang, S. J.; Park, M.; Kim, S. K.

    2013-11-01

    The accurate measurement of fast neutral particles from high energy ion tails is very important since it is a measure of ion cyclotron range of frequency (ICRF) or neutral beam (NB) ion heating. In KSTAR, fast neutral measurements have been carried out using a compact neutral particle analyzer based on the silicon photo diode since 2010. As a result, the fast neutral spectrum was observed consistent with the ion temperature, diamagnetic energy, and neutron flux in 2011. However, there was fast neutral count beyond the injected neutral beam energy in NB-only heating. Since it is difficult to expect the count unless the temperature is high enough to diffuse the fast ions beyond the beam energy it was required to identify what it is. During the 2012 campaign, the two-channel diode detectors with and without a particle stopper were used to distinguish fast neutral counts and other counts by a hard X-ray or neutrons. As a result, it was confirmed that the high energy component beyond the beam energy originated from a hard X-ray or neutrons. Finally, it was observed that faster neutrals are generated by ICRF heating and enhanced by electron cyclotron heating compared to NB-only heating.

  5. An initial measurement of a fast neutral spectrum for ion cyclotron range of frequency heated plasma using two-channel compact neutral particle analyzers in KSTAR

    SciTech Connect

    Kim, S. H.; Park, M.; Kim, S. K.; Wang, S. J.

    2013-11-15

    The accurate measurement of fast neutral particles from high energy ion tails is very important since it is a measure of ion cyclotron range of frequency (ICRF) or neutral beam (NB) ion heating. In KSTAR, fast neutral measurements have been carried out using a compact neutral particle analyzer based on the silicon photo diode since 2010. As a result, the fast neutral spectrum was observed consistent with the ion temperature, diamagnetic energy, and neutron flux in 2011. However, there was fast neutral count beyond the injected neutral beam energy in NB-only heating. Since it is difficult to expect the count unless the temperature is high enough to diffuse the fast ions beyond the beam energy it was required to identify what it is. During the 2012 campaign, the two-channel diode detectors with and without a particle stopper were used to distinguish fast neutral counts and other counts by a hard X-ray or neutrons. As a result, it was confirmed that the high energy component beyond the beam energy originated from a hard X-ray or neutrons. Finally, it was observed that faster neutrals are generated by ICRF heating and enhanced by electron cyclotron heating compared to NB-only heating.

  6. Atmospheric Boundary Layer and Clouds wind speed profile measurements with the new compact long range wind Lidar WindCube(TM) WLS70

    NASA Astrophysics Data System (ADS)

    Boquet, M.; Cariou, J. P.; Sauvage, L.; Lolli, S.; Parmentier, R.; Loaec, S.

    2009-04-01

    To fully understand atmospheric dynamics, climate studies, energy transfer, and weather prediction the wind field is one of the most important atmospheric state variables. Small scales variability and low atmospheric layers are not described with sufficient resolution up to now. To answer these needs, the WLS70 long-range wind Lidar is a new generation of wind Lidars developed by LEOSPHERE, derived from the commercial WindCube™ Lidar widely used by the wind power industry and well-known for its great accuracy and data availability. The WLS70 retrieves the horizontal and vertical wind speed profiles as well as the wind direction at various heights simultaneously inside the boundary layer and cloud layers. The amplitude and spectral content of the backscattering signal are also available. From raw data, the embedded signal processing software performs the computation of the aerosol Doppler shift and backscattering coefficient. Higher values of normalized relative backscattering (NRB) are proportional to higher aerosol concentration. At 1540 nm, molecular scattering being negligible, it is then possible to directly retrieve the Boundary Layer height evolution observing the height at which the WindCube NRB drops drastically. In this work are presented the results of the measurements obtained during the LUAMI campaign that took place in Lindenberg, at the DWD (Deutscher WetterDienst) meteorological observatory, from November 2008 to January 2009. The WLS70 Lidar instrument was placed close together with an EZ Lidar™ ALS450, a rugged and compact eye safe aerosol Lidar that provides a real time measurement of backscattering and extinction coefficients, aerosol optical depth (AOD), automatic detection of the planetary boundary layer (PBL) height and clouds base and top from 100m up to more than 20km. First results put in evidence wind shear and veer phenomena as well as strong convective effects during the raise of the mixing layer or before rain periods. Wind speed

  7. On the polymer physics origins of protein folding thermodynamics

    NASA Astrophysics Data System (ADS)

    Taylor, Mark P.; Paul, Wolfgang; Binder, Kurt

    2016-11-01

    A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.

  8. On the polymer physics origins of protein folding thermodynamics.

    PubMed

    Taylor, Mark P; Paul, Wolfgang; Binder, Kurt

    2016-11-07

    A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.

  9. All-or-none folding of a polymer in confinement

    NASA Astrophysics Data System (ADS)

    Taylor, Mark

    A flexible homopolymer chain with sufficiently short-range interactions undergoes a discontinuous transition from an expanded coil to a compact crystallite analogous to the all-or-none folding transition exhibited by fast-folding proteins. One anticipates that geometric confinement will reduce the entropy of the unfolded chain, thereby stabilizing the folded state and shifting the transition to higher temperature. In this work we study a flexible square-well N-mer chain (monomer diameter d) located between two hard walls forming a slit-like pore (width W) with the chain end-tethered to one wall. We carry out Monte simulations with Wang-Landau sampling to construct the single-chain density of states and use both microcanonical and canonical analyses to characterize phase transitions. When the slit width is similar to the size of the folded chain we observe a modest stabilization effect. Further reduction of the slit width geometrically prohibits the chain from folding into the free-chain ground state. However, a discontinuous all-or-none folding transition still occurs to a flattened crystallite that spans the pore. All-or-none folding persists even to the limit of a very narrow pore (W d) where the ground-state structure is a quasi-two-dimensional crystal. Funding: NSF DMR-1204747.

  10. Mesoscale Modeling of Chromatin Folding

    NASA Astrophysics Data System (ADS)

    Schlick, Tamar

    2009-03-01

    Eukaryotic chromatin is the fundamental protein/nucleic acid unit that stores the genetic material. Understanding how chromatin fibers fold and unfold in physiological conditions is important for interpreting fundamental biological processes like DNA replication and transcription regulation. Using a mesoscopic model of oligonucleosome chains and tailored sampling protocols, we elucidate the energetics of oligonucleosome folding/unfolding and the role of each histone tail, linker histones, and divalent ions in regulating chromatin structure. The resulting compact topologies reconcile features of the zigzag model with straight linker DNAs with the solenoid model with bent linker DNAs for optimal fiber organization and reveal dynamic and energetic aspects involved.

  11. Multiscale anisotropy controlled by folding: the example of the Chaudrons fold (Corbières, France)

    NASA Astrophysics Data System (ADS)

    Louis, Laurent; Robion, Philippe; David, Christian; Frizon de Lamotte, Dominique

    2006-04-01

    In this paper, anisotropies developed in silicoclastic continental deposits during the building of the Chaudrons anticline (Corbières, France) are studied. A microstructural analysis of the deformational features in three different panels within the fold (crest, hinge, and forelimb, respectively) is reported and compared with early field observations (distribution and orientation of cleavage) and laboratory measurements (estimation of magnetic and acoustic anisotropies). The main finding of this investigation is the preservation of unwelded joints between grains of calcite promoted by the presence of quartz grains. These joints, which appear as discontinuities in a matrix of calcite, are analyzed in orientation and composition. In the three panels of the fold that are investigated, a range of dip angles is observed with at least two major generations of joints, the average orientation of which is found to be consistent with both macroscopic cleavage and magnetic and acoustic fabrics. To account for the multimodal distribution of the joints orientation, we suggest an original scenario in which they are successively generated by sets. Two processes have operated simultaneously during the development of the fold: (1) horizontal rock mass compaction inducing pressure solution and twinning in calcite; (2) preservation of unwelded calcite/calcite grain joints due to stress heterogeneities associated with quartz inclusions. From these results, we suggest that microstructural processes are the same before and during folding, ruling out a passive shearing of cleavage plane formed during a first step of layer parallel shortening.

  12. Electrostatic origin of salt-induced nucleosome array compaction.

    PubMed

    Korolev, Nikolay; Allahverdi, Abdollah; Yang, Ye; Fan, Yanping; Lyubartsev, Alexander P; Nordenskiöld, Lars

    2010-09-22

    The physical mechanism of the folding and unfolding of chromatin is fundamentally related to transcription but is incompletely characterized and not fully understood. We experimentally and theoretically studied chromatin compaction by investigating the salt-mediated folding of an array made of 12 positioning nucleosomes with 177 bp repeat length. Sedimentation velocity measurements were performed to monitor the folding provoked by addition of cations Na(+), K(+), Mg(2+), Ca(2+), spermidine(3+), Co(NH(3))(6)(3+), and spermine(4+). We found typical polyelectrolyte behavior, with the critical concentration of cation needed to bring about maximal folding covering a range of almost five orders of magnitude (from 2 μM for spermine(4+) to 100 mM for Na(+)). A coarse-grained model of the nucleosome array based on a continuum dielectric description and including the explicit presence of mobile ions and charged flexible histone tails was used in computer simulations to investigate the cation-mediated compaction. The results of the simulations with explicit ions are in general agreement with the experimental data, whereas simple Debye-Hückel models are intrinsically incapable of describing chromatin array folding by multivalent cations. We conclude that the theoretical description of the salt-induced chromatin folding must incorporate explicit mobile ions that include ion correlation and ion competition effects.

  13. Two-state protein-like folding of a homopolymer chain

    NASA Astrophysics Data System (ADS)

    Taylor, Mark P.; Paul, Wolfgang; Binder, Kurt

    Many small proteins fold via a first-order 'all-or-none' transition directly from an expanded coil to a compact native state. Here we study an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple flexible homopolymer. Wang-Landau sampling is used to construct the 1D density of states for square-well chains of length 128. Analysis within both the micro-canonical and canonical ensembles shows that, for a chain with sufficiently short-range interactions, the usual polymer collapse transition is preempted by a direct freezing or 'folding' transition. A 2D free-energy landscape, built via subsequent multi-canonical sampling, reveals a dominant folding pathway over a single free-energy barrier. This barrier separates a high entropy ensemble of unfolded states from a low entropy set of crystallite states and the transition proceeds via the formation of a transition-state folding nucleus. Despite the non-unique homopolymer ground state, the thermodynamics of this direct freezing transition are identical to the thermodynamics of two-state protein folding. The model chain satisfies the van't Hoff calorimetric criterion for two-state folding and an Arrhenius analysis of the folding/unfolding free energy barrier yields a Chevron plot characteristic of small proteins.

  14. VIBRATION COMPACTION

    DOEpatents

    Hauth, J.J.

    1962-07-01

    A method of compacting a powder in a metal container is described including the steps of vibrating the container at above and below the resonant frequency and also sweeping the frequency of vibration across the resonant frequency several times thereby following the change in resonant frequency caused by compaction of the powder. (AEC)

  15. Compact dimension of denatured states of staphylococcal nuclease.

    PubMed

    Chow, C-Y; Wu, Ming-Chya; Fang, Huey-Jen; Hu, Chin-Kun; Chen, Hueih-Min; Tsong, Tian-Yow

    2008-08-15

    Fluorescence and circular dichroism stopped-flow have been widely used to determine the kinetics of protein folding including folding rates and possible folding pathways. Yet, these measurements are not able to provide spatial information of protein folding/unfolding. Especially, conformations of denatured states cannot be elaborated in detail. In this study, we apply the method of fluorescence energy transfer with a stopped-flow technique to study global structural changes of the staphylococcal nuclease (SNase) mutant K45C, where lysine 45 is replaced by cysteine, during folding and unfolding. By labeling the thiol group of cysteine with TNB (5,5'-dithiobis-2-nitrobenzoic acid) as an energy acceptor and the tryptophan at position 140 as a donor, distance changes between the acceptor and the donor during folding and unfolding are measured from the efficiency of energy transfer. Results indicate that the denatured states of SNase are highly compact regardless of how the denatured states (pH-induced or GdmCl-induced) are induced. The range of distance changes between two probes is between 25.6 and 25.4 A while it is 20.4 A for the native state. Furthermore, the folding process consists of three kinetic phases while the unfolding process is a single phase. These observations agree with our previous sequential model: N(0) left arrow over right arrow D(1) left arrow over right arrow D(2) left arrow over right arrow D(3) (Chen et al., J Mol Biol 1991;220:771-778). The efficiency of protein folding may be attributed to initiating the folding process from these compact denatured structures.

  16. Folded dielectric elastomer actuators

    NASA Astrophysics Data System (ADS)

    Carpi, Federico; Salaris, Claudio; DeRossi, Danilo

    2007-04-01

    Polymer-based linear actuators with contractile ability are currently demanded for several types of applications. Within the class of dielectric elastomer actuators, two basic configurations are available today for such a purpose: the multi-layer stack and the helical structure. The first consists of several layers of elementary planar actuators stacked in series mechanically and parallel electrically. The second configuration relies on a couple of helical compliant electrodes alternated with a couple of helical dielectrics. The fabrication of both these configurations presents some specific drawbacks today, arising from the peculiarity of each structure. Accordingly, the availability of simpler solutions may boost the short-term use of contractile actuators in practical applications. For this purpose, a new configuration is here described. It consists of a monolithic structure made of an electroded sheet, which is folded up and compacted. The resulting device is functionally equivalent to a multi-layer stack with interdigitated electrodes. However, with respect to a stack the new configuration is advantageously not discontinuous and can be manufactured in one single phase, avoiding layer-by-layer multi-step procedures. The development and preliminary testing of prototype samples of this new actuator made of a silicone elastomer are presented here.

  17. Detecting equilibrium cytochrome c folding intermediates by electrospray ionisation mass spectrometry: Two partially folded forms populate the molten-globule state

    PubMed Central

    Grandori, Rita

    2002-01-01

    Nanoelectrospray ionization mass spectrometry (nano-ESI-MS) is applied to the characterization of ferric cytochromec (cytc) conformational states under different solvent conditions. The methanol-induced molten-globule state in the pH range 2.6–3.0 is found to be populated by two distinct, partially folded conformers IA and IB. The more compact intermediate IB resembles that induced by glycerol in acid-unfolded cytc. The less compact one, IA, also can be induced by destabilization of the native structure by trifluoroethanol. IA and IB can be detected, in the absence of additives, around the midpoint of the acid-induced unfolding transition, providing direct evidence for involvement of equilibrium folding intermediates in cytc conformational transitions at low pH. This study shows that mass spectrometry can contribute to the characterization of molten-globule states of proteins by detection of distinct, although poorly populated, conformations involved in a dynamic equilibrium. PMID:11847268

  18. Quantitative Morphology of Epithelial Folds

    PubMed Central

    Štorgel, Nick; Krajnc, Matej; Mrak, Polona; Štrus, Jasna; Ziherl, Primož

    2016-01-01

    The shape of spatially modulated epithelial morphologies such as villi and crypts is usually associated with the epithelium-stroma area mismatch leading to buckling. We propose an alternative mechanical model based on intraepithelial stresses generated by differential tensions of apical, lateral, and basal sides of cells as well as on the elasticity of the basement membrane. We use it to theoretically study longitudinal folds in simple epithelia and we identify four types of corrugated morphologies: compact, invaginated, evaginated, and wavy. The obtained tissue contours and thickness profiles are compared to epithelial folds observed in invertebrates and vertebrates, and for most samples, the agreement is within the estimated experimental error. Our model establishes the groove-crest modulation of tissue thickness as a morphometric parameter that can, together with the curvature profile, be used to estimate the relative differential apicobasal tension in the epithelium. PMID:26745429

  19. Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding.

    PubMed Central

    Tsai, C. J.; Maizel, J. V.; Nussinov, R.

    1999-01-01

    We describe here an algorithm for distinguishing sequential from nonsequentially folding proteins. Several experiments have recently suggested that most of the proteins that are synthesized in the eukaryotic cell may fold sequentially. This proposed folding mechanism in vivo is particularly advantageous to the organism. In the absence of chaperones, the probability that a sequentially folding protein will misfold is reduced significantly. The problem we address here is devising a procedure that would differentiate between the two types of folding patterns. Footprints of sequential folding may be found in structures where consecutive fragments of the chain interact with each other. In such cases, the folding complexity may be viewed as being lower. On the other hand, higher folding complexity suggests that at least a portion of the polypeptide backbone folds back upon itself to form three-dimensional (3D) interactions with noncontiguous portion(s) of the chain. Hence, we look at the mechanism of folding of the molecule via analysis of its complexity, that is, through the 3D interactions formed by contiguous segments on the polypeptide chain. To computationally splice the structure into consecutively interacting fragments, we either cut it into compact hydrophobic folding units or into a set of hypothetical, transient, highly populated, contiguous fragments ("building blocks" of the structure). In sequential folding, successive building blocks interact with each other from the amino to the carboxy terminus of the polypeptide chain. Consequently, the results of the parsing differentiate between sequentially vs. nonsequentially folded chains. The automated assessment of the folding complexity provides insight into both the likelihood of misfolding and the kinetic folding rate of the given protein. In terms of the funnel free energy landscape theory, a protein that truly follows the mechanism of sequential folding, in principle, encounters smoother free energy barriers

  20. Hydraulic conductivity of compacted zeolites.

    PubMed

    Oren, A Hakan; Ozdamar, Tuğçe

    2013-06-01

    Hydraulic conductivities of compacted zeolites were investigated as a function of compaction water content and zeolite particle size. Initially, the compaction characteristics of zeolites were determined. The compaction test results showed that maximum dry unit weight (γ(dmax)) of fine zeolite was greater than that of granular zeolites. The γ(dmax) of compacted zeolites was between 1.01 and 1.17 Mg m(-3) and optimum water content (w(opt)) was between 38% and 53%. Regardless of zeolite particle size, compacted zeolites had low γ(dmax) and high w(opt) when compared with compacted natural soils. Then, hydraulic conductivity tests were run on compacted zeolites. The hydraulic conductivity values were within the range of 2.0 × 10(-3) cm s(-1) to 1.1 × 10(-7) cm s(-1). Hydraulic conductivity of all compacted zeolites decreased almost 50 times as the water content increased. It is noteworthy that hydraulic conductivity of compacted zeolite was strongly dependent on the zeolite particle size. The hydraulic conductivity decreased almost three orders of magnitude up to 39% fine content; then, it remained almost unchanged beyond 39%. Only one report was found in the literature on the hydraulic conductivity of compacted zeolite, which is in agreement with the findings of this study.

  1. Asymmetric hindwing foldings in rove beetles.

    PubMed

    Saito, Kazuya; Yamamoto, Shuhei; Maruyama, Munetoshi; Okabe, Yoji

    2014-11-18

    Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use.

  2. How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway.

    PubMed

    Dyson, H Jane; Wright, Peter E

    2017-01-17

    Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (∼2 s) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ∼ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the

  3. Folding gravitational-wave interferometers

    NASA Astrophysics Data System (ADS)

    Sanders, J. R.; Ballmer, Stefan W.

    2017-01-01

    The sensitivity of kilometer-scale terrestrial gravitational wave interferometers is limited by mirror coating thermal noise. Alternative interferometer topologies can mitigate the impact of thermal noise on interferometer noise curves. In this work, we explore the impact of introducing a single folding mirror into the arm cavities of dual-recycled Fabry–Perot interferometers. While simple folding alone does not reduce the mirror coating thermal noise, it makes the folding mirror the critical mirror, opening up a variety of design and upgrade options. Improvements to the folding mirror thermal noise through crystalline coatings or cryogenic cooling can increase interferometer range by as much as a factor of two over the Advanced LIGO reference design.

  4. Improving protein fold recognition by random forest

    PubMed Central

    2014-01-01

    Background Recognizing the correct structural fold among known template protein structures for a target protein (i.e. fold recognition) is essential for template-based protein structure modeling. Since the fold recognition problem can be defined as a binary classification problem of predicting whether or not the unknown fold of a target protein is similar to an already known template protein structure in a library, machine learning methods have been effectively applied to tackle this problem. In our work, we developed RF-Fold that uses random forest - one of the most powerful and scalable machine learning classification methods - to recognize protein folds. Results RF-Fold consists of hundreds of decision trees that can be trained efficiently on very large datasets to make accurate predictions on a highly imbalanced dataset. We evaluated RF-Fold on the standard Lindahl's benchmark dataset comprised of 976 × 975 target-template protein pairs through cross-validation. Compared with 17 different fold recognition methods, the performance of RF-Fold is generally comparable to the best performance in fold recognition of different difficulty ranging from the easiest family level, the medium-hard superfamily level, and to the hardest fold level. Based on the top-one template protein ranked by RF-Fold, the correct recognition rate is 84.5%, 63.4%, and 40.8% at family, superfamily, and fold levels, respectively. Based on the top-five template protein folds ranked by RF-Fold, the correct recognition rate increases to 91.5%, 79.3% and 58.3% at family, superfamily, and fold levels. Conclusions The good performance achieved by the RF-Fold demonstrates the random forest's effectiveness for protein fold recognition. PMID:25350499

  5. All-or-none protein-like folding of a homopolymer chain

    NASA Astrophysics Data System (ADS)

    Taylor, Mark; Paul, Wolfgang; Binder, Kurt

    2009-10-01

    Many small proteins fold via a first-order ``all-or-none'' transition directly from an expanded coil to a compact native state. Here we report an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple flexible homopolymer. Wang-Landau sampling is used to construct the complete density of states for square-well chains up to length 256. Analysis within both the microcanonical and canonical ensembles shows that, for a chain with sufficiently short-range interactions, the usual polymer collapse transition is preempted by a direct freezing transition. Despite the non-unique homopolymer ground state, the thermodynamics of this direct freezing transition are identical to the thermodynamics of two-state protein folding. A free energy barrier separates a high entropy ensemble of unfolded states from a low entropy set of crystallite states and the transition proceeds via the formation of a transition-state folding nucleus. An Arrhenius analysis of the folding/unfolding free energy barrier yields a Chevron plot characteristic of proteins and the model chain satisfies the van't Hoff calorimetric criterion for two-state folding.

  6. Oil shale compaction experimental results

    SciTech Connect

    Fahy, L.J.

    1985-11-01

    Oil shale compaction reduces the void volume available for gas flow in vertical modified in situ (VMIS) retorts. The mechanical forces caused by the weight of the overlying shale can equal 700 kPa near the bottom of commercial retorts. Clear evidence of shale compaction was revealed during postburn investigation of the Rio Blanco retorts at the C-a lease tract in Colorado. Western Research Institute conducted nine laboratory experiments to measure the compaction of Green River oil shale rubble during retorting. The objectives of these experiments were (1) to determine the effects of particle size, (2) to measure the compaction of different shale grades with 12 to 25 percent void volume and (3) to study the effects of heating rate on compaction. The compaction recorded in these experiments can be separated into the compaction that occurred during retorting and the compaction that occurred as the retort cooled down. The leaner oil shale charges compacted about 3 to 4 percent of the bed height at the end of retorting regardless of the void volume or heating rate. The richer shale charges compacted by 6.6 to 22.9 percent of the bed height depending on the shale grade and void volume used. Additional compaction of approximately 1.5 to 4.3 percent of the bed height was measured as the oil shale charges cooled down. Compaction increased with an increase in void volume for oil shale grades greater than 125 l/Mg. The particle size of the oil shale brick and the heating rate did not have a significant effect on the amount of compaction measured. Kerogen decomposition is a major factor in the compaction process. The compaction may be influenced by the bitumen intermediate acting as a lubricant, causing compaction to occur over a narrow temperature range between 315 and 430/sup 0/C. While the majority of the compaction occurs early in the retorting phase, mineral carbonate decomposition may also increase the amount of compaction. 14 refs., 12 figs., 4 tabs.

  7. Compact vortices

    NASA Astrophysics Data System (ADS)

    Bazeia, D.; Losano, L.; Marques, M. A.; Menezes, R.; Zafalan, I.

    2017-02-01

    We study a family of Maxwell-Higgs models, described by the inclusion of a function of the scalar field that represent generalized magnetic permeability. We search for vortex configurations which obey first-order differential equations that solve the equations of motion. We first deal with the asymptotic behavior of the field configurations, and then implement a numerical study of the solutions, the energy density and the magnetic field. We work with the generalized permeability having distinct profiles, giving rise to new models, and we investigate how the vortices behave, compared with the solutions of the corresponding standard models. In particular, we show how to build compact vortices, that is, vortex solutions with the energy density and magnetic field vanishing outside a compact region of the plane.

  8. Compact accelerator

    DOEpatents

    Caporaso, George J.; Sampayan, Stephen E.; Kirbie, Hugh C.

    2007-02-06

    A compact linear accelerator having at least one strip-shaped Blumlein module which guides a propagating wavefront between first and second ends and controls the output pulse at the second end. Each Blumlein module has first, second, and third planar conductor strips, with a first dielectric strip between the first and second conductor strips, and a second dielectric strip between the second and third conductor strips. Additionally, the compact linear accelerator includes a high voltage power supply connected to charge the second conductor strip to a high potential, and a switch for switching the high potential in the second conductor strip to at least one of the first and third conductor strips so as to initiate a propagating reverse polarity wavefront(s) in the corresponding dielectric strip(s).

  9. Mechanics of Curved Folds

    NASA Astrophysics Data System (ADS)

    Dias, Marcelo A.; Santangelo, Christian D.

    2011-03-01

    Despite an almost two thousand year history, origami, the art of folding paper, remains a challenge both artistically and scientifically. Traditionally, origami is practiced by folding along straight creases. A whole new set of shapes can be explored, however, if, instead of straight creases, one folds along arbitrary curves. We present a mechanical model for curved fold origami in which the energy of a plastically-deformed crease is balanced by the bending energy of developable regions on either side of the crease. Though geometry requires that a sheet buckle when folded along a closed curve, its shape depends on the elasticity of the sheet. NSF DMR-0846582.

  10. Compact CFB: The next generation CFB boiler

    SciTech Connect

    Utt, J.

    1996-12-31

    The next generation of compact circulating fluidized bed (CFB) boilers is described in outline form. The following topics are discussed: compact CFB = pyroflow + compact separator; compact CFB; compact separator is a breakthrough design; advantages of CFB; new design with substantial development history; KUHMO: successful demo unit; KUHMO: good performance over load range with low emissions; KOKKOLA: first commercial unit and emissions; KOKKOLA: first commercial unit and emissions; compact CFB installations; next generation CFB boiler; grid nozzle upgrades; cast segmented vortex finders; vortex finder installation; ceramic anchors; pre-cast vertical bullnose; refractory upgrades; and wet gunning.

  11. Compact magnetograph

    NASA Technical Reports Server (NTRS)

    Title, A. M.; Gillespie, B. A.; Mosher, J. W.

    1982-01-01

    A compact magnetograph system based on solid Fabry-Perot interferometers as the spectral isolation elements was studied. The theory of operation of several Fabry-Perot systems, the suitability of various magnetic lines, signal levels expected for different modes of operation, and the optimal detector systems were investigated. The requirements that the lack of a polarization modulator placed upon the electronic signal chain was emphasized. The PLZT modulator was chosen as a satisfactory component with both high reliability and elatively low voltage requirements. Thermal control, line centering and velocity offset problems were solved by a Fabry-Perot configuration.

  12. Elbow Synovial Fold Syndrome

    DTIC Science & Technology

    2007-12-01

    Density MR with arrows The clinical differential diagnosis of plica syndrome includes lateral epicondylitis (aka tennis elbow ), loose bodies... Elbow Synovial Fold Syndrome Radiology Corner Elbow Synovial Fold Syndrome Guarantor: CPT Amit Sanghi, USA, MC FS Contributors: CPT Amit...the case of a 17 year old female with elbow synovial fold syndrome (aka plica synovialis). The etiology is thought to be related to repetitive

  13. Fast protein folding kinetics

    PubMed Central

    Gelman, Hannah; Gruebele, Martin

    2014-01-01

    Fast folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast folding proteins has provided insight into the mechanisms which allow some proteins to find their native conformation well less than 1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even “slow” folding processes: fast folders are small, relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast folding proteins and provides an overview of the major findings of fast folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general as well as some work that is left to do. PMID:24641816

  14. A galaxy of folds

    PubMed Central

    Alva, Vikram; Remmert, Michael; Biegert, Andreas; Lupas, Andrei N; Söding, Johannes

    2010-01-01

    Many protein classification systems capture homologous relationships by grouping domains into families and superfamilies on the basis of sequence similarity. Superfamilies with similar 3D structures are further grouped into folds. In the absence of discernable sequence similarity, these structural similarities were long thought to have originated independently, by convergent evolution. However, the growth of databases and advances in sequence comparison methods have led to the discovery of many distant evolutionary relationships that transcend the boundaries of superfamilies and folds. To investigate the contributions of convergent versus divergent evolution in the origin of protein folds, we clustered representative domains of known structure by their sequence similarity, treating them as point masses in a virtual 2D space which attract or repel each other depending on their pairwise sequence similarities. As expected, families in the same superfamily form tight clusters. But often, superfamilies of the same fold are linked with each other, suggesting that the entire fold evolved from an ancient prototype. Strikingly, some links connect superfamilies with different folds. They arise from modular peptide fragments of between 20 and 40 residues that co-occur in the connected folds in disparate structural contexts. These may be descendants of an ancestral pool of peptide modules that evolved as cofactors in the RNA world and from which the first folded proteins arose by amplification and recombination. Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains. PMID:19937658

  15. A galaxy of folds.

    PubMed

    Alva, Vikram; Remmert, Michael; Biegert, Andreas; Lupas, Andrei N; Söding, Johannes

    2010-01-01

    Many protein classification systems capture homologous relationships by grouping domains into families and superfamilies on the basis of sequence similarity. Superfamilies with similar 3D structures are further grouped into folds. In the absence of discernable sequence similarity, these structural similarities were long thought to have originated independently, by convergent evolution. However, the growth of databases and advances in sequence comparison methods have led to the discovery of many distant evolutionary relationships that transcend the boundaries of superfamilies and folds. To investigate the contributions of convergent versus divergent evolution in the origin of protein folds, we clustered representative domains of known structure by their sequence similarity, treating them as point masses in a virtual 2D space which attract or repel each other depending on their pairwise sequence similarities. As expected, families in the same superfamily form tight clusters. But often, superfamilies of the same fold are linked with each other, suggesting that the entire fold evolved from an ancient prototype. Strikingly, some links connect superfamilies with different folds. They arise from modular peptide fragments of between 20 and 40 residues that co-occur in the connected folds in disparate structural contexts. These may be descendants of an ancestral pool of peptide modules that evolved as cofactors in the RNA world and from which the first folded proteins arose by amplification and recombination. Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains.

  16. Compact fixed wavelength femtosecond oscillators as an add-on for tunable Ti:sapphire lasers extend the range of applications towards multimodal imaging and optogenetics

    NASA Astrophysics Data System (ADS)

    Hakulinen, T.; Klein, J.

    2016-03-01

    Two-photon (2P) microscopy based on tunable Ti:sapphire lasers has become a widespread tool for 3D imaging with sub-cellular resolution in living tissues. In recent years multi-photon microscopy with simpler fixed-wavelength femtosecond oscillators using Yb-doped tungstenates as gain material has raised increasing interest in life-sciences, because these lasers offer one order of magnitude more average power than Ti:sapphire lasers in the wavelength range around 1040 nm: Two-photon (2P) excitation of mainly red or yellow fluorescent dyes and proteins (e.g. YFP, mFruit series) simultaneously has been proven with a single IR laser wavelength. A new approach is to extend the usability of existing tunable Titanium sapphire lasers by adding a fixed IR wavelength with an Yb femtosecond oscillator. By that means a multitude of applications for multimodal imaging and optogenetics can be supported. Furthermore fs Yb-lasers are available with a repetition rate of typically 10 MHz and an average power of typically 5 W resulting in pulse energy of typically 500 nJ, which is comparably high for fs-oscillators. This makes them an ideal tool for two-photon spinning disk laser scanning microscopy and holographic patterning for simultaneous photoactivation of large cell populations. With this work we demonstrate that economical, small-footprint Yb fixed-wavelength lasers can present an interesting add-on to tunable lasers that are commonly used in multiphoton microscopy. The Yb fs-lasers hereby offer higher power for imaging of red fluorescent dyes and proteins, are ideally enhancing existing Ti:sapphire lasers with more power in the IR, and are supporting pulse energy and power hungry applications such as spinning disk microscopy and holographic patterning.

  17. Compact Torsatron configurations

    SciTech Connect

    Carreras, B. A.; Dominguez, N.; Garcia, L.; Lynch, V. E.; Lyon, J. F.; Cary, J. R.; Hanson, J. D.; Navarro, A. P.

    1987-09-01

    Low-aspect-ratio stellarator configurations can be realized by using torsatron winding. Plasmas with aspect ratios in the range of 3.5 to 5 can be confined by these Compact Torsatron configurations. Stable operation at high BETA should be possible in these devices, if a vertical field coil system is adequately designed to avoid breaking of the magnetic surfaces at finite BETA. 17 refs., 21 figs., 1 tab.

  18. Compact power reactor

    DOEpatents

    Wetch, Joseph R.; Dieckamp, Herman M.; Wilson, Lewis A.

    1978-01-01

    There is disclosed a small compact nuclear reactor operating in the epithermal neutron energy range for supplying power at remote locations, as for a satellite. The core contains fuel moderator elements of Zr hydride with 7 w/o of 93% enriched uranium alloy. The core has a radial beryllium reflector and is cooled by liquid metal coolant such as NaK. The reactor is controlled and shut down by moving portions of the reflector.

  19. Functional cooperation between BiP and calreticulin in the folding maturation of a glycoprotein in Trypanosoma cruzi

    PubMed Central

    Labriola, Carlos A.; Villamil Giraldo, Ana M.; Parodi, Armando J.; Caramelo, Julio J.

    2011-01-01

    Proteins may adopt diverse conformations during their folding in vivo, ranging from extended chains when they emerge from the ribosome to compact intermediates near the end of the folding process. Accordingly, a variety of chaperones and folding assisting enzymes have evolved to deal with this diversity. Chaperone selection by a particular substrate depends on the structural features of its folding intermediates. In addition, this process may be modulated by competitive effects between chaperones. Here we address this issue by using TcrCATL as model substrate. TcrCATL is an abundant Trypanosoma cruzi lysosomal protease and it was the first identified endogenous UDP-Glc:glycoprotein glucosyltransferase (UGGT) substrate. We found that TcrCATL associated sequentially with BiP and calreticulin (CRT) during its folding process. Early, extended conformations were bound to BiP, while more advanced and compact folding intermediates associated to CRT. The interaction between TcrCATL and CRT was impeded by deletion of the UGGT-encoding gene but, similarly to what was observed in wild type cells, in mutant cells TcrCATL associated to BiP only when displaying extended conformations. The absence of TcrCATL–CRT interactions in UGGT null cells resulted in a drastic reduction of TcrCATL folding efficiency and triggered the aggregation of TcrCATL through intermolecular disulfide bonds. These observations show that BiP and CRT activities complement each other to supervise a complete and efficient TcrCATL folding process. The present report provides further evidence on the early evolutionary acquisition of the basic tenets of the N-glycan dependent quality control mechanism of glycoprotein folding. PMID:20934456

  20. Protein-like folding and free energy landscape of a homopolymer chain

    NASA Astrophysics Data System (ADS)

    Taylor, Mark; Paul, Wolfgang; Binder, Kurt

    2011-03-01

    Many small proteins fold via a first-order ``all-or-none'' transition directly from an expanded coil to a compact native state. We have recently reported an analogous direct coil-to-crystallite transition for a flexible homopolymer. Wang-Landau sampling was used to construct the 1D density of states for square-well chains up to length 256 and a microcanonical analysis shows that for short-range interactions the usual polymer collapse transition is preempted by a direct freezing transition. A 2D configurational probability landscape, built via multi-canonical sampling, reveals a dominant folding pathway and an inherent configurational barrier to folding. Despite the non-unique homopolymer ground state, the thermodynamics of this direct freezing transition are identical to those of two-state protein folding. Homopolymer folding proceeds over a free energy barrier via a transition state folding nucleus, displays a protein-like Chevron plot, and satisfies the van't Hoff two-state criterion. Funding: NSF DMR-0804370, DFG SFB-625/A3.

  1. Protein-like folding and free energy landscape of a homopolymer chain

    NASA Astrophysics Data System (ADS)

    Taylor, Mark; Paul, Wolfgang; Binder, Kurt

    2011-04-01

    Many small proteins fold via a first-order "all-or-none" transition directly from an expanded coil to a compact native state. We have recently reported an analogous direct coil-to-crystallite transition for a flexible homopolymer [1]. Wang-Landau sampling was used to construct the 1D density of states for square-well chains up to length 256 and a microcanonical analysis shows that for short-range interactions the usual polymer collapse transition is preempted by a direct freezing transition. A 2D configurational probability landscape, built via multi-canonical sampling, reveals a dominant folding pathway and an inherent configurational barrier to folding. Despite the non-unique homopolymer ground state, the thermodynamics of this direct freezing transition are identical to those of two-state protein folding. Homopolymer folding proceeds over a free energy barrier via a transition state folding nucleus, displays a protein-like Chevron plot, and satisfies the van't Hoff two-state criterion.[4pt] [1] Phys. Rev. E 79, 050801(R) (2009); J. Chem. Phys. 131, 114907 (2009).

  2. The Role of Atomic Level Steric Effects and Attractive Forces in Protein Folding

    PubMed Central

    Lammert, Heiko; Wolynes, Peter G.; Onuchic, José N.

    2011-01-01

    Protein folding into tertiary structures is controlled by an interplay of attractive contact interactions and steric effects. We investigate the balance between these contributions using structure-based models using an all-atom representation of the structure combined with a coarse-grained contact potential. Tertiary contact interactions between atoms are collected into a single broad attractive well between the Cβ atoms between each residue pair in a native contact. Through the width of these contact potentials we control their tolerance for deviations from the ideal structure and the spatial range of attractive interactions. In the compact native state dominant packing constraints limit the effects of a coarse-grained contact potential. During folding however the broad attractive potentials allow an early collapse that starts before the native local structure is completely adopted. As a consequence the folding transition is broadened and the free energy barrier is decreased. Eventually two-state folding behavior is lost completely for systems with very broad attractive potentials. The stabilization of native-like residue interactions in non-perfect geometries early in the folding process frequently leads to structural traps. Global mirror images are a notable example. These traps are penalized by the details of the repulsive interactions only after further collapse. Successful folding to the native state requires simultaneous guidance from both attractive and repulsive interactions. PMID:22081451

  3. Turbulent phenomena in protein folding.

    PubMed

    Kalgin, Igor V; Chekmarev, Sergei F

    2011-01-01

    Protein folding and hydrodynamic turbulence are two long-standing challenges, in molecular biophysics and fluid dynamics, respectively. The theories of these phenomena have been developed independently and used different formalisms. Here we show that the protein folding flows can be surprisingly similar to turbulent fluid flows. Studying a benchmark model protein (an SH3 domain), we have found that the flows for the slow folding trajectories of the protein, in which a partly formed N- and C-terminal β sheet hinders the RT loop from attaching to the protein core, have many properties of turbulent flows of a fluid. The flows are analyzed in a three-dimensional (3D) space of collective variables, which are the numbers of native contacts between the terminal β strands, between the RT loop and the protein core, and the rest of the native contacts. We have found that the flows have fractal nature and are filled with 3D eddies; the latter contain strange attractors, at which the tracer flow paths behave as saddle trajectories. Two regions of the space increment have been observed, in which the flux variations are self-similar with the scaling exponent h=1/3, in surprising agreement with the Kolmogorov inertial range theory of turbulence. In one region, the cascade of protein rearrangements is directed from larger to smaller scales (net folding), and in the other, it is oppositely directed (net unfolding). Folding flows for the fast trajectories are essentially "laminar" and do not have the property of self-similarity. Based on the results of our study, we infer, and support this inference by simulations, that the origin of the similarity between the protein folding and turbulent motion of a fluid is in a cascade mechanism of structural transformations in the systems that underlies these phenomena.

  4. Viral RNAs Are Unusually Compact

    PubMed Central

    Gopal, Ajaykumar; Egecioglu, Defne E.; Yoffe, Aron M.; Ben-Shaul, Avinoam; Rao, Ayala L. N.; Knobler, Charles M.; Gelbart, William M.

    2014-01-01

    A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly. PMID:25188030

  5. Viral RNAs are unusually compact.

    PubMed

    Gopal, Ajaykumar; Egecioglu, Defne E; Yoffe, Aron M; Ben-Shaul, Avinoam; Rao, Ayala L N; Knobler, Charles M; Gelbart, William M

    2014-01-01

    A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly.

  6. Statistical thermodynamics of protein folding: Comparison of a mean-field theory with Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Hao, Ming-Hong; Scheraga, Harold A.

    1995-01-01

    A comparative study of protein folding with an analytical theory and computer simulations, respectively, is reported. The theory is based on an improved mean-field formalism which, in addition to the usual mean-field approximations, takes into account the distributions of energies in the subsets of conformational states. Sequence-specific properties of proteins are parametrized in the theory by two sets of variables, one for the energetics of mean-field interactions and one for the distribution of energies. Simulations are carried out on model polypeptides with different sequences, with different chain lengths, and with different interaction potentials, ranging from strong biases towards certain local chain states (bond angles and torsional angles) to complete absence of local conformational preferences. Theoretical analysis of the simulation results for the model polypeptides reveals three different types of behavior in the folding transition from the statistical coiled state to the compact globular state; these include a cooperative two-state transition, a continuous folding, and a glasslike transition. It is found that, with the fitted theoretical parameters which are specific for each polypeptide under a different potential, the mean-field theory can describe the thermodynamic properties and folding behavior of the different polypeptides accurately. By comparing the theoretical descriptions with simulation results, we verify the basic assumptions of the theory and, thereby, obtain new insights about the folding transitions of proteins. It is found that the cooperativity of the first-order folding transition of the model polypeptides is determined mainly by long-range interactions, in particular the dipolar orientation; the local interactions (e.g., bond-angle and torsion-angle potentials) have only marginal effect on the cooperative characteristic of the folding, but have a large impact on the difference in energy between the folded lowest-energy structure and

  7. Description, host range and distribution of a new Macrodiplosis species (Diptera: Cecidomyiidae) that induces leaf-margin fold galls on deciduous Quercus (Fagaceae) with comparative notes on Palaearctic congeners.

    PubMed

    Kim, Wanggyu; Yukawa, Junichi; Harris, Keith M; Minami, Tsuneo; Matsuo, Kazunori; Skrzypczyńska, Małgorzata

    2014-06-20

    A gall midge that induces upwardly folded leaf-margin galls on Quercus serrata, Q. mongolica and Q. dentata (Fagaceae) in Japan and South Korea is described as Macrodiplosis selenis sp. n. (Diptera: Cecidomyiidae). M. selenis is distinguished from Palaearctic congeners by a combination of morphological characters. Genetic differences supported the result of morphological comparison and indicated that M. selenis is closely related to the European M. roboris, whose gall is similar to that of M. selenis.

  8. Folding of polyglutamine chains

    NASA Astrophysics Data System (ADS)

    Chopra, Manan; Reddy, Allam S.; Abbott, N. L.; de Pablo, J. J.

    2008-10-01

    Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntington's disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a β-helical structure. Transition path sampling Monte Carlo simulations are used to generate unbiased reactive pathways between unfolded configurations and the folded β-helical structure of the polyglutamine chain. The folding process is examined in both explicit water and an implicit solvent. Both models reveal that the formation of a few critical contacts is necessary and sufficient for the molecule to fold. Once the primary contacts are formed, the fate of the protein is sealed and it is largely committed to fold. We find that, consistent with emerging hypotheses about PolyQ aggregation, a stable β-helical structure could serve as the nucleus for subsequent polymerization of amyloid fibrils. Our results indicate that PolyQ sequences shorter than 36 residues cannot form that nucleus, and it is also shown that specific mutations inferred from an analysis of the simulated folding pathway exacerbate its stability.

  9. Compaction behavior of roller compacted ibuprofen.

    PubMed

    Patel, Sarsvatkumar; Kaushal, Aditya Mohan; Bansal, Arvind Kumar

    2008-06-01

    The effect of roller compaction pressure on the bulk compaction of roller compacted ibuprofen was investigated using instrumented rotary tablet press. Three different roller pressures were utilized to prepare granules and Heckel analysis, Walker analysis, compressibility, and tabletability were performed to derive densification, deformation, course of volume reduction and bonding phenomenon of different pressure roller compacted granules. Nominal single granule fracture strength was obtained by micro tensile testing. Heckel analysis indicated that granules prepared using lower pressure during roller compaction showed lower yield strength. The reduction in tabletability was observed for higher pressure roller compacted granules. The reduction in tabletability supports the results of granule size enlargement theory. Apart from the granule size enlargement theory, the available fines and relative fragmentation during compaction is responsible for higher bonding strength and provide larger areas for true particle contact at constant porosity for lower pressure roller compacted granules. Overall bulk compaction parameters indicated that granules prepared by lower roller compaction pressure were advantageous in terms of tabletability and densification. Overall results suggested that densification during roller compaction affects the particle level properties of specific surface area, nominal fracture strength, and compaction behavior.

  10. Compact Reactor

    SciTech Connect

    Williams, Pharis E.

    2007-01-30

    Weyl's Gauge Principle of 1929 has been used to establish Weyl's Quantum Principle (WQP) that requires that the Weyl scale factor should be unity. It has been shown that the WQP requires the following: quantum mechanics must be used to determine system states; the electrostatic potential must be non-singular and quantified; interactions between particles with different electric charges (i.e. electron and proton) do not obey Newton's Third Law at sub-nuclear separations, and nuclear particles may be much different than expected using the standard model. The above WQP requirements lead to a potential fusion reactor wherein deuterium nuclei are preferentially fused into helium nuclei. Because the deuterium nuclei are preferentially fused into helium nuclei at temperatures and energies lower than specified by the standard model there is no harmful radiation as a byproduct of this fusion process. Therefore, a reactor using this reaction does not need any shielding to contain such radiation. The energy released from each reaction and the absence of shielding makes the deuterium-plus-deuterium-to-helium (DDH) reactor very compact when compared to other reactors, both fission and fusion types. Moreover, the potential energy output per reactor weight and the absence of harmful radiation makes the DDH reactor an ideal candidate for space power. The logic is summarized by which the WQP requires the above conditions that make the prediction of DDH possible. The details of the DDH reaction will be presented along with the specifics of why the DDH reactor may be made to cause two deuterium nuclei to preferentially fuse to a helium nucleus. The presentation will also indicate the calculations needed to predict the reactor temperature as a function of fuel loading, reactor size, and desired output and will include the progress achieved to date.

  11. Estimating woody aboveground biomass in an area of agroforestry using airborne light detection and ranging and compact airborne spectrographic imager hyperspectral data: individual tree analysis incorporating tree species information

    NASA Astrophysics Data System (ADS)

    Wang, Zhihui; Liu, Liangyun; Peng, Dailiang; Liu, Xinjie; Zhang, Su; Wang, Yingjie

    2016-07-01

    Until now, there have been only a few studies that have made estimates of the woody aboveground biomass (AGB) in an area of agroforestry using remote sensing technology. The woody AGB density was estimated using individual tree analysis (ITA) that incorporated tree species information using a combination of airborne light detection and ranging (LiDAR) and compact airborne spectrographic imagery acquired over a typical agroforestry in northwestern China. First, a series of improved LiDAR processing algorithms was applied to achieve individual tree segmentation, and accurate plot-level canopy heights and crown diameters were obtained. The individual tree species were then successfully classified using both spectral and shape characteristics with an overall accuracy of 0.97 and a kappa coefficient of 0.85. Finally, the tree-level AGB (kg) was estimated based on the ITA; the AGB density (Mg/ha) was then upscaled based on the tree-level AGB values. It is concluded that, compared with the commonly used area-based method combining LiDAR and spectral metrics [root mean square error (RMSE)=19.58 Mg/ha], the ITA method performs better at estimating AGB density (RMSE=10.56 Mg/ha). The tree species information also improved the accuracy of the AGB estimation even though the species are not well diversified in this study area.

  12. Programmable matter by folding

    PubMed Central

    Hawkes, E.; An, B.; Benbernou, N. M.; Tanaka, H.; Kim, S.; Demaine, E. D.; Rus, D.; Wood, R. J.

    2010-01-01

    Programmable matter is a material whose properties can be programmed to achieve specific shapes or stiffnesses upon command. This concept requires constituent elements to interact and rearrange intelligently in order to meet the goal. This paper considers achieving programmable sheets that can form themselves in different shapes autonomously by folding. Past approaches to creating transforming machines have been limited by the small feature sizes, the large number of components, and the associated complexity of communication among the units. We seek to mitigate these difficulties through the unique concept of self-folding origami with universal crease patterns. This approach exploits a single sheet composed of interconnected triangular sections. The sheet is able to fold into a set of predetermined shapes using embedded actuation. To implement this self-folding origami concept, we have developed a scalable end-to-end planning and fabrication process. Given a set of desired objects, the system computes an optimized design for a single sheet and multiple controllers to achieve each of the desired objects. The material, called programmable matter by folding, is an example of a system capable of achieving multiple shapes for multiple functions. PMID:20616049

  13. Measurement of local chromatin compaction by spectral precision distance microscopy

    NASA Astrophysics Data System (ADS)

    Rauch, Joachim; Hausmann, Michael; Solovei, Irina; Horsthemke, Bernhard; Cremer, Thomas; Cremer, Christoph G.

    2000-12-01

    Fluorescence in situ hybridization (FISH) offers an appropriate technique to specifically label any given chromatin region by multi spectrally labeled, specific DNA probes. Using confocal laser scanning microscopy, quantitative measurements on the spatial distribution of labeling sites can be performed in 3D conserved cell nuclei. Recently, 'Spectral Precision Distance Microscopy' has been developed that allows 3D distance measurements between point-like fluorescence objects of different spectral signatures far beyond the diffraction limited resolution. In a well characterized and sequenced DNA region, the Prader- Willi/Angelman region q11-13 on chromosome 15, geometric distances between the fluorescence intensity bary centers of four different 'point-like' labeling sites were measured. More than 300 cell nuclei were evaluated with a 3D resolution equivalent better than 100 nm. The geometric bary center distances in nanometers were compared with the genomic bary center distance in kilobases (kb). A direct correlation, for instance linear correlation between geometric and genomic distances was not observed. From the measured values, a local compaction factor for the high order chromatin folding in the analyzed genome region was calculated. Along the 1000 kb chromatin segment analyzed, which spans nearly the compete Prader-Willi/Angelman region, different compaction factors were found. The compaction factor 40 typical for a straight 30 nm chromatin fiber was not observed. This shows that chromatin folding and compaction in intact nuclei may be more complex. With SPDM, however, a microscopical technique is available that can sensitively analyze chromatin organization in the 100 nm range in 3D conserved cell nuclei.

  14. Folded supersymmetry with a twist

    DOE PAGES

    Cohen, Timothy; Craig, Nathaniel; Lou, Hou Keong; ...

    2016-03-30

    Folded supersymmetry (f-SUSY) stabilizes the weak scale against radiative corrections from the top sector via scalar partners whose gauge quantum numbers differ from their Standard Model counterparts. This non-trivial pairing of states can be realized in extra-dimensional theories with appropriate supersymmetry-breaking boundary conditions. We present a class of calculable f-SUSY models that are parametrized by a non-trivial twist in 5D boundary conditions and can accommodate the observed Higgs mass and couplings. Although the distinctive phenomenology associated with the novel folded states should provide strong evidence for this mechanism, the most stringent constraints are currently placed by conventional supersymmetry searches. Asmore » a result, these models remain minimally fine-tuned in light of LHC8 data and provide a range of both standard and exotic signatures accessible at LHC13.« less

  15. Folded supersymmetry with a twist

    SciTech Connect

    Cohen, Timothy; Craig, Nathaniel; Lou, Hou Keong; Pinner, David

    2016-03-30

    Folded supersymmetry (f-SUSY) stabilizes the weak scale against radiative corrections from the top sector via scalar partners whose gauge quantum numbers differ from their Standard Model counterparts. This non-trivial pairing of states can be realized in extra-dimensional theories with appropriate supersymmetry-breaking boundary conditions. We present a class of calculable f-SUSY models that are parametrized by a non-trivial twist in 5D boundary conditions and can accommodate the observed Higgs mass and couplings. Although the distinctive phenomenology associated with the novel folded states should provide strong evidence for this mechanism, the most stringent constraints are currently placed by conventional supersymmetry searches. As a result, these models remain minimally fine-tuned in light of LHC8 data and provide a range of both standard and exotic signatures accessible at LHC13.

  16. Fold assessment for comparative protein structure modeling

    PubMed Central

    Melo, Francisco; Sali, Andrej

    2007-01-01

    Accurate and automated assessment of both geometrical errors and incompleteness of comparative protein structure models is necessary for an adequate use of the models. Here, we describe a composite score for discriminating between models with the correct and incorrect fold. To find an accurate composite score, we designed and applied a genetic algorithm method that searched for a most informative subset of 21 input model features as well as their optimized nonlinear transformation into the composite score. The 21 input features included various statistical potential scores, stereochemistry quality descriptors, sequence alignment scores, geometrical descriptors, and measures of protein packing. The optimized composite score was found to depend on (1) a statistical potential z-score for residue accessibilities and distances, (2) model compactness, and (3) percentage sequence identity of the alignment used to build the model. The accuracy of the composite score was compared with the accuracy of assessment by single and combined features as well as by other commonly used assessment methods. The testing set was representative of models produced by automated comparative modeling on a genomic scale. The composite score performed better than any other tested score in terms of the maximum correct classification rate (i.e., 3.3% false positives and 2.5% false negatives) as well as the sensitivity and specificity across the whole range of thresholds. The composite score was implemented in our program MODELLER-8 and was used to assess models in the MODBASE database that contains comparative models for domains in approximately 1.3 million protein sequences. PMID:17905832

  17. Fold assessment for comparative protein structure modeling.

    PubMed

    Melo, Francisco; Sali, Andrej

    2007-11-01

    Accurate and automated assessment of both geometrical errors and incompleteness of comparative protein structure models is necessary for an adequate use of the models. Here, we describe a composite score for discriminating between models with the correct and incorrect fold. To find an accurate composite score, we designed and applied a genetic algorithm method that searched for a most informative subset of 21 input model features as well as their optimized nonlinear transformation into the composite score. The 21 input features included various statistical potential scores, stereochemistry quality descriptors, sequence alignment scores, geometrical descriptors, and measures of protein packing. The optimized composite score was found to depend on (1) a statistical potential z-score for residue accessibilities and distances, (2) model compactness, and (3) percentage sequence identity of the alignment used to build the model. The accuracy of the composite score was compared with the accuracy of assessment by single and combined features as well as by other commonly used assessment methods. The testing set was representative of models produced by automated comparative modeling on a genomic scale. The composite score performed better than any other tested score in terms of the maximum correct classification rate (i.e., 3.3% false positives and 2.5% false negatives) as well as the sensitivity and specificity across the whole range of thresholds. The composite score was implemented in our program MODELLER-8 and was used to assess models in the MODBASE database that contains comparative models for domains in approximately 1.3 million protein sequences.

  18. Folds and Etudes

    ERIC Educational Resources Information Center

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  19. Implicit modeling of folds and overprinting deformation

    NASA Astrophysics Data System (ADS)

    Laurent, Gautier; Ailleres, Laurent; Grose, Lachlan; Caumon, Guillaume; Jessell, Mark; Armit, Robin

    2016-12-01

    Three-dimensional structural modeling is gaining importance for a broad range of quantitative geoscientific applications. However, existing approaches are still limited by the type of structural data they are able to use and by their lack of structural meaning. Most techniques heavily rely on spatial data for modeling folded layers, but are unable to completely use cleavage and lineation information for constraining the shape of modeled folds. This lack of structural control is generally compensated by expert knowledge introduced in the form of additional interpretive data such as cross-sections and maps. With this approach, folds are explicitly designed by the user instead of being derived from data. This makes the resulting structures subjective and deterministic. This paper introduces a numerical framework for modeling folds and associated foliations from typical field data. In this framework, a parametric description of fold geometry is incorporated into the interpolation algorithm. This way the folded geometry is implicitly derived from observed data, while being controlled through structural parameters such as fold wavelength, amplitude and tightness. A fold coordinate system is used to support the numerical description of fold geometry and to modify the behavior of classical structural interpolators. This fold frame is constructed from fold-related structural elements such as axial foliations, intersection lineations, and vergence. Poly-deformed terranes are progressively modeled by successively modeling each folding event going backward through time. The proposed framework introduces a new modeling paradigm, which enables the building of three-dimensional geological models of complex poly-deformed terranes. It follows a process based on the structural geologist approach and is able to produce geomodels that honor both structural data and geological knowledge.

  20. Extended Structures in RNA Folding Intermediates Are Due to Nonnative Interactions Rather than Electrostatic Repulsion

    SciTech Connect

    Baird, Nathan J.; Gong, Haipeng; Zaheer, Syed S.; Freed, Karl F.; Pan, Tao; Sosnick, Tobin R.

    2010-05-25

    RNA folding occurs via a series of transitions between metastable intermediate states for Mg{sup 2+} concentrations below those needed to fold the native structure. In general, these folding intermediates are considerably less compact than their respective native states. Our previous work demonstrates that the major equilibrium intermediate of the 154-residue specificity domain (S-domain) of the Bacillus subtilis RNase P RNA is more extended than its native structure. We now investigate two models with falsifiable predictions regarding the origins of the extended intermediate structures in the S-domains of the B. subtilis and the Escherichia coli RNase P RNA that belong to different classes of P RNA and have distinct native structures. The first model explores the contribution of electrostatic repulsion, while the second model probes specific interactions in the core of the folding intermediate. Using small-angle X-ray scattering and Langevin dynamics simulations, we show that electrostatics plays only a minor role, whereas specific interactions largely account for the extended nature of the intermediate. Structural contacts in the core, including a nonnative base pair, help to stabilize the intermediate conformation. We conclude that RNA folding intermediates adopt extended conformations due to short-range, nonnative interactions rather than generic electrostatic repulsion of helical domains. These principles apply to other ribozymes and riboswitches that undergo functionally relevant conformational changes.

  1. Rapid Sintering of Nano-Diamond Compacts

    SciTech Connect

    Osipov, A.; Nauyoks, S; Zerda, T; Zaporozhets, O

    2009-01-01

    Diamond compacts were sintered from nano-size diamond crystals at high pressure, 8 GPa, and temperature above 1500 degrees C for very short times ranging from 5 to 11 s. Structure and mechanical properties of the compacts have been characterized. Although we have not completely avoided graphitization of diamonds, the amount of graphite produced was low, less than 2%, and despite relatively high porosity, the compacts were characterized by high hardness, bulk and Young moduli.

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

    SciTech Connect

    Eliezer, D.

    1994-06-01

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

  3. Modelling of lateral fold growth and fold linkage: Applications to fold-and-thrust belt tectonics

    NASA Astrophysics Data System (ADS)

    Grasemann, Bernhard; Schmalholz, Stefan

    2013-04-01

    We use a finite element model to investigate the three-dimensional fold growth and interference of two initially isolated fold segments. The most critical parameter, which controls the fold linkage mode, is the phase difference between the laterally growing fold hinge lines: 1) "Linear-linkage" yields a sub-cylindrical fold with a saddle at the location where the two initial folds linked. 2) "Oblique-linkage" produces a curved fold resembling a Type II refold structure. 3) "Oblique-no-linkage" results in two curved folds with fold axes plunging in opposite directions. 4) "Linear-no-linkage" yields a fold train of two separate sub-cylindrical folds with fold axes plunging in opposite directions. The transition from linkage to no-linkage occurs when the fold separation between the initially isolated folds is slightly larger than one half of the low-amplitude fold wavelength. The model results compare well with previously published plasticine analogue models and can be directly applied to the investigation of fold growth history in fold-and-thust belts. An excellent natural example of lateral fold linkage is described from the Zagros fold-and-thrust belt in the Kurdistan Region of Iraq. The fold growth in this region is not controlled by major thrust faults but the shortening of the Paleozoic to Cenozoic passive margin sediments of the Arabian plate occurred mainly by detachment folding. The sub-cylindrical anticlines with hinge-parallel lengths of more than 50 km have not developed from single sub-cylindrical embryonic folds but they have merged from different fold segments that joined laterally during fold amplification and lateral fold growth. Linkage points are marked by geomorphological saddle points which are structurally the lowermost points of antiforms and points of principal curvatures with opposite sign. Linkage points can significantly influence the migration of mineral-rich fluids and hydrocarbons and are therefore of great economic importance.

  4. Folded waveguide coupler

    DOEpatents

    Owens, Thomas L.

    1988-03-01

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

  5. The protein folding network

    NASA Astrophysics Data System (ADS)

    Rao, Francesco; Caflisch, Amedeo

    2004-03-01

    Networks are everywhere. The conformation space of a 20-residue antiparallel beta-sheet peptide [1], sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. As previously found for the World-Wide Web as well as for social and biological networks , the conformation space contains highly connected hubs like the native state which is the most populated free energy basin. Furthermore, the network shows a hierarchical modularity [2] which is consistent with the funnel mechanism of folding [3] and is not observed for a random heteropolymer lacking a native state. Here we show that the conformation space network describes the free energy landscape without requiring projections into arbitrarily chosen reaction coordinates. The network analysis provides a basis for understanding the heterogeneity of the folding transition state and the existence of multiple pathways. [1] P. Ferrara and A. Caflisch, Folding simulations of a three-stranded antiparallel beta-sheet peptide, PNAS 97, 10780-10785 (2000). [2] Ravasz, E. and Barabási, A. L. Hierarchical organization in complex networks. Phys. Rev. E 67, 026112 (2003). [3] Dill, K. and Chan, H From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10-19 (1997)

  6. Ab initio RNA folding

    NASA Astrophysics Data System (ADS)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

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

  7. Ab initio RNA folding.

    PubMed

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

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

  8. Guiding the folding pathway of DNA origami

    NASA Astrophysics Data System (ADS)

    Dunn, Katherine E.; Dannenberg, Frits; Ouldridge, Thomas E.; Kwiatkowska, Marta; Turberfield, Andrew J.; Bath, Jonathan

    2015-09-01

    DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short `staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

  9. Folding and faulting of an elastic continuum

    PubMed Central

    Gourgiotis, Panos A.

    2016-01-01

    Folding is a process in which bending is localized at sharp edges separated by almost undeformed elements. This process is rarely encountered in Nature, although some exceptions can be found in unusual layered rock formations (called ‘chevrons’) and seashell patterns (for instance Lopha cristagalli). In mechanics, the bending of a three-dimensional elastic solid is common (for example, in bulk wave propagation), but folding is usually not achieved. In this article, the route leading to folding is shown for an elastic solid obeying the couple-stress theory with an extreme anisotropy. This result is obtained with a perturbation technique, which involves the derivation of new two-dimensional Green's functions for applied concentrated force and moment. While the former perturbation reveals folding, the latter shows that a material in an extreme anisotropic state is also prone to a faulting instability, in which a displacement step of finite size emerges. Another failure mechanism, namely the formation of dilation/compaction bands, is also highlighted. Finally, a geophysical application to the mechanics of chevron formation shows how the proposed approach may explain the formation of natural structures. PMID:27118925

  10. Folding funnels, binding funnels, and protein function.

    PubMed Central

    Tsai, C. J.; Kumar, S.; Ma, B.; Nussinov, R.

    1999-01-01

    Folding funnels have been the focus of considerable attention during the last few years. These have mostly been discussed in the general context of the theory of protein folding. Here we extend the utility of the concept of folding funnels, relating them to biological mechanisms and function. In particular, here we describe the shape of the funnels in light of protein synthesis and folding; flexibility, conformational diversity, and binding mechanisms; and the associated binding funnels, illustrating the multiple routes and the range of complexed conformers. Specifically, the walls of the folding funnels, their crevices, and bumps are related to the complexity of protein folding, and hence to sequential vs. nonsequential folding. Whereas the former is more frequently observed in eukaryotic proteins, where the rate of protein synthesis is slower, the latter is more frequent in prokaryotes, with faster translation rates. The bottoms of the funnels reflect the extent of the flexibility of the proteins. Rugged floors imply a range of conformational isomers, which may be close on the energy landscape. Rather than undergoing an induced fit binding mechanism, the conformational ensembles around the rugged bottoms argue that the conformers, which are most complementary to the ligand, will bind to it with the equilibrium shifting in their favor. Furthermore, depending on the extent of the ruggedness, or of the smoothness with only a few minima, we may infer nonspecific, broad range vs. specific binding. In particular, folding and binding are similar processes, with similar underlying principles. Hence, the shape of the folding funnel of the monomer enables making reasonable guesses regarding the shape of the corresponding binding funnel. Proteins having a broad range of binding, such as proteolytic enzymes or relatively nonspecific endonucleases, may be expected to have not only rugged floors in their folding funnels, but their binding funnels will also behave similarly

  11. Folding at the birth of the nascent chain: coordinating translation with co-translational folding.

    PubMed

    Zhang, Gong; Ignatova, Zoya

    2011-02-01

    In the living cells, the folding of many proteins is largely believed to begin co-translationally, during their biosynthesis at the ribosomes. In the ribosomal tunnel, the nascent peptide may establish local interactions and stabilize α-helical structures. Long-range contacts are more likely outside the ribosomes after release of larger segments of the nascent chain. Examples suggest that domains can attain native-like structure on the ribosome with and without population of folding intermediates. The co-translational folding is limited by the speed of the gradual extrusion of the nascent peptide which imposes conformational restraints on its folding landscape. Recent experimental and in silico modeling studies indicate that translation kinetics fine-tunes co-translational folding by providing a time delay for sequential folding of distinct portions of the nascent chain.

  12. Information from folds: A review

    NASA Astrophysics Data System (ADS)

    Hudleston, Peter J.; Treagus, Susan H.

    2010-12-01

    Folds are spectacular geological structures that are seen in layered rock on many different scales. To mark 30 years of the Journal of Structural Geology, we review the information that can be gained from studies of folds in theory, experiment and nature. We first review theoretical considerations and modeling, from classical approaches to current developments. The subject is dominated by single-layer fold theory, with the assumption of perfect layer-parallel shortening, but we also review multilayer fold theory and modeling, and folding of layers that are oblique to principal stresses and strains. This work demonstrates that viscosity ratio, degree of non-linearity of the flow law, anisotropy, and the thickness and spacing distribution of layers of different competence are all important in determining the nature and strength of the folding instability. Theory and modeling provide the basis for obtaining rheological information from natural folds, through analysis of wavelength/thickness ratios of single layer folds, and fold shapes. They also provide a basis for estimating the bulk strain from folded layers. Information about folding mechanisms can be obtained by analysis of cleavage and fabric patterns in folded rocks, and the history of deformation can be revealed by understanding how asymmetry can develop in folds, by how folds develop in shear zones, and how folds develop in more complex three-dimensional deformations.

  13. Fold and thrust systems in Mass Transport Deposits

    NASA Astrophysics Data System (ADS)

    Alsop, G. I.; Marco, S.; Levi, T.; Weinberger, R.

    2017-01-01

    Improvements in seismic reflection data from gravity-driven fold and thrust systems developed in offshore Mass Transport Deposits (MTDs) reveal a number of significant features relating to displacement along thrusts. However, the data are still limited by the resolution of the seismic method, and are unable to provide detail of local fold and thrust processes. Investigation of exceptional gravity-driven contractional structures forming part of MTDs in lacustrine deposits of the Dead Sea Basin, enables us to present the first detailed outcrop analysis of fold and thrust systems cutting unlithified 'soft' sediments. We employ a range of established geometric techniques to our case study, including dip isogons, fault-propagation fold charts and displacement-distance diagrams previously developed for investigation of thrusts and folds in lithified rocks. Fault-propagation folds in unlithified sediments display tighter interlimb angles compared to models developed for lithified sequences. Values of stretch, which compares the relative thickness of equivalent hangingwall and footwall sequences measured along the fault plane, may be as low as only 0.3, which is significantly less than the minimum 0.5 values reported from thrusts cutting lithified rocks, and reflects the extreme variation in stratigraphic thickness around thrust-related folds. We suggest that the simple shear component of deformation in unlithified sediments may modify the forelimb thickness and interlimb angles to a greater extent than in lithified rocks. The average spacing of thrust ramps and the thickness of the thrust sequence display an approximate 5:1 ratio across a range of scales in MTDs. In general, thicker hangingwall and footwall sequences occur with larger thrust displacements, although displacement patterns on thrusts cutting unlithified (yet cohesive) sediments are more variable than those in lithified rocks. Line-length restoration of thrust systems in MTDs reveals 42% shortening, which

  14. Toward understanding driving forces in membrane protein folding.

    PubMed

    Hong, Heedeok

    2014-12-15

    α-Helical membrane proteins are largely composed of nonpolar residues that are embedded in the lipid bilayer. An enigma in the folding of membrane proteins is how a polypeptide chain can be condensed into the compact folded state in the environment where the hydrophobic effect cannot strongly drive molecular interactions. Probably other forces such as van der Waals packing, hydrogen bonding, and weakly polar interactions, which are regarded less important in the folding of water-soluble proteins, should emerge. However, it is not clearly understood how those individual forces operate and how they are balanced for stabilizing membrane proteins. Studying this problem is not a trivial task mainly because of the methodological challenges in controlling the reversible folding of membrane proteins in the lipid bilayer. Overcoming the hurdles, meaningful progress has been made in the field in the last few decades. This review will focus on recent studies tackling the problem of driving forces in membrane protein folding.

  15. The Compact for Education.

    ERIC Educational Resources Information Center

    Harrington, Fred Harvey

    The Compact for Education is not yet particularly significant either for good or evil. Partly because of time and partly because of unreasonable expectations, the Compact is not yet a going concern. Enthusiasts have overestimated Compact possibilities and opponents have overestimated its dangers, so if the organization has limited rather than…

  16. Effects of heme on the structure of the denatured state and folding kinetics of cytochrome b562.

    PubMed

    Garcia, Pascal; Bruix, Marta; Rico, Manuel; Ciofi-Baffoni, Simone; Banci, Lucia; Ramachandra Shastry, M C; Roder, Heinrich; de Lumley Woodyear, Thierry; Johnson, Christopher M; Fersht, Alan R; Barker, Paul D

    2005-02-11

    Heme-linked proteins, such as cytochromes, are popular subjects for protein folding studies. There is the underlying question of whether the heme affects the structure of the denatured state by cross-linking it and forming other interactions, which would perturb the folding pathway. We have studied wild-type and mutant cytochrome b562 from Escherichia coli, a 106 residue four-alpha-helical bundle. The holo protein apparently refolds with a half-life of 4 micros in its ferrous state. We have analysed the folding of the apo protein using continuous-flow fluorescence as well as stopped-flow fluorescence and CD. The apo protein folded much more slowly with a half-life of 270 micros that was unaffected by the presence of exogenous heme. We examined the nature of the denatured states of both holo and apo proteins by NMR methods over a range of concentrations of guanidine hydrochloride. The starting point for folding of the holo protein in concentrations of denaturant around the denaturation transition was a highly ordered native-like species with heme bound. Fully denatured holo protein at higher concentrations of denaturant consisted of denatured apo protein and free heme. Our results suggest that the very fast folding species of denatured holo protein is in a compact state, whereas the normal folding pathway from fully denatured holo protein consists of the slower folding of the apo protein followed by the binding of heme. These data should be considered in the analysis of folding of heme proteins.

  17. Folds on Europa

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This image, acquired by NASA's Galileo spacecraft on September 26, 1998, shows features on the surface of Jupiter's moon Europa that a scientific report published today interprets as signs of compressive folding.

    The imaged area is in the Astypalaea Linea region of Europa's southern hemisphere, seen with low-angle sunshine coming from the upper right. North is toward the top.

    Astypalaea Linea is the smooth, gray area that stretches from north to south across the image mosaic. It is thought to have formed by a combination of pulling apart and sliding of the icy surface. The telltale fold features are within the smoother portions of the surface between the more dominant ridges, which are attributed to upwelling of material through surface ice. In the smooth areas, the surface has gentle swells and dips, which show most clearly in the version on the right, processed to accentuate broader-scale shapes. For example, a dip about 15 kilometers (about 10 miles) wide cuts diagonally across the northern half of the largest smooth area, and a rise runs parallel to that in the southern half of the smooth area. closeup detail

    Louise M. Prockter, at Johns Hopkins University, and Robert T. Pappalardo, at Brown University, report in the journal Science today that those rises, or anticlines, and dips, or synclines, appear to be the result of compression causing the crust to fold.

    Additional evidence comes from smaller features more visible in the version on the left, covering the same area. At the crest of the gentle rise in the largest smooth area are small fractures that could be caused by the stretching stress of bending the surface layer upwards. Similarly, at the bottom of the adjacent dip are small, wrinkle-like ridges that could be caused by stress from bending the surface layer downwards.

    The Jet Propulsion Laboratory, Pasadena, Calif., manages the Galileo mission for NASA's Office of Space Science, Washington, D.C. JPL is a division of the California

  18. Protein photo-folding and quantum folding theory.

    PubMed

    Luo, Liaofu

    2012-06-01

    The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from quantum folding theory by use of a field-theoretical method. All protein photo-folding processes are compared with common protein folding without the interaction of photons (non-radiative folding). It is demonstrated that there exists a common factor (thermo-averaged overlap integral of the vibration wave function, TAOI) for protein folding and protein photo-folding. Based on this finding it is predicted that (i) the stimulated photo-folding rates and the photon-protein resonance Raman scattering sections show the same temperature dependence as protein folding; (ii) the spectral line of the electronic transition is broadened to a band that includes an abundant vibration spectrum without and with conformational transitions, and the width of each vibration spectral line is largely reduced. The particular form of the folding rate-temperature relation and the abundant spectral structure imply the existence of quantum tunneling between protein conformations in folding and photo-folding that demonstrates the quantum nature of the motion of the conformational-electronic system.

  19. Statistical properties of a folded elastic rod

    NASA Astrophysics Data System (ADS)

    Bayart, Elsa; Deboeuf, Stéphanie; Boué, Laurent; Corson, Francis; Boudaoud, Arezki; Adda-Bedia, Mokhtar

    2010-03-01

    A large variety of elastic structures naturally seem to be confined into environments too small to accommodate them; the geometry of folded structures span a wide range of length-scales. The elastic properties of these confined systems are further constrained by self-avoidance as well as by the dimensionality of both structures and container. To mimic crumpled paper, we devised an experimental setup to study the packing of a dimensional elastic object in 2D geometries: an elastic rod is folded at the center of a circular Hele-Shaw cell by a centripetal force. The initial configuration of the rod and the acceleration of the rotating disk allow to span different final folded configurations while the final rotation speed controls the packing intensity. Using image analysis we measure geometrical and mechanical properties of the folded configurations, focusing on length, curvature and energy distributions.

  20. Folding of Nucleosome Arrays

    NASA Astrophysics Data System (ADS)

    Howell, Steven; Jimenez-Useche, Isabel; Andresen, Kurt; Yuan, Chongli; Qiu, Xiangyun

    2014-03-01

    Chromatin conformation and dynamics is central to gene functions including packaging, regulation, and repair. At the molecular level, the basic building block of chromatin is a nucleosome core particle (NCP) made of 147 base pairs (bp) of dsDNA wrapped around an octamer of histone proteins. These NCPs are connected by short 10-90 bps of linker DNA as beads on a string. Key factors determining the packaging of NCP arrays to form chromatin include ionic condition, linker DNA length, and epigenetic modifications, especially of the histone tails. We have investigated how the conformations of model tetra-NCP arrays are modulated by these factors using small angle x-ray scattering (SAXS). Here we present recent studies of the effects of ion (KCl and MgCl2), linker length, and histone modification (tail deletions) on NCP arrays. Our SAXS measurement makes it possible to learn about both the global compaction of NCP arrays and local inter-NCP spatial correlations within the same array.

  1. Critical State Finite Element Models of Contractional Fault-Related Folding: Structural and Mechanical Analyses

    NASA Astrophysics Data System (ADS)

    Albertz, M.; Lingrey, S.; Sanz, P. F.

    2011-12-01

    -length methods are grossly in error. Therefore, for a more accurate inverse model of fault-related folding, residual non-flexural-slip strains need to be applied; dilatation strains range between -0.1 and -0.3. These results suggest that appreciable discrepancies exist between simplistic flexural-slip based kinematic restoration techniques and more complicated strain paths for lithologically diverse fault-related folds in nature. In addition, we examine in detail the mechanical basis for the characteristic deformation styles. We track stress paths through time, investigate the complex stress fields developed throughout different fault-related folds and explain in a critical state mechanics framework under what circumstances failure results in shear band formation (and hence localized deformation) versus mechanical compaction (and thus distributed deformation).

  2. Cross folding in southern Bighorn basin

    SciTech Connect

    Gubbels, T.L.

    1986-08-01

    Analysis of Landsat Thematic Mapper imagery coupled with surface structural investigations of well-exposed folds in the southern Bighorn basin have revealed two northwest-trending folds that have been refolded. The eastern boundary of the Owl Creek Mountains is characterized by a well-defined alignment of folds that extend north-northwest from the Owl Creek thrust front. Bridger monocline, Wildhorse Butte anticline, and Red Hole anticline lie along this trend. Initial Laramide folding, probably during latest Cretaceous time, resulted in a single, continuous, north-northwest-trending anticline with a southwestward vergence. This anticline was progressively unfolded from south to north as the Owl Creek Range was thrust southward over the Wind River basin in earliest Eocene time; scissors-like vertical motion along this flexure rotated the axial surface of the early formed Bridger anticline, resulting in a monocline with a reversed vergence (northeastward). Formation of the Thermopolis/East Warm Springs anticline parallel to the north flank of the range accompanied thrusting and effectively refolded the northern end of the Wildhorse Butte anticline along an east-west axis. Faulting of the oversteepened south limb of the Red Hole cross fold was contemporaneous with folding. Cross-cutting fold axes in this area and the Mud Creek area to the west are best explained by a counterclockwise change in stress direction during the latest phase of the Laramide orogeny. Vertical movement along the eastern side of the Owl Creek Range results from differential motion in the hanging wall of the crystalline thrust sheet.

  3. How the genome folds

    NASA Astrophysics Data System (ADS)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  4. Folding of non-Euclidean curved shells

    NASA Astrophysics Data System (ADS)

    Bende, Nakul; Evans, Arthur; Innes-Gold, Sarah; Marin, Luis; Cohen, Itai; Santangelo, Christian; Hayward, Ryan

    2015-03-01

    Origami-based folding of 2D sheets has been of recent interest for a variety of applications ranging from deployable structures to self-folding robots. Though folding of planar sheets follows well-established principles, folding of curved shells involves an added level of complexity due to the inherent influence of curvature on mechanics. In this study, we use principles from differential geometry and thin shell mechanics to establish fundamental rules that govern folding of prototypical creased shells. In particular, we show how the normal curvature of a crease line controls whether the deformation is smooth or discontinuous, and investigate the influence of shell thickness and boundary conditions. We show that snap-folding of shells provides a route to rapid actuation on time-scales dictated by the speed of sound. The simple geometric design principles developed can be applied at any length-scale, offering potential for bio-inspired soft actuators for tunable optics, microfluidics, and robotics. This work was funded by the National Science Foundation through EFRI ODISSEI-1240441 with additional support to S.I.-G. through the UMass MRSEC DMR-0820506 REU program.

  5. Folding and hydrodynamics of a DNA i-motif from the c-MYC promoter determined by fluorescent cytidine analogs.

    PubMed

    Reilly, Samantha M; Lyons, Daniel F; Wingate, Sara E; Wright, Robert T; Correia, John J; Jameson, David M; Wadkins, Randy M

    2014-10-07

    The four-stranded i-motif (iM) conformation of cytosine-rich DNA has importance to a wide variety of biochemical systems that range from their use in nanomaterials to potential roles in oncogene regulation. The iM structure is formed at slightly acidic pH, where hemiprotonation of cytosine results in a stable C-C(+) basepair. Here, we performed fundamental studies to examine iM formation from a C-rich strand from the promoter of the human c-MYC gene. We used a number of biophysical techniques to characterize both the hydrodynamic properties and folding kinetics of a folded iM. Our hydrodynamic studies using fluorescence anisotropy decay and analytical ultracentrifugation show that the iM structure has a compact size in solution and displays the rigidity of a double strand. By studying the rates of circular dichroism spectral changes and quenching of fluorescent cytidine analogs, we also established a mechanism for the folding of a random coil oligo into the iM. In the course of determining this folding pathway, we established that the fluorescent dC analogs tC° and PdC can be used to monitor individual residues of an iM structure and to determine the pKa of an iM. We established that the C-C(+) hydrogen bonding of certain bases initiates the folding of the iM structure. We also showed that substitutions in the loop regions of iMs give a distinctly different kinetic signature during folding compared with bases that are intercalated. Our data reveal that the iM passes through a distinct intermediate form between the unfolded and folded forms. Taken together, our results lay the foundation for using fluorescent dC analogs to follow structural changes during iM formation. Our technique may also be useful for examining folding and structural changes in more complex iMs.

  6. The folding of an ``average'' beta trefoil protein.

    NASA Astrophysics Data System (ADS)

    Gosavi, Shachi; Jennings, Pat; Onuchic, Jose

    2007-03-01

    The beta-trefoil fold is characterized by twelve beta strands folded into three similar beta-beta-beta-loop-beta (trefoil) units. The overall fold has pseudo-threefold symmetry and consists of a six stranded-barrel, capped by a triangular hairpin triplet. The loops connecting the beta-strands vary in length and structure. It is these loops that give the fold its varied binding capability and the binding sites lie in different parts of the fold. The beta-trefoil proteins have little sequence similarity (sometimes less than 17%) and bind a range of molecules, including other proteins, DNA, membranes and carbohydrates. Protein folding experiments have been performed on four of the beta trefoils, namely, interleukin-1 (IL1B), acidic and basic fibroblast growth factors (FGF-1 and FGF-2) and hisactophilin (HIS). These experiments indicate that the proteins fold by different routes. Folding simulations of the proteins identify the possible folding routes and also show that the shapes of the barriers are different for the different proteins. In this work, we design a model protein which contains only the core fold elements of the beta-trefoil fold. We compare the folding of this ``average'' protein to the folding of His, FGF and IL1B and make some connections with function.

  7. Predicting protein folds with fold-specific PSSM libraries.

    PubMed

    Hong, Yoojin; Chintapalli, Sree Vamsee; Ko, Kyung Dae; Bhardwaj, Gaurav; Zhang, Zhenhai; van Rossum, Damian; Patterson, Randen L

    2011-01-01

    Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies. Herein, we outline an effective method for fold recognition using sets of PSSMs, each of which is constructed for different protein folds. Our analyses demonstrate that FSL (Fold-specific Position Specific Scoring Matrix Libraries) can predict/relate structures given only their amino acid sequences of highly divergent proteins. This ability to detect distant relationships is dependent on low-identity sequence alignments obtained from FSL. Results from our experiments demonstrate that FSL perform well in recognizing folds from the "twilight-zone" SABmark dataset. Further, this method is capable of accurate fold prediction in newly determined structures. We suggest that by building complete PSSM libraries for all unique folds within the Protein Database (PDB), FSL can be used to rapidly and reliably annotate a large subset of protein folds at proteomic level. The related programs and fold-specific PSSMs for our FSL are publicly available at: http://ccp.psu.edu/download/FSLv1.0/.

  8. Evolutionary Optimization of Protein Folding

    PubMed Central

    Debès, Cédric; Wang, Minglei; Caetano-Anollés, Gustavo; Gräter, Frauke

    2013-01-01

    Nature has shaped the make up of proteins since their appearance, 3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last 1.5 billion years that began during the “big bang” of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions. PMID:23341762

  9. Electrotransfection of Polyamine Folded DNA Origami Structures.

    PubMed

    Chopra, Aradhana; Krishnan, Swati; Simmel, Friedrich C

    2016-10-12

    DNA origami structures are artificial molecular nanostructures in which DNA double helices are forced into a closely packed configuration by a multitude of DNA strand crossovers. We show that three different types of origami structures (a flat sheet, a hollow tube, and a compact origami block) can be formed in magnesium-free buffer solutions containing low (<1 mM) concentrations of the condensing agent spermidine. Much like in DNA condensation, the amount of spermidine required for origami folding is proportional to the DNA concentration. At excessive amounts, the structures aggregate and precipitate. In contrast to origami structures formed in conventional buffers, the resulting structures are stable in the presence of high electric field pulses, such as those commonly used for electrotransfection experiments. We demonstrate that spermidine-stabilized structures are stable in cell lysate and can be delivered into mammalian cells via electroporation.

  10. Disappearance of the negative charge in giant DNA with a folding transition.

    PubMed Central

    Yamasaki, Y; Teramoto, Y; Yoshikawa, K

    2001-01-01

    In the present study we measure the electrophoretic mobility of giant T4 DNA (166 kbp) by electrophoretic light scattering for the elongated and folded compact states at different spermidine (trivalent cation) concentrations in 50 mM sodium maleate buffer (pH 6.0). It is found that the electrophoretic mobility of elongated DNA in the absence of the multivalent cation is seven times greater than that of fully folded compact DNA, where, with the increase of the concentration of spermidine, an abrupt transition is generated after a gradual decrease of the mobility. An analysis of the electrophoretic mobility suggests that the folded compact DNA chains almost completely lose their negative charges, by taking into account the difference of friction mechanism between an elongated and folded compact state. From the single chain observation by use of fluorescence microscopy, it is found that a phase-segregated structure is generated at intermediate concentrations of spermidine. The gradual decrease of the electrophoretic mobility in the transition region is, thus, attributed to the formation of the segregated state, exhibiting partial electroneutralization in the folded part. Disappearance of the negative charges in the completely folded compact DNAs is discussed in relation to the mechanism of transition, in terms of a first-order phase transition. PMID:11371456

  11. Folding paper-based lithium-ion batteries for higher areal energy densities.

    PubMed

    Cheng, Qian; Song, Zeming; Ma, Teng; Smith, Bethany B; Tang, Rui; Yu, Hongyu; Jiang, Hanqing; Chan, Candace K

    2013-10-09

    Paper folding techniques are used in order to compact a Li-ion battery and increase its energy per footprint area. Full cells were prepared using Li4Ti5O12 and LiCoO2 powders deposited onto current collectors consisting of paper coated with carbon nanotubes. Folded cells showed higher areal capacities compared to the planar versions with a 5 × 5 cell folded using the Miura-ori pattern displaying a ~14× increase in areal energy density.

  12. Detachment folding, fold amplification, and diapirism in thrust wedge experiments

    NASA Astrophysics Data System (ADS)

    Bonini, Marco

    2003-12-01

    The relations between detachment folding, fold amplification, and salt diapirism in contractional settings have been investigated by means of scaled analogue models. The viscosity of the silicone layer simulating salt in nature and the shortening rates were combined in order to reproduce weak (type 1 models) and strong (type 2 models) décollements. Deformation patterns in the roof sequence exhibited two contrasting styles, (1) outward propagation of detachment folding along the décollement (OFP mode) and (2) passive roof duplex (PRD mode). In type 2 models, detachment folding propagated away from the most external thrust in the floor sequence, while in type 1 models, long-lived detachment folds almost invariably localized amplified above a floor thrust tip as a result of strain localization. A silicone wall intruded occasionally into the crestal graben of detachment folds in type 1 and OFP models. Best fitting of transition models data points indicates nonlinear relations with regression curves close to the equilateral hyperbola equation for both OFP-PRD and amplified detachment folds-box folds transitions. A quantitative comparison of model results with nature has been attempted by plotting salt-based fold-and-thrust belts data points on the scaled transition curves obtained from the modeling. Such a comparison relates shear stress products and ratios to the conditions favoring the amplification of detachment folds and the potential emplacement of ductile diapirs in their core. By reducing the roof sequence strength, pore fluid pressure λb is inferred to shift the equilibrium of fold-and-thrust belts toward the field of OFP and diapirism.

  13. Graphene folding on flat substrates

    SciTech Connect

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

    2014-10-28

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

  14. Changes of protein stiffness during folding detect protein folding intermediates.

    PubMed

    Małek, Katarzyna E; Szoszkiewicz, Robert

    2014-01-01

    Single-molecule force-quench atomic force microscopy (FQ-AFM) is used to detect folding intermediates of a simple protein by detecting changes of molecular stiffness of the protein during its folding process. Those stiffness changes are obtained from shape and peaks of an autocorrelation of fluctuations in end-to-end length of the folding molecule. The results are supported by predictions of the equipartition theorem and agree with existing Langevin dynamics simulations of a simplified model of a protein folding. In the light of the Langevin simulations the experimental data probe an ensemble of random-coiled collapsed states of the protein, which are present both in the force-quench and thermal-quench folding pathways.

  15. Dynamical compactness and sensitivity

    NASA Astrophysics Data System (ADS)

    Huang, Wen; Khilko, Danylo; Kolyada, Sergiĭ; Zhang, Guohua

    2016-05-01

    To link the Auslander point dynamics property with topological transitivity, in this paper we introduce dynamically compact systems as a new concept of a chaotic dynamical system (X , T) given by a compact metric space X and a continuous surjective self-map T : X → X. Observe that each weakly mixing system is transitive compact, and we show that any transitive compact M-system is weakly mixing. Then we discuss the relationships between it and other several stronger forms of sensitivity. We prove that any transitive compact system is Li-Yorke sensitive and furthermore multi-sensitive if it is not proximal, and that any multi-sensitive system has positive topological sequence entropy. Moreover, we show that multi-sensitivity is equivalent to both thick sensitivity and thickly syndetic sensitivity for M-systems. We also give a quantitative analysis for multi-sensitivity of a dynamical system.

  16. Stabilization of compactible waste

    SciTech Connect

    Franz, E.M.; Heiser, J.H. III; Colombo, P.

    1990-09-01

    This report summarizes the results of series of experiments performed to determine the feasibility of stabilizing compacted or compactible waste with polymers. The need for this work arose from problems encountered at disposal sites attributed to the instability of this waste in disposal. These studies are part of an experimental program conducted at Brookhaven National Laboratory (BNL) investigating methods for the improved solidification/stabilization of DOE low-level wastes. The approach taken in this study was to perform a series of survey type experiments using various polymerization systems to find the most economical and practical method for further in-depth studies. Compactible dry bulk waste was stabilized with two different monomer systems: styrene-trimethylolpropane trimethacrylate (TMPTMA) and polyester-styrene, in laboratory-scale experiments. Stabilization was accomplished by wetting or soaking compactible waste (before or after compaction) with monomers, which were subsequently polymerized. Three stabilization methods are described. One involves the in-situ treatment of compacted waste with monomers in which a vacuum technique is used to introduce the binder into the waste. The second method involves the alternate placement and compaction of waste and binder into a disposal container. In the third method, the waste is treated before compaction by wetting the waste with the binder using a spraying technique. A series of samples stabilized at various binder-to-waste ratios were evaluated through water immersion and compression testing. Full-scale studies were conducted by stabilizing two 55-gallon drums of real compacted waste. The results of this preliminary study indicate that the integrity of compacted waste forms can be readily improved to ensure their long-term durability in disposal environments. 9 refs., 10 figs., 2 tabs.

  17. Compact Proton Accelerator for Cancer Therapy

    SciTech Connect

    Chen, Y; Paul, A C

    2007-06-12

    An investigation is being made into the feasibility of making a compact proton dielectric wall (DWA) accelerator for medical radiation treatment based on the high gradient insulation (HGI) technology. A small plasma device is used for the proton source. Using only electric focusing fields for transporting and focusing the beam on the patient, the compact DWA proton accelerator m system can deliver wide and independent variable ranges of beam currents, energies and spot sizes.

  18. Structural Bridges through Fold Space

    PubMed Central

    Edwards, Hannah; Deane, Charlotte M.

    2015-01-01

    Several protein structure classification schemes exist that partition the protein universe into structural units called folds. Yet these schemes do not discuss how these units sit relative to each other in a global structure space. In this paper we construct networks that describe such global relationships between folds in the form of structural bridges. We generate these networks using four different structural alignment methods across multiple score thresholds. The networks constructed using the different methods remain a similar distance apart regardless of the probability threshold defining a structural bridge. This suggests that at least some structural bridges are method specific and that any attempt to build a picture of structural space should not be reliant on a single structural superposition method. Despite these differences all representations agree on an organisation of fold space into five principal community structures: all-α, all-β sandwiches, all-β barrels, α/β and α + β. We project estimated fold ages onto the networks and find that not only are the pairings of unconnected folds associated with higher age differences than bridged folds, but this difference increases with the number of networks displaying an edge. We also examine different centrality measures for folds within the networks and how these relate to fold age. While these measures interpret the central core of fold space in varied ways they all identify the disposition of ancestral folds to fall within this core and that of the more recently evolved structures to provide the peripheral landscape. These findings suggest that evolutionary information is encoded along these structural bridges. Finally, we identify four highly central pivotal folds representing dominant topological features which act as key attractors within our landscapes. PMID:26372166

  19. Pseudoknots in RNA folding landscapes

    PubMed Central

    Kucharík, Marcel; Hofacker, Ivo L.; Stadler, Peter F.; Qin, Jing

    2016-01-01

    Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these questions. Efficient coarse-graining methods are required to reduce the intractably vast energy landscapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuristic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary structures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded. Results: We generalize the BHG framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures. The occurrence and influence of pseudoknotted intermediates on the folding pathway, however, appear to depend very strongly on the individual RNAs so that no general rule can be inferred. Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and Supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html. Contact: qin@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID

  20. Shock compaction of molybdenum powder

    NASA Technical Reports Server (NTRS)

    Ahrens, T. J.; Kostka, D.; Vreeland, T., Jr.; Schwarz, R. B.; Kasiraj, P.

    1983-01-01

    Shock recovery experiments which were carried out in the 9 to 12 GPa range on 1.4 distension Mo and appear adequate to compact to full density ( 45 (SIGMA)m) powders were examined. The stress levels, however, are below those calculated to be from 100 to approx. 22 GPa which a frictional heating model predicts are required to consolidate approx. 10 to 50 (SIGMA)m particles. The model predicts that powders that have a distension of m=1.6 shock pressures of 14 to 72 GPa are required to consolidate Mo powders in the 50 to 10 (SIGMA)m range.

  1. Visualizing chaperone-assisted protein folding

    PubMed Central

    Horowitz, Scott; Salmon, Loïc; Koldewey, Philipp; Ahlstrom, Logan S.; Martin, Raoul; Quan, Shu; Afonine, Pavel V.; van den Bedem, Henry; Wang, Lili; Xu, Qingping; Trievel, Raymond C.; Brooks, Charles L.; Bardwell, James CA

    2016-01-01

    Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding, where obtaining structural ensembles of chaperone:substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a novel structural biology approach based on X-ray crystallography, termed Residual Electron and Anomalous Density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the E. coli chaperone Spy. This study resulted in a series of snapshots depicting the various folding states of Im7 while bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded and native-like states, and reveals how a substrate can explore its folding landscape while bound to a chaperone. PMID:27239796

  2. Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability

    PubMed Central

    Pancsa, Rita; Varadi, Mihaly; Tompa, Peter; Vranken, Wim F.

    2016-01-01

    Proteins fulfil a wide range of tasks in cells; understanding how they fold into complex three-dimensional (3D) structures and how these structures remain stable while retaining sufficient dynamics for functionality is essential for the interpretation of overall protein behaviour. Since the 1950's, solvent exchange-based methods have been the most powerful experimental means to obtain information on the folding and stability of proteins. Considerable expertise and care were required to obtain the resulting datasets, which, despite their importance and intrinsic value, have never been collected, curated and classified. Start2Fold is an openly accessible database (http://start2fold.eu) of carefully curated hydrogen/deuterium exchange (HDX) data extracted from the literature that is open for new submissions from the community. The database entries contain (i) information on the proteins investigated and the underlying experimental procedures and (ii) the classification of the residues based on their exchange protection levels, also allowing for the instant visualization of the relevant residue groups on the 3D structures of the corresponding proteins. By providing a clear hierarchical framework for the easy sharing, comparison and (re-)interpretation of HDX data, Start2Fold intends to promote a better understanding of how the protein sequence encodes folding and structure as well as the development of new computational methods predicting protein folding and stability. PMID:26582925

  3. Analysis of folded pulse forming line operation.

    PubMed

    Domonkos, M T; Watrous, J; Parker, J V; Cavazos, T; Slenes, K; Heidger, S; Brown, D; Wilson, D

    2014-09-01

    A compact pulse forming line (CPFL) concept based on a folded transmission line and high-breakdown strength dielectric was explored through an effort combining proof-of-principle experiments with electromagnetic modeling. A small-scale folded CPFL was fabricated using surface-mount ceramic multilayer capacitors. The line consisted of 150 capacitors close-packed in parallel and delivered a 300 ns flat-top pulse. The concept was carried to a 10 kV class device using a polymer-ceramic nanocomposite dielectric with a permittivity of 37.6. The line was designed for a 161 ns FWHM length pulse into a matched load. The line delivered a 110 ns FWHM pulse, and the pulse peak amplitude exceeded the matched load ideal. Transient electromagnetic analysis using the particle-in-cell code ICEPIC was conducted to examine the nature of the unexpected pulse shortening and distortion. Two-dimensional analysis failed to capture the anomalous behavior. Three-dimensional analysis replicated the pulse shape and revealed that the bends were largely responsible for the pulse shortening. The bends not only create the expected reflection of the incident TEM wave but also produce a non-zero component of the Poynting vector perpendicular to the propagation direction of the dominant electromagnetic wave, resulting in power flow largely external to the PFL. This analysis explains both the pulse shortening and the amplitude of the pulse.

  4. Problem Solving through Paper Folding

    ERIC Educational Resources Information Center

    Wares, Arsalan

    2014-01-01

    The purpose of this article is to describe a couple of challenging mathematical problems that involve paper folding. These problem-solving tasks can be used to foster geometric and algebraic thinking among students. The context of paper folding makes some of the abstract mathematical ideas involved relatively concrete. When implemented…

  5. How do chaperonins fold protein?

    PubMed Central

    Motojima, Fumihiro

    2015-01-01

    Protein folding is a biological process that is essential for the proper functioning of proteins in all living organisms. In cells, many proteins require the assistance of molecular chaperones for their folding. Chaperonins belong to a class of molecular chaperones that have been extensively studied. However, the mechanism by which a chaperonin mediates the folding of proteins is still controversial. Denatured proteins are folded in the closed chaperonin cage, leading to the assumption that denatured proteins are completely encapsulated inside the chaperonin cage. In contrast to the assumption, we recently found that denatured protein interacts with hydrophobic residues at the subunit interfaces of the chaperonin, and partially protrude out of the cage. In this review, we will explain our recent results and introduce our model for the mechanism by which chaperonins accelerate protein folding, in view of recent findings. PMID:27493521

  6. Denatured proteins and early folding intermediates simulated in a reduced conformational space.

    PubMed

    Kmiecik, Sebastian; Kurcinski, Mateusz; Rutkowska, Aleksandra; Gront, Dominik; Kolinski, Andrzej

    2006-01-01

    Conformations of globular proteins in the denatured state were studied using a high-resolution lattice model of proteins and Monte Carlo dynamics. The model assumes a united-atom and high-coordination lattice representation of the polypeptide conformational space. The force field of the model mimics the short-range protein-like conformational stiffness, hydrophobic interactions of the side chains and the main-chain hydrogen bonds. Two types of approximations for the short-range interactions were compared: simple statistical potentials and knowledge-based protein-specific potentials derived from the sequence-structure compatibility of short fragments of protein chains. Model proteins in the denatured state are relatively compact, although the majority of the sampled conformations are globally different from the native fold. At the same time short protein fragments are mostly native-like. Thus, the denatured state of the model proteins has several features of the molten globule state observed experimentally. Statistical potentials induce native-like conformational propensities in the denatured state, especially for the fragments located in the core of folded proteins. Knowledge-based protein-specific potentials increase only slightly the level of similarity to the native conformations, in spite of their qualitatively higher specificity in the native structures. For a few cases, where fairly accurate experimental data exist, the simulation results are in semiquantitative agreement with the physical picture revealed by the experiments. This shows that the model studied in this work could be used efficiently in computational studies of protein dynamics in the denatured state, and consequently for studies of protein folding pathways, i.e. not only for the modeling of folded structures, as it was shown in previous studies. The results of the present studies also provide a new insight into the explanation of the Levinthal's paradox.

  7. Compressive laser ranging.

    PubMed

    Babbitt, Wm Randall; Barber, Zeb W; Renner, Christoffer

    2011-12-15

    Compressive sampling has been previously proposed as a technique for sampling radar returns and determining sparse range profiles with a reduced number of measurements compared to conventional techniques. By employing modulation on both transmission and reception, compressive sensing in ranging is extended to the direct measurement of range profiles without intermediate measurement of the return waveform. This compressive ranging approach enables the use of pseudorandom binary transmit waveforms and return modulation, along with low-bandwidth optical detectors to yield high-resolution ranging information. A proof-of-concept experiment is presented. With currently available compact, off-the-shelf electronics and photonics, such as high data rate binary pattern generators and high-bandwidth digital optical modulators, compressive laser ranging can readily achieve subcentimeter resolution in a compact, lightweight package.

  8. 3D fold growth rates in transpressional tectonic settings

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel

    2015-04-01

    Geological folds are inherently three-dimensional (3D) structures; hence, they also grow in 3D. In this study, fold growth in all three dimensions is quantified numerically using a finite-element algorithm for simulating deformation of Newtonian media in 3D. The presented study is an extension and generalization of the work presented in Frehner (2014), which only considered unidirectional layer-parallel compression. In contrast, the full range from strike slip settings (i.e., simple shear) to unidirectional layer-parallel compression is considered here by varying the convergence angle of the boundary conditions; hence the results are applicable to general transpressional tectonic settings. Only upright symmetrical single-layer fold structures are considered. The horizontal higher-viscous layer exhibits an initial point-like perturbation. Due to the mixed pure- and simple shear boundary conditions a mechanical buckling instability grows from this perturbation in all three dimensions, described by: Fold amplification (vertical growth): Fold amplification describes the growth from a fold shape with low limb-dip angle to a shape with higher limb-dip angle. Fold elongation (growth parallel to fold axis): Fold elongation describes the growth from a dome-shaped (3D) structure to a more cylindrical fold (2D). Sequential fold growth (growth perpendicular to fold axial plane): Sequential fold growth describes the growth of secondary (and further) folds adjacent to the initial isolated fold. The term 'lateral fold growth' is used as an umbrella term for both fold elongation and sequential fold growth. In addition, the orientation of the fold axis is tracked as a function of the convergence angle. Even though the absolute values of all three growth rates are markedly reduced with increasing simple-shear component at the boundaries, the general pattern of the quantified fold growth under the studied general-shear boundary conditions is surprisingly similar to the end

  9. Inframammary fold: a histologic reappraisal.

    PubMed

    Muntan, C D; Sundine, M J; Rink, R D; Acland, R D

    2000-02-01

    The inframammary fold is a defining element in the shape and structure of the female breast. It should be preserved whenever possible in ablative procedures and recreated accurately when the breast is reconstructed after mastectomy. To date, no accurate anatomic description of this essential structure exists. Previous studies have suggested that the fold is produced by a supporting ligament running from the dermis in the fold region to a variety of locations on the rib cage. This clinic's experience with mastectomy, augmentation mammaplasty, and breast reconstruction does not support the existence of a ligamentous structure. To define the structure of the inframammary fold, 10 female and 2 male cadavers were studied. The anterior chest wall was removed en bloc and frozen in orthostatic position. Parasagittal sections were made of the inframammary fold with the chest wall intact. After decalcification of the ribs and routine histologic preparation, thin sections were stained with Gomori's trichrome. On light microscopic examination, no demonstrable ligamentous structure of dense regular connective tissue could be identified in the fold region in any of the 12 specimens. Superficial and deep fascial layers were uniformly observed anterior to the pectoralis major and serratus anterior muscles. The superficial fascia was connected to the dermis in the fold region in a variety of configurations. In some cases, the deep fascia fused with the superficial fascia and dermis at the fold level. In other cases, bundles of collagen fibers arising from the superficial fascial layer were found to insert into the dermis at the inframammary fold, slightly inferior to it, or both. These bundles were observed consistently in sections from the sternum to the middle axillary line. They were distinct from Cooper's suspensory ligaments, which are seen more superiorly in the glandular tissue.

  10. Compact microchannel system

    DOEpatents

    Griffiths, Stewart

    2003-09-30

    The present invention provides compact geometries for the layout of microchannel columns through the use of turns and straight channel segments. These compact geometries permit the use of long separation or reaction columns on a small microchannel substrate or, equivalently, permit columns of a fixed length to occupy a smaller substrate area. The new geometries are based in part on mathematical analyses that provide the minimum turn radius for which column performance in not degraded. In particular, we find that straight channel segments of sufficient length reduce the required minimum turn radius, enabling compact channel layout when turns and straight segments are combined. The compact geometries are obtained by using turns and straight segments in overlapped or nested arrangements to form pleated or coiled columns.

  11. Phased array compaction cell for measurement of the transversely isotropic elastic properties of compacting sediments

    SciTech Connect

    Nihei, K.T.; Nakagawa, S.; Reverdy, F.; Meyer, L.R.; Duranti, L.; Ball, G.

    2010-12-15

    Sediments undergoing compaction typically exhibit transversely isotropic (TI) elastic properties. We present a new experimental apparatus, the phased array compaction cell, for measuring the TI elastic properties of clay-rich sediments during compaction. This apparatus uses matched sets of P- and S-wave ultrasonic transducers located along the sides of the sample and an ultrasonic P-wave phased array source, together with a miniature P-wave receiver on the top and bottom ends of the sample. The phased array measurements are used to form plane P-waves that provide estimates of the phase velocities over a range of angles. From these measurements, the five TI elastic constants can be recovered as the sediment is compacted, without the need for sample unloading, recoring, or reorienting. This paper provides descriptions of the apparatus, the data processing, and an application demonstrating recovery of the evolving TI properties of a compacting marine sediment sample.

  12. The role of stress on chemical compaction of illite shale: An experimental study

    NASA Astrophysics Data System (ADS)

    Bruijn, R. H. C.; Almqvist, B. S. G.; Benson, P. M.; Hirt, A. M.

    2012-04-01

    range from 1.0 to 17.1 % in porosity, reflecting variation in experimental conditions. SEM investigation identifies chemical compaction as an increasing amount of authigenic phengite and biotite, coupled with a decrease in detrital illite and related sub-micron clay-micropores as a function of porosity. Ultrafine (< 2 μm) quartz and biotite form with a shape-preferred orientation, which gives rise to foliation. This microstructure development is ascribed to fluid-assisted mass transfer, which is controlled by permeability anisotropy. The presence of micro-folds and kinks in both isostatically compacted samples, and samples that were compacted by axial compression, is explained by exhausted pore closure. Pore closure is the dominant strain accommodation mechanism in all compressed samples. Magnetic fabric and crystallographic texture show a linear evolution with compaction, regardless of the applied stress field. We observe that differential stress accelerates chemical compaction, without modifying the evolution of fabric and the measured properties, and state that laboratory strain rates did not change the mechanisms of compaction. We conclude that tectonic forces have no effect on the development of magnetic properties and texture in chemically compacting pelites when strain is accommodated primarily by pore closing.

  13. Theory of RNA Folding: From Hairpins to Ribozymes

    NASA Astrophysics Data System (ADS)

    Thirumalai, D.; Hyeon, Changbong

    The rugged nature of the RNA folding landscape is determined by a number of conflicting interactions like repulsive electrostatic potential between the charges on the phosphate groups, constraints due to loop entropy, base stacking, and hydrogen bonding that operate on various length scales. As a result the kinetics of self-assembly of RNA is complex, but can be easily modulated by varying the concentrations, sizes, and shapes of the counterions. Here, we provide a theoretical description of RNA folding that is rooted in the energy landscape perspective and polyelectrolyte theory. A consequence of the rugged folding landscape is that, self-assembly of RNA into compact three-dimensional structures occurs by parallel routes, and is best described by the kinetic partitioning mechanism (KPM). According to KPM one fraction of molecules (Φ) folds rapidly while the remaining gets trapped in one of several competing basins of attraction. The partition factor Φ can be altered by point mutations as well as by changing the initial conditions such as ion concentration, size and valence of ions. We show that even hairpin formation, either by temperature or force quench, captures much of the features of folding of large RNA molecules. Despite the complexity of the folding process, we show that the KPM concepts from polyelectrolyte theory, and charge density of ions can be used to explain the stability, pathways and their diversity, and the plastiCity of the transition State ensemble of RNA self-assembly.

  14. Ion specificity in α-helical folding kinetics.

    PubMed

    von Hansen, Yann; Kalcher, Immanuel; Dzubiella, Joachim

    2010-11-04

    The influence of the salts KCl, NaCl, and NaI at molar concentrations on the α-helical folding kinetics of the alanine-based oligopeptide Ace-AEAAAKEAAAKA-Nme is investigated by means of (explicit-water) molecular dynamics simulations and a diffusional analysis. The mean first passage times for folding and unfolding are found to be highly salt-specific. In particular, the folding times increase about 1 order of magnitude for the sodium salts. The drastic slowing can be traced to long-lived, compact configurations of the partially folded peptide, in which sodium ions are tightly bound by several carbonyl and carboxylate groups. This multiple trapping leads to a nonexponential residence time distribution of the cations in the first solvation shell of the peptide. The analysis of α-helical folding in the framework of diffusion in a reduced (one-dimensional) free energy landscape further shows that the salt not only specifically modifies equilibrium properties but also induces kinetic barriers due to individual ion binding. In the sodium salts, for instance, the peptide's configurational mobility (or "diffusivity") can decrease about 1 order of magnitude. This study demonstrates the highly specific action of ions and highlights the intimate coupling of intramolecular friction and solvent effects in protein folding.

  15. Fog spontaneously folds mosquito wings

    NASA Astrophysics Data System (ADS)

    Dickerson, Andrew K.; Liu, Xing; Zhu, Ting; Hu, David L.

    2015-02-01

    The flexibility of insect wings confers aerodynamic benefits, but can also present a hazard if exposed to fog or dew. Fog can cause water to accumulate on wings, bending them into tight taco shapes and rendering them useless for flight. In this combined experimental and theoretical study, we use high-speed video to film the spontaneous folding of isolated mosquito wings due to the evaporation of a water drop. We predict shapes of the deformed wing using two-dimensional elastica theory, considering both surface tension and Laplace pressure. We also recommend fold-resistant geometries for the wings of flapping micro-aerial vehicles. Our work reveals the mechanism of insect wing folding and provides a framework for further study of capillarity-driven folding in both natural and biomimetic systems at small scales.

  16. Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation

    PubMed Central

    Chen, Mark M.; Bartlett, Alice I.; Nerenberg, Paul S.; Friel, Claire T.; Hackenberger, Christian P. R.; Stultz, Collin M.; Radford, Sheena E.; Imperiali, Barbara

    2010-01-01

    N-linked glycosylation modulates protein folding and stability through a variety of mechanisms. As such there is considerable interest in the development of general rules to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in the design and development of modified proteins with advantageous properties. In this study, expressed protein ligation is used to create site-specifically glycosylated variants of the bacterial immunity protein Im7 modified with the chitobiose disaccharide (GlcNAc-GlcNAc). Glycans were introduced at seven solvent exposed sites within the Im7 sequence and the kinetic and thermodynamic consequences of N-linked glycosylation analyzed. The values for glycan incorporation were found to range from +5.2 to -3.8 kJ·mol-1. In several cases, glycosylation influences folding by modulating the local conformational preferences of the glycosylated sequence. These locally mediated effects are most prominent in the center of α-helices where glycosylation negatively effects folding and in compact turn motifs between segments of ordered secondary structure where glycosylation promotes folding and enhances the overall stability of the native protein. The studies also provide insight into why glycosylation is commonly identified at the transition between different types of secondary structure and when glycosylation may be used to elaborate protein structure to protect disordered sequences from proteolysis or immune system recognition. PMID:21148421

  17. Compact telescope for free-space communications

    NASA Astrophysics Data System (ADS)

    Draganov, Vladimir; James, Daryl G.

    2002-10-01

    Several types of telescopes are used for free space telecommunications. The most common are Cassegrain and Gregorian telescopes. The main difference between Cassegrain and Gregorian optical systems is that Gregorian telescopes employ a concave secondary mirror located beyond the focus of the primary mirror. This results in longer tube lengths, as the distance between mirrors is slightly more than the sum of their focal lengths, which is the reason Cassegrain systems are the most common. In addition, Gregorian telescopes produce an upright image, while Cassegrain telescopes produce an inverted image. FSONA is presenting a new compact optical system, which can be described as a modified Gregorian telescope. This telescope is ideally suited for free space optical communications but also has many other applications. The compact telescope is created from a standard Gregorian system by flipping the secondary mirror over a folding mirror installed approximately in the middle of the optical path between primary and secondary mirrors. In this manner, the primary mirror is constructed with a concentric "double curved" geometry, and a central obscuring folding mirror which matches the diameter of the smaller curve of the primary is mounted a short distance in front. This "double curved" geometry is easily produced using diamond turning technology, and the result is a compact telescope approximately 1/2 the length of a regular Gregorian telescope and roughly 2/3 the length of a Cassegrain telescope. There are several advantages to using this type of telescope: 1. The system is very compact. Telescope can be as short as 1/7 of the focal length of the system. 2. For Cassegrain and Gregorian systems it is very critical to keep tight tolerances on the centration between primary and secondary mirrors. The modified Gregorian telescope will always have perfect centration because both curved surfaces are machined at the same time on a diamond turning lathe. The folding mirror is flat

  18. Protein folding by motion planning

    NASA Astrophysics Data System (ADS)

    Thomas, Shawna; Song, Guang; Amato, Nancy M.

    2005-12-01

    We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMs). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structures, assuming we know the native fold. A feature of our PRM-based framework is that the large sets of folding pathways in the roadmaps it produces, in just a few hours on a desktop PC, provide global information about the protein's energy landscape. This is an advantage over other simulation methods such as molecular dynamics or Monte Carlo methods which require more computation and produce only a single trajectory in each run. In our initial studies, we obtained encouraging results for several small proteins. In this paper, we investigate more sophisticated techniques for analyzing the folding pathways in our roadmaps. In addition to more formally revalidating our previous results, we present a case study showing that our technique captures known folding differences between the structurally similar proteins G and L. This research was supported in part by NSF CAREER Award CCR-9624315, NSF Grants ACI-9872126, EIA-9975018, EIA-0103742, EIA-9805823, ACR-0113971, CCR-0113974, EIA-9810937, EIA-0079874 and the Texas Higher Education Coordinating Board grant ATP-000512-0261-2001. ST was supported in part by an NSF Graduate Research Fellowship. GS was supported in part by an IBM PhD Fellowship.

  19. On hydrodynamic interpretation of folding of an α-helical protein

    NASA Astrophysics Data System (ADS)

    Andryushchenko, V. A.; Chekmarev, S. F.

    2016-11-01

    Using the method of molecular dynamics, the simulation of folding of an α-helical protein from the unfolded to compact and functional (native) state is performed. The protein folding is interpreted as a stationary motion of a compressible "folding fluid". It is shown that the densities of folding fluxes obey the same similarity relations as the velocities of an incompressible fluid in the Kolmogorov's turbulence theory, except that instead of the rate of change of kinetic energy per mass unit, the rate of change of flux variance per volume unit plays the role of the key parameter.

  20. Self-folding graphene-polymer bilayers

    SciTech Connect

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

    2015-05-18

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

  1. Structure of a Folding Intermediate Reveals the Interplay Between Core and Peripheral Elements in RNA Folding

    SciTech Connect

    Baird, Nathan J.; Westhof, Eric; Qin, Hong; Pan, Tao; Sosnick, Tobin R.

    2010-07-13

    Though the molecular architecture of many native RNA structures has been characterized, the structures of folding intermediates are poorly defined. Here, we present a nucleotide-level model of a highly structured equilibrium folding intermediate of the specificity domain of the Bacillus subtilis RNase P RNA, obtained using chemical and nuclease mapping, circular dichroism spectroscopy, small-angle X-ray scattering and molecular modeling. The crystal structure indicates that the 154 nucleotide specificity domain is composed of several secondary and tertiary structural modules. The structure of the intermediate contains modules composed of secondary structures and short-range tertiary interactions, implying a sequential order of tertiary structure formation during folding. The intermediate lacks the native core and several long-range interactions among peripheral regions, such as a GAAA tetraloop and its receptor. Folding to the native structure requires the local rearrangement of a T-loop in the core in concert with the formation of the GAAA tetraloop-receptor interaction. The interplay of core and peripheral structure formation rationalizes the high degree of cooperativity observed in the folding transition leading to the native structure.

  2. Compact Star Time Scales

    NASA Astrophysics Data System (ADS)

    Swank, J. H.

    1996-12-01

    A major goal of RXTE is to investigate the fastest timing signals from compact stars, especially neutron stars and black holes. Signals have now been found from many (at least nine) low mass X-ray binaries containing neutron stars in the frequency range (100-1200 Hz) expected for the rotation period of the neutron star after being spun up by accretion over a long period. The kilohertz frequency domain for these sources is simpler than the domain of oscillations below about 50 Hz in that a few isolated features can dominate over white noise. However there are three main features to consider (not all present at the same time) and at least two are quasiperiodic with varying widths and frequencies. Several models are pitting their predictions against the behavior of these features, but the bursters, especially, appear to be revealing the neutron stars's spin. It is consistent with our beliefs that no black hole candidate has shown the same complex of signals, although at least one QPO frequency of a few hundred Hz could be expected in black hole candidates by analogy to the 67 Hz observed from GRS 1915+105. The observations also provide critical tests of the interpretions of the lower frequency (5-50 Hz) QPO and the variable noise seen in both low magnetic field neutron stars and black hole candidates. The kilohertz features have not been seen from the accreting pulsars with relatively high magnetic fields, but high luminosity pulsars (such as last year's transient, GRO J1744-28) reveal signatures of the dynamic interaction between the accretion flow, the magnetic field, and perhaps the neutron star surface in addition to their coherent pulsations.

  3. Mitotic chromosome compaction via active loop extrusion

    NASA Astrophysics Data System (ADS)

    Goloborodko, Anton; Imakaev, Maxim; Marko, John; Mirny, Leonid; MIT-Northwestern Team

    During cell division, two copies of each chromosome are segregated from each other and compacted more than hundred-fold into the canonical X-shaped structures. According to earlier microscopic observations and the recent Hi-C study, chromosomes are compacted into arrays of consecutive loops of ~100 kilobases. Mechanisms that lead to formation of such loop arrays are largely unknown. Here we propose that, during cell division, chromosomes can be compacted by enzymes that extrude loops on chromatin fibers. First, we use computer simulations and analytical modeling to show that a system of loop-extruding enzymes on a chromatin fiber self-organizes into an array of consecutive dynamic loops. Second, we model the process of loop extrusion in 3D and show that, coupled with the topo II strand-passing activity, it leads to robust compaction and segregation of sister chromatids. This mechanism of chromosomal condensation and segregation does not require additional proteins or specific DNA markup and is robust against variations in the number and properties of such loop extruding enzymes. Work at NU was supported by the NSF through Grants DMR-1206868 and MCB-1022117, and by the NIH through Grants GM105847 and CA193419. Work at MIT was supported by the NIH through Grants GM114190 R01HG003143.

  4. Retention of local conformational compactness in unfolding of barnase; Contribution of end-to-end interactions within quasi-modules.

    PubMed

    Shinoda, Kazuki; Takahashi, Ken-Ichi; Go, Mitiko

    2007-01-01

    To understand how protein reduces the conformational space to be searched for the native structure, it is crucial to characterize ensembles of conformations on the way of folding processes, in particular ensembles of relatively long-range structures connecting between an extensively unfolded state and a state with a native-like overall chain topology. To analyze such intermediate conformations, we performed multiple unfolding molecular dynamics simulations of barnase at 498K. Some short-range structures such as part of helix and turn were well sustained while most of the secondary structures and the hydrophobic cores were eventually lost, which is consistent with the results by other experimental and computational studies. The most important novel findings were persistence of long-range relatively compact substructures, which was captured by exploiting the concept of module. Module is originally introduced to describe the hierarchical structure of a globular protein in the native state. Modules are conceptually such relatively compact substructures that are resulted from partitioning the native structure of a globular protein completely into several contiguous segments with the least extended conformations. We applied this concept of module to detect a possible hierarchical structure of each snapshot structure in unfolding processes as well. Along with this conceptual extension, such detected relatively compact substructures are named quasi-modules. We found almost perfect persistence of quasi-module boundaries that are positioned close to the native module boundaries throughout the unfolding trajectories. Relatively compact conformations of the quasi-modules seemed to be retained mainly by hydrophobic interactions formed between residues located at both terminal regions within each module. From these results, we propose a hypothesis that hierarchical folding with the early formation of quasi-modules effectively reduces search space for the native structure.

  5. Physically detached 'compact groups'

    NASA Technical Reports Server (NTRS)

    Hernquist, Lars; Katz, Neal; Weinberg, David H.

    1995-01-01

    A small fraction of galaxies appear to reside in dense compact groups, whose inferred crossing times are much shorter than a Hubble time. These short crossing times have led to considerable disagreement among researchers attempting to deduce the dynamical state of these systems. In this paper, we suggest that many of the observed groups are not physically bound but are chance projections of galaxies well separated along the line of sight. Unlike earlier similar proposals, ours does not require that the galaxies in the compact group be members of a more diffuse, but physically bound entity. The probability of physically separated galaxies projecting into an apparent compact group is nonnegligible if most galaxies are distributed in thin filaments. We illustrate this general point with a specific example: a simulation of a cold dark matter universe, in which hydrodynamic effects are included to identify galaxies. The simulated galaxy distribution is filamentary and end-on views of these filaments produce apparent galaxy associations that have sizes and velocity dispersions similar to those of observed compact groups. The frequency of such projections is sufficient, in principle, to explain the observed space density of groups in the Hickson catalog. We discuss the implications of our proposal for the formation and evolution of groups and elliptical galaxies. The proposal can be tested by using redshift-independent distance estimators to measure the line-of-sight spatial extent of nearby compact groups.

  6. UFO (UnFold Operator) computer program abstract

    SciTech Connect

    Kissel, L.; Biggs, F.

    1982-11-01

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

  7. Design and Evaluation of Compact Antennae for Ionospheric Sounding

    NASA Astrophysics Data System (ADS)

    Erjavec, T. J.; Vierinen, J.

    2014-12-01

    Compact high frequency (HF) antennas are crucial for enabling the use of HF radar sounding for ionospheric remote sensing using a dense network of sounders. Current ionosonde antennas are large and expensive. In this study, we investigate two compact HF antenna designs through modeling and prototypes: a folded resistively loaded dipole, and a capacitively tuned small magnetic loop. Both antennas were modeled using FEKO to investigate antenna efficiency and beam patterns. The folded dipole was bought off the shelf, while the compact magnetic loop prototype was built in house. In this study, we present both modeling and measurements of the antenna characteristics. We also present the first ionospheric soundings obtained using the prototype antennas.

  8. NoFold: RNA structure clustering without folding or alignment.

    PubMed

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.

  9. NoFold: RNA structure clustering without folding or alignment

    PubMed Central

    Middleton, Sarah A.

    2014-01-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function—for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. PMID:25234928

  10. Folded orthogonal frequency division multiplexing.

    PubMed

    Corcoran, Bill; Zhu, Chen; Song, Binhuang; Lowery, Arthur J

    2016-12-26

    We propose and demonstrate a new sub-carrier multiplexing scheme, utilizing orthogonal, periodic-sinc-shaped sub-carrier spectra. This 'folded' OFDM allows for multi-carrier bands to be generated with the precise, rectangular frequency definition of Nyquist WDM. We show that this scheme can be implemented with 10 GHz sub-bands, showing a 0.5-dB implementation penalty and successful transmission over 4160-km. We further investigate 40-GHz bands in an add/drop multiplexing scenario on a 50-GHz WDM grid, and show that folded OFDM can provided advantages over conventional OFDM in bandwidth-limited systems.

  11. Protein folding in the cell

    NASA Astrophysics Data System (ADS)

    Gething, Mary-Jane; Sambrook, Joseph

    1992-01-01

    In the cell, as in vitro, the final conformation of a protein is determined by its amino-acid sequence. But whereas some isolated proteins can be denatured and refolded in vitro in the absence of other macromolecular cellular components, folding and assembly of polypeptides in vivo involves other proteins, many of which belong to families that have been highly conserved during evolution.

  12. Use of Protein Folding Reagents.

    PubMed

    2016-04-01

    The reagents and methods for purification and use of the most commonly used denaturants, guanidine hydrochloride (guanidine-HCl) and urea, are described. Other protein denaturants and reagents used to fold proteins are briefly mentioned. Sulfhydryl reagents (reducing agents) and "oxido-shuffling" (or oxidative regeneration) systems are also described.

  13. Compact optical transconductance varistor

    SciTech Connect

    Sampayan, Stephen

    2015-09-22

    A compact radiation-modulated transconductance varistor device having both a radiation source and a photoconductive wide bandgap semiconductor material (PWBSM) integrally formed on a substrate so that a single interface is formed between the radiation source and PWBSM for transmitting PWBSM activation radiation directly from the radiation source to the PWBSM.

  14. Compact rotating cup anemometer

    NASA Technical Reports Server (NTRS)

    Wellman, J. B.

    1968-01-01

    Compact, collapsible rotating cup anemometer is used in remote locations where portability and durability are factors in the choice of equipment. This lightweight instrument has a low wind-velocity threshold, is capable of withstanding large mechanical shocks while in its stowed configuration, and has fast response to wind fluctuations.

  15. Compact, Integrated Photoelectron Linacs

    NASA Astrophysics Data System (ADS)

    Yu, David

    2000-12-01

    The innovative compact high energy iniector which has been developed by DULY Research Inc., will have wide scientific industrial and medical applications. The new photoelectron injector integrates the photocathode directly into a multicell linear accelerator with no drift space between the injector and the linac. By focusing the beam with solenoid or permanent magnets, and producing high current with low emittance, extremely high brightness is achieved. In addition to providing a small footprint and improved beam quality in an integrated structure, the compact system considerably simplifies external subsystems required to operate the photoelectron linac, including rf power transport, beam focusing, vacuum and cooling. The photoelectron linac employs an innovative Plane-Wave-Transformer (PWT) design, which provides strong cell-to-cell coupling, relaxes manufacturing tolerance and facilitates the attachment of external ports to the compact structure with minimal field interference. DULY Research Inc. under the support of the DOE Small Business Innovation Research (SBIR) program, has developed, constructed and installed a 20-MeV, S-band compact electron source at UCLA. DULY Research is also presently engaged in the development of an X-band photoelectron linear accelerator in another SBIR project. The higher frequency structure when completed will be approximately three times smaller, and capable of a beam brightness ten times higher than the S-band structure.

  16. Compact Solar Camera.

    ERIC Educational Resources Information Center

    Juergens, Albert

    1980-01-01

    Describes a compact solar camera built as a one-semester student project. This camera is used for taking pictures of the sun and moon and for direct observation of the image of the sun on a screen. (Author/HM)

  17. COMPACT SCHOOL AND $$ SAVINGS.

    ERIC Educational Resources Information Center

    BAIR, W.G.

    A REVIEW OF THE CRITERIA FOR CONSIDERING THE USE OF A TOTAL ENERGY SYSTEM WITHIN A SCHOOL BUILDING STATES THE WINDOWLESS, COMPACT SCHOOL OFFERS MORE EFFICIENT SPACE UTILIZATION WITH LESS AREA REQUIRED FOR GIVEN STUDENT POPULATION AND LOWER OPERATION COSTS. THE AUTHOR RECOMMENDS THAT THESE BUILDINGS BE WINDOWLESS TO REDUCE HEAT COSTS, HOWEVER, AT…

  18. Limestone compaction: an enigma

    USGS Publications Warehouse

    Shinn, Eugene A.; Halley, Robert B.; Hudson, J. Harold; Lidz, Barbara H.

    1977-01-01

    Compression of an undisturbed carbonate sediment core under a pressure of 556 kg/cm2 produced a “rock” with sedimentary structures similar to typical ancient fine-grained limestones. Surprisingly, shells, foraminifera, and other fossils were not noticeably crushed, which indicates that absence of crushed fossils in ancient limestones can no longer be considered evidence that limestones do not compact.

  19. Compact Information Representations

    DTIC Science & Technology

    2016-08-02

    proposal aims at developing mathematically rigorous and general- purpose statistical methods based on stable random projections, to achieve compact...faced with very large, inherently high-dimensional, or naturally streaming datasets. This pro- posal aims at developing mathematically rigorous and

  20. Compact Electric- And Magnetic-Field Sensor

    NASA Technical Reports Server (NTRS)

    Winterhalter, Daniel; Smith, Edward

    1994-01-01

    Compact sensor measures both electric and magnetic fields. Includes both short electric-field dipole and search-coil magnetometer. Three mounted orthogonally providing triaxial measurements of electromagnetic field at frequencies ranging from near 0 to about 10 kHz.

  1. Analysis of Technology for Compact Coherent Lidar

    NASA Technical Reports Server (NTRS)

    Amzajerdian, Farzin

    1997-01-01

    In view of the recent advances in the area of solid state and semiconductor lasers has created new possibilities for the development of compact and reliable coherent lidars for a wide range of applications. These applications include: Automated Rendezvous and Capture, wind shear and clear air turbulence detection, aircraft wake vortex detection, and automobile collision avoidance. The work performed by the UAH personnel under this Delivery Order, concentrated on design and analyses of a compact coherent lidar system capable of measuring range and velocity of hard targets, and providing air mass velocity data. The following is the scope of this work. a. Investigate various laser sources and optical signal detection configurations in support of a compact and lightweight coherent laser radar to be developed for precision range and velocity measurements of hard and fuzzy targets. Through interaction with MSFC engineers, the most suitable laser source and signal detection technique that can provide a reliable compact and lightweight laser radar design will be selected. b. Analyze and specify the coherent laser radar system configuration and assist with its optical and electronic design efforts. Develop a system design including its optical layout design. Specify all optical components and provide the general requirements of the electronic subsystems including laser beam modulator and demodulator drivers, detector electronic interface, and the signal processor. c. Perform a thorough performance analysis to predict the system measurement range and accuracy. This analysis will utilize various coherent laser radar sensitivity formulations and different target models.

  2. RNAiFold: a web server for RNA inverse folding and molecular design.

    PubMed

    Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

    2013-07-01

    Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.

  3. Microfluidic Mixers for Studying Protein Folding

    PubMed Central

    Waldauer, Steven A.; Wu, Ling; Yao, Shuhuai; Bakajin, Olgica; Lapidus, Lisa J.

    2012-01-01

    The process by which a protein folds into its native conformation is highly relevant to biology and human health yet still poorly understood. One reason for this is that folding takes place over a wide range of timescales, from nanoseconds to seconds or longer, depending on the protein1. Conventional stopped-flow mixers have allowed measurement of folding kinetics starting at about 1 ms. We have recently developed a microfluidic mixer that dilutes denaturant ~100-fold in ~8 μs2. Unlike a stopped-flow mixer, this mixer operates in the laminar flow regime in which turbulence does not occur. The absence of turbulence allows precise numeric simulation of all flows within the mixer with excellent agreement to experiment3-4. Laminar flow is achieved for Reynolds numbers Re ≤100. For aqueous solutions, this requires micron scale geometries. We use a hard substrate, such as silicon or fused silica, to make channels 5-10 μm wide and 10 μm deep (See Figure 1). The smallest dimensions, at the entrance to the mixing region, are on the order of 1 μm in size. The chip is sealed with a thin glass or fused silica coverslip for optical access. Typical total linear flow rates are ~1 m/s, yielding Re~10, but the protein consumption is only ~0.5 nL/s or 1.8 μL/hr. Protein concentration depends on the detection method: For tryptophan fluorescence the typical concentration is 100 μM (for 1 Trp/protein) and for FRET the typical concentration is ~100 nM. The folding process is initiated by rapid dilution of denaturant from 6 M to 0.06 M guanidine hydrochloride. The protein in high denaturant flows down a central channel and is met on either side at the mixing region by buffer without denaturant moving ~100 times faster (see Figure 2). This geometry causes rapid constriction of the protein flow into a narrow jet ~100 nm wide. Diffusion of the light denaturant molecules is very rapid, while diffusion of the heavy protein molecules is much slower, diffusing less than 1 μm in 1 ms

  4. Human Frataxin Folds Via an Intermediate State. Role of the C-Terminal Region

    PubMed Central

    Faraj, Santiago E.; González-Lebrero, Rodolfo M.; Roman, Ernesto A.; Santos, Javier

    2016-01-01

    The aim of this study is to investigate the folding reaction of human frataxin, whose deficiency causes the neurodegenerative disease Friedreich’s Ataxia (FRDA). The characterization of different conformational states would provide knowledge about how frataxin can be stabilized without altering its functionality. Wild-type human frataxin and a set of mutants, including two highly destabilized FRDA-associated variants were studied by urea-induced folding/unfolding in a rapid mixing device and followed by circular dichroism. The analysis clearly indicates the existence of an intermediate state (I) in the folding route with significant secondary structure content but relatively low compactness, compared with the native ensemble. However, at high NaCl concentrations I-state gains substantial compaction, and the unfolding barrier is strongly affected, revealing the importance of electrostatics in the folding mechanism. The role of the C-terminal region (CTR), the key determinant of frataxin stability, was also studied. Simulations consistently with experiments revealed that this stretch is essentially unstructured, in the most compact transition state ensemble (TSE2). The complete truncation of the CTR drastically destabilizes the native state without altering TSE2. Results presented here shed light on the folding mechanism of frataxin, opening the possibility of mutating it to generate hyperstable variants without altering their folding kinetics. PMID:26856628

  5. Human Frataxin Folds Via an Intermediate State. Role of the C-Terminal Region.

    PubMed

    Faraj, Santiago E; González-Lebrero, Rodolfo M; Roman, Ernesto A; Santos, Javier

    2016-02-09

    The aim of this study is to investigate the folding reaction of human frataxin, whose deficiency causes the neurodegenerative disease Friedreich's Ataxia (FRDA). The characterization of different conformational states would provide knowledge about how frataxin can be stabilized without altering its functionality. Wild-type human frataxin and a set of mutants, including two highly destabilized FRDA-associated variants were studied by urea-induced folding/unfolding in a rapid mixing device and followed by circular dichroism. The analysis clearly indicates the existence of an intermediate state (I) in the folding route with significant secondary structure content but relatively low compactness, compared with the native ensemble. However, at high NaCl concentrations I-state gains substantial compaction, and the unfolding barrier is strongly affected, revealing the importance of electrostatics in the folding mechanism. The role of the C-terminal region (CTR), the key determinant of frataxin stability, was also studied. Simulations consistently with experiments revealed that this stretch is essentially unstructured, in the most compact transition state ensemble (TSE2). The complete truncation of the CTR drastically destabilizes the native state without altering TSE2. Results presented here shed light on the folding mechanism of frataxin, opening the possibility of mutating it to generate hyperstable variants without altering their folding kinetics.

  6. Human Frataxin Folds Via an Intermediate State. Role of the C-Terminal Region

    NASA Astrophysics Data System (ADS)

    Faraj, Santiago E.; González-Lebrero, Rodolfo M.; Roman, Ernesto A.; Santos, Javier

    2016-02-01

    The aim of this study is to investigate the folding reaction of human frataxin, whose deficiency causes the neurodegenerative disease Friedreich’s Ataxia (FRDA). The characterization of different conformational states would provide knowledge about how frataxin can be stabilized without altering its functionality. Wild-type human frataxin and a set of mutants, including two highly destabilized FRDA-associated variants were studied by urea-induced folding/unfolding in a rapid mixing device and followed by circular dichroism. The analysis clearly indicates the existence of an intermediate state (I) in the folding route with significant secondary structure content but relatively low compactness, compared with the native ensemble. However, at high NaCl concentrations I-state gains substantial compaction, and the unfolding barrier is strongly affected, revealing the importance of electrostatics in the folding mechanism. The role of the C-terminal region (CTR), the key determinant of frataxin stability, was also studied. Simulations consistently with experiments revealed that this stretch is essentially unstructured, in the most compact transition state ensemble (TSE2). The complete truncation of the CTR drastically destabilizes the native state without altering TSE2. Results presented here shed light on the folding mechanism of frataxin, opening the possibility of mutating it to generate hyperstable variants without altering their folding kinetics.

  7. Cooling of Compact Stars with Color Superconducting Quark Matter

    NASA Astrophysics Data System (ADS)

    Noda, T.; Yasutake, N.; Hashimoto, M.; Maruyama, T.; Tatsumi, T.; Fujimoto, M. Y.

    2015-11-01

    We show a scenario for the cooling of compact stars considering the central source of Cassiopeia A (Cas A).The Cas A observation shows that the central source is a compact star with a high effective temperature, and it is consistent with the cooling without exotic phases. The Cas A observation also gives the mass range of M ≥ 1.5 M_⊙.It may conflict with the current cooling scenarios of compact stars that heavy stars show rapid cooling. We include the effect of the color superconducting (CSC) quark matter phase on the thermal evolution of compact stars.We assume the gap energy of CSC quark phase is large (Δ ≳ 10 MeV),and we simulate the cooling of compact stars. We present cooling curves obtained from the evolutionary calculations of compact stars: while heavier stars cool slowly, and lighter ones indicate the opposite tendency.

  8. Energy landscape in protein folding and unfolding

    PubMed Central

    Mallamace, Francesco; Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Vasi, Cirino; Baglioni, Piero; Buldyrev, Sergey V.; Chen, Sow-Hsin; Stanley, H. Eugene

    2016-01-01

    We use 1H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295

  9. Folding Elastic Thermal Surface - FETS

    NASA Technical Reports Server (NTRS)

    Urquiza, Eugenio; Zhang, Burt X.; Thelen, Michael P.; Rodriquez, Jose I.; Pellegrino, Sergio

    2013-01-01

    The FETS is a light and compact thermal surface (sun shade, IR thermal shield, cover, and/or deployable radiator) that is mounted on a set of offset tape-spring hinges. The thermal surface is constrained during launch and activated in space by a thermomechanical latch such as a wax actuator. An application-specific embodiment of this technology developed for the MATMOS (Mars Atmospheric Trace Molecule Occultation Spectrometer) project serves as a deployable cover and thermal shield for its passive cooler. The FETS fits compactly against the instrument within the constrained launch envelope, and then unfolds into a larger area once in space. In this application, the FETS protects the passive cooler from thermal damage and contamination during ground operations, launch, and during orbit insertion. Once unfolded or deployed, the FETS serves as a heat shield, intercepting parasitic heat loads by blocking the passive cooler s view of the warm spacecraft. The technology significantly enhances the capabilities of instruments requiring either active or passive cooling of optical detectors. This can be particularly important for instruments where performance is limited by the available radiator area. Examples would be IR optical instruments on CubeSATs or those launched as hosted payloads because radiator area is limited and views are often undesirable. As a deployable radiator, the panels making up the FETS are linked thermally by thermal straps and heat pipes; the structural support and deployment energy is provided using tape-spring hinges. The FETS is a novel combination of existing technologies. Prior art for deployable heat shields uses rotating hinges that typically must be lubricated to avoid cold welding or static friction. By using tape-spring hinges, the FETS avoids the need for lubricants by avoiding friction altogether. This also eliminates the potential for contamination of nearby cooled optics by outgassing lubricants. Furthermore, the tape-spring design of

  10. Folding propensity of intrinsically disordered proteins by osmotic stress

    SciTech Connect

    Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.; Pino, James C.; Chennubhotla, S. Chakra; Ramanathan, Arvind; O'Neill, Hugh Michael; Berthelier, Valerie; Stanley, Christopher B.

    2016-10-11

    Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scattering (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.

  11. Two Piece Compaction Die Design

    SciTech Connect

    Coffey, Ethan N

    2010-03-01

    Compaction dies used to create europium oxide and tantalum control plates were modeled using ANSYS 11.0. Two-piece designs were considered in order to make the dies easier to assemble than the five-piece dies that were previously used. The two areas of concern were the stresses at the interior corner of the die cavity and the distortion of the cavity wall due to the interference fit between the two pieces and the pressure exerted on the die during the compaction process. A successful die design would have stresses less than the yield stress of the material and a maximum wall distortion on the order of 0.0001 in. Design factors that were investigated include the inner corner radius, the value of the interference fit, the compaction force, the size of the cavity, and the outer radius and geometry of the outer ring. The results show that for the europium oxide die, a 0.01 in. diameter wire can be used to create the cavity, leading to a 0.0055 in. radius corner, if the radial interference fit is 0.003 in. For the tantalum die, the same wire can be used with a radial interference fit of 0.001 in. Also, for the europium oxide die with a 0.003 in. interference fit, it is possible to use a wire with a diameter of 0.006 in. for the wire burning process. Adding a 10% safety factor to the compaction force tends to lead to conservative estimates of the stresses but not for the wall distortion. However, when the 10% safety factor is removed, the wall distortion is not affected enough to discard the design. Finally, regarding the europium oxide die, when the cavity walls are increased by 0.002 in. per side or the outer ring is made to the same geometry as the tantalum die, all the stresses and wall distortions are within the desired range. Thus, the recommendation is to use a 0.006 in. diameter wire and a 0.003 in. interference fit for the europium oxide die and a 0.01 in. diameter wire and a 0.001 in. interference fit for the tantalum die. The dies can also be made to have the

  12. Incompletely compacted equilibrated ordinary chondrites

    SciTech Connect

    Sasso, M.R.; Macke, R.J.; Boesenberg, J.S.; Britt, D.T.; Rovers, M.L.; Ebel, D.S.; Friedrich, J.M.

    2010-01-22

    We document the size distributions and locations of voids present within five highly porous equilibrated ordinary chondrites using high-resolution synchrotron X-ray microtomography ({mu}CT) and helium pycnometry. We found total porosities ranging from {approx}10 to 20% within these chondrites, and with {mu}CT we show that up to 64% of the void space is located within intergranular voids within the rock. Given the low (S1-S2) shock stages of the samples and the large voids between mineral grains, we conclude that these samples experienced unusually low amounts of compaction and shock loading throughout their entire post accretionary history. With Fe metal and FeS metal abundances and grain size distributions, we show that these chondrites formed naturally with greater than average porosities prior to parent body metamorphism. These materials were not 'fluffed' on their parent body by impact-related regolith gardening or events caused by seismic vibrations. Samples of all three chemical types of ordinary chondrites (LL, L, H) are represented in this study and we conclude that incomplete compaction is common within the asteroid belt.

  13. Folded waveguide gyrotron traveling-wave-tube amplifier

    SciTech Connect

    Choi, J.J.; Armstrong, C.M.; Ganguly, A.K.; Calise, F.

    1995-03-01

    A compact, low cost gyrotron traveling-wave-tube (gyro-TWT) amplifier capable of producing high-power, broadband, millimeter wave radiation is reported. The interaction circuit is a periodic, magnetic field plane (H plane) bend, transverse folded waveguide employed with a high-power axis-encircling electron beam. Transverse beam modulation and wave amplification in the folded waveguide gyro-TWT are observed in both linear theory and large signal simulations. Calculations from an equivalent circuit model and a three-dimensional electromagnetic code predict a mode coalescing of the first stop-band in a periodic structure. The mode coalescing is verified from experimental measurements. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  14. Compaction dynamics of wet granular packings

    NASA Astrophysics Data System (ADS)

    Vandewalle, Nicolas; Ludewig, Francois; Fiscina, Jorge E.; Lumay, Geoffroy

    2013-03-01

    The extremely slow compaction dynamics of wet granular assemblies has been studied experimentally. The cohesion, due to capillary bridges between neighboring grains, has been tuned using different liquids having specific surface tension values. The characteristic relaxation time for compaction τ grows strongly with cohesion. A kinetic model, based on a free volume kinetic equations and the presence of a capillary energy barrier (due to liquid bridges), is able to reproduce quantitatively the experimental curves. This model allows one to describe the cohesion in wet granular packing. The influence of relative humidity (RH) on the extremely slow compaction dynamics of a granular assembly has also been investigated in the range 20 % - 80 % . Triboelectric and capillary condensation effects have been introduced in the kinetic model. Results confirm the existence of an optimal condition at RH ~ 45 % for minimizing cohesive interactions between glass beads.

  15. Compact Spreader Schemes

    SciTech Connect

    Placidi, M.; Jung, J. -Y.; Ratti, A.; Sun, C.

    2014-07-25

    This paper describes beam distribution schemes adopting a novel implementation based on low amplitude vertical deflections combined with horizontal ones generated by Lambertson-type septum magnets. This scheme offers substantial compactness in the longitudinal layouts of the beam lines and increased flexibility for beam delivery of multiple beam lines on a shot-to-shot basis. Fast kickers (FK) or transverse electric field RF Deflectors (RFD) provide the low amplitude deflections. Initially proposed at the Stanford Linear Accelerator Center (SLAC) as tools for beam diagnostics and more recently adopted for multiline beam pattern schemes, RFDs offer repetition capabilities and a likely better amplitude reproducibility when compared to FKs, which, in turn, offer more modest financial involvements both in construction and operation. Both solutions represent an ideal approach for the design of compact beam distribution systems resulting in space and cost savings while preserving flexibility and beam quality.

  16. Compact spreader schemes

    NASA Astrophysics Data System (ADS)

    Placidi, M.; Jung, J.-Y.; Ratti, A.; Sun, C.

    2014-12-01

    This paper describes beam distribution schemes adopting a novel implementation based on low amplitude vertical deflections combined with horizontal ones generated by Lambertson-type septum magnets. This scheme offers substantial compactness in the longitudinal layouts of the beam lines and increased flexibility for beam delivery of multiple beam lines on a shot-to-shot basis. Fast kickers (FK) or transverse electric field RF Deflectors (RFD) provide the low amplitude deflections. Initially proposed at the Stanford Linear Accelerator Center (SLAC) as tools for beam diagnostics and more recently adopted for multiline beam pattern schemes, RFDs offer repetition capabilities and a likely better amplitude reproducibility when compared to FKs, which, in turn, offer more modest financial involvements both in construction and operation. Both solutions represent an ideal approach for the design of compact beam distribution systems resulting in space and cost savings while preserving flexibility and beam quality.

  17. Compact optical isolator.

    PubMed

    Sansalone, F J

    1971-10-01

    This paper describes a compact Faraday rotation isolator using terbium aluminum garnet (TAG) as the Faraday rotation material and small high field permanent magnets made of copper-rare earth alloys. The nominal isolation is 26 dB with a 0.4-dB forward loss. The present isolator can be adjusted to provide effective isolation from 4880 A to 5145 A. Details of the design, fabrication, and performance of the isolator are presented.

  18. Folding Dynamics and Pathways of the Trp-Cage Miniproteins

    PubMed Central

    2015-01-01

    Using alternate measures of fold stability for a wide variety of Trp-cage mutants has raised the possibility that prior dynamics T-jump measures may not be reporting on complete cage formation for some species. NMR relaxation studies using probes that only achieve large chemical shift difference from unfolded values on complete cage formation indicate slower folding in some but not all cases. Fourteen species have been examined, with cage formation time constants (1/kF) ranging from 0.9–7.5 μs at 300 K. The present study does not change the status of the Trp-cage as a fast folding, essentially two-state system, although it does alter the stage at which this description applies. A diversity of prestructuring events, depending on the specific analogue examined, may appear in the folding scenario, but in all cases, formation of the N-terminal helix is complete either at or before the cage-formation transition state. In contrast, the fold-stabilizing H-bonding interactions of the buried Ser14 side chain and the Arg/Asp salt bridge are post-transition state features on the folding pathway. The study has also found instances in which a [P12W] mutation is fold destabilizing but still serves to accelerate the folding process. PMID:25184759

  19. The Australia Telescope Compact Array Broad-band Backend: description and first results

    NASA Astrophysics Data System (ADS)

    Wilson, Warwick E.; Ferris, R. H.; Axtens, P.; Brown, A.; Davis, E.; Hampson, G.; Leach, M.; Roberts, P.; Saunders, S.; Koribalski, B. S.; Caswell, J. L.; Lenc, E.; Stevens, J.; Voronkov, M. A.; Wieringa, M. H.; Brooks, K.; Edwards, P. G.; Ekers, R. D.; Emonts, B.; Hindson, L.; Johnston, S.; Maddison, S. T.; Mahony, E. K.; Malu, S. S.; Massardi, M.; Mao, M. Y.; McConnell, D.; Norris, R. P.; Schnitzeler, D.; Subrahmanyan, R.; Urquhart, J. S.; Thompson, M. A.; Wark, R. M.

    2011-09-01

    Here, we describe the Compact Array Broad-band Backend (CABB) and present first results obtained with the upgraded Australia Telescope Compact Array (ATCA). The 16-fold increase in observing bandwidth, from 2 × 128 to 2 × 2048 MHz, high-bit sampling and the addition of 16 zoom windows (each divided into further 2048 channels) provide major improvements for all ATCA observations. The benefits of the new system are: (1) hugely increased radio continuum and polarization sensitivity as well as image fidelity; (2) substantially improved capability to search for and map emission and absorption lines over large velocity ranges; (3) simultaneous multi-line and continuum observations; (4) increased sensitivity, survey speed and dynamic range due to high-bit sampling and (5) high-velocity resolution, while maintaining full polarization output. The new CABB system encourages all observers to make use of both spectral line and continuum data to achieve their full potential. Given the dramatic increase of the ATCA capabilities in all bands (ranging from 1.1 to 105 GHz) CABB enables scientific projects that were not feasible before the upgrade, such as simultaneous observations of multiple spectral lines, on-the-fly mapping, fast follow-up of radio transients (e.g. the radio afterglow of new supernovae) and maser observation at high-velocity resolution and full polarization. The first science results presented here include wide-band spectra, high dynamic-range images and polarization measurements, highlighting the increased capability and discovery potential of the ATCA. The Australia Telescope Compact Array is part of the Australia Telescope National Facility which is funded by the Commonwealth of Australia for operation as a National Facility managed by CSIRO.

  20. Where's the Bend? Locating the First Folded Structure in Straight Chain Alkylbenzenes in a Supersonic Jet Expansion

    NASA Astrophysics Data System (ADS)

    Hewett, Daniel M.; Bocklitz, Sebastian; Suhm, Martin A.; Zwier, Timothy S.

    2016-06-01

    Alkylbenzenes make up 20-30% of petroleum fuels and are important intermediates in combustion. In gasoline, these alkyl chains are relatively short, but extend to 20 or more carbons in length in diesel fuels. While one tends to think of these chains as extending out away from the phenyl ring in an all-trans configuration, dispersive interactions between segments of the alkyl chain and between the alkyl chain and the ring will stabilize more compact geometries in which the alkyl chain folds back on itself and extends over the aromatic π cloud. This talk seeks to answer the following question: How long must the alkyl chain be before it starts to fold back over itself? Studies of the pure n-alkanes by the Suhm group have shown the turn to favorably occur for a chain about 17 carbon atoms in length. The studies presented here focus on the affect the aromatic ring has on when this turn becomes favorable. Jet-cooled laser-induced fluorescence excitation and single-conformation IR spectra have been recorded in the alkyl CH stretch region for a series of alkylbenzenes with chain lengths ranging from two to ten carbon atoms. We show, through a combination of experiment, high level calculation, and theoretical modeling, that conformations begin to form that fold back over the aromatic ring at about n=8.

  1. Slowing Down Downhill Folding: A Three-Probe Study

    SciTech Connect

    Kim, Seung Joong; Matsumura, Yoshitaka; Dumont, Charles; Kihara, Hiroshi; Gruebele, Martin

    2009-09-11

    The mutant Tyr{sup 22}Trp/Glu{sup 33}Tyr/Gly{sup 46}Ala/Gly{sup 48}Ala of {lambda} repressor fragment {lambda}6-85 was previously assigned as an incipient downhill folder. We slow down its folding in a cryogenic water-ethylene-glycol solvent (-18 to -28 C). The refolding kinetics are probed by small-angle x-ray scattering, circular dichroism, and fluorescence to measure the radius of gyration, the average secondary structure content, and the native packing around the single tryptophan residue. The main resolved kinetic phase of the mutant is probe independent and faster than the main phase observed for the pseudo-wild-type. Excess helical structure formed early on by the mutant may reduce the formation of turns and prevent the formation of compact misfolded states, speeding up the overall folding process. Extrapolation of our main cryogenic folding phase and previous T-jump measurements to 37 C yields nearly the same refolding rate as extrapolated by Oas and co-workers from NMR line-shape data. Taken together, all the data consistently indicate a folding speed limit of {approx}4.5 {micro}s for this fast folder.

  2. Some physical approaches to protein folding

    NASA Astrophysics Data System (ADS)

    Bascle, J.; Garel, T.; Orland, H.

    1993-02-01

    To understand how a protein folds is a problem which has important biological implications. In this article, we would like to present a physics-oriented point of view, which is twofold. First of all, we introduce simple statistical mechanics models which display, in the thermodynamic limit, folding and related transitions. These models can be divided into (i) crude spin glass-like models (with their Mattis analogs), where one may look for possible correlations between the chain self-interactions and the folded structure, (ii) glass-like models, where one emphasizes the geometrical competition between one- or two-dimensional local order (mimicking α helix or β sheet structures), and the requirement of global compactness. Both models are too simple to predict the spatial organization of a realistic protein, but are useful for the physicist and should have some feedback in other glassy systems (glasses, collapsed polymers .... ). These remarks lead us to the second physical approach, namely a new Monte-Carlo method, where one grows the protein atom-by-atom (or residue-by-residue), using a standard form (CHARMM .... ) for the total energy. A detailed comparison with other Monte-Carlo schemes, or Molecular Dynamics calculations, is then possible; we will sketch such a comparison for poly-alanines. Our twofold approach illustrates some of the difficulties one encounters in the protein folding problem, in particular those associated with the existence of a large number of metastable states. Le repliement des protéines est un problème qui a de nombreuses implications biologiques. Dans cet article, nous présentons, de deux façons différentes, un point de vue de physicien. Nous introduisons tout d'abord des modèles simples de mécanique statistique qui exhibent, à la limite thermodynamique, des transitions de repliement. Ces modèles peuvent être divisés en (i) verres de spin (éventuellement à la Mattis), où l'on peut chercher des corrélations entre les

  3. Ventricular-Fold Dynamics in Human Phonation

    ERIC Educational Resources Information Center

    Bailly, Lucie; Bernardoni, Nathalie Henrich; Müller, Frank; Rohlfs, Anna-Katharina; Hess, Markus

    2014-01-01

    Purpose: In this study, the authors aimed (a) to provide a classification of the ventricular-fold dynamics during voicing, (b) to study the aerodynamic impact of these motions on vocal-fold vibrations, and (c) to assess whether ventricular-fold oscillations could be sustained by aerodynamic coupling with the vocal folds. Method: A 72-sample…

  4. Mesozoic folds, fossil fields, and future finds ( )

    SciTech Connect

    Newman, G.W.; Witter, G.G.

    1988-02-01

    Drilling and surface geologic mapping have shown that pre-Tertiary, post-Triassic folds and upthrusted anticlines in an eastern Nevada fold-belt have accumulated major oil columns. This Mesozoic foldbelt involves a Cambrian through Triassic section, which has hundreds of feet of porosity in Ordovician sandstones, Silurian and Devonian carbonates, and Mississippian sandstones. In addition to the Devonian Pilot and Mississippian Chainman shales, source rocks are found in Cambrian and Ordovician shales and in some Paleozoic carbonates. The occurrence of live and dead oil shows in hundreds of vertical feet of porosity in wells drilled on several of these Mesozoic structures is interpreted as evidence that these structures were giant oil fields prior to being breached by Tertiary Basin and Range extensional faulting, which allowed vertical hydrocarbon leakage. Noting that undrilled Mesozoic structures still exist in the foldbelt and noting that natural processes are seldom 100% efficient - including, probably, the disruptive effects of Basin and range extensional faulting - the authors suggest that there is a very good chance of finding one or more giant fields in the remaining structures of this foldbelt.

  5. Gravitational waves from compact objects

    NASA Astrophysics Data System (ADS)

    de Freitas Pacheco, José Antonio

    2010-11-01

    Large ground-based laser beam interferometers are presently in operation both in the USA (LIGO) and in Europe (VIRGO) and potential sources that might be detected by these instruments are revisited. The present generation of detectors does not have a sensitivity high enough to probe a significant volume of the universe and, consequently, predicted event rates are very low. The planned advanced generation of interferometers will probably be able to detect, for the first time, a gravitational signal. Advanced LIGO and EGO instruments are expected to detect few (some): binary coalescences consisting of either two neutron stars, two black holes or a neutron star and a black hole. In space, the sensitivity of the planned LISA spacecraft constellation will allow the detection of the gravitational signals, even within a “pessimistic" range of possible signals, produced during the capture of compact objects by supermassive black holes, at a rate of a few tens per year.

  6. Folded MEMS approach to NMRG

    NASA Astrophysics Data System (ADS)

    Gundeti, Venu Madhav

    Atomic gyroscopes have a potential for good performance advantages and several attempts are being made to miniaturize them. This thesis describes the efforts made in implementing a Folded MEMS based NMRG. The micro implementations of all the essential components for NMRG (Nuclear Magnetic Resonance Gyroscope) are described in detail in regards to their design, fabrication, and characterization. A set of micro-scale Helmholtz coils are described and the homogeneity of the generated magnetic field is analyzed for different designs of heaters. The dielectric mirrors and metallic mirrors are compared in terms of reflectivity and polarization change up on reflection. A pyramid shaped folded backbone structure is designed, fabricated, and assembled along with all the required components. A novel double-folded structure 1/4th the size of original version is fabricated and assembled. Design and modeling details of a 5 layered shield with shielding factor > 106 and total volume of around 90 cc are also presented. A table top setup for characterization of atomic vapor cell is described in detail. A micro vapor cell based Rb magnetometer with a sensitivity of 108 pT/√Hz is demonstrated. The challenges due to DC heating are addressed and mitigated using an AC heater. Several experiments related to measuring the relaxation time of Xe are provided along with results. For Xe131, relaxation times of T1 = 23.78 sec, T2 = 18.06 sec and for Xe129, T1 = 21.65 sec and T2 = 20.45 sec are reported.

  7. Chaperonin-mediated Protein Folding

    PubMed Central

    Horwich, Arthur L.

    2013-01-01

    We have been studying chaperonins these past twenty years through an initial discovery of an action in protein folding, analysis of structure, and elucidation of mechanism. Some of the highlights of these studies were presented recently upon sharing the honor of the 2013 Herbert Tabor Award with my early collaborator, Ulrich Hartl, at the annual meeting of the American Society for Biochemistry and Molecular Biology in Boston. Here, some of the major findings are recounted, particularly recognizing my collaborators, describing how I met them and how our great times together propelled our thinking and experiments. PMID:23803606

  8. Radar Cross Section Studies/Compact Range Research

    NASA Technical Reports Server (NTRS)

    Burnside, W. D.; Dominek, A. K.; Gupta, I. J.; Newman, E. H.; Pathak, P. H.; Peters, L., Jr.

    1988-01-01

    A summary is given of the achievements of NASA Grant NsG-1613 by Ohio State University from May 1, 1987 to April 30, 1988. The major topics covered are as follows: (1) electromagnetic scattering analysis; (2) indoor scattering measurement systems; (3) RCS control; (4) waveform processing techniques; (5) material scattering and design studies; (6) design and evaluation of design studies; and (7) antenna studies. Major progress has been made in each of these areas as verified by the numerous publications produced.

  9. Radar cross section studies/compact range research

    NASA Technical Reports Server (NTRS)

    Burnside, W. D.; Dominek, A. K.; Gupta, I. J.; Newman, E. H.; Pathak, P. H.; Peters, L., Jr.

    1989-01-01

    Achievements in advancing the state-of-the-art in the measurement, control, and analysis of electromagnetic scattering from general aerodynamic targets are summarized. The major topics associated with this study include: (1) electromagnetic scattering analysis; (2) indoor scattering measurement systems; (3) RCS control; (4) waveform processing techniques; (5) material scattering and design studies; (6) design and evaluation of standard targets; and (7) antenna studies. Progress in each of these areas is reported and related publications are listed.

  10. User's manual for semi-circular compact range reflector code

    NASA Technical Reports Server (NTRS)

    Gupta, Inder J.; Burnside, Walter D.

    1986-01-01

    A computer code was developed to analyze a semi-circular paraboloidal reflector antenna with a rolled edge at the top and a skirt at the bottom. The code can be used to compute the total near field of the antenna or its individual components at a given distance from the center of the paraboloid. Thus, it is very effective in computing the size of the sweet spot for RCS or antenna measurement. The operation of the code is described. Various input and output statements are explained. Some results obtained using the computer code are presented to illustrate the code's capability as well as being samples of input/output sets.

  11. Compact gate valve

    DOEpatents

    Bobo, Gerald E.

    1977-01-01

    This invention relates to a double-disc gate valve which is compact, comparatively simple to construct, and capable of maintaining high closing pressures on the valve discs with low frictional forces. The valve casing includes axially aligned ports. Mounted in the casing is a sealed chamber which is pivotable transversely of the axis of the ports. The chamber contains the levers for moving the valve discs axially, and an actuator for the levers. When an external drive means pivots the chamber to a position where the discs are between the ports and axially aligned therewith, the actuator for the levers is energized to move the discs into sealing engagement with the ports.

  12. COMPACT CASCADE IMPACTS

    DOEpatents

    Lippmann, M.

    1964-04-01

    A cascade particle impactor capable of collecting particles and distributing them according to size is described. In addition the device is capable of collecting on a pair of slides a series of different samples so that less time is required for the changing of slides. Other features of the device are its compactness and its ruggedness making it useful under field conditions. Essentially the unit consists of a main body with a series of transverse jets discharging on a pair of parallel, spaced glass plates. The plates are capable of being moved incremental in steps to obtain the multiple samples. (AEC)

  13. Compact laser amplifier system

    DOEpatents

    Carr, R.B.

    1974-02-26

    A compact laser amplifier system is described in which a plurality of face-pumped annular disks, aligned along a common axis, independently radially amplify a stimulating light pulse. Partially reflective or lasing means, coaxially positioned at the center of each annualar disk, radially deflects a stimulating light directed down the common axis uniformly into each disk for amplification, such that the light is amplified by the disks in a parallel manner. Circumferential reflecting means coaxially disposed around each disk directs amplified light emission, either toward a common point or in a common direction. (Official Gazette)

  14. Effects of Initial Powder Compact Thickness, Lubrication, and Particle Morphology on the Cold Compaction Behavior of Ti Powder

    NASA Astrophysics Data System (ADS)

    Lou, Jia; Gabbitas, Brian; Zhang, Deliang; Yang, Fei

    2015-08-01

    This work investigates the compaction behavior of hydride-dehydride CP-Ti powder from green density/compaction pressure curves. These were obtained through a modification of selected processing conditions, such as variation in compact thickness, the use of internal lubrication, and additions of plasma rotating electrode process powder. A modified Cooper-Eaton equation, which treats the compaction process to be a combination of particle rearrangement (PR) and plastic deformation (PD) mechanisms, was used to simulate the curves. A comparison with aluminum and iron compaction is also carried out in this study. The research indicated that the cold compaction of titanium powder can be separated into two stages: a PR stage (stage I), which occurs at a compacting pressure in the range of 0 to 200 MPa, followed by a further PR stage initiated by PD, when the compaction pressure is in the range of 200 to 1000 MPa. The existence of stage II is due to the low plastic deformability of titanium and low density achieved at the end of stage I.

  15. Synthetic circuit for exact adaptation and fold-change detection.

    PubMed

    Kim, Jongmin; Khetarpal, Ishan; Sen, Shaunak; Murray, Richard M

    2014-05-01

    Biological organisms use their sensory systems to detect changes in their environment. The ability of sensory systems to adapt to static inputs allows wide dynamic range as well as sensitivity to input changes including fold-change detection, a response that depends only on fold changes in input, and not on absolute changes. This input scale invariance underlies an important strategy for search that depends solely on the spatial profile of the input. Synthetic efforts to reproduce the architecture and response of cellular circuits provide an important step to foster understanding at the molecular level. We report the bottom-up assembly of biochemical systems that show exact adaptation and fold-change detection. Using a malachite green aptamer as the output, a synthetic transcriptional circuit with the connectivity of an incoherent feed-forward loop motif exhibits pulse generation and exact adaptation. A simple mathematical model was used to assess the amplitude and duration of pulse response as well as the parameter regimes required for fold-change detection. Upon parameter tuning, this synthetic circuit exhibits fold-change detection for four successive rounds of two-fold input changes. The experimental realization of fold-change detection circuit highlights the programmability of transcriptional switches and the ability to obtain predictive dynamical systems in a cell-free environment for technological applications.

  16. Elasticity and stress relaxation of a very small vocal fold

    PubMed Central

    Riede, Tobias; York, Alexander; Furst, Stephen; Müller, Rolf; Seelecke, Stefan

    2011-01-01

    Across mammals many vocal sounds are produced by airflow induced vocal fold oscillation. We tested the hypothesis that stress-strain and stress-relaxation behavior of rat vocal folds can be used to predict the fundamental frequency range of the species’ vocal repertoire. In a first approximation vocal fold oscillation has been modeled by the string model but it is not known whether this concept equally applies to large and small species. The shorter the vocal fold, the more the ideal string law may underestimate normal mode frequencies. To accommodate the very small size of the tissue specimen, a custom-built miniaturized tensile test apparatus was developed. Tissue properties of 6 male rat vocal folds were measured. Rat vocal folds demonstrated the typical linear stress-strain behavior in the low strain region and an exponential stress response at strains larger than about 40%. Approximating the rat’s vocal fold oscillation with the string model suggests that fundamental frequencies up to about 6 kHz can be produced, which agrees with frequencies reported for audible rat vocalization. Individual differences and time-dependent changes in the tissue properties parallel findings in other species, and are interpreted as universal features of the laryngeal sound source. PMID:21550608

  17. Synthetic circuit for exact adaptation and fold-change detection

    PubMed Central

    Kim, Jongmin; Khetarpal, Ishan; Murray, Richard M.

    2014-01-01

    Biological organisms use their sensory systems to detect changes in their environment. The ability of sensory systems to adapt to static inputs allows wide dynamic range as well as sensitivity to input changes including fold-change detection, a response that depends only on fold changes in input, and not on absolute changes. This input scale invariance underlies an important strategy for search that depends solely on the spatial profile of the input. Synthetic efforts to reproduce the architecture and response of cellular circuits provide an important step to foster understanding at the molecular level. We report the bottom-up assembly of biochemical systems that show exact adaptation and fold-change detection. Using a malachite green aptamer as the output, a synthetic transcriptional circuit with the connectivity of an incoherent feed-forward loop motif exhibits pulse generation and exact adaptation. A simple mathematical model was used to assess the amplitude and duration of pulse response as well as the parameter regimes required for fold-change detection. Upon parameter tuning, this synthetic circuit exhibits fold-change detection for four successive rounds of two-fold input changes. The experimental realization of fold-change detection circuit highlights the programmability of transcriptional switches and the ability to obtain predictive dynamical systems in a cell-free environment for technological applications. PMID:24728988

  18. Unraveling metamaterial properties in zigzag-base folded sheets

    PubMed Central

    Eidini, Maryam; Paulino, Glaucio H.

    2015-01-01

    Creating complex spatial objects from a flat sheet of material using origami folding techniques has attracted attention in science and engineering. In the present work, we use the geometric properties of partially folded zigzag strips to better describe the kinematics of known zigzag/herringbone-base folded sheet metamaterials such as Miura-ori. Inspired by the kinematics of a one–degree of freedom zigzag strip, we introduce a class of cellular folded mechanical metamaterials comprising different scales of zigzag strips. This class of patterns combines origami folding techniques with kirigami. Using analytical and numerical models, we study the key mechanical properties of the folded materials. We show that our class of patterns, by expanding on the design space of Miura-ori, is appropriate for a wide range of applications from mechanical metamaterials to deployable structures at small and large scales. We further show that, depending on the geometry, these materials exhibit either negative or positive in-plane Poisson’s ratios. By introducing a class of zigzag-base materials in the current study, we unify the concept of in-plane Poisson’s ratio for similar materials in the literature and extend it to the class of zigzag-base folded sheet materials. PMID:26601253

  19. Unraveling metamaterial properties in zigzag-base folded sheets.

    PubMed

    Eidini, Maryam; Paulino, Glaucio H

    2015-09-01

    Creating complex spatial objects from a flat sheet of material using origami folding techniques has attracted attention in science and engineering. In the present work, we use the geometric properties of partially folded zigzag strips to better describe the kinematics of known zigzag/herringbone-base folded sheet metamaterials such as Miura-ori. Inspired by the kinematics of a one-degree of freedom zigzag strip, we introduce a class of cellular folded mechanical metamaterials comprising different scales of zigzag strips. This class of patterns combines origami folding techniques with kirigami. Using analytical and numerical models, we study the key mechanical properties of the folded materials. We show that our class of patterns, by expanding on the design space of Miura-ori, is appropriate for a wide range of applications from mechanical metamaterials to deployable structures at small and large scales. We further show that, depending on the geometry, these materials exhibit either negative or positive in-plane Poisson's ratios. By introducing a class of zigzag-base materials in the current study, we unify the concept of in-plane Poisson's ratio for similar materials in the literature and extend it to the class of zigzag-base folded sheet materials.

  20. Scalable Nonlinear Compact Schemes

    SciTech Connect

    Ghosh, Debojyoti; Constantinescu, Emil M.; Brown, Jed

    2014-04-01

    In this work, we focus on compact schemes resulting in tridiagonal systems of equations, specifically the fifth-order CRWENO scheme. We propose a scalable implementation of the nonlinear compact schemes by implementing a parallel tridiagonal solver based on the partitioning/substructuring approach. We use an iterative solver for the reduced system of equations; however, we solve this system to machine zero accuracy to ensure that no parallelization errors are introduced. It is possible to achieve machine-zero convergence with few iterations because of the diagonal dominance of the system. The number of iterations is specified a priori instead of a norm-based exit criterion, and collective communications are avoided. The overall algorithm thus involves only point-to-point communication between neighboring processors. Our implementation of the tridiagonal solver differs from and avoids the drawbacks of past efforts in the following ways: it introduces no parallelization-related approximations (multiprocessor solutions are exactly identical to uniprocessor ones), it involves minimal communication, the mathematical complexity is similar to that of the Thomas algorithm on a single processor, and it does not require any communication and computation scheduling.

  1. Compaction of Titanium Powders

    SciTech Connect

    Gerdemann, Stephen,J; Jablonski, Paul, J

    2011-05-01

    Accurate modeling of powder densification has been an area of active research for more than 60 years. The earliest efforts were focused on linearization of the data because computers were not readily available to assist with curve-fitting methods. In this work, eight different titanium powders (three different sizes of sponge fines<150 {micro}m,<75 {micro}m, and<45 {micro}m; two different sizes of a hydride-dehydride [HDH]<75 {micro}m and<45 {micro}m; an atomized powder; a commercially pure [CP] Ti powder from International Titanium Powder [ITP]; and a Ti 6 4 alloy powder) were cold pressed in a single-acting die instrumented to collect stress and deformation data during compaction. From these data, the density of each compact was calculated and then plotted as a function of pressure. The results show that densification of all the powders, regardless of particle size, shape, or chemistry, can be modeled accurately as the sum of an initial density plus the sum of a rearrangement term and a work-hardening term. These last two terms are found to be a function of applied pressure and take the form of an exponential rise.

  2. Compact electrostatic comb actuator

    DOEpatents

    Rodgers, M. Steven; Burg, Michael S.; Jensen, Brian D.; Miller, Samuel L.; Barnes, Stephen M.

    2000-01-01

    A compact electrostatic comb actuator is disclosed for microelectromechanical (MEM) applications. The actuator is based upon a plurality of meshed electrostatic combs, some of which are stationary and others of which are moveable. One or more restoring springs are fabricated within an outline of the electrostatic combs (i.e. superposed with the moveable electrostatic combs) to considerably reduce the space required for the actuator. Additionally, a truss structure is provided to support the moveable electrostatic combs and prevent bending or distortion of these combs due to unbalanced electrostatic forces or external loading. The truss structure formed about the moveable electrostatic combs allows the spacing between the interdigitated fingers of the combs to be reduced to about one micron or less, thereby substantially increasing the number of active fingers which can be provided in a given area. Finally, electrostatic shields can be used in the actuator to substantially reduce unwanted electrostatic fields to further improve performance of the device. As a result, the compact electrostatic comb actuator of the present invention occupies only a fraction of the space required for conventional electrostatic comb actuators, while providing a substantial increase in the available drive force (up to one-hundred times).

  3. Compaction of Titanium Powders

    SciTech Connect

    Stephen J. Gerdemann; Paul D. Jablonski

    2010-11-01

    Accurate modeling of powder densification has been an area of active research for more than 60 years. The earliest efforts were focused on linearization of the data because computers were not readily available to assist with curve-fitting methods. In this work, eight different titanium powders (three different sizes of sponge fines <150 μm, <75 μm, and < 45 μm; two different sizes of a hydride-dehydride [HDH] <75 μm and < 45 μm; an atomized powder; a commercially pure [CP] Ti powder from International Titanium Powder [ITP]; and a Ti 6 4 alloy powder) were cold pressed in a single-acting die instrumented to collect stress and deformation data during compaction. From these data, the density of each compact was calculated and then plotted as a function of pressure. The results show that densification of all the powders, regardless of particle size, shape, or chemistry, can be modeled accurately as the sum of an initial density plus the sum of a rearrangement term and a work-hardening term. These last two terms are found to be a function of applied pressure and take the form of an exponential rise.

  4. Compact Infrasonic Windscreen

    NASA Technical Reports Server (NTRS)

    Zuckerwar, Allan J.; Shams, Qamar A.; Sealey, Bradley S.; Comeaux, Toby

    2005-01-01

    A compact windscreen has been conceived for a microphone of a type used outdoors to detect atmospheric infrasound from a variety of natural and manmade sources. Wind at the microphone site contaminates received infrasonic signals (defined here as sounds having frequencies <20 Hz), because a microphone cannot distinguish between infrasonic pressures (which propagate at the speed of sound) and convective pressure fluctuations generated by wind turbulence. Hence, success in measurement of outdoor infrasound depends on effective screening of the microphone from the wind. The present compact windscreen is based on a principle: that infrasound at sufficiently large wavelength can penetrate any barrier of practical thickness. Thus, a windscreen having solid, non-porous walls can block convected pressure fluctuations from the wind while transmitting infrasonic acoustic waves. The transmission coefficient depends strongly upon the ratio between the acoustic impedance of the windscreen and that of air. Several materials have been found to have impedance ratios that render them suitable for use in constructing walls that have practical thicknesses and are capable of high transmission of infrasound. These materials (with their impedance ratios in parentheses) are polyurethane foam (222), space shuttle tile material (332), balsa (323), cedar (3,151), and pine (4,713).

  5. Kinematics and thermodynamics of a folding heteropolymer.

    PubMed Central

    Fukugita, M; Lancaster, D; Mitchard, M G

    1993-01-01

    In order to elucidate the folding dynamics of protein, we have carried out numerical simulations of a heteropolymer model of self-interacting random chains. We find that folding propensity depends strongly on sequence and that both folding and nonfolding sequences exist. Furthermore we show that folding is a two-step process: the transition from coil state to unique folded state takes place through a globule phase. In addition to the continuous coil-globule transition, there exists an abrupt transition that separates the unique folded state from the globule state and ensures the stability of the native state. PMID:8327518

  6. Preparation of bulk superhard B-C-N nanocomposite compact

    DOEpatents

    Zhao, Yusheng; He, Duanwei

    2011-05-10

    Bulk, superhard, B--C--N nanocomposite compacts were prepared by ball milling a mixture of graphite and hexagonal boron nitride, encapsulating the ball-milled mixture at a pressure in a range of from about 15 GPa to about 25 GPa, and sintering the pressurized encapsulated ball-milled mixture at a temperature in a range of from about 1800-2500 K. The product bulk, superhard, nanocomposite compacts were well sintered compacts with nanocrystalline grains of at least one high-pressure phase of B--C--N surrounded by amorphous diamond-like carbon grain boundaries. The bulk compacts had a measured Vicker's hardness in a range of from about 41 GPa to about 68 GPa.

  7. Compact Focal Plane Assembly for Planetary Science

    NASA Technical Reports Server (NTRS)

    Brown, Ari; Aslam, Shahid; Huang, Wei-Chung; Steptoe-Jackson, Rosalind

    2013-01-01

    A compact radiometric focal plane assembly (FPA) has been designed in which the filters are individually co-registered over compact thermopile pixels. This allows for construction of an ultralightweight and compact radiometric instrument. The FPA also incorporates micromachined baffles in order to mitigate crosstalk and low-pass filter windows in order to eliminate high-frequency radiation. Compact metal mesh bandpass filters were fabricated for the far infrared (FIR) spectral range (17 to 100 microns), a game-changing technology for future planetary FIR instruments. This fabrication approach allows the dimensions of individual metal mesh filters to be tailored with better than 10- micron precision. In contrast, conventional compact filters employed in recent missions and in near-term instruments consist of large filter sheets manually cut into much smaller pieces, which is a much less precise and much more labor-intensive, expensive, and difficult process. Filter performance was validated by integrating them with thermopile arrays. Demonstration of the FPA will require the integration of two technologies. The first technology is compact, lightweight, robust against cryogenic thermal cycling, and radiation-hard micromachined bandpass filters. They consist of a copper mesh supported on a deep reactive ion-etched silicon frame. This design architecture is advantageous when constructing a lightweight and compact instrument because (1) the frame acts like a jig and facilitates filter integration with the FPA, (2) the frame can be designed so as to maximize the FPA field of view, (3) the frame can be simultaneously used as a baffle for mitigating crosstalk, and (4) micron-scale alignment features can be patterned so as to permit high-precision filter stacking and, consequently, increase the filter bandwidth and sharpen the out-of-band rolloff. The second technology consists of leveraging, from another project, compact and lightweight Bi0.87Sb0.13/Sb arrayed thermopiles

  8. Prediction of folding pathway and kinetics among plant hemoglobins using an average distance map method.

    PubMed

    Nakajima, Shunsuke; Alvarez-Salgado, Emma; Kikuchi, Takeshi; Arredondo-Peter, Raúl

    2005-11-15

    Computational methods, such as the ADM (average distance map) method, have been developed to predict folding of homologous proteins. In this work we used the ADM method to predict the folding pathway and kinetics among selected plant nonsymbiotic (nsHb), symbiotic (Lb), and truncated (tHb) hemoglobins (Hbs). Results predicted that (1) folding of plant Hbs occurs throughout the formation of compact folding modules mostly formed by helices A, B, and C, and E, F, G, and H (folding modules A/C and E/H, respectively), and (2) primitive (moss) nsHbs fold in the C-->N direction, evolved (monocot and dicot) nsHbs fold either in the C-->N or N-->C direction, and Lbs and plant tHbs fold in the C-->N direction. We also predicted relative folding rates of plant Hbs from qualitative analyses of the stability of subdomains and classified plant Hbs into fast and moderate folding. ADM analysis of nsHbs predicted that prehelix A plays a role during folding of the N-terminal domain of Ceratodon nsHb, and that CD-loop plays a role in folding of primitive (Physcomitrella and Ceratodon) but not evolved nsHbs. Modeling of the rice Hb1 A/C and E/H modules showed that module E/H overlaps to the Mycobacterium tuberculosis HbO two-on-two folding. This observation suggests that module E/H is an ancient tertiary structure in plant Hbs.

  9. Ions and RNAs: Free Energies of Counterion-Mediated RNA Fold Stabilities.

    PubMed

    Mak, C H; Henke, Paul S

    2013-01-08

    We present an implicit ion model fo the calculation of the electrostatic free energies of RNA conformations in the presence of divalent counterions such as Mg(2+). The model was applied to the native and several non-native structures of the hammerhead ribozyme and the group I intron in Tetrahymena to study the stability of candidate unfolding intermediates. Based on a rigorous statistical mechanical treatment of the counterions that are closely associated with the RNA while handling the rest of the ions in the solution via a mean field theory in the Grand Canonical ensemble, the implicit ion model accurately reproduces the ordering of their free energies, correctly identifying the native fold as the most stable structure out of the other alternatives. For RNA concentrations in the range below 0.1 μM, divalent concentrations of ∼0.5 mM or above, and over a wide range of solvent dielectric constants, the equilibrium number of divalent ions associated with the RNA remains close to what is needed to exactly neutralize the phosphate negative charges, but the stability of compact RNA folds can be reversed when the divalent ion concentration is lower than ∼0.1 mM, causing the number of associated ions to underneutralize the RNA. In addition to calculating counterion-mediated free energies, the model is also able to identify potential high-affinity electronegative ion binding pockets on the RNA. The model can be easily integrated into an all-atom Monte Carlo RNA simulation as an implicit counterion model.

  10. Compact grating interferometer for producing photoresist gratings with incoherent light.

    PubMed

    Post, D; Patorski, K; Ning, P

    1987-03-15

    An achromatic interferometer was developed to produce 1200-lines/mm crossed-line photoresist gratings with a mercury arc light source. It is a compact reflection system of outstanding stability. Alignment procedures are described. The most stringent requirement, coplanar alignment of two folding gratings, was accomplished with the aid of a Twyman-Green interferometer. The grating interferometer produced crossed-line photoresist gratings with first-order diffraction efficiency exceeding 20%.

  11. METHOD OF FORMING ELONGATED COMPACTS

    DOEpatents

    Larson, H.F.

    1959-05-01

    A powder compacting procedure and apparatus which produces elongated compacts of Be is described. The powdered metal is placed in a thin metal tube which is chemically compatible to lubricant, powder, atmosphere, and die material and will undergo a high degree of plastic deformation and have intermediate hardness. The tube is capped and placed in the die, and punches are applied to the ends. During the compacting stroke the powder seizes the tube and a thickening and shortening of the tube occurs. The tube is easily removed from the die, split, and peeled from the compact. (T.R.H.)

  12. HI absorption in nearby compact radio galaxies

    NASA Astrophysics Data System (ADS)

    Glowacki, M.; Allison, J. R.; Sadler, E. M.; Moss, V. A.; Curran, S. J.; Musaeva, A.; Deng, C.; Parry, R.; Sligo, M. C.

    2017-01-01

    HI absorption studies yield information on both AGN feeding and feedback processes. This AGN activity interacts with the neutral gas in compact radio sources, which are believed to represent the young or recently re-triggered AGN population. We present the results of a survey for HI absorption in a sample of 66 compact radio sources at 0.040 < z < 0.096 with the Australia Telescope Compact Array. In total, we obtained seven detections, five of which are new, with a large range of peak optical depths (3% to 87%). Of the detections, 71% exhibit asymmetric, broad (ΔvFWHM > 100 km s-1) features, indicative of disturbed gas kinematics. Such broad, shallow and offset features are also found within low-excitation radio galaxies which is attributed to disturbed circumnuclear gas, consistent with early-type galaxies typically devoid of a gas-rich disk. Comparing mid-infrared colours of our galaxies with HI detections indicates that narrow and deep absorption features are preferentially found in late-type and high-excitation radio galaxies in our sample. These features are attributed to gas in galactic disks. By combining XMM-Newton archival data with 21-cm data, we find support that absorbed X-ray sources may be good tracers of HI content within the host galaxy. This sample extends previous HI surveys in compact radio galaxies to lower radio luminosities and provides a basis for future work exploring the higher redshift universe.

  13. Geometry of Miura-folded metamaterials

    PubMed Central

    Schenk, Mark; Guest, Simon D.

    2013-01-01

    This paper describes two folded metamaterials based on the Miura-ori fold pattern. The structural mechanics of these metamaterials are dominated by the kinematics of the folding, which only depends on the geometry and therefore is scale-independent. First, a folded shell structure is introduced, where the fold pattern provides a negative Poisson’s ratio for in-plane deformations and a positive Poisson’s ratio for out-of-plane bending. Second, a cellular metamaterial is described based on a stacking of individual folded layers, where the folding kinematics are compatible between layers. Additional freedom in the design of the metamaterial can be achieved by varying the fold pattern within each layer. PMID:23401549

  14. Folding tools for flat conductor cable harnesses

    NASA Technical Reports Server (NTRS)

    Loggins, R.

    1971-01-01

    Vise grip pliers have detachable metal gripping plates which are changed to accommodate cables from 1 to 3 in. wide and to form any desired fold angle. A second tool squeezes cable along crease to complete the fold.

  15. Mesozoic folds, fossil fields, and future finds

    SciTech Connect

    Newman, G.W.; Witter, G.G.

    1988-01-01

    Drilling and surface geologic mapping have shown that pre-Tertiary, post-Triassic folds and upthrusted anticlines in an eastern Nevada foldbelt have accumulated major oil columns. This Mesozoic foldbelt involves a Cambrian through Triassic section, which has hundreds of feet of porosity in Ordovician sandstones, Silurian and Devonian carbonates, and Mississippian sandstones. In addition to the Devonian Pilot and Mississippian Chainman Shales, source rocks are found in Cambrian and Ordovician shales and in some Paleozoic carbonates. The occurrence of live and dead oil shows in hundreds of vertical feet of porosity in wells drilled on several of these Mesozoic structures is interpreted as evidence that these structures were giant oil fields prior to being breached by Tertiary Basin and Range extensional faulting, which allowed vertical hydrocarbon leakage.

  16. The topomer-sampling model of protein folding

    PubMed Central

    Debe, Derek A.; Carlson, Matt J.; Goddard, William A.

    1999-01-01

    Clearly, a protein cannot sample all of its conformations (e.g., ≈3100 ≈ 1048 for a 100 residue protein) on an in vivo folding timescale (<1 s). To investigate how the conformational dynamics of a protein can accommodate subsecond folding time scales, we introduce the concept of the native topomer, which is the set of all structures similar to the native structure (obtainable from the native structure through local backbone coordinate transformations that do not disrupt the covalent bonding of the peptide backbone). We have developed a computational procedure for estimating the number of distinct topomers required to span all conformations (compact and semicompact) for a polypeptide of a given length. For 100 residues, we find ≈3 × 107 distinct topomers. Based on the distance calculated between different topomers, we estimate that a 100-residue polypeptide diffusively samples one topomer every ≈3 ns. Hence, a 100-residue protein can find its native topomer by random sampling in just ≈100 ms. These results suggest that subsecond folding of modest-sized, single-domain proteins can be accomplished by a two-stage process of (i) topomer diffusion: random, diffusive sampling of the 3 × 107 distinct topomers to find the native topomer (≈0.1 s), followed by (ii) intratopomer ordering: nonrandom, local conformational rearrangements within the native topomer to settle into the precise native state. PMID:10077555

  17. Compact acoustic refrigerator

    SciTech Connect

    Bennett, G.A.

    1991-12-31

    This invention is comprised of a compact acoustic refrigeration system that actively cools components, e.g., electrical circuits, in a borehole environment. An acoustic engine includes first thermodynamic elements for generating a standing acoustic wave in a selected medium. An acoustic refrigerator includes second thermodynamic elements located in the standing wave for generating a relatively cold temperature at a first end of the second thermodynamic elements and a relatively hot temperature at a second end of the second thermodynamic elements. A resonator volume cooperates with the first and second thermodynamic elements to support the standing wave. To accommodate the high heat fluxes required for heat transfer to/from the first and second thermodynamic elements, first heat pipes transfer heat from the heat load to the second thermodynamic elements and second heat pipes transfer heat from first and second thermodynamic elements to the borehole environment.

  18. Multipurpose Compact Spectrometric Unit

    SciTech Connect

    Bocarov, Viktor; Cermak, Pavel; Mamedov, Fadahat; Stekl, Ivan

    2009-11-09

    A new standalone compact spectrometer was developed. The device consists of analog (peamplifier, amplifier) and digital parts. The digital part is based on the 160 MIPS Digital Signal Processor. It contains 20 Msps Flash-ADC, 1 MB RAM for spectra storage, 128 KB Flash/ROM for firmware storage, Real Time Clock and several voltage regulators providing the power for user peripherals (e.g. amplifier, temperature sensors, etc.). Spectrometer is connected with a notebook via high-speed USB 2.0 bus. The spectrometer is multipurpose device, which is planned to be used for measurements of Rn activities, energy of detected particles by CdTe pixel detector or for coincidence measurements.

  19. Compact photonic spin filters

    NASA Astrophysics Data System (ADS)

    Ke, Yougang; Liu, Zhenxing; Liu, Yachao; Zhou, Junxiao; Shu, Weixing; Luo, Hailu; Wen, Shuangchun

    2016-10-01

    In this letter, we propose and experimentally demonstrate a compact photonic spin filter formed by integrating a Pancharatnam-Berry phase lens (focal length of ±f ) into a conventional plano-concave lens (focal length of -f). By choosing the input port of the filter, photons with a desired spin state, such as the right-handed component or the left-handed one, propagate alone its original propagation direction, while the unwanted spin component is quickly diverged after passing through the filter. One application of the filter, sorting the spin-dependent components of vector vortex beams on higher-order Poincaré sphere, is also demonstrated. Our scheme provides a simple method to manipulate light, and thereby enables potential applications for photonic devices.

  20. Compact vacuum insulation

    DOEpatents

    Benson, David K.; Potter, Thomas F.

    1993-01-01

    An ultra-thin compact vacuum insulation panel is comprised of two hard, but bendable metal wall sheets closely spaced apart from each other and welded around the edges to enclose a vacuum chamber. Glass or ceramic spacers hold the wall sheets apart. The spacers can be discrete spherical beads or monolithic sheets of glass or ceramic webs with nodules protruding therefrom to form essentially "point" or "line" contacts with the metal wall sheets. In the case of monolithic spacers that form "line" contacts, two such spacers with the line contacts running perpendicular to each other form effectively "point" contacts at the intersections. Corrugations accommodate bending and expansion, tubular insulated pipes and conduits, and preferred applications are also included.

  1. Compact vacuum insulation embodiments

    DOEpatents

    Benson, David K.; Potter, Thomas F.

    1992-01-01

    An ultra-thin compact vacuum insulation panel is comprised of two hard, but bendable metal wall sheets closely spaced apart from each other and welded around the edges to enclose a vacuum chamber. Glass or ceramic spacers hold the wall sheets apart. The spacers can be discrete spherical beads or monolithic sheets of glass or ceramic webs with nodules protruding therefrom to form essentially "point" or "line" contacts with the metal wall sheets. In the case of monolithic spacers that form "line" contacts, two such spacers with the line contacts running perpendicular to each other form effectively "point" contacts at the intersections. Corrugations accommodate bending and expansion, tubular insulated pipes and conduits, and preferred applications are also included.

  2. Compact vacuum insulation embodiments

    DOEpatents

    Benson, D.K.; Potter, T.F.

    1992-04-28

    An ultra-thin compact vacuum insulation panel is comprised of two hard, but bendable metal wall sheets closely spaced apart from each other and welded around the edges to enclose a vacuum chamber. Glass or ceramic spacers hold the wall sheets apart. The spacers can be discrete spherical beads or monolithic sheets of glass or ceramic webs with nodules protruding therefrom to form essentially point' or line' contacts with the metal wall sheets. In the case of monolithic spacers that form line' contacts, two such spacers with the line contacts running perpendicular to each other form effectively point' contacts at the intersections. Corrugations accommodate bending and expansion, tubular insulated pipes and conduits, and preferred applications are also included. 26 figs.

  3. Compact vacuum insulation

    DOEpatents

    Benson, D.K.; Potter, T.F.

    1993-01-05

    An ultra-thin compact vacuum insulation panel is comprised of two hard, but bendable metal wall sheets closely spaced apart from each other and welded around the edges to enclose a vacuum chamber. Glass or ceramic spacers hold the wall sheets apart. The spacers can be discrete spherical beads or monolithic sheets of glass or ceramic webs with nodules protruding therefrom to form essentially point'' or line'' contacts with the metal wall sheets. In the case of monolithic spacers that form line'' contacts, two such spacers with the line contacts running perpendicular to each other form effectively point'' contacts at the intersections. Corrugations accommodate bending and expansion, tubular insulated pipes and conduits, and preferred applications are also included.

  4. Compact acoustic refrigerator

    DOEpatents

    Bennett, G.A.

    1992-11-24

    A compact acoustic refrigeration system actively cools components, e.g., electrical circuits, in a borehole environment. An acoustic engine includes first thermodynamic elements for generating a standing acoustic wave in a selected medium. An acoustic refrigerator includes second thermodynamic elements located in the standing wave for generating a relatively cold temperature at a first end of the second thermodynamic elements and a relatively hot temperature at a second end of the second thermodynamic elements. A resonator volume cooperates with the first and second thermodynamic elements to support the standing wave. To accommodate the high heat fluxes required for heat transfer to/from the first and second thermodynamic elements, first heat pipes transfer heat from the heat load to the second thermodynamic elements and second heat pipes transfer heat from first and second thermodynamic elements to the borehole environment. 18 figs.

  5. Compact acoustic refrigerator

    DOEpatents

    Bennett, Gloria A.

    1992-01-01

    A compact acoustic refrigeration system actively cools components, e.g., electrical circuits (22), in a borehole environment. An acoustic engine (12, 14) includes first thermodynamic elements (12) for generating a standing acoustic wave in a selected medium. An acoustic refrigerator (16, 26, 28) includes second thermodynamic elements (16) located in the standing wave for generating a relatively cold temperature at a first end of the second thermodynamic elements (16) and a relatively hot temperature at a second end of the second thermodynamic elements (16). A resonator volume (18) cooperates with the first and second thermodynamic elements (12, 16) to support the standing wave. To accommodate the high heat fluxes required for heat transfer to/from the first and second thermodynamic elements (12, 16), first heat pipes (24, 26) transfer heat from the heat load (22) to the second thermodynamic elements (16) and second heat pipes (28, 32) transfer heat from first and second thermodynamic elements (12, 16) to the borehole environment.

  6. Compact artificial hand

    NASA Technical Reports Server (NTRS)

    Wiker, G. A.; Mann, W. A. (Inventor)

    1979-01-01

    A relatively simple, compact artificial hand, is described which includes hooks pivotally mounted on first frame to move together and apart. The first frame is rotatably mounted on a second frame to enable "turning at the wrist" movement without limitation. The second frame is pivotally mounted on a third frame to permit 'flexing at the wrist' movement. A hook-driving motor is fixed to the second frame but has a shaft that drives a speed reducer on the first frame which, in turn, drives the hooks. A second motor mounted on the second frame, turns a gear on the first frame to rotate the first frame and the hooks thereon. A third motor mounted on the third frame, turns a gear on a second frame to pivot it.

  7. Extracting Information from Folds in Rocks.

    ERIC Educational Resources Information Center

    Hudleston, Peter John

    1986-01-01

    Describes the three processes of folding in rocks: buckling, bending, and passive folding. Discusses how geometrical properties and strain distributions help to identify which processes produce natural folds, and also provides information about the mechanical properties of rocks, and the sense of shear in shear zones. (TW)

  8. Dynamics of Folds in the Plane

    ERIC Educational Resources Information Center

    Krylov, Nikolai A.; Rogers, Edwin L.

    2011-01-01

    Take a strip of paper and fold a crease intersecting the long edges, creating two angles. Choose one edge and consider the angle with the crease. Fold the opposite edge along the crease, creating a new crease that bisects the angle. Fold again, this time using the newly created crease and the initial edge, creating a new angle along the chosen…

  9. Intradomain Confinement of Disulfides in the Folding of Two Consecutive Modules of the LDL Receptor

    PubMed Central

    Martínez-Oliván, Juan; Fraga, Hugo; Arias-Moreno, Xabier; Ventura, Salvador; Sancho, Javier

    2015-01-01

    The LDL receptor internalizes circulating LDL and VLDL particles for degradation. Its extracellular binding domain contains ten (seven LA and three EGF) cysteine-rich modules, each bearing three disulfide bonds. Despite the enormous number of disulfide combinations possible, LDLR oxidative folding leads to a single native species with 30 unique intradomain disulfides. Previous folding studies of the LDLR have shown that non native disulfides are initially formed that lead to compact species. Accordingly, the folding of the LDLR has been described as a "coordinated nonvectorial” reaction, and it has been proposed that early compaction funnels the reaction toward the native structure. Here we analyze the oxidative folding of LA4 and LA5, the modules critical for ApoE binding, isolated and in the LA45 tandem. Compared to LA5, LA4 folding is slow and inefficient, resembling that of LA5 disease-linked mutants. Without Ca++, it leads to a mixture of many two-disulfide scrambled species and, with Ca++, to the native form plus two three-disulfide intermediates. The folding of the LA45 tandem seems to recapitulate that of the individual repeats. Importantly, although the folding of the LA45 tandem takes place through formation of scrambled isomers, no interdomain disulfides are detected, i.e. the two adjacent modules fold independently without the assistance of interdomain covalent interactions. Reduction of incredibly large disulfide combinatorial spaces, such as that in the LDLR, by intradomain confinement of disulfide bond formation might be also essential for the efficient folding of other homologous disulfide-rich receptors. PMID:26168158

  10. Towards a geomechanics classification of folded layered rock masses

    NASA Astrophysics Data System (ADS)

    Agliardi, Federico; Zanchi, Andrea; Bianchi, Federico; Crosta, Giovanni B.

    2016-04-01

    Several schemes have been proposed in the last decades to account for the effects of structure and alteration of rock masses on their geo-mechanical properties. Among these, the Geological Strength Index (GSI) turned out as the most effective to account for complex geological conditions, including heavily fractured, heterogeneous (e.g. flysch-like) or tectonically disturbed rock masses. It is well known that folding has a direct impact on the type and degree of fracturing. Nevertheless, no classification scheme has been developed to introduce explicitly the effects of folding and associated fracturing on rock mass strength and deformability. In this perspective, we carried out an exploratory study aimed at establishing relationships between outcrop-scale folding and GSI in layered carbonate rock masses, exceptionally well exposed in a quarry near Bergamo (Lombardia, Southern Alps). A N-S trending, 350m long and 115m high benched rock face exposes a complete cross section of a sub-horizontal inclined fold involving Lower Jurassic cherty mudstones (Moltrasio Lms.) and marly limestones successions (Domaro Lms.). The main fold has an axial surface moderately dipping to the north and is characterised by polyharmonic folds at scales of metres to tens of metres. The site was documented by producing a digital outcrop through a high-resolution terrestrial photogrammetric survey from distances ranging from 70 to 130 m (18 camera stations, 395 pictures), using RTK GNSS measurements for camera station geo-referencing. Data processing by Structure-from-Motion (SfM) techniques resulted in detailed point clouds covering the entire slope with a cm-scale accuracy. In order to establish relationships between lithology, folding styles, and geomechanical properties of folded rock masses we performed a detailed structural analysis at 25 survey stations spread over all the different fold sectors. These surveys include: lithology, bedding attitude and thickness, brittle structures (e

  11. Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model.

    PubMed

    Reddy, Govardhan; Thirumalai, D

    2015-08-27

    Folding of Ubiquitin (Ub), a functionally important protein found in eukaryotic organisms, is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained self-organized-polymer model with side chains (SOP-SC). The melting temperatures (Tm's), identified with the peaks in the heat capacity curves, decrease as pH decreases, in qualitative agreement with experiments. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At Tm, Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at Tm, with multiple transitions between the folded and unfolded states, shows a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long-range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of microseconds, then Ub folding follows the diffusion-collision mechanism with intermediates, many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a Pfold analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings for

  12. Understanding Protein Non-Folding

    PubMed Central

    Uversky, Vladimir N.; Dunker, A. Keith

    2010-01-01

    This review describes the family of intrinsically disordered proteins, members of which fail to form rigid 3-D structures under physiological conditions, either along their entire lengths or only in localized regions. Instead, these intriguing proteins/regions exist as dynamic ensembles within which atom positions and backbone Ramachandran angles exhibit extreme temporal fluctuations without specific equilibrium values. Many of these intrinsically disordered proteins are known to carry out important biological functions which, in fact, depend on the absence of specific 3-D structure. The existence of such proteins does not fit the prevailing structure-function paradigm, which states that unique 3-D structure is a prerequisite to function. Thus, the protein structure-function paradigm has to be expanded to include intrinsically disordered proteins and alternative relationships among protein sequence, structure, and function. This shift in the paradigm represents a major breakthrough for biochemistry, biophysics and molecular biology, as it opens new levels of understanding with regard to the complex life of proteins. This review will try to answer the following questions: How were intrinsically disordered proteins discovered? Why don't these proteins fold? What is so special about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases? PMID:20117254

  13. Role of mRNA structure in the control of protein folding

    PubMed Central

    Faure, Guilhem; Ogurtsov, Aleksey Y.; Shabalina, Svetlana A.; Koonin, Eugene V.

    2016-01-01

    Specific structures in mRNA modulate translation rate and thus can affect protein folding. Using the protein structures from two eukaryotes and three prokaryotes, we explore the connections between the protein compactness, inferred from solvent accessibility, and mRNA structure, inferred from mRNA folding energy (ΔG). In both prokaryotes and eukaryotes, the ΔG value of the most stable 30 nucleotide segment of the mRNA (ΔGmin) strongly, positively correlates with protein solvent accessibility. Thus, mRNAs containing exceptionally stable secondary structure elements typically encode compact proteins. The correlations between ΔG and protein compactness are much more pronounced in predicted ordered parts of proteins compared to the predicted disordered parts, indicative of an important role of mRNA secondary structure elements in the control of protein folding. Additionally, ΔG correlates with the mRNA length and the evolutionary rate of synonymous positions. The correlations are partially independent and were used to construct multiple regression models which explain about half of the variance of protein solvent accessibility. These findings suggest a model in which the mRNA structure, particularly exceptionally stable RNA structural elements, act as gauges of protein co-translational folding by reducing ribosome speed when the nascent peptide needs time to form and optimize the core structure. PMID:27466388

  14. Sediment compaction rates and subsidence in deltaic plains: Numerical constraints and stratigraphic influences

    USGS Publications Warehouse

    Meckel, T.A.; ten Brink, U.S.; Williams, S.J.

    2007-01-01

    Natural sediment compaction in deltaic plains influences subsidence rates and the evolution of deltaic morphology. Determining compaction rates requires detailed knowledge of subsurface geotechnical properties and depositional history, neither of which is often readily available. To overcome this lack of knowledge, we numerically forward model the incremental sedimentation and compaction of stochastically generated stratigraphies with geotechnical properties typical of modern depositional environments in the Mississippi River delta plain. Using a Monte Carlo approach, the range of probable compaction rates for stratigraphies with compacted thicknesses −1. The fastest compacting stratigraphies are composed primarily of peat and bar sand, whereas the slowest compacting stratigraphies are composed of prodelta mud and natural levee deposits. These results suggest that compaction rates can significantly influence vertical and lateral stratigraphic trends during deltaic evolution.

  15. Recovery of compacted soils in Mojave Desert ghost towns.

    USGS Publications Warehouse

    Webb, R.H.; Steiger, J.W.; Wilshire, H.G.

    1986-01-01

    Residual compaction of soils was measured at seven sites in five Mojave Desert ghost towns. Soils in these Death Valley National Monument townsites were compacted by vehicles, animals, and human trampling, and the townsites had been completely abandoned and the buildings removed for 64 to 75 yr. Recovery times extrapolated using a linear recovery model ranged from 80 to 140 yr and averaged 100 yr. The recovery times were related to elevation, suggesting freeze-thaw loosening as an important factor in ameliorating soil compaction in the Mojave Desert. -from Authors

  16. Elastic properties of granular materials under uniaxial compaction cycles

    NASA Technical Reports Server (NTRS)

    Warren, N.; Anderson, O. L.

    1973-01-01

    Data on andesitic and basaltic sands are presented showing compressional sound velocity, density, and creep as functions of uniaxial loading through several compaction cycles. Maximum pressures over which acoustic measurements were made were in the range from 600 to 700 bars. The dynamic elastic modulus varies with pressure in a manner analogous to that of a static elastic modulus defined by small pressure perturbations on a typical compaction cycle. After several compaction cycles, two compressional elastic moduli apparently exist at low pressure (thus two modes of compressional wave propagation through the samples are indicated). The elastic moduli observations are briefly discussed in terms of a general expression for compressibility.

  17. 3D fold growth in transpression

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel

    2016-12-01

    Geological folds in transpression are inherently 3D structures; hence their growth and rotation behavior is studied using 3D numerical finite-element simulations. Upright single-layer buckle folds in Newtonian materials are considered, which grow from an initial point-like perturbation due to a combination of in-plane shortening and shearing (i.e., transpression). The resulting fold growth exhibits three components: (1) fold amplification (vertical), (2) fold elongation (parallel to fold axis), and (3) sequential fold growth (perpendicular to axial plane) of new anti- and synforms adjacent to the initial fold. Generally, the fold growth rates are smaller for shearing-dominated than for shortening-dominated transpression. In spite of the growth rate, the folding behavior is very similar for the different convergence angles. The two lateral directions always exhibit similar growth rates implying that the bulk fold structure occupies an increasing roughly circular area. Fold axes are always parallel to the major horizontal principal strain axis (λ→max, i.e., long axis of the horizontal finite strain ellipse), which is initially also parallel to the major horizontal instantaneous stretching axis (ISA→max). After initiation, the fold axes rotate together with λ→max. Sequential folds appearing later do not initiate parallel to ISA→max, but parallel to λ→max, i.e. parallel to the already existing folds, and also rotate with λ→max. Therefore, fold axes do not correspond to passive material lines and hinge migration takes place as a consequence. The fold axis orientation parallel to λ→max is independent of convergence angle and viscosity ratio. Therefore, a triangular relationship between convergence angle, amount of shortening, and fold axis orientation exists. If two of these values are known, the third can be determined. This relationship is applied to the Zagros fold-and-thrust-belt to estimate the degree of strain partitioning between the Simply

  18. Folding of viscous sheets and filaments

    NASA Astrophysics Data System (ADS)

    Skorobogatiy, M.; Mahadevan, L.

    2000-12-01

    We consider the nonlinear folding behavior of a viscous filament or a sheet under the influence of an external force such as gravity. Everyday examples of this phenomenon are provided by the periodic folding of a sheet of honey as it impinges on toast, or the folding of a stream of shampoo as it falls on one's hand. To understand the evolution of a fold, we formulate and solve a free-boundary problem for the phenomenon, give scaling laws for the size of the folds and the frequency with which they are laid out, and verify these experimentally.

  19. Compaction with Automatic Jog Introduction,

    DTIC Science & Technology

    1985-10-01

    The compaction algorithm This section defines mathematically the problem of compaction with auto- matk jog introduction, and presents a practical...t(5) of potential cuts of S, and usng their mutability cmndi to constrain the positiokn of modulo in S. The proof that this technique gen - erates a

  20. Dynamically Scaled Glottal Flow Through Symmetrically Oscillating Vocal Fold Models

    NASA Astrophysics Data System (ADS)

    Halvorson, Lori; Baitinger, Andrew; Sherman, Erica; Krane, Michael; Zhang, Lucy; Wei, Timothy

    2011-11-01

    Experimental results derived from DPIV measurements in a scaled up dynamic human vocal fold model are presented. The 10x scale vocal fold model is a new design that incorporates key features of vocal fold oscillatory motion. This includes coupling of down/upstream rocking as well as the oscillatory open/close motions. Experiments were dynamically scaled to examine a range of frequencies, 100 - 200 Hz, corresponding to the male and female voice. By using water as the working fluid, very high resolution, both spatial and temporal resolution, was achieved. Time resolved movies of flow through symmetrically oscillating vocal folds will be presented. Both individual realizations as well as phase-averaged data will be shown. Key features, such as randomness and development time of the Coanda effect, vortex shedding, and volume flow rate data will be shown. In this talk, effects associated with paralysis of one vocal fold will be discussed. This talk provides the baseline fluid dynamics for the vocal fold paralysis study presented in Sherman, et al. Supported by the NIH.

  1. Anatomy and Histology of an Epicanthal Fold.

    PubMed

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  2. Controlled Folding of Single Crystal Graphene.

    PubMed

    Wang, Bin; Huang, Ming; Kim, Na Yeon; Cunning, Benjamin V; Huang, Yuan; Qu, Deshun; Chen, Xianjue; Jin, Sunghwan; Biswal, Mandakini; Zhang, Xu; Lee, Sun Hwa; Lim, Hyunseob; Yoo, Won Jong; Lee, Zonghoon; Ruoff, Rodney S

    2017-03-08

    Folded graphene in which two layers are stacked with a twist angle between them has been predicted to exhibit unique electronic, thermal, and magnetic properties. We report the folding of a single crystal monolayer graphene film grown on a Cu(111) substrate by using a tailored substrate having a hydrophobic region and a hydrophilic region. Controlled film delamination from the hydrophilic region was used to prepare macroscopic folded graphene with good uniformity on the millimeter scale. This process was used to create many folded sheets each with a defined twist angle between the two sheets. By identifying the original lattice orientation of the monolayer graphene on Cu foil, or establishing the relation between the fold angle and twist angle, this folding technique allows for the preparation of twisted bilayer graphene films with defined stacking orientations and may also be extended to create folded structures of other two-dimensional nanomaterials.

  3. Compact designer TALENs for efficient genome engineering.

    PubMed

    Beurdeley, Marine; Bietz, Fabian; Li, Jin; Thomas, Severine; Stoddard, Thomas; Juillerat, Alexandre; Zhang, Feng; Voytas, Daniel F; Duchateau, Philippe; Silva, George H

    2013-01-01

    Transcription activator-like effector nucleases are readily targetable 'molecular scissors' for genome engineering applications. These artificial nucleases offer high specificity coupled with simplicity in design that results from the ability to serially chain transcription activator-like effector repeat arrays to target individual DNA bases. However, these benefits come at the cost of an appreciably large multimeric protein complex, in which DNA cleavage is governed by the nonspecific FokI nuclease domain. Here we report a significant improvement to the standard transcription activator-like effector nuclease architecture by leveraging the partially specific I-TevI catalytic domain to create a new class of monomeric, DNA-cleaving enzymes. In vivo yeast, plant and mammalian cell assays demonstrate that the half-size, single-polypeptide compact transcription activator-like effector nucleases exhibit overall activity and specificity comparable to currently available designer nucleases. In addition, we harness the catalytic mechanism of I-TevI to generate novel compact transcription activator-like effector nuclease-based nicking enzymes that display a greater than 25-fold increase in relative targeted gene correction efficacy.

  4. Autonomous folding of the excised coenzyme-binding domain of D-glyceraldehyde 3-phosphate dehydrogenase from Thermotoga maritima.

    PubMed Central

    Jecht, M.; Tomschy, A.; Kirschner, K.; Jaenicke, R.

    1994-01-01

    An important question in protein folding is whether compact substructures or domains are autonomous units of folding and assembly. The protomer of the tetrameric D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima has a complex coenzyme-binding domain, in which residues 1-146 form a compact substructure with the last 31 residues (313-333). Here it is shown that the gene of a single-chain protein can be expressed in Escherichia coli after deleting the 163 codons corresponding to the interspersed catalytic domain (150-312). The purified gene product is a soluble, monomeric protein that binds both NAD+ and NADH strongly and possesses the same unfolding transition induced by guanidinium chloride as the native tetramer. The autonomous folding of the coenzyme-binding domain has interesting implications for the folding, assembly, function, and evolution of the native enzyme. PMID:8019412

  5. The Arterial Folding Point During Flexion of the Hip Joint

    SciTech Connect

    Park, Sung Il; Won, Je Hwan Kim, Byung Moon; Kim, Jae Keun; Lee, Do Yun

    2005-04-15

    Purpose: Endovascular stents placed in periarticular vessels may be at a greater risk of neointimal hyperplasia and eventual occlusion than those placed in non-periarticular vessels. The purpose of this study was to investigate the location of maximal conformational change along the iliac and femoral artery, the folding point, during flexion of the hip joint and its location relative to the hip joint and the inguinal ligament. Methods: Seventy patients undergoing femoral artery catheterization were evaluated. The patients were 47 men and 23 women and ranged in age from 26 to 75 years (mean 54 years). The arteries (right:left = 34:36) were measured using a marked catheter for sizing vessels. Fluoroscopic images were obtained in anteroposterior and lateral projections in neutral position, and in the lateral projection in flexed position of the hip joint. The folding point was determined by comparing the lateral projection images in the neutral and flexed positions. The distance from the acetabular roof to the folding point and the distance from the inguinal ligament to the folding point was evaluated. Results: : The folding point was located 42.8 {+-} 28.6 mm cranial to the acetabular roof and 35.1 {+-} 30.1 mm cranial to the inguinal ligament. As the patient's age increased, the folding point was located more cranially (p < 0.001). Conclusions: The folding point during flexion of the hip joint was located 42.8 {+-} 28.6 mm cranial to the acetabular roof and 35.1 {+-} 30.1 mm cranial to the inguinal ligament. As the patient's age increased, the folding point was located more cranially. When a stent is inserted over this region, more attention may be needed during follow-up to monitor possible occlusion and stent failure.

  6. Hierarchical classification of protein folds using a novel ensemble classifier.

    PubMed

    Lin, Chen; Zou, Ying; Qin, Ji; Liu, Xiangrong; Jiang, Yi; Ke, Caihuan; Zou, Quan

    2013-01-01

    The analysis of biological information from protein sequences is important for the study of cellular functions and interactions, and protein fold recognition plays a key role in the prediction of protein structures. Unfortunately, the prediction of protein fold patterns is challenging due to the existence of compound protein structures. Here, we processed the latest release of the Structural Classification of Proteins (SCOP, version 1.75) database and exploited novel techniques to impressively increase the accuracy of protein fold classification. The techniques proposed in this paper include ensemble classifying and a hierarchical framework, in the first layer of which similar or redundant sequences were deleted in two manners; a set of base classifiers, fused by various selection strategies, divides the input into seven classes; in the second layer of which, an analogous ensemble method is adopted to predict all protein folds. To our knowledge, it is the first time all protein folds can be intelligently detected hierarchically. Compared with prior studies, our experimental results demonstrated the efficiency and effectiveness of our proposed method, which achieved a success rate of 74.21%, which is much higher than results obtained with previous methods (ranging from 45.6% to 70.5%). When applied to the second layer of classification, the prediction accuracy was in the range between 23.13% and 46.05%. This value, which may not be remarkably high, is scientifically admirable and encouraging as compared to the relatively low counts of proteins from most fold recognition programs. The web server Hierarchical Protein Fold Prediction (HPFP) is available at http://datamining.xmu.edu.cn/software/hpfp.

  7. Hierarchical Classification of Protein Folds Using a Novel Ensemble Classifier

    PubMed Central

    Qin, Ji; Liu, Xiangrong; Jiang, Yi; Ke, Caihuan; Zou, Quan

    2013-01-01

    The analysis of biological information from protein sequences is important for the study of cellular functions and interactions, and protein fold recognition plays a key role in the prediction of protein structures. Unfortunately, the prediction of protein fold patterns is challenging due to the existence of compound protein structures. Here, we processed the latest release of the Structural Classification of Proteins (SCOP, version 1.75) database and exploited novel techniques to impressively increase the accuracy of protein fold classification. The techniques proposed in this paper include ensemble classifying and a hierarchical framework, in the first layer of which similar or redundant sequences were deleted in two manners; a set of base classifiers, fused by various selection strategies, divides the input into seven classes; in the second layer of which, an analogous ensemble method is adopted to predict all protein folds. To our knowledge, it is the first time all protein folds can be intelligently detected hierarchically. Compared with prior studies, our experimental results demonstrated the efficiency and effectiveness of our proposed method, which achieved a success rate of 74.21%, which is much higher than results obtained with previous methods (ranging from 45.6% to 70.5%). When applied to the second layer of classification, the prediction accuracy was in the range between 23.13% and 46.05%. This value, which may not be remarkably high, is scientifically admirable and encouraging as compared to the relatively low counts of proteins from most fold recognition programs. The web server Hierarchical Protein Fold Prediction (HPFP) is available at http://datamining.xmu.edu.cn/software/hpfp. PMID:23437146

  8. Compact dusty clouds in a cosmic environment

    SciTech Connect

    Tsytovich, V. N.; Ivlev, A. V.; Burkert, A.; Morfill, G. E.

    2014-01-10

    A novel mechanism of the formation of compact dusty clouds in astrophysical environments is discussed. It is shown that the balance of collective forces operating in space dusty plasmas can result in the effect of dust self-confinement, generating equilibrium spherical clusters. The distribution of dust and plasma density inside such objects and their stability are investigated. Spherical dusty clouds can be formed in a broad range of plasma parameters, suggesting that this process of dust self-organization might be a generic phenomenon occurring in different astrophysical media. We argue that compact dusty clouds can represent condensation seeds for a population of small-scale, cold, gaseous clumps in the diffuse interstellar medium. They could play an important role in regulating its small-scale structure and its thermodynamical evolution.

  9. Stress and strain evolution of folding rocks

    NASA Astrophysics Data System (ADS)

    Llorens, Maria-Gema; Griera, Albert; Bons, Paul; Gomez-Rivas, Enrique; Weikusat, Ilka

    2015-04-01

    One of the main objectives of structural geology is to unravel rock deformation histories. Fold shapes can be used to estimate the orientation and amount of strain associated with folding. However, much more information on rheology and kinematics can potentially be extracted from fold geometries (Llorens et al., 2013a). We can study the development of folds, quantify the relationships between the different parameters that determine their geometries and estimate their mechanical evolution. This approach allows us to better understand and predict not only rock but also ice deformation. One of the main parameters in fold development is the viscosity contrast between the folding layer and the matrix in which it is embedded (m), since it determines the initial fold wavelength and the amplification rate of the developing folds. Moreover, non-linear viscous rheology influences fold geometry too (Llorens et al., 2013b). We present a series of 2-dimensional simulations of folding of viscous single layers in pure and simple shear. We vary different parameters in order to compare and determine their influence on the resulting fold patterns and the associated mechanical response of the material. To perform these simulations we use the software platform ELLE (www.elle.ws) with the non-linear viscous finite element code BASIL. The results show that layers thicken at the beginning of deformation in all simulations, and visible folds start earlier or later depending on the viscosity contrast. When folds start to nucleate the layer maximum shear strain decreases, moving away from the theoretical trend for homogeneous strain (no folding). This allows the accurate determination of the onset of folding. Maximum deviatoric stresses are higher in power-law than in linear-viscosity materials, and it is initially double in pure shear than in simple shear conditions. Therefore, folding a competent layer requires less work in simple than in pure shear. The maximum deviatoric stress

  10. Compact vacuum insulation

    DOEpatents

    Benson, David K.; Potter, Thomas F.

    1992-01-01

    Improved compact insulation panel is provided which is comprised of two adjacent metal sheets spaced close together with a plurality of spherical, or other discretely shaped, glass or ceramic beads optimally positioned between the sheets to provide support and maintain the spacing between the metal sheets when the gases therebetween are evacuated to form a vacuum. These spherical glass beads provide the maximum support while minimizing thermal conductance. In its preferred embodiment; these two metal sheets are textured with ribs or concave protrusions in conjunction with the glass beads to maximize the structural integrity of the panels while increasing the spacing between beads, thereby reducing the number of beads and the number of thermal conduction paths. Glass or porcelain-enameled liners in combination with the glass spacers and metal sidewalls effectively decrease thermal conductivity, and variious laminates, including wood, porcelain-enameled metal, and others effectively increase the strength and insulation capabilities of the panels. Also, a metal web is provided to hold the spacers in place, and strategic grooves are shown to accommodate expansion and contraction or shaping of the panels.

  11. Compact vacuum insulation

    DOEpatents

    Benson, D.K.; Potter, T.F.

    1992-10-27

    Improved compact insulation panel is provided which is comprised of two adjacent metal sheets spaced close together with a plurality of spherical, or other discretely shaped, glass or ceramic beads optimally positioned between the sheets to provide support and maintain the spacing between the metal sheets when the gases there between are evacuated to form a vacuum. These spherical glass beads provide the maximum support while minimizing thermal conductance. In its preferred embodiment; these two metal sheets are textured with ribs or concave protrusions in conjunction with the glass beads to maximize the structural integrity of the panels while increasing the spacing between beads, thereby reducing the number of beads and the number of thermal conduction paths. Glass or porcelain-enameled liners in combination with the glass spacers and metal sidewalls effectively decrease thermal conductivity, and various laminates, including wood, porcelain-enameled metal, and others effectively increase the strength and insulation capabilities of the panels. Also, a metal web is provided to hold the spacers in place, and strategic grooves are shown to accommodate expansion and contraction or shaping of the panels. 35 figs.

  12. Compact Dexterous Robotic Hand

    NASA Technical Reports Server (NTRS)

    Lovchik, Christopher Scott (Inventor); Diftler, Myron A. (Inventor)

    2001-01-01

    A compact robotic hand includes a palm housing, a wrist section, and a forearm section. The palm housing supports a plurality of fingers and one or more movable palm members that cooperate with the fingers to grasp and/or release an object. Each flexible finger comprises a plurality of hingedly connected segments, including a proximal segment pivotally connected to the palm housing. The proximal finger segment includes at least one groove defining first and second cam surfaces for engagement with a cable. A plurality of lead screw assemblies each carried by the palm housing are supplied with power from a flexible shaft rotated by an actuator and output linear motion to a cable move a finger. The cable is secured within a respective groove and enables each finger to move between an opened and closed position. A decoupling assembly pivotally connected to a proximal finger segment enables a cable connected thereto to control movement of an intermediate and distal finger segment independent of movement of the proximal finger segment. The dexterous robotic hand closely resembles the function of a human hand yet is light weight and capable of grasping both heavy and light objects with a high degree of precision.

  13. Compact plasma accelerator

    NASA Technical Reports Server (NTRS)

    Foster, John E. (Inventor)

    2004-01-01

    A compact plasma accelerator having components including a cathode electron source, an anodic ionizing gas source, and a magnetic field that is cusped. The components are held by an electrically insulating body having a central axis, a top axial end, and a bottom axial end. The cusped magnetic field is formed by a cylindrical magnet having an axis of rotation that is the same as the axis of rotation of the insulating body, and magnetized with opposite poles at its two axial ends; and an annular magnet coaxially surrounding the cylindrical magnet, magnetized with opposite poles at its two axial ends such that a top axial end has a magnetic polarity that is opposite to the magnetic polarity of a top axial end of the cylindrical magnet. The ionizing gas source is a tubular plenum that has been curved into a substantially annular shape, positioned above the top axial end of the annular magnet such that the plenum is centered in a ring-shaped cusp of the magnetic field generated by the magnets. The plenum has one or more capillary-like orifices spaced around its top such that an ionizing gas supplied through the plenum is sprayed through the one or more orifices. The plenum is electrically conductive and is positively charged relative to the cathode electron source such that the plenum functions as the anode; and the cathode is positioned above and radially outward relative to the plenum.

  14. Compact neutron generator

    DOEpatents

    Leung, Ka-Ngo; Lou, Tak Pui

    2005-03-22

    A compact neutron generator has at its outer circumference a toroidal shaped plasma chamber in which a tritium (or other) plasma is generated. A RF antenna is wrapped around the plasma chamber. A plurality of tritium ion beamlets are extracted through spaced extraction apertures of a plasma electrode on the inner surface of the toroidal plasma chamber and directed inwardly toward the center of neutron generator. The beamlets pass through spaced acceleration and focusing electrodes to a neutron generating target at the center of neutron generator. The target is typically made of titanium tubing. Water is flowed through the tubing for cooling. The beam can be pulsed rapidly to achieve ultrashort neutron bursts. The target may be moved rapidly up and down so that the average power deposited on the surface of the target may be kept at a reasonable level. The neutron generator can produce fast neutrons from a T-T reaction which can be used for luggage and cargo interrogation applications. A luggage or cargo inspection system has a pulsed T-T neutron generator or source at the center, surrounded by associated gamma detectors and other components for identifying explosives or other contraband.

  15. Investigation of HMA compactability using GPR technique

    NASA Astrophysics Data System (ADS)

    Plati, Christina; Georgiou, Panos; Loizos, Andreas

    2014-05-01

    In-situ field density is often regarded as one of the most important controls used to ensure that an asphalt pavement being placed is of high quality. The achieved density results from the effectiveness of the applied compaction mode on the Hot Mix Asphalt (HMA) layer. It is worthwhile mentioning that the proper compaction of HMA increases pavement fatigue life, decreases the amount of permanent deformation or rutting, reduces the amount of oxidation or aging, decreases moisture damage or stripping, increases strength and internal stability, and may decrease slightly the amount of low-temperature cracking that may occur in the mix. Conventionally, the HMA density in the field is assessed by direct destructive methods, including through the cutting of samples or drilling cores. These methods are characterized by a high accuracy, although they are intrusive and time consuming. In addition, they provide local information, i.e. information only for the exact test location. To overcome these limitations, the use of non-intrusive techniques is often recommended. The Ground Penetrating Radar (GPR) technique is an example of a non-intrusive technique that has been increasingly used for pavement investigations over the years. GPR technology is practical and application-oriented with the overall design concept, as well as the hardware, usually dependent on the target type and the material composing the target and its surroundings. As the sophistication of operating practices increases, the technology matures and GPR becomes an intelligent sensor system. The intelligent sensing deals with the expanded range of GPR applications in pavements such as determining layer thickness, detecting subsurface distresses, estimating moisture content, detecting voids and others. In addition, the practice of using GPR to predict in-situ field density of compacted asphalt mixture material is still under development and research; however the related research findings seem to be promising

  16. Kinetic partitioning mechanism of HDV ribozyme folding.

    PubMed

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  17. Kinetic partitioning mechanism of HDV ribozyme folding

    SciTech Connect

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  18. Kinetic partitioning mechanism of HDV ribozyme folding

    NASA Astrophysics Data System (ADS)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-01

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  19. Viscoelastic properties of the false vocal fold

    NASA Astrophysics Data System (ADS)

    Chan, Roger W.

    2004-05-01

    The biomechanical properties of vocal fold tissues have been the focus of many previous studies, as vocal fold viscoelasticity critically dictates the acoustics and biomechanics of phonation. However, not much is known about the viscoelastic response of the ventricular fold or false vocal fold. It has been shown both clinically and in computer simulations that the false vocal fold may contribute significantly to the aerodynamics and sound generation processes of human voice production, with or without flow-induced oscillation of the false fold. To better understand the potential role of the false fold in phonation, this paper reports some preliminary measurements on the linear and nonlinear viscoelastic behavior of false vocal fold tissues. Linear viscoelastic shear properties of human false fold tissue samples were measured by a high-frequency controlled-strain rheometer as a function of frequency, and passive uniaxial tensile stress-strain response of the tissue samples was measured by a muscle lever system as a function of strain and loading rate. Elastic moduli (Young's modulus and shear modulus) of the false fold tissues were calculated from the measured data. [Work supported by NIH.

  20. The ion-induced folding of the hammerhead ribozyme: core sequence changes that perturb folding into the active conformation.

    PubMed Central

    Bassi, G S; Murchie, A I; Lilley, D M

    1996-01-01

    The hammerhead ribozyme undergoes an ion-dependent folding process into the active conformation. We find that the folding can be blocked at specific stages by changes of sequence or functionality within the core. In the the absence of added metal ions, the global structure of the hammerhead is extended, with a large angle subtended between stems I and II. No core sequence changes appear to alter this geometry, consistent with an unstructured core under these conditions. Upon addition of low concentrations of magnesium ions, the hammerhead folds by an association of stems II and III, to include a large angle between them. This stage is inhibited or altered by mutations within the oligopurine sequence lying between stems II and III, and folding is completely prevented by an A14G mutation. Further increase in magnesium ion concentration brings about a second stage of folding in the natural sequence hammerhead, involving a reorientation of stem I, which rotates around into the same direction of stem II. Because this transition occurs over the same range of magnesium ion concentration over which the hammerhead ribozyme becomes active, it is likely that the final conformation is most closely related to the active form of the structure. Magnesium ion-dependent folding into this conformation is prevented by changes at G5, notably removal of the 2'-hydroxyl group and replacement of the base by cytidine. The ability to dissect the folding process by means of sequence changes suggests that two separate ion-dependent stages are involved in the folding of the hammerhead ribozyme into the active conformation. PMID:8752086

  1. Folding of synthetic homogeneous glycoproteins in the presence of a glycoprotein folding sensor enzyme.

    PubMed

    Dedola, Simone; Izumi, Masayuki; Makimura, Yutaka; Seko, Akira; Kanamori, Akiko; Sakono, Masafumi; Ito, Yukishige; Kajihara, Yasuhiro

    2014-03-10

    UDP-glucose:glycoprotein glucosyltransferase (UGGT) plays a key role in recognizing folded and misfolded glycoproteins in the glycoprotein quality control system of the endoplasmic reticulum. UGGT detects misfolded glycoproteins and re-glucosylates them as a tag for misfolded glycoproteins. A flexible model to reproduce in vitro folding of a glycoprotein in the presence of UGGT in a mixture containing correctly folded, folding intermediates, and misfolded glycoproteins is described. The data demonstrates that UGGT can re-glucosylate all intermediates in the in vitro folding experiments, thus indicating that UGGT inspects not only final folded products, but also the glycoprotein folding intermediates.

  2. High energy microlaser and compact MOPA transmitter

    NASA Astrophysics Data System (ADS)

    Brickeen, Brian K.; Bernot, Dave; Geathers, Eliot; Mosovsky, Joseph

    2011-06-01

    A compact micro-oscillator incorporating a dual-bounce, grazing incidence gain module with a folded resonator cavity is presented. The gain module, previously developed for Nd:YVO4, is embodied in highly doped ceramic Nd:YAG to generate improved Q-switch performance while maintaining localized pump absorption. The cavity design utilizes a doubly folded optics path around the gain crystal to increase the intra-cavity mode for a more optimum overlap with the pump light volume produced by standard lensed laser diode bars. A modified CS-package diode mount is developed to facilitate the reduced size of the oscillator without sacrificing the ability to use a high-energy, side-pumping arrangement. The oscillator is combined with a high gain, high energy extraction VHGM amplifier to generate a transmitter source on the order of 50 mJ. Cooling for both the oscillator and amplifier modules is provided via a conductive path through the base of the package. Both devices are mounted on opposite sides of a phase-change cooling reservoir to enable self-contained, burst-mode operation. Beam shaping of the oscillator output, in preparation for injection into the amplifier, is contained in a small cut-away path on the reservoir side.

  3. Thermodynamic characterization of an equilibrium folding intermediate of staphylococcal nuclease.

    PubMed Central

    Xie, D.; Fox, R.; Freire, E.

    1994-01-01

    High-sensitivity differential scanning calorimetry and CD spectroscopy have been used to probe the structural stability and measure the folding/unfolding thermodynamics of a Pro117-->Gly variant of staphylococcal nuclease. It is shown that at neutral pH the thermal denaturation of this protein is well accounted for by a 2-state mechanism and that the thermally denatured state is a fully hydrated unfolded polypeptide. At pH 3.5, thermal denaturation results in a compact denatured state in which most, if not all, of the helical structure is missing and the beta subdomain apparently remains largely intact. At pH 3.0, no thermal transition is observed and the molecule exists in the compact denatured state within the 0-100 degrees C temperature interval. At high salt concentration and pH 3.5, the thermal unfolding transition exhibits 2 cooperative peaks in the heat capacity function, the first one corresponding to the transition from the native to the intermediate state and the second one to the transition from the intermediate to the unfolded state. As is the case with other proteins, the enthalpy of the intermediate is higher than that of the unfolded state at low temperatures, indicating that, under those conditions, its stabilization must be of an entropic origin. The folding intermediate has been modeled by structural thermodynamic calculations. Structure-based thermodynamic calculations also predict that the most probable intermediate is one in which the beta subdomain is essentially intact and the rest of the molecule unfolded, in agreement with the experimental data. The structural features of the equilibrium intermediate are similar to those of a kinetic intermediate previously characterized by hydrogen exchange and NMR spectroscopy. PMID:7756977

  4. Compaction managed mirror bend achromat

    DOEpatents

    Douglas, David

    2005-10-18

    A method for controlling the momentum compaction in a beam of charged particles. The method includes a compaction-managed mirror bend achromat (CMMBA) that provides a beamline design that retains the large momentum acceptance of a conventional mirror bend achromat. The CMMBA also provides the ability to tailor the system momentum compaction spectrum as desired for specific applications. The CMMBA enables magnetostatic management of the longitudinal phase space in Energy Recovery Linacs (ERLs) thereby alleviating the need for harmonic linearization of the RF waveform.

  5. Compactness of lateral shearing interferometers

    NASA Astrophysics Data System (ADS)

    Ferrec, Yann; Taboury, Jean; Sauer, Hervé; Chavel, Pierre

    2011-08-01

    Imaging lateral shearing interferometers are good candidates for airborne or spaceborne Fourier-transform spectral imaging. For such applications, compactness is one key parameter. In this article, we compare the size of four mirror-based interferometers, the Michelson interferometer with roof-top (or corner-cube) mirrors, and the cyclic interferometers with two, three, and four mirrors, focusing more particularly on the last two designs. We give the expression of the translation they induce between the two exiting rays. We then show that the cyclic interferometer with three mirrors can be made quite compact. Nevertheless, the Michelson interferometer is the most compact solution, especially for highly diverging beams.

  6. Optical methods for measuring DNA folding

    NASA Astrophysics Data System (ADS)

    Smith, Adam D.; Ukogu, Obinna A.; Devenica, Luka M.; White, Elizabeth D.; Carter, Ashley R.

    2017-03-01

    One of the most important biological processes is the dynamic folding and unfolding of deoxyribonucleic acid (DNA). The folding process is crucial for DNA to fit within the boundaries of the cell, while the unfolding process is essential for DNA replication and transcription. To accommodate both processes, the cell employs a highly active folding mechanism that has been the subject of intense study over the last few decades. Still, many open questions remain. What are the pathways for folding or unfolding? How does the folding equilibrium shift? And, what is the energy landscape for a particular process? Here, we review these emerging questions and the in vitro, optical methods that have provided answers, introducing the topic for those physicists seeking to step into biology. Specifically, we discuss two iconic experiments for DNA folding, the tethered particle motion (TPM) experiment and the optical tweezers experiment.

  7. Structural features of protein folding nuclei.

    PubMed

    Garbuzynskiy, S O; Kondratova, M S

    2008-03-05

    A crucial event of protein folding is the formation of a folding nucleus. We demonstrate the presence of a considerable coincidence between the location of folding nuclei and the location of so-called "root structural motifs", which have unique overall folds and handedness. In the case of proteins with a single root structural motif, the involvement in the formation of a folding nucleus is in average significantly higher for amino acids residues that are in root structural motifs, compared to residues in other parts of the protein. The tests carried out revealed that the observed difference is statistically reliable. Thus, a structural feature that corresponds to the protein folding nucleus is now found.

  8. Compact, Reliable EEPROM Controller

    NASA Technical Reports Server (NTRS)

    Katz, Richard; Kleyner, Igor

    2010-01-01

    A compact, reliable controller for an electrically erasable, programmable read-only memory (EEPROM) has been developed specifically for a space-flight application. The design may be adaptable to other applications in which there are requirements for reliability in general and, in particular, for prevention of inadvertent writing of data in EEPROM cells. Inadvertent writes pose risks of loss of reliability in the original space-flight application and could pose such risks in other applications. Prior EEPROM controllers are large and complex and do not provide all reasonable protections (in many cases, few or no protections) against inadvertent writes. In contrast, the present controller provides several layers of protection against inadvertent writes. The controller also incorporates a write-time monitor, enabling determination of trends in the performance of an EEPROM through all phases of testing. The controller has been designed as an integral subsystem of a system that includes not only the controller and the controlled EEPROM aboard a spacecraft but also computers in a ground control station, relatively simple onboard support circuitry, and an onboard communication subsystem that utilizes the MIL-STD-1553B protocol. (MIL-STD-1553B is a military standard that encompasses a method of communication and electrical-interface requirements for digital electronic subsystems connected to a data bus. MIL-STD- 1553B is commonly used in defense and space applications.) The intent was to both maximize reliability while minimizing the size and complexity of onboard circuitry. In operation, control of the EEPROM is effected via the ground computers, the MIL-STD-1553B communication subsystem, and the onboard support circuitry, all of which, in combination, provide the multiple layers of protection against inadvertent writes. There is no controller software, unlike in many prior EEPROM controllers; software can be a major contributor to unreliability, particularly in fault

  9. Folded Cassegrain sets of the Gran Telescopio Canarias (GTC)

    NASA Astrophysics Data System (ADS)

    Gomez, Alberto; Sanquirce, Rubén.; Murga, Gaizka; Etxeita, Borja; Vizcargüenaga, Alberto; San Vicente, Ander; Fernandez, Esther; Vega, Oscar; Siegel, Benjamín.

    2012-09-01

    The Gran Telescopio Canarias (GTC) has been recently received two Folded Cassegrain Sets (FC-Sets) composed of an instrument rotator and the corresponding Acquisition and Guiding (AG) optomechanics. IDOM has been the responsible for the design, manufacturing, assembly and commissioning of the two units of FC-Sets. The design combines a compact layout of the mechanical system, enhanced by an innovative cable wrap design, resulting in a smooth and precise movement, whilst guaranteeing good access to important components and maximizing the maintainability. The custom design of the cable wrap as an evolution of the rolling loop type eliminates the need for a cable chain static housing, minimizing weight and impact on the telescope tube. The AG Mechanics provides the required pointing and focusing capabilities in a compact configuration. In January 2010, IDOM is awarded the design and procurement of the two FC-Sets. The final design is approved by GRANTECAN and the fabrication process starts in Nov 2011. The assembly and commissioning of both units are completed in April 2011. Once the Factory Acceptance Tests finishes in Dec 2011, all the elements are delivered to the Observatorio del Roque de los Muchachos (ORM). The Site Acceptance Tests are completed in Feb 2012.

  10. Deterministic Folding in Stiff Elastic Membranes

    NASA Astrophysics Data System (ADS)

    Tallinen, T.; Åström, J. A.; Timonen, J.

    2008-09-01

    Crumpled membranes have been found to be characterized by complex patterns of spatially seemingly random facets separated by narrow ridges of high elastic energy. We demonstrate by numerical simulations that compression of stiff elastic membranes with small randomness in their initial configurations leads to either random ridge configurations (high entropy) or nearly deterministic folds (low elastic energy). For folding with symmetric ridge configurations to appear in part of the crumpling processes, the crumpling rate must be slow enough. Folding stops when the thickness of the folded structure becomes important, and crumpling continues thereafter as a random process.

  11. Protein Folding and Self-Organized Criticality

    NASA Astrophysics Data System (ADS)

    Bajracharya, Arun; Murray, Joelle

    Proteins are known to fold into tertiary structures that determine their functionality in living organisms. However, the complex dynamics of protein folding and the way they consistently fold into the same structures is not fully understood. Self-organized criticality (SOC) has provided a framework for understanding complex systems in various systems (earthquakes, forest fires, financial markets, and epidemics) through scale invariance and the associated power law behavior. In this research, we use a simple hydrophobic-polar lattice-bound computational model to investigate self-organized criticality as a possible mechanism for generating complexity in protein folding.

  12. Compact Infrared Spectrometers

    NASA Technical Reports Server (NTRS)

    Mouroulis, Pantazis

    2009-01-01

    Concentric spectrometer forms are advantageous for constructing a variety of systems spanning the entire visible to infrared range. Spectrometer examples are given, including broadband or high resolution forms. Some issues associated with the Dyson catadioptric type are also discussed.

  13. 16 CFR Appendix F2 to Part 305 - Compact Clothes Washers

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 1 2014-01-01 2014-01-01 false Compact Clothes Washers F2 Appendix F2 to... LABELING RULEâ) Pt. 305, App. F2 Appendix F2 to Part 305—Compact Clothes Washers Range Information “Compact” includes all household clothes washers with a tub capacity of less than 1.6 cu. ft. Capacity Range...

  14. DNA quadruplex folding formalism--a tutorial on quadruplex topologies.

    PubMed

    Karsisiotis, Andreas Ioannis; O'Kane, Christopher; Webba da Silva, Mateus

    2013-11-01

    Quadruplexes of DNA adopt a large variety of topologies that are dependent on their environment. We have been developing a formalism for quadruplex folding based on the relationship between base and its sugar--as defined by the glycosidic bond angle. By reducing the quadruplex stem to a description based on two finite states of the range of angles the glycosidic bond angle may adopt, the description of the relationships of type of loop and groove widths of a quadruplex stem are possible. In its current form this formalism has allowed for the prediction of some unimolecular quadruplex topologies. Its rules, whilst developed for unimolecular quadruplexes of three loops, are of general utility in understanding the interdependency of structural characteristics of multimolecular folds, as well as unimolecular quadruplexes of more than three loops. Here we describe current understanding of the interdependent structural features that define the quadruplex fold, and provide a tutorial for the use and application of this formalism.

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

    SciTech Connect

    Stillinger, F.H.; Head-Gordon, T.

    1995-09-01

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

  16. Compact Shelving Ten Years Later.

    ERIC Educational Resources Information Center

    Morris, Leslie R.

    1998-01-01

    Discusses experiences at the Niagara University Library with compact shelving. Highlights include citations to other relevant articles; patron use; selection of vendor; reliability; possible problems; and installation considerations, such as floor-load requirements. (LRW)

  17. An isolated compact galaxy triplet

    NASA Astrophysics Data System (ADS)

    Feng, Shuai; Shao, Zheng-Yi; Shen, Shi-Yin; Argudo-Fernández, Maria; Wu, Hong; Lam, Man-I.; Yang, Ming; Yuan, Fang-Ting

    2016-05-01

    We report the discovery of an isolated compact galaxy triplet SDSS J084843.45+164417.3, which is first detected by the LAMOST spectral survey and then confirmed by a spectroscopic observation of the BFOSC mounted on the 2.16 meter telescope located at Xinglong Station, which is administered by National Astronomical Observatories, Chinese Academy of Sciences. It is found that this triplet is an isolated and extremely compact system, which has an aligned configuration and very small radial velocity dispersion. The member galaxies have similar colors and show marginal star formation activities. These results support the opinion that the compact triplets are well-evolved systems rather than hierarchically forming structures. This serendipitous discovery reveals the limitations of fiber spectral redshift surveys in studying such a compact system, and demonstrates the necessity of additional observations to complete the current redshift sample.

  18. A Compact Beam Measurement Setup

    NASA Astrophysics Data System (ADS)

    Graf, Urs U.

    2016-08-01

    We present the design of a compact measurement device to determine the position of a beam in a radio optical setup. The unit is used to align the Terahertz optics of the GREAT instrument on the airborne astronomical observatory SOFIA.

  19. What Is Business's Social Compact?

    ERIC Educational Resources Information Center

    Avishai, Bernard

    1994-01-01

    Under the "new" social compact, businesses must focus on continuous learning and thus have both an obligation to support teaching and an opportunity to profit from it. Learning organizations must also be teaching organizations. (SK)

  20. Design of RNAs: comparing programs for inverse RNA folding.

    PubMed

    Churkin, Alexander; Retwitzer, Matan Drory; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny

    2017-01-03

    Computational programs for predicting RNA sequences with desired folding properties have been extensively developed and expanded in the past several years. Given a secondary structure, these programs aim to predict sequences that fold into a target minimum free energy secondary structure, while considering various constraints. This procedure is called inverse RNA folding. Inverse RNA folding has been traditionally used to design optimized RNAs with favorable properties, an application that is expected to grow considerably in the future in light of advances in the expanding new fields of synthetic biology and RNA nanostructures. Moreover, it was recently demonstrated that inverse RNA folding can successfully be used as a valuable preprocessing step in computational detection of novel noncoding RNAs. This review describes the most popular freeware programs that have been developed for such purposes, starting from RNAinverse that was devised when formulating the inverse RNA folding problem. The most recently published ones that consider RNA secondary structure as input are antaRNA, RNAiFold and incaRNAfbinv, each having different features that could be beneficial to specific biological problems in practice. The various programs also use distinct approaches, ranging from ant colony optimization to constraint programming, in addition to adaptive walk, simulated annealing and Boltzmann sampling. This review compares between the various programs and provides a simple description of the various possibilities that would benefit practitioners in selecting the most suitable program. It is geared for specific tasks requiring RNA design based on input secondary structure, with an outlook toward the future of RNA design programs.

  1. Structure, function and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding.

    NASA Astrophysics Data System (ADS)

    Samiotakis, Antonios; Dhar, Apratim; Ebbinghaus, Simon; Nienhaus, Lea; Homouz, Dirar; Gruebele, Martin; Cheung, Margaret

    2010-10-01

    We combine experiment and computer simulation to show how macromolecular crowding dramatically affects the structure, function and folding landscape of phosphoglycerate kinase (PGK). Fluorescence labeling shows that compact states of yeast PGK are populated as the amount of crowding agents (Ficoll 70) increases. Coarse-grained molecular simulations reveal three compact ensembles: C (crystal structure), CC (collapsed crystal) and Sph (spherical compact). With an adjustment for viscosity, crowded wild type PGK and fluorescent PGK are about 15 times or more active in 200 mg/ml Ficoll than in aqueous solution. Our results suggest a new solution to the classic problem of how the ADP and diphosphoglycerate binding sites of PGK come together to make ATP: rather than undergoing a hinge motion, the ADP and substrate sites are already located in proximity under crowded conditions that mimic the in vivo conditions under which the enzyme actually operates.

  2. The number density of quiescent compact galaxies at intermediate redshift

    SciTech Connect

    Damjanov, Ivana; Hwang, Ho Seong; Geller, Margaret J.; Chilingarian, Igor

    2014-09-20

    Massive compact systems at 0.2 < z < 0.6 are the missing link between the predominantly compact population of massive quiescent galaxies at high redshift and their analogs and relics in the local volume. The evolution in number density of these extreme objects over cosmic time is the crucial constraining factor for the models of massive galaxy assembly. We select a large sample of ∼200 intermediate-redshift massive compacts from the Baryon Oscillation Spectroscopic Survey (BOSS) spectroscopy by identifying point-like Sloan Digital Sky Survey photometric sources with spectroscopic signatures of evolved redshifted galaxies. A subset of our targets have publicly available high-resolution ground-based images that we use to augment the dynamical and stellar population properties of these systems by their structural parameters. We confirm that all BOSS compact candidates are as compact as their high-redshift massive counterparts and less than half the size of similarly massive systems at z ∼ 0. We use the completeness-corrected numbers of BOSS compacts to compute lower limits on their number densities in narrow redshift bins spanning the range of our sample. The abundance of extremely dense quiescent galaxies at 0.2 < z < 0.6 is in excellent agreement with the number densities of these systems at high redshift. Our lower limits support the models of massive galaxy assembly through a series of minor mergers over the redshift range 0 < z < 2.

  3. The Number Density of Quiescent Compact Galaxies at Intermediate Redshift

    NASA Astrophysics Data System (ADS)

    Damjanov, Ivana; Hwang, Ho Seong; Geller, Margaret J.; Chilingarian, Igor

    2014-09-01

    Massive compact systems at 0.2 < z < 0.6 are the missing link between the predominantly compact population of massive quiescent galaxies at high redshift and their analogs and relics in the local volume. The evolution in number density of these extreme objects over cosmic time is the crucial constraining factor for the models of massive galaxy assembly. We select a large sample of ~200 intermediate-redshift massive compacts from the Baryon Oscillation Spectroscopic Survey (BOSS) spectroscopy by identifying point-like Sloan Digital Sky Survey photometric sources with spectroscopic signatures of evolved redshifted galaxies. A subset of our targets have publicly available high-resolution ground-based images that we use to augment the dynamical and stellar population properties of these systems by their structural parameters. We confirm that all BOSS compact candidates are as compact as their high-redshift massive counterparts and less than half the size of similarly massive systems at z ~ 0. We use the completeness-corrected numbers of BOSS compacts to compute lower limits on their number densities in narrow redshift bins spanning the range of our sample. The abundance of extremely dense quiescent galaxies at 0.2 < z < 0.6 is in excellent agreement with the number densities of these systems at high redshift. Our lower limits support the models of massive galaxy assembly through a series of minor mergers over the redshift range 0 < z < 2.

  4. Compact Ho:YLF Laser

    NASA Technical Reports Server (NTRS)

    Hemmati, H.

    1988-01-01

    Longitudinal pumping by laser diodes increases efficiency. Improved holmium:yttrium lithium fluoride laser radiates as much as 56 mW of power at wavelength of 2.1 micrometer. New Ho:YLF laser more compact and efficient than older, more powerful devices of this type. Compact, efficient Ho:YLF laser based on recent successes in use of diode lasers to pump other types of solid-state lasers.

  5. Monolithic Nanocrystalline Au Fabricated by the Compaction of Nanoscale Foam

    SciTech Connect

    Hodge, A M; Biener, J; Hsiung, L M; Hamza, A V; Satcher Jr., J H

    2004-07-28

    We describe a two-step dealloying/compaction process to produce nanocrystalline Au. First, nanocrystalline/nanoporous Au foam is synthesized by electrochemically-driven dealloying. The resulting Au foams exhibit porosities of 60 and 70% with pore sizes of {approx} 40 and 100 nm, respectively, and a typical grain size of <50 nm. Second, the nanoporous foams are fully compacted to produce nanocrystalline monolithic Au. The compacted Au was characterized by TEM and X-ray diffraction and tested by depth-sensing nanoindentation. The compacted nanocrystalline Au exhibits an average grain size of <50 nm and hardness values ranging from 1.4 to 2.0 GPa, which are up to 4.5 times higher than the hardness values obtained from polycrystalline Au.

  6. Soil compaction and structural morphology under tractor wheelings

    NASA Astrophysics Data System (ADS)

    Shanahan, Peter; Quinton, John; Binley, Andrew; Silgram, Martyn

    2010-05-01

    Compaction of cultivated soils is a major problem for agriculture in terms of yield decline and sustainable soil resource management. Tramline wheelings exacerbate runoff and increase erosion from arable land. The UK Department for Environment, Food and Rural Affairs (Defra) LINK Project - a joint venture between agri-business, land managers and research groups - is currently evaluating a number of methods for alleviating compaction in tractor wheelings across a range of soil types in England. Using innovative applications of agri-geophysics (e.g. ground penetrating radar, electrical resistivity, acoustics and x-ray tomography), this current project aims to determine relationships between properties derived from geophysical methods (e.g. soil moisture, porosity), soil compaction and structural morphology. Such relationships are important for a clearer understanding of hydrological and biogeochemical processes in compacted soils, to address land management practices and develop cost-effective mitigation measures. Our poster will present some early results of this study.

  7. Role of local and nonlocal interactions in folding and misfolding of globular proteins

    NASA Astrophysics Data System (ADS)

    Kumar, Adesh; Baruah, Anupaul; Biswas, Parbati

    2017-02-01

    A Monte Carlo simulation based sequence design method is proposed to study the role of the local and the nonlocal interactions with varying secondary structure content in protein folding, misfolding and unfolding. A statistical potential is developed from the compilation of a data set of proteins, which accounts for the respective contribution of local and the nonlocal interactions. Sequences are designed through a combination of positive and negative design by a Monte Carlo simulation in the sequence space. The weights of the local and the nonlocal interactions are tuned appropriately to study the role of the local and the nonlocal interactions in the folding, unfolding and misfolding of the designed sequences. Results suggest that the nonlocal interactions are the primary determinant of protein folding while the local interactions may be required but not always necessary. The nonlocal interactions mainly guide the polypeptide chain to form compact structures but do not differentiate between the native-like conformations, while the local interactions stabilize the target conformation against the native-like competing conformations. The study concludes that the local interactions govern the fold-misfold transition, while the nonlocal interactions regulate the fold-unfold transition of proteins. However, for proteins with predominantly β-sheet content, the nonlocal interactions control both fold-misfold and fold-unfold transitions.

  8. Retinal and Choroidal Folds in Papilledema

    PubMed Central

    Sibony, Patrick A.; Kupersmith, Mark J.; Feldon, Steven E.; Wang, Jui-Kai; Garvin, Mona

    2015-01-01

    Purpose To determine the frequency, patterns, associations, and biomechanical implications of retinal and choroidal folds in papilledema due to idiopathic intracranial hypertension (IIH). Methods Retinal and choroidal folds were studied in patients enrolled in the IIH Treatment Trial using fundus photography (n = 165 study eyes) and spectral-domain optical coherence tomography (SD-OCT; n = 125). We examined the association between folds and peripapillary shape, retinal nerve fiber layer (RNFL) thickness, disc volume, Frisén grade, acuity, perimetric mean deviation, intraocular pressure, intracranial pressure, and refractive error. Results We identified three types of folds in IIH patients with papilledema: peripapillary wrinkles (PPW), retinal folds (RF), and choroidal folds (CF). Frequency, with photos, was 26%, 19%, and 1%, respectively; SD-OCT frequency was 46%, 47%, and 10%. At least one type of fold was present in 41% of patients with photos and 73% with SD-OCT. Spectral-domain OCT was more sensitive. Structural parameters related to the severity of papilledema were associated with PPW and RF, whereas anterior deformation of the peripapillary RPE/basement membrane layer was associated with CF and RF. Folds were not associated with vision loss at baseline. Conclusions Folds in papilledema are biomechanical signs of stress/strain on the optic nerve head and load-bearing structures induced by intracranial hypertension. Folds are best imaged with SD-OCT. The patterns of retinal and choroidal folds are the products of a complex interplay between the degree of papilledema and anterior deformation of the load-bearing structures (sclera and possibly the lamina cribrosa), both modulated by structural geometry and material properties of the optic nerve head. (ClinicalTrials.gov number, NCT01003639.) PMID:26335066

  9. Folding propensity of intrinsically disordered proteins by osmotic stress

    DOE PAGES

    Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.; ...

    2016-10-11

    Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scatteringmore » (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.« less

  10. Folding propensity of intrinsically disordered proteins by osmotic stress†

    PubMed Central

    Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.; Pino, James C.; Chennubhotla, S. Chakra; Ramanathan, Arvind; O’Neill, Hugh M.; Berthelier, Valerie

    2017-01-01

    Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR) separate from their mutual binding. Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain α-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scattering (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. By focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding. PMID:27752679

  11. The relationship of cortical folding and brain arteriovenous malformations

    PubMed Central

    Shah, Manish N.; Smith, Sarah E.; Dierker, Donna L.; Herbert, Joseph P.; Coalson, Timothy S.; Bruck, Brent S.; Zipfel, Gregory J.; Van Essen, David C.; Dacey, Ralph G.

    2016-01-01

    Background The pathogenesis of human intracranial arteriovenous malformations (AVMs) is not well understood; this study aims to quantitatively assess cortical folding in patients with these lesions. Methods Seven adult participants, 4 male and 3 female, with unruptured, surgically unresectable intracranial AVMs were prospectively enrolled in the study, with a mean age of 42.1 years and Spetzler-Martin grade range of II–IV. High-resolution brain MRI T1 and T2 sequences were obtained. After standard preprocessing, segmentation and registration techniques, three measures of cortical folding, the depth difference index (DDI), coordinate distance index (CDI) and gyrification index (GI)), were calculated for the affected and unaffected hemispheres of each subject as well as a healthy control subject set. Results Of the three metrics, CDI, DDI and GI, used for cortical folding assessment, none demonstrated significant differences between the participants and previously studied healthy adults. There was a significant negative correlation between the DDI ratio between affected and unaffected hemispheres and AVM volume (correlation coefficient r = −0.74, p = 0.04). Conclusion This study is the first to quantitatively assess human brain cortical folding in the presence of intracranial AVMs and no significant differences between AVM-affected versus unaffected hemispheres were found in a small dataset. We suggest longitudinal, larger human MRI-based cortical folding studies to assess whether AVMs are congenital lesions of vascular development or de novo, dynamic lesions. PMID:28009020

  12. Design of optics for compact star sensors

    NASA Astrophysics Data System (ADS)

    Xu, Minyi; Shi, Rongbao; Shen, Weimin

    2016-10-01

    In order to adapt to small size and low cost space platform such as mini-satellites, this paper studies the design of optics for compact star sensor. At first, the relationship between limiting magnitude and optical system specifications which includes field of view and entrance pupil diameter is analyzed, based on its Pyramid identification algorithm and signal-to-noise ratio requirement. The specifications corresponding to different limiting magnitude can be obtained after the detector is selected, and both of the complexity of optical lens and the size of baffle can be estimated. Then the range of the limiting magnitude can be determined for the miniaturization of the optical system. Taking STAR1000 CMOS detector as an example, the compact design of the optical system can be realized when the limiting magnitude is in the interval of 4.9Mv 5.5Mv. At last, the lens and baffle of a CMOS compact star sensor is optimally designed, of which length and weight is respectively 124 millimeters and 300 grams.

  13. Compaction with automatic jog introduction

    NASA Astrophysics Data System (ADS)

    Maley, F. M.

    1985-10-01

    A novel polynomial-time algorithm for compacting a VLSI layout is presented. Compared to previous algorithms, the algorithm promises to produce higher quality output while reducing the need for designer intervention. The performance gain is realized by converting wires into constraints on the positions of the active devices. These constraints can be solved by graph-theoretic techniques to yield optimal positions for chip components. A single-layer router is then used to restore the wires to the layout, using as many as jogs as necessary. An automated compaction procedure is an effective tool for cutting production costs of a VLSI circuit at low cost to the designer, because the yield of fabricated chips is strongly dependent on the total circuit area. Sect 1 is an introduction. Sect 2 states the definitions and theoretical results that underlie the new compaction method. Sect 3 shows how the circuit layout is converted to a data structure appropriate for compaction, and Sect 4 details the body of the compaction algorithm. Sect 5 covers several improvements to the algorithm that should make it run considerably faster. Sect 6 comments on the algorithms of results, and a discussion of the practical value of the compaction algorithm.

  14. Persistent homology analysis of protein structure, flexibility and folding

    PubMed Central

    Xia, Kelin; Wei, Guo-Wei

    2014-01-01

    Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is, for the first time, introduced for extracting molecular topological fingerprints (MTFs) based on the persistence of molecular topological invariants. MTFs are utilized for protein characterization, identification and classification. The method of slicing is proposed to track the geometric origin of protein topological invariants. Both all-atom and coarse-grained representations of MTFs are constructed. A new cutoff-like filtration is proposed to shed light on the optimal cutoff distance in elastic network models. Based on the correlation between protein compactness, rigidity and connectivity, we propose an accumulated bar length generated from persistent topological invariants for the quantitative modeling of protein flexibility. To this end, a correlation matrix based filtration is developed. This approach gives rise to an accurate prediction of the optimal characteristic distance used in protein B-factor analysis. Finally, MTFs are employed to characterize protein topological evolution during protein folding and quantitatively predict the protein folding stability. An excellent consistence between our persistent homology prediction and molecular dynamics simulation is found. This work reveals the topology-function relationship of proteins. PMID:24902720

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

    PubMed Central

    Hofmann, Hagen; Hillger, Frank; Pfeil, Shawn H.; Hoffmann, Armin; Streich, Daniel; Haenni, Dominik; Nettels, Daniel; Lipman, Everett A.; Schuler, Benjamin

    2010-01-01

    Molecular chaperones are known to be essential for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms. We use single-molecule Förster resonance energy transfer to follow the folding of a protein inside the GroEL/GroES chaperonin cavity over a time range from milliseconds to hours. Our results show that confinement in the chaperonin decelerates the folding of the C-terminal domain in the substrate protein rhodanese, but leaves the folding rate of the N-terminal domain unaffected. Microfluidic mixing experiments indicate that strong interactions of the substrate with the cavity walls impede the folding process, but the folding hierarchy is preserved. Our results imply that no universal chaperonin mechanism exists. Rather, a competition between intra- and intermolecular interactions determines the folding rates and mechanisms of a substrate inside the GroEL/GroES cage. PMID:20547872

  16. A Computational Model of Cerebral Cortex Folding

    PubMed Central

    Nie, Jingxin; Guo, Lei; Li, Gang; Faraco, Carlos; Miller, L Stephen; Liu, Tianming

    2010-01-01

    The geometric complexity and variability of the human cerebral cortex has long intrigued the scientific community. As a result, quantitative description of cortical folding patterns and the understanding of underlying folding mechanisms have emerged as important research goals. This paper presents a computational 3-dimensional geometric model of cerebral cortex folding initialized by MRI data of a human fetal brain and deformed under the governance of a partial differential equation modeling cortical growth. By applying different simulation parameters, our model is able to generate folding convolutions and shape dynamics of the cerebral cortex. The simulations of this 3D geometric model provide computational experimental support to the following hypotheses: 1) Mechanical constraints of the skull regulate the cortical folding process. 2) The cortical folding pattern is dependent on the global cell growth rate of the whole cortex. 3) The cortical folding pattern is dependent on relative rates of cell growth in different cortical areas. 4) The cortical folding pattern is dependent on the initial geometry of the cortex. PMID:20167224

  17. Fractures Sets Associated to Buckle Folds

    NASA Astrophysics Data System (ADS)

    Liu, X.; Eckert, A.; Connolly, P. T.

    2014-12-01

    Buckle folds of single and multilayered sedimentary strata in the literature are commonly associated to a variety of different fracture sets, both shear and tensile. Amongst the most noticeable fractures are tensile fractures occurring in the outer hinges of the fold crest and shear fractures in the bottom of fold hinge zones. These fractures are well explained and understood by the extensional and compressional strain/stress pattern in the fold hinge. However, tensile fractures parallel to the fold axis, tensile fractures cutting through the limb, normal faults on the fold hinge, and shear fractures of different orientations in the fold limb cannot intuitively be linked to the stress regime occurring during the buckling process. This study utilizes a 2D and 3D finite element modeling approach using Maxwell visco-elastic rheology to study the stress conditions during single and multilayer buckling for each fracture set to occur. The numerical simulations include sensitivity analyses on material parameters such as permeability, viscosity and overburden thickness. For fracture sets not likely to occur during the buckling process pre- and post folding processes such as initial overpressure, extensional unfolding, and erosional unloading are studied.

  18. Stochastic Resonance in Protein Folding Dynamics.

    PubMed

    Davtyan, Aram; Platkov, Max; Gruebele, Martin; Papoian, Garegin A

    2016-05-04

    Although protein folding reactions are usually studied under static external conditions, it is likely that proteins fold in a locally fluctuating cellular environment in vivo. To mimic such behavior in in vitro experiments, the local temperature of the solvent can be modulated either harmonically or using correlated noise. In this study, coarse-grained molecular simulations are used to investigate these possibilities, and it is found that both periodic and correlated random fluctuations of the environment can indeed accelerate folding kinetics if the characteristic frequencies of the applied fluctuations are commensurate with the internal timescale of the folding reaction; this is consistent with the phenomenon of stochastic resonance observed in many other condensed-matter processes. To test this theoretical prediction, the folding dynamics of phosphoglycerate kinase under harmonic temperature fluctuations are experimentally probed using Förster resonance energy transfer fluorescence measurements. To analyze these experiments, a combination of theoretical approaches is developed, including stochastic simulations of folding kinetics and an analytical mean-field kinetic theory. The experimental observations are consistent with the theoretical predictions of stochastic resonance in phosphoglycerate kinase folding. When combined with an alternative experiment on the protein VlsE using a power spectrum analysis, elaborated in Dave et al., ChemPhysChem 2016, 10.1002/cphc.201501041, the overall data overwhelmingly point to the experimental confirmation of stochastic resonance in protein folding dynamics.

  19. Protein folding: When ribosomes pick the structure

    NASA Astrophysics Data System (ADS)

    Sivertsson, Elin M.; Itzhaki, Laura S.

    2014-05-01

    Anfinsen's principle tells us that the folded structure of a protein is determined solely by its sequence. Now, it has been shown that the rate at which a polypeptide chain is synthesized in the cell can affect which of two alternative folded structures it adopts.

  20. Local vs global motions in protein folding

    PubMed Central

    Maisuradze, Gia G.; Liwo, Adam; Senet, Patrick; Scheraga, Harold A.

    2013-01-01

    It is of interest to know whether local fluctuations in a polypeptide chain play any role in the mechanism by which the chain folds to the native structure of a protein. This question is addressed by analyzing folding and non-folding trajectories of a protein; as an example, the analysis is applied to the 37-residue triple β-strand WW domain from the Formin binding protein 28 (FBP28) (PDB ID: 1E0L). Molecular dynamics (MD) trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue, and principal components, respectively, were analyzed. The key residues involved in the folding of the FBP28 WW domain are elucidated by this analysis. The correlations between local and global motions are found. It is shown that most of the residues in the folding trajectories of the system studied here move in a concerted fashion, following the dynamics of the whole system. This demonstrates how the choice of a pathway has to involve concerted movements in order for this protein to fold. This finding also sheds light on the effectiveness of principal component analysis (PCA) for the description of the folding dynamics of the system studied. It is demonstrated that the FEL along the PCs, computed by considering only several critically-placed residues, can correctly describe the folding dynamics. PMID:23914144

  1. The effects of host galaxy properties on merging compact binaries detectable by LIGO

    NASA Astrophysics Data System (ADS)

    O'Shaughnessy, R.; Bellovary, J. M.; Brooks, A.; Shen, S.; Governato, F.; Christensen, C. R.

    2017-01-01

    Cosmological simulations of galaxy formation can produce present-day galaxies with a large range of assembly and star formation histories. A detailed study of the metallicity evolution and star formation history of such simulations can assist in predicting Laser Interferometer Gravitational-Wave Observatory (LIGO)-detectable compact object binary mergers. Recent simulations of compact binary evolution suggest that the compact object merger rate depends sensitively on the progenitor's metallicity. Rare low-metallicity star formation during galaxy assembly can produce more detected compact binaries than typical star formation. Using detailed simulations of galaxy and chemical evolution, we determine how sensitively the compact binary populations of galaxies with a similar present-day appearance depend on the details of their assembly. We also demonstrate by concrete example the extent to which dwarf galaxies overabundantly produce compact binary mergers, particularly binary black holes, relative to more massive galaxies. We discuss the implications for transient multimessenger astronomy with compact binary sources.

  2. Folding and Finding RNA Secondary Structure

    PubMed Central

    Mathews, David H.; Moss, Walter N.; Turner, Douglas H.

    2010-01-01

    SUMMARY Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed. PMID:20685845

  3. Fan-fold shielded electrical leads

    DOEpatents

    Rohatgi, Rajeev R.; Cowan, Thomas E.

    1996-01-01

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

  4. Cooperative Tertiary Interaction Network Guides RNA Folding

    SciTech Connect

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

    2013-04-08

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

  5. Fan-fold shielded electrical leads

    DOEpatents

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

    1996-06-11

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

  6. The origami of thioredoxin-like folds

    PubMed Central

    Pan, Jonathan L.; Bardwell, James C.A.

    2006-01-01

    Origami is the Japanese art of folding a piece of paper into complex shapes and forms. Much like origami of paper, Nature has used conserved protein folds to engineer proteins for a particular task. An example of a protein family, which has been used by Nature numerous times, is the thioredoxin superfamily. Proteins in the thioredoxin superfamily are all structured with a β-sheet core surrounded with α-helices, and most contain a canonical CXXC motif. The remarkable feature of these proteins is that the link between them is the fold; however, their reactivity is different for each member due to small variations in this general fold as well as their active site. This review attempts to unravel the minute differences within this protein family, and it also demonstrates the ingenuity of Nature to use a conserved fold to generate a diverse collection of proteins to perform a number of different biochemical tasks. PMID:17008712

  7. A Canonical Biomechanical Vocal Fold Model

    PubMed Central

    Bhattacharya, Pinaki; Siegmund, Thomas H.

    2012-01-01

    Summary The present article aimed at constructing a canonical geometry of the human vocal fold (VF) from subject-specific image slice data. A computer-aided design approach automated the model construction. A subject-specific geometry available in literature, three abstractions (which successively diminished in geometric detail) derived from it, and a widely used quasi two-dimensional VF model geometry were used to create computational models. The first three natural frequencies of the models were used to characterize their mechanical response. These frequencies were determined for a representative range of tissue biomechanical properties, accounting for underlying VF histology. Compared with the subject-specific geometry model (baseline), a higher degree of abstraction was found to always correspond to a larger deviation in model frequency (up to 50% in the relevant range of tissue biomechanical properties). The model we deemed canonical was optimally abstracted, in that it significantly simplified the VF geometry compared with the baseline geometry but can be recalibrated in a consistent manner to match the baseline response. Models providing only a marginally higher degree of abstraction were found to have significant deviation in predicted frequency response. The quasi two-dimensional model presented an extreme situation: it could not be recalibrated for its frequency response to match the subject-specific model. This deficiency was attributed to complex support conditions at anterior-posterior extremities of the VFs, accentuated by further issues introduced through the tissue biomechanical properties. In creating canonical models by leveraging advances in clinical imaging techniques, the automated design procedure makes VF modeling based on subject-specific geometry more realizable. PMID:22209063

  8. Compact proton spectrometers for measurements of shock

    SciTech Connect

    Mackinnon, A; Zylstra, A; Frenje, J A; Seguin, F H; Rosenberg, M J; Rinderknecht, H G; Johnson, M G; Casey, D T; Sinenian, N; Manuel, M; Waugh, C J; Sio, H W; Li, C K; Petrasso, R D; Friedrich, S; Knittel, K; Bionta, R; McKernan, M; Callahan, D; Collins, G; Dewald, E; Doeppner, T; Edwards, M J; Glenzer, S H; Hicks, D; Landen, O L; London, R; Meezan, N B

    2012-05-02

    The compact Wedge Range Filter (WRF) proton spectrometer was developed for OMEGA and transferred to the National Ignition Facility (NIF) as a National Ignition Campaign (NIC) diagnostic. The WRF measures the spectrum of protons from D-{sup 3}He reactions in tuning-campaign implosions containing D and {sup 3}He gas; in this work we report on the first proton spectroscopy measurement on the NIF using WRFs. The energy downshift of the 14.7-MeV proton is directly related to the total {rho}R through the plasma stopping power. Additionally, the shock proton yield is measured, which is a metric of the final merged shock strength.

  9. Compact Groups of Galaxies with Complete Spectroscopic Redshifts in the Local Universe

    NASA Astrophysics Data System (ADS)

    Sohn, Jubee; Hwang, Ho Seong; Geller, Margaret J.; Diaferio, Antonaldo; Rines, Kenneth J.; Lee, Myung Gyoon; Lee, Gwang-Ho

    2015-12-01

    Dynamical analysis of compact groups provides important tests of models of compact group formation and evolution. By compiling 2066 redshifts from FLWO/FAST, from the literature, and from SDSS DR12 in the fields of compact groups in tet{McC09}, we construct the largest sample of compact groups with complete spectroscopic redshifts in the redshift range 0.01 < z < 0.22. This large redshift sample shows that the interloper fraction in the tet{McC09} compact group candidates is ˜ 42%. A secure sample of 332 compact groups includes 192 groups with four or more member galaxies and 140 groups with three members. The fraction of early-type galaxies in these compact groups is 62%, higher than for the original Hickson compact groups. The velocity dispersions of early- and late-type galaxies in compact groups change little with groupcentric radius; the radii sampled are less than 100 h^{-1} kpc, smaller than the radii typically sampled by members of massive clusters of galaxies. The physical properties of our sample compact groups include size, number density, velocity dispersion, and local environment; these properties slightly differ from those derived for the original Hickson compact groups and for the DPOSS II compact groups. Differences result from subtle differences in the way the group candidates were originally selected. The abundance of the compact groups changes little with redshift over the range covered by this sample. The approximate constancy of the abundance for this sample is a potential constraint on the evolution of compact groups on a few Gigayear timescale.

  10. Compact Intracloud Discharges

    SciTech Connect

    Smith, David A.

    1998-11-01

    In November of 1993, mysterious signals recorded by a satellite-borne broadband VHF radio science experiment called Blackboard led to a completely unexpected discovery. Prior to launch of the ALEXIS satellite, it was thought that its secondary payload, Blackboard, would most often detect the radio emissions from lightning when its receiver was not overwhelmed by noise from narrowband communication carriers. Instead, the vast majority of events that triggered the instrument were isolated pairs of pulses that were one hundred times more energetic than normal thunderstorm electrical emissions. The events, which came to be known as TIPPs (for transionospheric pulse pairs), presented a true mystery to the geophysics community. At the time, it was not even known whether the events had natural or anthropogenic origins. After two and one half years of research into the unique signals, two ground-based receiver arrays in New Mexico first began to detect and record thunderstorm radio emissions that were consistent with the Blackboard observations. On two occasions, the ground-based systems and Blackboard even recorded emissions that were produced by the same exact events. From the ground based observations, it has been determined that TIPP events areproduced by brief, singular, isolated, intracloud electrical discharges that occur in intense regions of thunderstorms. These discharges have been dubbed CIDS, an acronym for compact intracloud discharges. During the summer of 1996, ground-based receiver arrays were used to record the electric field change signals and broadband HF emissions from hundreds of CIDS. Event timing that was accurate to within a few microseconds made possible the determination of source locations using methods of differential time of arrival. Ionospheric reflections of signals were recorded in addition to groundwave/line-of-sight signals and were used to determine accurate altitudes for the discharges. Twenty-four CIDS were recorded from three

  11. Compact intracloud discharges

    NASA Astrophysics Data System (ADS)

    Smith, David Adam

    In November of 1993, mysterious signals recorded by a satellite-borne broadband VHF radio science experiment called Blackbeard led to a completely unexpected discovery. Prior to launch of the ALEXIS satellite, it was thought that its secondary payload, Blackbeard, would most often detect the radio emissions from lightning when its receiver was not overwhelmed by noise from narrowband communication carriers. Instead, the vast majority of events that triggered the instrument were isolated pairs of pulses that were one hundred times more energetic than normal thunderstorm electrical emissions. The events, which came to be known as TIPPs (for transionospheric pulse pairs), presented a true mystery to the geophysics community. At the time, it was not even known whether the events had natural or anthropogenic origins. After two and one half years of research into the unique signals, two ground-based receiver arrays in New Mexico first began to detect and record thunderstorm radio emissions that were consistent with the Blackbeard observations. On two occasions, the ground-based systems and Blackbeard even recorded emissions that were produced by the same exact events. From the ground-based observations, it has been determined that TIPP events are produced by brief, singular, isolated, intracloud electrical discharges that occur in intense regions of thunderstorms. These discharges have been dubbed CIDs, an acronym for compact intracloud discharges. During the summer of 1996, ground- based receiver arrays were used to record the electric field change signals and broadband HF emissions from hundreds of CIDs. Event timing that was accurate to within a few microseconds made possible the determination of source locations using methods of differential time of arrival. Ionospheric reflections of signals were recorded in addition to groundwave/line-of-sight signals and were used to determine accurate altitudes for the discharges. Twenty-four CIDs were recorded from three

  12. Natural examples of Valdivia compact spaces

    NASA Astrophysics Data System (ADS)

    Kalenda, Ondrej F. K.

    2008-04-01

    We collect examples of Valdivia compact spaces, their continuous images and associated classes of Banach spaces which appear naturally in various branches of mathematics. We focus on topological constructions generating Valdivia compact spaces, linearly ordered compact spaces, compact groups, L1 spaces, Banach lattices and noncommutative L1 spaces.

  13. Hierarchical folding mechanism of apomyoglobin revealed by ultra-fast H/D exchange coupled with 2D NMR.

    PubMed

    Uzawa, Takanori; Nishimura, Chiaki; Akiyama, Shuji; Ishimori, Koichiro; Takahashi, Satoshi; Dyson, H Jane; Wright, Peter E

    2008-09-16

    The earliest steps in the folding of proteins are complete on an extremely rapid time scale that is difficult to access experimentally. We have used rapid-mixing quench-flow methods to extend the time resolution of folding studies on apomyoglobin and elucidate the structural and dynamic features of members of the ensemble of intermediate states that are populated on a submillisecond time scale during this process. The picture that emerges is of a continuum of rapidly interconverting states. Even after only 0.4 ms of refolding time a compact state is formed that contains major parts of the A, G, and H helices, which are sufficiently well folded to protect amides from exchange. The B, C, and E helix regions fold more slowly and fluctuate rapidly between open and closed states as they search docking sites on this core; the secondary structure in these regions becomes stabilized as the refolding time is increased from 0.4 to 6 ms. No further stabilization occurs in the A, G, H core at 6 ms of folding time. These studies begin to time-resolve a progression of compact states between the fully unfolded and native folded states and confirm the presence an ensemble of intermediates that interconvert in a hierarchical sequence as the protein searches conformational space on its folding trajectory.

  14. Quantification of a Helical Origami Fold

    NASA Astrophysics Data System (ADS)

    Dai, Eric; Han, Xiaomin; Chen, Zi

    2015-03-01

    Origami, the Japanese art of paper folding, is traditionally viewed as an amusing pastime and medium of artistic expression. However, in recent years, origami has served as a source of inspiration for innovations in science and engineering. Here, we present the geometric and mechanical properties of a twisting origami fold. The origami structure created by the fold exhibits several interesting properties, including rigid foldibility, local bistability and finely tunable helical coiling, with control over pitch, radius and handedness of the helix. In addition, the pattern generated by the fold closely mimics the twist buckling patterns shown by thin materials, for example, a mobius strip. We use six parameters of the twisting origami pattern to generate a fully tunable graphical model of the fold. Finally, we present a mathematical model of the local bistability of the twisting origami fold. Our study elucidates the mechanisms behind the helical coiling and local bistability of the twisting origami fold, with potential applications in robotics and deployable structures. Acknowledgment to Branco Weiss Fellowship for funding.

  15. GroEL-mediated protein folding.

    PubMed Central

    Fenton, W. A.; Horwich, A. L.

    1997-01-01

    I. Architecture of GroEL and GroES and the reaction pathway A. Architecture of the chaperonins B. Reaction pathway of GroEL-GroES-mediated folding II. Polypeptide binding A. A parallel network of chaperones binding polypeptides in vivo B. Polypeptide binding in vitro 1. Role of hydrophobicity in recognition 2. Homologous proteins with differing recognition-differences in primary structure versus effects on folding pathway 3. Conformations recognized by GroEL a. Refolding studies b. Binding of metastable intermediates c. Conformations while stably bound at GroEL 4. Binding constants and rates of association 5. Conformational changes in the substrate protein associated with binding by GroEL a. Observations b. Kinetic versus thermodynamic action of GroEL in mediating unfolding c. Crossing the energy landscape in the presence of GroEL III. ATP binding and hydrolysis-driving the reaction cycle IV. GroEL-GroES-polypeptide ternary complexes-the folding-active cis complex A. Cis and trans ternary complexes B. Symmetric complexes C. The folding-active intermediate of a chaperonin reaction-cis ternary complex D. The role of the cis space in the folding reaction E. Folding governed by a "timer" mechanism F. Release of nonnative polypeptides during the GroEL-GroES reaction G. Release of both native and nonnative forms under physiologic conditions H. A role for ATP binding, as well as hydrolysis, in the folding cycle V. Concluding remarks. PMID:9098884

  16. Cooperativity and modularity in protein folding

    PubMed Central

    Sasai, Masaki; Chikenji, George; Terada, Tomoki P.

    2016-01-01

    A simple statistical mechanical model proposed by Wako and Saitô has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Muñoz and Eaton and has since been referred to as the Wako-Saitô-Muñoz-Eaton (WSME) model. The success of the WSME model in explaining the folding of many proteins has verified the hypothesis that the folding is dominated by native interactions, which makes the energy landscape globally biased toward native conformation. Using the WSME and other related models, Saitô emphasized the importance of the hierarchical pathway in protein folding; folding starts with the creation of contiguous segments having a native-like configuration and proceeds as growth and coalescence of these segments. The Φ-values calculated for barnase with the WSME model suggested that segments contributing to the folding nucleus are similar to the structural modules defined by the pattern of native atomic contacts. The WSME model was extended to explain folding of multi-domain proteins having a complex topology, which opened the way to comprehensively understanding the folding process of multi-domain proteins. The WSME model was also extended to describe allosteric transitions, indicating that the allosteric structural movement does not occur as a deterministic sequential change between two conformations but as a stochastic diffusive motion over the dynamically changing energy landscape. Statistical mechanical viewpoint on folding, as highlighted by the WSME model, has been renovated in the context of modern methods and ideas, and will continue to provide insights on equilibrium and dynamical features of proteins.

  17. Folding pathways of the Tetrahymena ribozyme

    PubMed Central

    Mitchell, David; Russell, Rick

    2014-01-01

    Like many structured RNAs, the Tetrahymena group I intron ribozyme folds through multiple pathways and intermediates. Under standard conditions in vitro, a small fraction reaches the native state (N) with kobs ≈ 0.6 min–1, while the remainder forms a long-lived misfolded conformation (M) thought to differ in topology. These alternative outcomes reflect a pathway that branches late in folding, after disruption of a trapped intermediate (Itrap). Here, we use catalytic activity to probe the folding transitions from Itrap to the native and misfolded states. We show that mutations predicted to weaken the core helix P3 do not increase the rate of folding from Itrap but they increase the fraction that reaches the native state rather than forming the misfolded state. Thus, P3 is disrupted during folding to the native state but not to the misfolded state, and P3 disruption occurs after the rate-limiting step. Interestingly, P3-strengthening mutants also increase native folding. Additional experiments show that these mutants are rapidly committed to folding to the native state, although they reach the native state with approximately the same rate constant as the wild-type ribozyme (~1 min–1). Thus, the P3-strengthening mutants populate a distinct pathway that includes at least one intermediate but avoids the M state, most likely because P3 and the correct topology are formed early. Our results highlight multiple pathways in RNA folding and illustrate how kinetic competitions between rapid events can have long-lasting effects because the ‘choice’ is enforced by energy barriers that grow larger as folding progresses. PMID:24747051

  18. Gauge Theory and Calibrated Geometry for Calabi-Yau 4-folds

    NASA Astrophysics Data System (ADS)

    Cao, Yalong

    This thesis is devoted to the study of gauge theory and calibrated geometry for Calabi-Yau 4-folds. More specifically, our study is along the following five directions. 1. We develop Donaldson-Thomas type theory on Calabi-Yau 4-folds. Let X be a compact complex Calabi-Yau 4-fold. We define Donaldson-Thomas type deformation invariants (DT4 invariants) by studying moduli spaces of solutions to the Donaldson- Thomas equations on X. We also study sheaves counting problems on local Calabi-Yau 4-folds. We relate DT4 invariants of KY to the Donaldson-Thomas invariants of the associated Fano 3-fold Y. When the Calabi-Yau 4-fold is toric, we adapt the virtual localization formula to define the corresponding equivariant DT4 invariants. We also discuss the non-commutative version of DT4 invariants for quivers with relations. Finally, we compute DT4 invariants for certain Calabi-Yau 4-folds when moduli spaces are smooth and find a DT 4/GW correspondence for X. Examples of wall-crossing phenomenon in DT4 theory are also given. 2. Given a complex 4-fold X with an (Calabi-Yau 3-fold) anti-canonical divisor Y, we study relative Donaldson-Thomas invariants for this pair, which are elements in the Donaldson-Thomas cohomologies of Y. We also discuss gluing formulas which relate relative invariants and DT4 invariants for Calabi-Yau 4-folds. 3. We study orientability issues of moduli spaces from gauge theories on Calabi-Yau manifolds. Our results generalize and strengthen those for Donaldson-Thomas theory on Calabi-Yau manifolds of dimensions 3 and 4. We also prove a corresponding result in the relative situation which is relevant to the gluing formula in DT theory. 4. Motivated by Strominger-Yau-Zaslow's mirror symmetry proposal and Kontsevich's homological mirror symmetry conjecture, we study mirror phenomena (in A-model) of certain results from Donaldson-Thomas theory for Calabi-Yau 4-folds. More precisely, we study calibrated geometry in the sense of Harvey-Lawson and Lagrangian

  19. On the usefulness of sheath folds as kinematic indicators

    NASA Astrophysics Data System (ADS)

    Reber, J. E.; Galland, O.; Dabrowski, M.; Schmid, D. W.; Cobbold, P. R.

    2012-04-01

    even though they formed under a constant deformation direction. The resulting sheath folds show no limb thickening, which makes them difficult to use as shear sense indicators. Several studies on sheath folds suggest that the bulk strain type can be obtained by measuring the aspect ratio of the eye pattern. We performed the same measurements on the sheath folds simulated in our analytical and experimental models, in which the strain type was simple shear. The obtained values, however, covered the whole range characteristic for simple shear and pure shear bulk deformation. This procedure thus appears to be not very reliable. In addition, the aspect ratio of the eye-structures seems to be dependent on the layer thickness and the viscosity contrast between the layers. We conclude that sheath folds, though beautiful structures, are very unreliable kinematic indicators and should only be used with the utmost care.

  20. Compact and high-resolution optical orbital angular momentum sorter

    NASA Astrophysics Data System (ADS)

    Wan, Chenhao; Chen, Jian; Zhan, Qiwen

    2017-03-01

    A compact and high-resolution optical orbital angular momentum (OAM) sorter is proposed and demonstrated. The sorter comprises a quadratic fan-out mapper and a dual-phase corrector positioned in the pupil plane and the Fourier plane, respectively. The optical system is greatly simplified compared to previous demonstrations of OAM sorting, and the performance in resolution and efficiency is maintained. A folded configuration is set up using a single reflective spatial light modulator (SLM) to demonstrate the validity of the scheme. The two phase elements are implemented on the left and right halves of the SLM and connected by a right-angle prism. Experimental results demonstrate the high resolution of the compact OAM sorter, and the current limit in efficiency can be overcome by replacing with transmissive SLMs and removing the beam splitters. This novel scheme paves the way for the miniaturization and integration of high-resolution OAM sorters.

  1. Easy mounting interface for compact instruments at TNG

    NASA Astrophysics Data System (ADS)

    Ghedina, Adriano; Riverol Rodriguez, A. Luis

    2016-08-01

    The Telescopio Nazionale Galileo (TNG) is able to offer an F/11 Nasmyth focal station with an easy mount for small devices or compact instruments. The slit masks at the focal plane of the LRS spectrograph can be removed in few minutes from the selector stage. A FoV of 9x9arcmin2 is available and a small instrument can be mounted instead of the slit on a mechanical interface of 240x125mm. The size of the instrument along the optical axis is limited by the support of the collimation lens of the spectrograph. This solution has already been used for small devices like a CCD camera or a SH sensor and a compact Hamamatsu photometer. Furthermore from 2016 it will host the folding optical relay for the GIARPS Instrument. This interface is an opportunity to test new instruments, prototypes or demonstrators in a not invasive or time consuming manner at a 4m class telescope.

  2. Effects of osmolytes on protein folding and aggregation in cells.

    PubMed

    Ignatova, Zoya; Gierasch, Lila M

    2007-01-01

    Nature has developed many strategies to ensure that the complex and challenging protein folding reaction occurs in vivo with adequate efficiency and fidelity for the success of the organism. Among the strategies widely employed in a huge range of species and cell types is the elaboration of small organic molecules called osmolytes that offset the potentially damaging effects of osmotic stress. While considerable knowledge has been gained in vitro regarding the influence of osmolytes on protein structure and folding, it is of great interest to probe the effects of osmolytes in cells. We have developed an in-cell fluorescent-labeling method that enables the study of protein stability and also protein aggregation in vivo. We utilize a genetically encoded tag called a tetra-Cys motif that binds specifically to a bis-arsenical fluorescein-based dye "FlAsH"; we inserted the tetra-Cys motif into a protein of interest in such a way that the FlAsH signal reported on the state of folding or aggregation of the protein. Then, we designed protocols to assess how various osmolytes influence the stability and propensity to aggregate of our protein of interest. These are described here. Not only are there potential biotechnological applications of osmolytes in the quest to produce greater quantities of well-folded proteins, but also osmolytes may serve as tools and points of departure for therapeutic intervention in protein folding and aggregation diseases. Having in vivo methods to analyze how osmolytes affect folding and aggregation enhances our ability to further these goals greatly.

  3. Preliminary results of post-irradiation examination of the AGR-1 TRISO fuel compacts

    SciTech Connect

    Paul Demkowicz; John Hunn; Robert Morris; Jason Harp; Philip Winston; Charles Baldwin; Fred Montgomery; Scott Ploger; Isabella van Rooyen

    2012-10-01

    Five irradiated fuel compacts from the AGR-1 experiment have been examined in detail in order to assess in-pile fission product release behavior. Compacts were electrolytically deconsolidated and analyzed using the leach-burn-leach technique to measure fission product inventory in the compact matrix and identify any particles with a defective SiC layer. Loose particles were then gamma counted to measure the fission product inventory. One particle with a defective SiC layer was found in the five compacts examined. The fractional release of Ag 110m from the particles was significant. The total fraction of silver released from all the particles within a compact ranged from 0-0.63 and individual particles within a single compact often exhibited a very wide range of silver release. The average fractional release of Eu-154 from all particles in a compact was 2.4×10-4—1.3×10-2, which is indicative of release through intact coatings. The fractional Cs-134 inventory in the compact matrix was <2×10-5 when all coatings remained intact, indicating good cesium retention. Approximately 1% of the palladium inventory was found in the compact matrix for two of the compacts, indicating significant release through intact coatings.

  4. A bidirectional shape memory alloy folding actuator

    NASA Astrophysics Data System (ADS)

    Paik, Jamie K.; Wood, Robert J.

    2012-06-01

    This paper presents a low-profile bidirectional folding actuator based on annealed shape memory alloy sheets applicable for meso- and microscale systems. Despite the advantages of shape memory alloys—high strain, silent operation, and mechanical simplicity—their application is often limited to unidirectional operation. We present a bidirectional folding actuator that produces two opposing 180° motions. A laser-patterned nickel alloy (Inconel 600) heater localizes actuation to the folding sections. The actuator has a thin ( < 1 mm) profile, making it appropriate for use in robotic origami. Various design parameters and fabrication variants are described and experimentally explored in the actuator prototype.

  5. Network measures for protein folding state discrimination

    PubMed Central

    Menichetti, Giulia; Fariselli, Piero; Remondini, Daniel

    2016-01-01

    Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there is not a first-principle model to explain this different behavior. We exploit the network properties of protein structures by introducing novel observables to address the problem of classifying the different types of folding kinetics. These observables display a plain physical meaning, in terms of vibrational modes, possible configurations compatible with the native protein structure, and folding cooperativity. The relevance of these observables is supported by a classification performance up to 90%, even with simple classifiers such as discriminant analysis. PMID:27464796

  6. Mechanical Models of Fault-Related Folding

    SciTech Connect

    Johnson, A. M.

    2003-01-09

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

  7. Geometric formalism for DNA quadruplex folding.

    PubMed

    Webba da Silva, Mateus

    2007-01-01

    Understanding the control of self-assembly and stereochemical properties of DNA higher order architectural folds is of fundamental importance in biology as well as biochemical technological applications. Guanine-rich DNA sequences can form tetrahelical architectures termed quadruplexes. A formalism is presented describing the interdependency of a set of structural descriptors as a geometric basis for folding of unimolecular quadruplex topologies. It represents a standard for interpretation of structural characteristics of quadruplexes, and is comprehensive in explicitly harmonizing the results of published literature with a unified language. The formalism is a fundamental step towards prediction of unimolecular quadruplex folding topologies from primary sequence.

  8. A compact acousto-optic lens for 2D and 3D femtosecond based 2-photon microscopy

    PubMed Central

    Kirkby, Paul A.; Naga Srinivas, N.K.M.; Silver, R. Angus

    2010-01-01

    We describe a high speed 3D Acousto-Optic Lens Microscope (AOLM) for femtosecond 2-photon imaging. By optimizing the design of the 4 AO Deflectors (AODs) and by deriving new control algorithms, we have developed a compact spherical AOL with a low temporal dispersion that enables 2-photon imaging at 10-fold lower power than previously reported. We show that the AOLM can perform high speed 2D raster-scan imaging (>150 Hz) without scan rate dependent astigmatism. It can deflect and focus a laser beam in a 3D random access sequence at 30 kHz and has an extended focusing range (>137 μm; 40X 0.8NA objective). These features are likely to make the AOLM a useful tool for studying fast physiological processes distributed in 3D space PMID:20588506

  9. New compact neutron polarizer

    NASA Astrophysics Data System (ADS)

    Krist, Th; Kennedy, S. J.; Hicks, T. J.; Mezei, F.

    A new type of a neutron polarizing bender was developed in co-operation with BENSC and ANSTO. It is based upon bent thin silicon wafers coated on one side with SiFeCo polarizing supermirrors and on the other side with Gd. Initial tests at BENSC in a 300 Oe magnetic field yielded a transmission of spin-up neutrons of about 55% over an angle range of 0.75° and flipping ratios > 30. Subsequent tests at ANSTO at 1200 Oe yielded a transmission of 48% with a flipping ratio > 45.

  10. Equation for compaction of paleosols due to burial

    NASA Astrophysics Data System (ADS)

    Sheldon, Nathan D.; Retallack, Gregory J.

    2001-03-01

    Existing empirically derived compaction curves for marine sediments fail to estimate the compaction of paleosols, flood-plain sediments, and peats as indicated by deformation of clastic dikes, dinosaur footprints, and sandstone paleochannels. Yet compaction estimates are vital to reconstructing paleoclimate and geochemical profiles of paleosols, to modeling sediment accumulation rates of nonmarine rocks, and to tectonic flexural modeling of molasse facies. This paper presents a compaction equation and physically derived constants that make geologically realistic estimates of compaction of paleosols and other nonmarine sediments. A protocol for the application of the equation is suggested that would allow the following equation to solve for burial compaction (C as a fraction of original thickness) given depth of burial (D in km) as: C = -Si/[(F0/ eDk) - 1]. This equation can be applied to nonmarine sedimentary rocks or paleosols given appropriate empirical data on the physical constants in the equation, such as initial solidity (Si), initial porosity (F0), and the corresponding curve-fitting constant (k). Data on physical constants useful for this equation are compiled here for a range of paleosol and nonmarine sediment types.

  11. CYANATE ION IN COMPACT AMORPHOUS WATER ICE

    SciTech Connect

    Mate, Belen; Herrero, Victor J.; Rodriguez-Lazcano, Yamilet; Moreno, Miguel A.; Escribano, Rafael; Fernandez-Torre, Delia; Gomez, Pedro C.

    2012-11-10

    The 4.62 {mu}m infrared (2164.5 cm{sup -1}) absorption band, observed in ice mantels toward many young stellar objects, has been mostly attributed to the {nu}{sub 3} (CN stretch) band of OCN{sup -} ions. We present in this work a spectroscopic study of OCN{sup -} ions embedded in compact amorphous ice in a range of concentrations and temperatures relevant to astronomical observations together with quantum mechanical calculations of the {nu}{sub 3} band of OCN{sup -} in various H{sub 2}O environments. The ice samples containing the ions are prepared through hyperquenching of liquid droplets of K{sup +}OCN{sup -} solutions on a substrate at 14 K. The {nu}{sub 3} OCN{sup -} band appears as a broad feature peaking at 4.64 {mu}m with a secondary maximum at 4.54 {mu}m and is much weaker than the corresponding peak in the liquid solution or in the solid salt. A similar weakening is observed for other OCN{sup -} absorption peaks at 7.66 {mu}m (2{nu}{sub 2}) and 8.20 {mu}m ({nu}{sub 1}). The theoretical calculations for the {nu}{sub 3} vibration lead to a range of frequencies spanning the experimentally observed width. This frequency spread could help explain the pronounced drop in the band intensity in the ice. The OCN{sup -} {nu}{sub 3} band in the present compact ices is also broader and much weaker than that reported in the literature for OCN{sup -} ions obtained by variously processing porous ice samples containing suitable neutral precursors. The results of this study indicate that the astronomical detection of OCN{sup -} in ice mantels could be significantly impaired if the ion is embedded in a compact water network.

  12. A bionic approach to mathematical modeling the fold geometry of deployable reflector antennas on satellites

    NASA Astrophysics Data System (ADS)

    Feng, C. M.; Liu, T. S.

    2014-10-01

    Inspired from biology, this study presents a method for designing the fold geometry of deployable reflectors. Since the space available inside rockets for transporting satellites with reflector antennas is typically cylindrical in shape, and its cross-sectional area is considerably smaller than the reflector antenna after deployment, the cross-sectional area of the folded reflector must be smaller than the available rocket interior space. Membrane reflectors in aerospace are a type of lightweight structure that can be packaged compactly. To design membrane reflectors from the perspective of deployment processes, bionic applications from morphological changes of plants are investigated. Creating biologically inspired reflectors, this paper deals with fold geometry of reflectors, which imitate flower buds. This study uses mathematical formulation to describe geometric profiles of flower buds. Based on the formulation, new designs for deployable membrane reflectors derived from bionics are proposed. Adjusting parameters in the formulation of these designs leads to decreases in reflector area before deployment.

  13. Transmembrane segments form tertiary hairpins in the folding vestibule of the ribosome.

    PubMed

    Tu, Liwei; Khanna, Pooja; Deutsch, Carol

    2014-01-09

    Folding of membrane proteins begins in the ribosome as the peptide is elongated. During this process, the nascent peptide navigates along 100Å of tunnel from the peptidyltransferase center to the exit port. Proximal to the exit port is a "folding vestibule" that permits the nascent peptide to compact and explore conformational space for potential tertiary folding partners. The latter occurs for cytosolic subdomains but has not yet been shown for transmembrane segments. We now demonstrate, using an accessibility assay and an improved intramolecular crosslinking assay, that the helical transmembrane S3b-S4 hairpin ("paddle") of a voltage-gated potassium (Kv) channel, a critical region of the Kv voltage sensor, forms in the vestibule. S3-S4 hairpin interactions are detected at an early stage of Kv biogenesis. Moreover, this vestibule hairpin is consistent with a closed-state conformation of the Kv channel in the plasma membrane.

  14. Compact orthogonal NMR field sensor

    DOEpatents

    Gerald, II, Rex E.; Rathke, Jerome W.

    2009-02-03

    A Compact Orthogonal Field Sensor for emitting two orthogonal electro-magnetic fields in a common space. More particularly, a replacement inductor for existing NMR (Nuclear Magnetic Resonance) sensors to allow for NMR imaging. The Compact Orthogonal Field Sensor has a conductive coil and a central conductor electrically connected in series. The central conductor is at least partially surrounded by the coil. The coil and central conductor are electrically or electro-magnetically connected to a device having a means for producing or inducing a current through the coil and central conductor. The Compact Orthogonal Field Sensor can be used in NMR imaging applications to determine the position and the associated NMR spectrum of a sample within the electro-magnetic field of the central conductor.

  15. Comparison of the folded stripline and stacked stripline concepts to the folded waveguide launcher

    SciTech Connect

    Gardner, W.L.; Caughman, J.B.O.; Hoffman, D.J.; Probert, P.H.

    1993-12-31

    Two new concepts are being developed as possible upgrades to the folded waveguide launcher. The folded stripline is a folded waveguide with an additional conductor positioned inside. The term stripline refers to the resemblance of the design to microwave microstrip line. The conductor provides support for TEM mode propagation, which eliminates cutoff and the nonlinear frequency dependence of the waveguide impedance and phase velocity. A natural extension to the folded stripline is the stacked stripline, which comprises several stacked, independent TEM waveguides. Initial measurements indicate that both concepts have better magnetic flux coupling than the folded waveguide.

  16. Comparison of the folded stripline and stacked stripline concepts to the folded waveguide launcher

    SciTech Connect

    Gardner, W.L.; Caughman, J.B.O.; Hoffman, D.J. ); Probert, P.H. )

    1994-10-15

    Two new concepts are being developed as possible upgrades to the folded waveguide launcher. The folded stripline is a folded waveguide with an additional conductor positioned inside. The term [ital stripline] refers to the resemblance of the design to microwave microstrip line. The conductor provides support for TEM mode propagation, which eliminates cutoff and the nonlinear frequency dependence of the waveguide impedance and phase velocity. A natural extension to the folded stripline is the stacked stripline, which comprises several stacked, independent TEM waveguides. Initial measurements indicate that both concepts have better magnetic flux coupling than the folded waveguide.

  17. Paleomagnetic and structural evidence for oblique slip in a fault-related fold, Grayback monocline, Colorado

    USGS Publications Warehouse

    Tetreault, J.; Jones, C.H.; Erslev, E.; Larson, S.; Hudson, M.; Holdaway, S.

    2008-01-01

    Significant fold-axis-parallel slip is accommodated in the folded strata of the Grayback monocline, northeastern Front Range, Colorado, without visible large strike-slip displacement on the fold surface. In many cases, oblique-slip deformation is partitioned; fold-axis-normal slip is accommodated within folds, and fold-axis-parallel slip is resolved onto adjacent strike-slip faults. Unlike partitioning strike-parallel slip onto adjacent strike-slip faults, fold-axis-parallel slip has deformed the forelimb of the Grayback monocline. Mean compressive paleostress orientations in the forelimb are deflected 15??-37?? clockwise from the regional paleostress orientation of the northeastern Front Range. Paleomagnetic directions from the Permian Ingleside Formation in the forelimb are rotated 16??-42?? clockwise about a bedding-normal axis relative to the North American Permian reference direction. The paleostress and paleomagnetic rotations increase with the bedding dip angle and decrease along strike toward the fold tip. These measurements allow for 50-120 m of fold-axis-parallel slip within the forelimb, depending on the kinematics of strike-slip shear. This resolved horizontal slip is nearly equal in magnitude to the ???180 m vertical throw across the fold. For 200 m of oblique-slip displacement (120 m of strike slip and 180 m of reverse slip), the true shortening direction across the fold is N90??E, indistinguishable from the regionally inferred direction of N90??E and quite different from the S53??E fold-normal direction. Recognition of this deformational style means that significant amounts of strike slip can be accommodated within folds without axis-parallel surficial faulting. ?? 2008 Geological Society of America.

  18. Folding analysis of the most complex Stevedore’s protein knot

    PubMed Central

    Wang, Iren; Chen, Szu-Yu; Hsu, Shang-Te Danny

    2016-01-01

    DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore’s protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I’. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I’ to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures. PMID:27527519

  19. Thermal stability and folding kinetics analysis of intrinsically disordered protein, securin

    NASA Astrophysics Data System (ADS)

    Chang, Chia-Ching; Chu, Hsueh-Liang; Ho, Li-Ping

    2014-03-01

    Lacking a stable tertiary structure, intrinsically disordered proteins (IDPs) possess particular functions in cell regulation, signaling, and controlling pathways. The study of their unique structure features, thermal stabilities, and folding kinetics is intriguing. In this study, an identified IDP, securin, was used as a model protein. By using a quasi-static five-step (on-path) folding process, the function of securin was restored and analyzed by isothermal titration calorimetry. Fluorescence spectroscopy and particle size analysis indicated that securin possessed a compact hydrophobic core and particle size. The glass transition of securin was characterized using differential scanning microcalorimetry. Furthermore, the folding/unfolding rates (kobs) of securin were undetectable, implying that the folding/unfolding rate is very fast and that the conformation of securin is sensitive to solvent environment change. Therefore, securin may fold properly under specific physiological conditions. In summary, the thermal glass transition behavior and undetectable kobs of folding/unfolding reactions may be two of the indices of IDP. This study was supported in part by grants NSC 97-2112-M-009-009-YM3 and NSC 100-2112-M-009-004-MY3, Taiwan, R.O.C.

  20. Topology Explains Why Automobile Sunshades Fold Oddly

    ERIC Educational Resources Information Center

    Feist, Curtis; Naimi, Ramin

    2009-01-01

    Automobile sunshades always fold into an "odd" number of loops. The explanation why involves elementary topology (braid theory and linking number, both explained in detail here with definitions and examples), and an elementary fact from algebra about symmetric group.

  1. Cycle 22 COS/NUV Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, T.; Welty, A.

    2016-09-01

    We summarize the Cycle 22 COS/NUV Fold Distribution for the Cosmic Origins Spectrograph's (COS) MAMA detector on the Hubble Space Telescope. The detector micro-channel plate's health state is determined and the results are presented.

  2. Folded Resonant Horns for Power Ultrasonic Applications

    NASA Technical Reports Server (NTRS)

    Sherrit, Stewart; Askins, Stephen; Gradziel, Michael; Bao, Xiaoqi; Chang, Zensheu; Dolgin, Benjamin; Bar-Cohen, Yoseph; Peterson, Tom

    2003-01-01

    Folded horns have been conceived as alternatives to straight horns used as resonators and strain amplifiers in power ultrasonic systems. Such systems are used for cleaning, welding, soldering, cutting, and drilling in a variety of industries. In addition, several previous NASA Tech Briefs articles have described instrumented drilling, coring, and burrowing machines that utilize combinations of sonic and ultrasonic vibrational actuation. The main advantage of a folded horn, relative to a straight horn of the same resonance frequency, is that the folded horn can be made shorter (that is, its greatest linear dimension measured from the outside can be made smaller). Alternatively, for a given length, the resonance frequency can be reduced. Hence, the folded-horn concept affords an additional degree of design freedom for reducing the length of an ultrasonic power system that includes a horn.

  3. Folding, Binding, Misfolding and Aggregation with AWSEM

    NASA Astrophysics Data System (ADS)

    Schafer, Nicholas P.

    This thesis discusses our recent results using the Associative-memory, Water-mediated, Structure and Energy Model (AWSEM), an optimized, coarse-grained molecular dynamics protein folding model, to fold, bind, and predict the misfolding behavior of proteins. AWSEM is capable of performing de novo structure prediction on small alpha-helical protein domains and predict the binding interfaces of homo- and hetero-dimers. More recent work demonstrates how the misfolding behavior of tandem constructs in AWSEM is consistent with crucial aspects of ensemble and single molecule experiments on the aggregation and misfolding of these constructs. The first chapter is a review of the energy landscape theory of protein folding as it applies to the problem of protein structure prediction, and more specifically how energy landscape theory and the principle of minimal frustration can be used to optimize parameters of coarse-grained protein folding simulation models. The subsequent four chapters are reports of novel research performed with one such model.

  4. Self-folding miniature elastic electric devices

    NASA Astrophysics Data System (ADS)

    Miyashita, Shuhei; Meeker, Laura; Tolley, Michael T.; Wood, Robert J.; Rus, Daniela

    2014-09-01

    Printing functional materials represents a considerable impact on the access to manufacturing technology. In this paper we present a methodology and validation of print-and-self-fold miniature electric devices. Polyvinyl chloride laminated sheets based on metalized polyester film show reliable self-folding processes under a heat application, and it configures 3D electric devices. We exemplify this technique by fabricating fundamental electric devices, namely a resistor, capacitor, and inductor. Namely, we show the development of a self-folded stretchable resistor, variable resistor, capacitive strain sensor, and an actuation mechanism consisting of a folded contractible solenoid coil. Because of their pre-defined kinematic design, these devices feature elasticity, making them suitable as sensors and actuators in flexible circuits. Finally, an RLC circuit obtained from the integration of developed devices is demonstrated, in which the coil based actuator is controlled by reading a capacitive strain sensor.

  5. Origami: Paper Folding--The Algorithmic Way.

    ERIC Educational Resources Information Center

    Heukerott, Pamela Beth

    1988-01-01

    Describes origami, the oriental art of paper folding as an activity to teach upper elementary students concepts and skills in geometry involving polygons, angles, measurement, symmetry, and congruence. (PK)

  6. Frustration in Condensed Matter and Protein Folding

    NASA Astrophysics Data System (ADS)

    Li, Z.; Tanner, S.; Conroy, B.; Owens, F.; Tran, M. M.; Boekema, C.

    2014-03-01

    By means of computer modeling, we are studying frustration in condensed matter and protein folding, including the influence of temperature and Thomson-figure formation. Frustration is due to competing interactions in a disordered state. The key issue is how the particles interact to reach the lowest frustration. The relaxation for frustration is mostly a power function (randomly assigned pattern) or an exponential function (regular patterns like Thomson figures). For the atomic Thomson model, frustration is predicted to decrease with the formation of Thomson figures at zero kelvin. We attempt to apply our frustration modeling to protein folding and dynamics. We investigate the homogeneous protein frustration that would cause the speed of the protein folding to increase. Increase of protein frustration (where frustration and hydrophobicity interplay with protein folding) may lead to a protein mutation. Research is supported by WiSE@SJSU and AFC San Jose.

  7. The Ribosome Modulates Nascent Protein Folding

    PubMed Central

    Kaiser, Christian M.; Goldman, Daniel H.; Chodera, John D.; Tinoco, Ignacio; Bustamante, Carlos

    2014-01-01

    Proteins are synthesized by the ribosome and generally must fold to become functionally active. Although it is commonly assumed that the ribosome affects the folding process, this idea has been extremely difficult to demonstrate. We have developed an experimental system to investigate the folding of single ribosome-bound stalled nascent polypeptides with optical tweezers. In T4 lysozyme, synthesized in a reconstituted in vitro translation system, the ribosome slows the formation of stable tertiary interactions and the attainment of the native state relative to the free protein. Incomplete T4 lysozyme polypeptides misfold and aggregate when free in solution, but they remain folding-competent near the ribosomal surface. Altogether, our results suggest that the ribosome not only decodes the genetic information and synthesizes polypeptides, but also promotes efficient de novo attainment of the native state. PMID:22194581

  8. Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis.

    PubMed

    Uversky, Vladimir N

    2013-11-01

    For decades, protein function was intimately linked to the presence of a unique, aperiodic crystal-like structure in a functional protein. The two only places for conformational ensembles of under-folded (or partially folded) protein forms in this picture were either the end points of the protein denaturation processes or transiently populated folding intermediates. Recent years witnessed dramatic change in this perception and conformational ensembles, which the under-folded proteins are, have moved from the shadow. Accumulated to date data suggest that a protein can exist in at least three global forms-functional and folded, functional and intrinsically disordered (nonfolded), and nonfunctional and misfolded/aggregated. Under-folded protein states are crucial for each of these forms, serving as important folding intermediates of ordered proteins, or as functional states of intrinsically disordered proteins (IDPs) and IDP regions (IDPRs), or as pathology triggers of misfolded proteins. Based on these observations, conformational ensembles of under-folded proteins can be classified as transient (folding and misfolding intermediates) and permanent (IDPs and stable misfolded proteins). Permanently under-folded proteins can further be split into intentionally designed (IDPs and IDPRs) and unintentionally designed (misfolded proteins). Although intrinsic flexibility, dynamics, and pliability are crucial for all under-folded proteins, the different categories of under-foldedness are differently encoded in protein amino acid sequences.

  9. FOLD PROFILER: A MATLAB ®—based program for fold shape classification

    NASA Astrophysics Data System (ADS)

    Lisle, R. J.; Fernández Martínez, J. L.; Bobillo-Ares, N.; Menéndez, O.; Aller, J.; Bastida, F.

    2006-02-01

    FOLD PROFILER is a MATLAB code for classifying the shapes of profiles of folded surfaces. The classification is based on the comparison of the natural fold profile with curves representing mathematical functions. The user is offered a choice of four methods, each based on a different type of function: cubic Bezier curves, conic sections, power functions and superellipses. The comparison is carried out by the visual matching of the fold profile displayed on-screen from an imported digital image and computed theoretical curves which are superimposed on the image of the fold. To improve the fit with the real fold shape, the parameters of the theoretical curves are changed by simple mouse actions. The parameters of the mathematical function that best fits the real folds are used to classify the fold shape. FOLD PROFILER allows the rapid implementation of four existing methods for fold shape analysis. The attractiveness of this analytical tool lies in the way it gives an instant visual appreciation of the effect of changing the parameters that are used to classify fold geometry.

  10. Compact accelerator for medical therapy

    DOEpatents

    Caporaso, George J.; Chen, Yu-Jiuan; Hawkins, Steven A.; Sampayan, Stephen E.; Paul, Arthur C.

    2010-05-04

    A compact accelerator system having an integrated particle generator-linear accelerator with a compact, small-scale construction capable of producing an energetic (.about.70-250 MeV) proton beam or other nuclei and transporting the beam direction to a medical therapy patient without the need for bending magnets or other hardware often required for remote beam transport. The integrated particle generator-accelerator is actuable as a unitary body on a support structure to enable scanning of a particle beam by direction actuation of the particle generator-accelerator.

  11. Compact monolithic capacitive discharge unit

    DOEpatents

    Roesler, Alexander W.; Vernon, George E.; Hoke, Darren A.; De Marquis, Virginia K.; Harris, Steven M.

    2007-06-26

    A compact monolithic capacitive discharge unit (CDU) is disclosed in which a thyristor switch and a flyback charging circuit are both sandwiched about a ceramic energy storage capacitor. The result is a compact rugged assembly which provides a low-inductance current discharge path. The flyback charging circuit preferably includes a low-temperature co-fired ceramic transformer. The CDU can further include one or more ceramic substrates for enclosing the thyristor switch and for holding various passive components used in the flyback charging circuit. A load such as a detonator can also be attached directly to the CDU.

  12. Compressibility Characteristics of Compacted Snow

    DTIC Science & Technology

    1976-06-01

    Cornpressibility characteristics 7Jj i C’p of compacted snowifAG2� 004 t Cover: ~ ~ ~ ~ ~ ~ ~ ~ a - Thn***o htgrp fpoyrsaliekAmgife i ote rm...nwcmrse to7 asa 10 Phtgahb nhn Gow1 CRREL Report 76-21 Compressibility characteristics of compacted snow %i" Gunars Abele and Anthony J. Cow I ~ June 1976 A ...c , I fu. A AD,:j ly M3rs CORPS OF ENGINEERS, U.S. ARMY COLD REGIONS RESEARCH AND ENGINEERZ]NG LABORATORY HANOVER, NEW HAMPSHIRE Approved for public

  13. The hydrogen exchange core and protein folding.

    PubMed Central

    Li, R.; Woodward, C.

    1999-01-01

    A database of hydrogen-deuterium exchange results has been compiled for proteins for which there are published rates of out-exchange in the native state, protection against exchange during folding, and out-exchange in partially folded forms. The question of whether the slow exchange core is the folding core (Woodward C, 1993, Trends Biochem Sci 18:359-360) is reexamined in a detailed comparison of the specific amide protons (NHs) and the elements of secondary structure on which they are located. For each pulsed exchange or competition experiment, probe NHs are shown explicitly; the large number and broad distribution of probe NHs support the validity of comparing out-exchange with pulsed-exchange/competition experiments. There is a strong tendency for the same elements of secondary structure to carry NHs most protected in the native state, NHs first protected during folding, and NHs most protected in partially folded species. There is not a one-to-one correspondence of individual NHs. Proteins for which there are published data for native state out-exchange and theta values are also reviewed. The elements of secondary structure containing the slowest exchanging NHs in native proteins tend to contain side chains with high theta values or be connected to a turn/loop with high theta values. A definition for a protein core is proposed, and the implications for protein folding are discussed. Apparently, during folding and in the native state, nonlocal interactions between core sequences are favored more than other possible nonlocal interactions. Other studies of partially folded bovine pancreatic trypsin inhibitor (Barbar E, Barany G, Woodward C, 1995, Biochemistry 34:11423-11434; Barber E, Hare M, Daragan V, Barany G, Woodward C, 1998, Biochemistry 37:7822-7833), suggest that developing cores have site-specific energy barriers between microstates, one disordered, and the other(s) more ordered. PMID:10452602

  14. [Congenital retinal folds in different clinical cases].

    PubMed

    Munteanu, M

    2005-01-01

    We present 12 clinical cases of congenital retinal folds with different etiologies: posterior primitive vitreous persistency and hyperplasia (7 cases),retinocytoma (1 case). retinopathy of prematurity (1 case), astrocytoma of the retina (1 case), retinal vasculitis (1 case), Goldmann-Favre syndrome (1 case). Etiopathogenic and nosological aspects are discussed; the congenital retinal folds are interpreted as a symptom in a context of a congenital or acquired vitreo-retinal pathology.

  15. Geometric Folding Algorithms: Bridging Theory to Practice

    DTIC Science & Technology

    2009-11-03

    Proved that any orthogonal polyhedron can be folded from a single, universal crease pattern (box pleating). 1.2 Origami Design • Developed...mathematical theory for what happens in paper between creases, in partic- ular for the case of circular creases. • Circular crease origami on permanent...sheet of paper. • Developing mathematical theory of Robert Lang’s TreeMaker framework for efficiently folding tree-shaped origami "bases

  16. Protein folding and misfolding: mechanism and principles.

    PubMed

    Englander, S Walter; Mayne, Leland; Krishna, Mallela M G

    2007-11-01

    Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors

  17. Recovery of severely compacted soils in the Mojave Desert, California, USA

    USGS Publications Warehouse

    Webb, R.H.

    2002-01-01

    Often as a result of large-scale military maneuvers in the past, many soils in the Mojave Desert are highly vulnerable to soil compaction, particularly when wet. Previous studies indicate that natural recovery of severely compacted desert soils is extremely slow, and some researchers have suggested that subsurface compaction may not recover. Poorly sorted soils, particularly those with a loamy sand texture, are most vulnerable to soil compaction, and these soils are the most common in alluvial fans of the Mojave Desert. Recovery of compacted soil is expected to vary as a function of precipitation amounts, wetting-and-drying cycles, freeze-thaw cycles, and bioturbation, particularly root growth. Compaction recovery, as estimated using penetration depth and bulk density, was measured at 19 sites with 32 site-time combinations, including the former World War II Army sites of Camps Ibis, Granite, Iron Mountain, Clipper, and Essex. Although compaction at these sites was caused by a wide variety of forces, ranging from human trampling to tank traffic, the data do not allow segregation of differences in recovery rates for different compaction forces. The recovery rate appears to be logarithmic, with the highest rate of change occurring in the first few decades following abandonment. Some higher-elevation sites have completely recovered from soil compaction after 70 years. Using a linear model of recovery, the full recovery time ranges from 92 to 100 years; using a logarithmic model, which asymptotically approaches full recovery, the time required for 85% recovery ranges from 105-124 years.

  18. Optimum folding pathways for growing protein chains.

    PubMed

    Senturk, Serife; Baday, Sefer; Arkun, Yaman; Erman, Burak

    2007-11-26

    The folding of a protein is studied as it grows residue by residue from the N-terminus and enters an environment that stabilizes the folded state. This mode of folding of a growing chain is different from refolding where the full chain folds from a disordered initial configuration to the native state. We propose a sequential dynamic optimization method that computes the evolution of optimum folding pathways as amino acid residues are added to the peptide chain one by one. The dynamic optimization formulation is deterministic and uses Newton's equations of motion and a Go-type potential that establishes the native contacts and excluded volume effects. The method predicts the optimal energy-minimizing path among all the alternative feasible pathways. As two examples, the folding of the chicken villin headpiece, a 36-residue protein, and chymotrypsin inhibitor 2 (CI2), a 64-residue protein, are studied. Results on the villin headpiece show significant differences from the refolding of the same chain studied previously. Results on CI2 mostly agree with the results of refolding experiments and computational work.

  19. Cortical Folding Patterns and Predicting Cytoarchitecture

    PubMed Central

    Rajendran, Niranjini; Busa, Evelina; Augustinack, Jean; Hinds, Oliver; Yeo, B.T. Thomas; Mohlberg, Hartmut; Amunts, Katrin; Zilles, Karl

    2008-01-01

    The human cerebral cortex is made up of a mosaic of structural areas, frequently referred to as Brodmann areas (BAs). Despite the widespread use of cortical folding patterns to perform ad hoc estimations of the locations of the BAs, little is understood regarding 1) how variable the position of a given BA is with respect to the folds, 2) whether the location of some BAs is more variable than others, and 3) whether the variability is related to the level of a BA in a putative cortical hierarchy. We use whole-brain histology of 10 postmortem human brains and surface-based analysis to test how well the folds predict the locations of the BAs. We show that higher order cortical areas exhibit more variability than primary and secondary areas and that the folds are much better predictors of the BAs than had been previously thought. These results further highlight the significance of cortical folding patterns and suggest a common mechanism for the development of the folds and the cytoarchitectonic fields. PMID:18079129

  20. "Wet" Versus "Dry" Folding of Polyproline

    NASA Astrophysics Data System (ADS)

    Shi, Liuqing; Holliday, Alison E.; Bohrer, Brian C.; Kim, Doyong; Servage, Kelly A.; Russell, David H.; Clemmer, David E.

    2016-06-01

    When the all- cis polyproline-I helix (PPI, favored in 1-propanol) of polyproline-13 is introduced into water, it folds into the all- trans polyproline-II (PPII) helix through at least six intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we show that the solvent-free intermediates refold into the all- cis PPI helix with high (>90%) efficiency. Moreover, in the absence of solvent, each intermediate appears to utilize the same small set of pathways observed for the solution-phase PPII → PPI transition upon immersion of PPIIaq in 1-propanol. That folding in solution (under conditions where water is displaced by propanol) and folding in vacuo (where energy required for folding is provided by collisional activation) occur along the same pathway is remarkable. Implicit in this statement is that 1-propanol mimics a "dry" environment, similar to the gas phase. We note that intermediates with structures that are similar to PPIIaq can form PPII under the most gentle activation conditions—indicating that some transitions observed in water (i.e. , "we t" folding, are accessible (albeit inefficient) in vacuo. Lastly, these "dry" folding experiments show that PPI (all cis) is favored under "dry" conditions, which underscores the role of water as the major factor promoting preference for trans proline.

  1. Superposed fold-thrust events at the Nevada Test Site

    USGS Publications Warehouse

    Cashman, Patricia H.; Cole, James C.; Trexler, James H.

    2000-01-01

    The Nevada Test Site (NTS), in southern Nye County, Nevada, straddles significant pre-Tertiary structural and stratigraphic boundaries. Detailed stratigraphy and biostratigraphy of the Upper Paleozoic section delineates the regional trust sheets and constrains their burial histories. The Paleozoic rocks record three phases of contractional deformation, overprinted by strike-slip faulting. These occured in the folloing order: (1) foreland-vergant folding and imbricate thrusting in the footwall of the Belted Range thrust; (2) hinterland-vergent folding and thrusting; and (3) north-vergant folding that we interpret as footwall deformation below a third major thrust system. Sinistral slip, typically accompanied by minor east-west shortening, has occured along a series of north-northeast--north-northwest--striking faults around Yucca Flat. This strike-slip faulting postdates both foreland-vergent and hinterland-vergent deformation, and predates the Cretaceous Climax stock; its age relative to the north-vergent folding and thrusting is unknown. Our new understanding of the geometry of these structures provides new insights into the correlation and interpretation of regional structural features. Field trip stops will examine: (1) the stratigraphic differences that allow us to distinguish the regional thrust sheets and constrain their burial histories; and (2) the field relationships that document the kinematics and relative ages of the penetrative deformational events.

  2. 76 FR 66326 - Meeting of the Compact Council for the National Crime Prevention and Privacy Compact

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-26

    ... address this session of the Council should notify the Federal Bureau Of Investigation (FBI) Compact..., FBI Compact Officer, Compact Council Office, Module D3, 1000 Custer Hollow Road, Clarksburg,...

  3. 75 FR 62568 - Meeting of the Compact Council for the National Crime Prevention and Privacy Compact

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-12

    ... of the Council should notify the Federal Bureau of Investigation (FBI) Compact Officer, Mr. Gary S..., FBI Compact Officer, Compact Council Office, Module D3, 1000 Custer Hollow Road, Clarksburg,...

  4. Compacting biomass waste materials for use as fuel

    NASA Astrophysics Data System (ADS)

    Zhang, Ou

    Every year, biomass waste materials are produced in large quantity. The combustibles in biomass waste materials make up over 70% of the total waste. How to utilize these waste materials is important to the nation and the world. The purpose of this study is to test optimum processes and conditions of compacting a number of biomass waste materials to form a densified solid fuel for use at coal-fired power plants or ordinary commercial furnaces. Successful use of such fuel as a substitute for or in cofiring with coal not only solves a solid waste disposal problem but also reduces the release of some gases from burning coal which cause health problem, acid rain and global warming. The unique punch-and-die process developed at the Capsule Pipeline Research Center, University of Missouri-Columbia was used for compacting the solid wastes, including waste paper, plastics (both film and hard products), textiles, leaves, and wood. The compaction was performed to produce strong compacts (biomass logs) under room temperature without binder and without preheating. The compaction conditions important to the commercial production of densified biomass fuel logs, including compaction pressure, pressure holding time, back pressure, moisture content, particle size, binder effects, and mold conditions were studied and optimized. The properties of the biomass logs were evaluated in terms of physical, mechanical, and combustion characteristics. It was found that the compaction pressure and the initial moisture content of the biomass material play critical roles in producing high-quality biomass logs. Under optimized compaction conditions, biomass waste materials can be compacted into high-quality logs with a density of 0.8 to 1.2 g/cm3. The logs made from the combustible wastes have a heating value in the range 6,000 to 8,000 Btu/lb which is only slightly (10 to 30%) less than that of subbituminous coal. To evaluate the feasibility of cofiring biomass logs with coal, burn tests were

  5. A Compact Polarization Imager

    NASA Technical Reports Server (NTRS)

    Thompson, Karl E.; Rust, David M.; Chen, Hua

    1995-01-01

    A new type of image detector has been designed to analyze the polarization of light simultaneously at all picture elements (pixels) in a scene. The Integrated Dual Imaging Detector (IDID) consists of a polarizing beamsplitter bonded to a custom-designed charge-coupled device with signal-analysis circuitry, all integrated on a silicon chip. The IDID should simplify the design and operation of imaging polarimeters and spectroscopic imagers used, for example, in atmospheric and solar research. Other applications include environmental monitoring and robot vision. Innovations in the IDID include two interleaved 512 x 1024 pixel imaging arrays (one for each polarization plane), large dynamic range (well depth of 10(exp 6) electrons per pixel), simultaneous readout and display of both images at 10(exp 6) pixels per second, and on-chip analog signal processing to produce polarization maps in real time. When used with a lithium niobate Fabry-Perot etalon or other color filter that can encode spectral information as polarization, the IDID can reveal tiny differences between simultaneous images at two wavelengths.

  6. Specific energy requirement for compacting corn stover.

    PubMed

    Mani, Sudhagar; Tabil, Lope G; Sokhansanj, Shahab

    2006-08-01

    Corn stover is a major crop residue for biomass conversion to produce chemicals and fuels. One of the problems associated with the supply of corn stover to conversion plants is the delivery of feedstock at a low cost. Corn stover has low bulk density and it is difficult to handle. In this study, chopped corn stover samples were compacted in a piston cylinder under three pressure levels (5, 10, 15 MPa) and at three moisture content levels (5%, 10%, 15% (wb)) to produce briquettes. The total energy requirement to compress and extrude briquette ranged from 12 to 30 MJ/t. The briquette density ranged from 650 to 950 kg/m3 increasing with pressure. Moisture content had also a significant effect on briquette density, durability and stability. Low moisture stover (5-10%) resulted in denser, more stable and more durable briquettes than high moisture stover (15%).

  7. Passive Ranging

    DTIC Science & Technology

    1988-08-01

    1981). 5. R. Courant and D. Hilbert, Methods of Mathematical Physics , Vol. I, English ed., * Interscience, New York, 1953. 32 32 APPENDIX A CALCULATION...K Courant and D. Hilbert, Methods of Mathematical Physics , Vol. I, English ed., * Interscience, New York, 1953. A-8 APPENDIX B * RANGING ACCURACY IN

  8. Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements

    PubMed Central

    PENEDO, J. CARLOS; WILSON, TIMOTHY J.; JAYASENA, SUMEDHA D.; KHVOROVA, ANASTASIA; LILLEY, DAVID M.J.

    2004-01-01

    It has been shown that the activity of the hammerhead ribozyme at μM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the μM range of magnesium ion concentration. Disruption of the loop–loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions. PMID:15100442

  9. Ranking vocal fold model parameters by their influence on modal frequencies

    PubMed Central

    Cook, Douglas D.; Nauman, Eric; Mongeau, Luc

    2009-01-01

    The purpose of this study was to identify, using computational models, the vocal fold parameters which are most influential in determining the vibratory characteristics of the vocal folds. The sensitivities of vocal folds modal frequencies to variations model parameters were used to determine the most influential parameters. A detailed finite element model of the human vocal fold was created. The model was defined by eight geometric and six material parameters. The model included transitional boundary regions to idealize the complex physiological structure of real human subjects. Parameters were simultaneously varied over ranges representative of actual human vocal folds. Three separate statistical analysis techniques were used to identify the most and least sensitive model parameters with respect to modal frequency. The results from all three methods consistently suggest that a set of five parameters are most influential in determining the vibratory characteristics of the vocal folds. PMID:19813811

  10. Compact Photon Source Conceptual Design

    SciTech Connect

    Degtyarenko, Pavel V.; Wojtsekhowski, Bogdan B.

    2016-04-01

    We describe options for the production of an intense photon beam at the CEBAF Hall D Tagger facility, needed for creating a high-quality secondary K 0 L delivered to the Hall D detector. The conceptual design for the Compact Photon Source apparatus is presented.

  11. Upwind Compact Finite Difference Schemes

    NASA Astrophysics Data System (ADS)

    Christie, I.

    1985-07-01

    It was shown by Ciment, Leventhal, and Weinberg ( J. Comput. Phys.28 (1978), 135) that the standard compact finite difference scheme may break down in convection dominated problems. An upwinding of the method, which maintains the fourth order accuracy, is suggested and favorable numerical results are found for a number of test problems.

  12. Adapted to roar: functional morphology of tiger and lion vocal folds.

    PubMed

    Klemuk, Sarah A; Riede, Tobias; Walsh, Edward J; Titze, Ingo R

    2011-01-01

    Vocal production requires active control of the respiratory system, larynx and vocal tract. Vocal sounds in mammals are produced by flow-induced vocal fold oscillation, which requires vocal fold tissue that can sustain the mechanical stress during phonation. Our understanding of the relationship between morphology and vocal function of vocal folds is very limited. Here we tested the hypothesis that vocal fold morphology and viscoelastic properties allow a prediction of fundamental frequency range of sounds that can be produced, and minimal lung pressure necessary to initiate phonation. We tested the hypothesis in lions and tigers who are well-known for producing low frequency and very loud roaring sounds that expose vocal folds to large stresses. In histological sections, we found that the Panthera vocal fold lamina propria consists of a lateral region with adipocytes embedded in a network of collagen and elastin fibers and hyaluronan. There is also a medial region that contains only fibrous proteins and hyaluronan but no fat cells. Young's moduli range between 10 and 2000 kPa for strains up to 60%. Shear moduli ranged between 0.1 and 2 kPa and differed between layers. Biomechanical and morphological data were used to make predictions of fundamental frequency and subglottal pressure ranges. Such predictions agreed well with measurements from natural phonation and phonation of excised larynges, respectively. We assume that fat shapes Panthera vocal folds into an advantageous geometry for phonation and it protects vocal folds. Its primary function is probably not to increase vocal fold mass as suggested previously. The large square-shaped Panthera vocal fold eases phonation onset and thereby extends the dynamic range of the voice.

  13. Dual folding pathways of an α /β protein from all-atom ab initio folding simulations

    NASA Astrophysics Data System (ADS)

    Lei, Hongxing; Wang, Zhi-Xiang; Wu, Chun; Duan, Yong

    2009-10-01

    Successful ab initio folding of proteins with both α-helix and β-sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any α /β proteins to within experimental error has yet to be reported. Here we demonstrate that it is an achievable goal to fold α /β proteins with a force field emphasizing the balance between the two major secondary structures. Using our newly developed force field, we conducted extensive ab initio folding simulations on an α /β protein full sequence design (FSD) employing both conventional molecular dynamics and replica exchange molecular dynamics in combination with a generalized-Born solvation model. In these simulations, the folding of FSD to the native state with high population (>64.2%) and high fidelity (Cα-Root Mean Square Deviation of 1.29 Å for the most sampled conformation when compared to the experimental structure) was achieved. The folding of FSD was found to follow two pathways. In the major pathway, the folding started from the formation of the helix. In the minor pathway, however, folding of the β-hairpin started first. Further examination revealed that the helix initiated from the C-terminus and propagated toward the N-terminus. The formation of the hydrophobic contacts coincided with the global folding. Therefore the hydrophobic force does not appear to be the driving force of the folding of this protein.

  14. The nature of protein folding pathways

    PubMed Central

    Englander, S. Walter; Mayne, Leland

    2014-01-01

    How do proteins fold, and why do they fold in that way? This Perspective integrates earlier and more recent advances over the 50-y history of the protein folding problem, emphasizing unambiguously clear structural information. Experimental results show that, contrary to prior belief, proteins are multistate rather than two-state objects. They are composed of separately cooperative foldon building blocks that can be seen to repeatedly unfold and refold as units even under native conditions. Similarly, foldons are lost as units when proteins are destabilized to produce partially unfolded equilibrium molten globules. In kinetic folding, the inherently cooperative nature of foldons predisposes the thermally driven amino acid-level search to form an initial foldon and subsequent foldons in later assisted searches. The small size of foldon units, ∼20 residues, resolves the Levinthal time-scale search problem. These microscopic-level search processes can be identified with the disordered multitrack search envisioned in the “new view” model for protein folding. Emergent macroscopic foldon–foldon interactions then collectively provide the structural guidance and free energy bias for the ordered addition of foldons in a stepwise pathway that sequentially builds the native protein. These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process. Additionally, these observations answer the “how” and the “why” questions. The protein folding pathway depends on the same foldon units and foldon–foldon interactions that construct the native structure. PMID:25326421

  15. 16 CFR Appendix F2 to Part 305 - Compact Clothes Washers

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 1 2012-01-01 2012-01-01 false Compact Clothes Washers F2 Appendix F2 to Part 305 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS RULE... Appendix F2 to Part 305—Compact Clothes Washers Range Information “Compact” includes all household...

  16. 16 CFR Appendix F2 to Part 305 - Compact Clothes Washers

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 16 Commercial Practices 1 2013-01-01 2013-01-01 false Compact Clothes Washers F2 Appendix F2 to Part 305 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS RULE... Appendix F2 to Part 305—Compact Clothes Washers Range Information “Compact” includes all household...

  17. 16 CFR Appendix F2 to Part 305 - Compact Clothes Washers

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 1 2011-01-01 2011-01-01 false Compact Clothes Washers F2 Appendix F2 to Part 305 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS RULE... Appendix F2 to Part 305—Compact Clothes Washers Range Information “Compact” includes all household...

  18. A Tracking Analysis of Compact Students within Level 1 of Their Higher Education Programmes

    ERIC Educational Resources Information Center

    Wakely, Katrina; Saunders, Danny

    2004-01-01

    This article presents a tracking analysis of level 1 undergraduates who entered the University of Glamorgan through the Compact schools initiative. The Compact initiative aims to widen access to higher education by encouraging young people from disadvantaged backgrounds to attend a range of preparatory activities and by offering lower entry…

  19. Petrofabric test of viscous folding theory

    NASA Astrophysics Data System (ADS)

    Onasch, Charles M.

    1984-06-01

    Compression and extension axes are deduced from quartz deformation lamellae in a quartzite and a graywacke folded into an asymetrical syncline. Deformation lamellae fabrics in the two sandstones are distinctly different. In the graywacke, regardless of bedding orientation or position on the fold, compression axes are normal or nearly normal to the axial planar rough cleavage. Extension axes generally lie in the cleavage plane, parallel to dip. In most quartzite samples, compression axes are parallel or subparallel to bedding, at high angles to the fold axis and extension axes are normal to bedding. Two samples from the very base of the formation indicate compression parallel to the fold axis with extension parallel to bedding, at high angles to the fold axis. One of these two shows both patterns. The lamellae fabric geometry in these two samples suggests the presence of a neutral surface in the quartzite. The lamellae-derived compression and extension axes are in good agreement with the buckling behavior of a viscous layer (quartzite) embedded in a less viscous medium (graywacke and shale below and shale and carbonate above).

  20. Computational and theoretical methods for protein folding.

    PubMed

    Compiani, Mario; Capriotti, Emidio

    2013-12-03

    A computational approach is essential whenever the complexity of the process under study is such that direct theoretical or experimental approaches are not viable. This is the case for protein folding, for which a significant amount of data are being collected. This paper reports on the essential role of in silico methods and the unprecedented interplay of computational and theoretical approaches, which is a defining point of the interdisciplinary investigations of the protein folding process. Besides giving an overview of the available computational methods and tools, we argue that computation plays not merely an ancillary role but has a more constructive function in that computational work may precede theory and experiments. More precisely, computation can provide the primary conceptual clues to inspire subsequent theoretical and experimental work even in a case where no preexisting evidence or theoretical frameworks are available. This is cogently manifested in the application of machine learning methods to come to grips with the folding dynamics. These close relationships suggested complementing the review of computational methods within the appropriate theoretical context to provide a self-contained outlook of the basic concepts that have converged into a unified description of folding and have grown in a synergic relationship with their computational counterpart. Finally, the advantages and limitations of current computational methodologies are discussed to show how the smart analysis of large amounts of data and the development of more effective algorithms can improve our understanding of protein folding.

  1. Protein Folding and Mechanisms of Proteostasis

    PubMed Central

    Díaz-Villanueva, José Fernando; Díaz-Molina, Raúl; García-González, Victor

    2015-01-01

    Highly sophisticated mechanisms that modulate protein structure and function, which involve synthesis and degradation, have evolved to maintain cellular homeostasis. Perturbations in these mechanisms can lead to protein dysfunction as well as deleterious cell processes. Therefore in recent years the etiology of a great number of diseases has been attributed to failures in mechanisms that modulate protein structure. Interconnections among metabolic and cell signaling pathways are critical for homeostasis to converge on mechanisms associated with protein folding as well as for the preservation of the native structure of proteins. For instance, imbalances in secretory protein synthesis pathways lead to a condition known as endoplasmic reticulum (ER) stress which elicits the adaptive unfolded protein response (UPR). Therefore, taking this into consideration, a key part of this paper is developed around the protein folding phenomenon, and cellular mechanisms which support this pivotal condition. We provide an overview of chaperone protein function, UPR via, spatial compartmentalization of protein folding, proteasome role, autophagy, as well as the intertwining between these processes. Several diseases are known to have a molecular etiology in the malfunction of mechanisms responsible for protein folding and in the shielding of native structure, phenomena which ultimately lead to misfolded protein accumulation. This review centers on our current knowledge about pathways that modulate protein folding, and cell responses involved in protein homeostasis. PMID:26225966

  2. A sweet code for glycoprotein folding.

    PubMed

    Caramelo, Julio J; Parodi, Armando J

    2015-11-14

    Glycoprotein synthesis is initiated in the endoplasmic reticulum (ER) lumen upon transfer of a glycan (Glc3Man9GlcNAc2) from a lipid derivative to Asn residues (N-glycosylation). N-Glycan-dependent quality control of glycoprotein folding in the ER prevents exit to Golgi of folding intermediates, irreparably misfolded glycoproteins and incompletely assembled multimeric complexes. It also enhances folding efficiency by preventing aggregation and facilitating formation of proper disulfide bonds. The control mechanism essentially involves four components, resident lectin-chaperones (calnexin and calreticulin) that recognize monoglucosylated polymannose protein-linked glycans, lectin-associated oxidoreductase acting on monoglucosylated glycoproteins (ERp57), a glucosyltransferase that creates monoglucosylated epitopes in protein-linked glycans (UGGT) and a glucosidase (GII) that removes the glucose units added by UGGT. This last enzyme is the only mechanism component sensing glycoprotein conformations as it creates monoglucosylated glycans exclusively in not properly folded glycoproteins or in not completely assembled multimeric glycoprotein complexes. Glycoproteins that fail to properly fold are eventually driven to proteasomal degradation in the cytosol following the ER-associated degradation pathway, in which the extent of N-glycan demannosylation by ER mannosidases play a relevant role in the identification of irreparably misfolded glycoproteins.

  3. Equilibrium unfolding of Escherichia coli ribonuclease H: characterization of a partially folded state.

    PubMed Central

    Dabora, J. M.; Marqusee, S.

    1994-01-01

    We have examined the equilibrium unfolding of Escherichia coli ribonuclease HI (RNase H), a member of a family of enzymes that cleaves RNA from RNA:DNA hybrids. A completely synthetic gene was constructed that expresses a variant of the wild-type sequence with all 3 cysteines replaced with alanine. The resulting recombinant protein is active and folds reversibly. Denaturation studies monitored by circular dichroism and tryptophan fluorescence yield coincident curves that suggest the equilibrium unfolding reaction is a 2-state process. Acid denaturation, however, reveals a cooperative transition at approximately pH 1.8 to a partially folded state. This acid state can be further denatured in a reversible manner by the addition of heat or urea as monitored by either CD or tryptophan fluorescence. Analytical ultracentrifugation studies indicate that the acid state of RNase H is both compact and monomeric. Although compact, the acid state does not resemble the native protein: the acid state displays a near-UV CD spectrum similar to the unfolded state and binds to and enhances the fluorescence of the dye 1-anilinonaphthalene, 8-sulfonate much more than either the native or unfolded states. Therefore, the acid state of E. coli RNase H has the characteristics of a molten globule: it retains a high degree of secondary structure, remains compact, yet does not appear to contain a tightly packed core. PMID:7833802

  4. Proteopedia: Rossmann Fold: A Beta-Alpha-Beta Fold at Dinucleotide Binding Sites

    ERIC Educational Resources Information Center

    Hanukoglu, Israel

    2015-01-01

    The Rossmann fold is one of the most common and widely distributed super-secondary structures. It is composed of a series of alternating beta strand (ß) and alpha helical (a) segments wherein the ß-strands are hydrogen bonded forming a ß-sheet. The initial beta-alpha-beta (ßaß) fold is the most conserved segment of Rossmann folds. As this segment…

  5. Palaeomagnetic analysis of plunging fold structures: Errors and a simple fold test

    NASA Astrophysics Data System (ADS)

    Stewart, Simon A.

    1995-02-01

    The conventional corrections for bedding dip in palaeomagnetic studies involve either untilting about strike or about some inclined axis—the choice is usually governed by the perceived fold hinge orientation. While it has been recognised that untilting bedding about strike can be erroneous if the beds lie within plunging fold structures, there are several types of fold which have plunging hinges, but whose limbs have rotated about horizontal axes. Examples are interference structures and forced folds; restoration about inclined axes may be incorrect in these cases. The angular errors imposed upon palaeomagnetic lineation data via the wrong choice of rotation axis during unfolding are calculated here and presented for lineations in any orientation which could be associated with an upright, symmetrical fold. This extends to palaeomagnetic data previous analyses which were relevant to bedding-parallel lineations. This numerical analysis highlights the influence of various parameters which describe fold geometry and relative lineation orientation upon the angular error imparted to lineation data by the wrong unfolding method. The effect of each parameter is described, and the interaction of the parameters in producing the final error is discussed. Structural and palaeomagnetic data are cited from two field examples of fold structures which illustrate the alternative kinematic histories. Both are from thin-skinned thrust belts, but the data show that one is a true plunging fold, formed by rotation about its inclined hinge, whereas the other is an interference structure produced by rotation of the limbs about non-parallel horizontal axes. Since the angle between the palaeomagnetic lineations and the inclined fold hinge is equal on both limbs in the former type of structure, but varies from limb to limb in the latter, a simple test can be defined which uses palaeomagnetic lineation data to identify rotation axes and hence fold type. This test can use pre- or syn-folding

  6. Magnetic Bunch Compression for a Compact Compton Source

    SciTech Connect

    Gamage, B.; Satogata, Todd J.

    2013-12-01

    A compact electron accelerator suitable for Compton source applications is in design at the Center for Accelerator Science at Old Dominion University and Jefferson Lab. Here we discuss two options for transverse magnetic bunch compression and final focus, each involving a 4-dipole chicane with M_{56} tunable over a range of 1.5-2.0m with independent tuning of final focus to interaction point $\\beta$*=5mm. One design has no net bending, while the other has net bending of 90 degrees and is suitable for compact corner placement.

  7. Compact networked radars for Army unattended ground sensors

    NASA Astrophysics Data System (ADS)

    Wikner, David A.; Viveiros, Edward A.; Wellman, Ronald; Clark, John; Kurtz, Jim; Pulskamp, Jeff; Proie, Robert; Ivanov, Tony; Polcawich, Ronald G.; Adler, Eric D.

    2010-04-01

    The Army Research Laboratory is in partnership with the University of Florida - Electronics Communications Laboratory to develop compact radar technology and demonstrate that it is scalable to a variety of ultra-lightweight platforms (<10 lbs.) to meet Army mission needs in persistent surveillance, unattended ground sensor (UGS), unmanned systems, and man-portable sensor applications. The advantage of this compact radar is its steerable beam technology and relatively long-range capability compared to other small, battery-powered radar concepts. This paper will review the ongoing development of the sensor and presents a sample of the collected data thus far.

  8. High Impact Technology Compact Combustion (HITCC) Compact Core Technologies

    DTIC Science & Technology

    2016-01-01

    correlation as the chemical “timescale.” The resulting correlation equation is Eq 22. Including laminar flame speed improved the R-squared value from...including: 1) ultra-compact combustors, 2) inter-turbine burner concepts, 3) bluff-body stabilized turbulent flames, 4) well-stirred reactors for... chemical kinetics, and 5) detonation-stabilized turbulent flames. Lean blowout data was collected on propane and jet fuel bluff-body stabilized flames

  9. Folding a protein by discretizing its backbone torsional dynamics

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel

    1999-05-01

    The aim of this work is to provide a coarse codification of local conformational constraints associated with each folding motif of a peptide chain in order to obtain a rough solution to the protein folding problem. This is accomplished by implementing a discretized version of the soft-mode dynamics on a personal computer (PC). Our algorithm mimics a parallel process as it evaluates concurrent folding possibilities by pattern recognition. It may be implemented in a PC as a sequence of perturbation-translation-renormalization (p-t-r) cycles performed on a matrix of local topological constraints (LTM). This requires suitable representational tools and a periodic quenching of the dynamics required for renormalization. We introduce a description of the peptide chain based on a local discrete variable the values of which label the basins of attraction of the Ramachandran map for each residue. Thus, the local variable indicates the basin in which the torsional coordinates of each residue lie at a given time. In addition, a coding of local topological constraints associated with each secondary and tertiary structural motif is introduced. Our treatment enables us to adopt a computation time step of 81 ps, a value far larger than hydrodynamic drag time scales. Folding pathways are resolved as transitions between patterns of locally encoded structural signals that change within the 10 μs-100 ms time scale range. These coarse folding pathways are generated by the periodic search for structural patterns in the time-evolving LTM. Each pattern is recorded as a contact matrix, an operation subject to a renormalization feedback loop. The validity of our approach is tested vis-a-vis experimentally-probed folding pathways eventually generating tertiary interactions in proteins which recover their active structure under in vitro renaturation conditions. As an illustration, we focus on determining significant folding intermediates and late kinetic bottlenecks that occur within the

  10. Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand.

    PubMed

    Chang, Yu-Chu; Oas, Terrence G

    2010-06-29

    Understanding the interconversion between thermodynamically distinguishable states present in a protein folding pathway provides not only the kinetics and energetics of protein folding but also insights into the functional roles of these states in biological systems. The protein component of the bacterial RNase P holoenzyme from Bacillus subtilis (P protein) was previously shown to be unfolded in the absence of its cognate RNA or other anionic ligands. P protein was used in this study as a model system to explore general features of intrinsically disordered protein (IDP) folding mechanisms. The use of trimethylamine N-oxide (TMAO), an osmolyte that stabilizes the unliganded folded form of the protein, enabled us to study the folding process of P protein in the absence of ligand. Transient stopped-flow kinetic traces at various final TMAO concentrations exhibited multiphasic kinetics. Equilibrium "cotitration" experiments were performed using both TMAO and urea during the titration to produce a urea-TMAO titration surface of P protein. Both kinetic and equilibrium studies show evidence of a previously undetected intermediate state in the P protein folding process. The intermediate state is significantly populated, and the folding rate constants are relatively slow compared to those of intrinsically folded proteins similar in size and topology. The experiments and analysis described serve as a useful example for mechanistic folding studies of other IDPs.

  11. Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

    NASA Astrophysics Data System (ADS)

    Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros mountains extends over 1800 km from Kurdistan in N-Iraq to the Strait of Hormuz in Iran and is one of the world most promising regions for the future hydrocarbon exploration. The Zagros Mountains started to form as a result of the collision between the Eurasian and Arabian Plates, whose convergence began in the Late Cretaceous as part of the Alpine-Himalayan orogenic system. Geodetic and seismological data document that both plates are still converging and that the fold and thrust belt of the Zagros is actively growing. Extensive hydrocarbon exploration mainly focuses on the antiforms of this fold and thrust belt and therefore the growth history of the folds is of great importance. This work investigates by means of structural field work and quantitative geomorphological techniques the progressive fold growth of the Permam, Bana Bawi- and Safeen- Anticlines located in the NE of the city of Erbil in the Kurdistan region of Northern Iraq. This part of the Zagros fold and thrust belt belongs to the so-called Simply Folded Belt, which is dominated by gentle to open folding. Faults or fault related folds have only minor importance. The mechanical anisotropy of the formations consisting of a succession of relatively competent (massive dolomite and limestone) and incompetent (claystone and siltstone) sediments essentially controls the deformation pattern with open to gentle parallel folding of the competent layers and flexural flow folding of the incompetent layers. The characteristic wavelength of the fold trains is around 10 km. Due to faster erosion of the softer rock layers in the folded sequence, the more competent lithologies form sharp ridges with steeply sloping sides along the eroded flanks of the anticlines. Using an ASTER digital elevation model in combination with geological field data we quantified 250 drainage basins along the different limbs of the subcylindrical Permam, Bana Bawi- and Safeen- Anticlines. Geomorphological indices of the drainage

  12. Transversal Clifford gates on folded surface codes

    SciTech Connect

    Moussa, Jonathan E.

    2016-10-12

    Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surface codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. Lastly, the specific application of these codes to universal quantum computation based on qubit fusion is also discussed.

  13. Transversal Clifford gates on folded surface codes

    DOE PAGES

    Moussa, Jonathan E.

    2016-10-12

    Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surfacemore » codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. Lastly, the specific application of these codes to universal quantum computation based on qubit fusion is also discussed.« less

  14. Exact folded-band chaotic oscillator.

    PubMed

    Corron, Ned J; Blakely, Jonathan N

    2012-06-01

    An exactly solvable chaotic oscillator with folded-band dynamics is shown. The oscillator is a hybrid dynamical system containing a linear ordinary differential equation and a nonlinear switching condition. Bounded oscillations are provably chaotic, and successive waveform maxima yield a one-dimensional piecewise-linear return map with segments of both positive and negative slopes. Continuous-time dynamics exhibit a folded-band topology similar to Rössler's oscillator. An exact solution is written as a linear convolution of a fixed basis pulse and a discrete binary sequence, from which an equivalent symbolic dynamics is obtained. The folded-band topology is shown to be dependent on the symbol grammar.

  15. Thermal stability of idealized folded carbyne loops

    PubMed Central

    2013-01-01

    Self-unfolding items provide a practical convenience, wherein ring-like frames are contorted into a state of equilibrium and subsequently  pop up’ or deploy when perturbed from a folded structure. Can the same process be exploited at the molecular scale? At the limiting scale is a closed chain of single atoms, used here to investigate the limits of stability of such folded ring structures via full atomistic molecular dynamics. Carbyne is a one-dimensional carbon allotrope composed of sp-hybridized carbon atoms. Here, we explore the stability of idealized carbyne loops as a function of chain length, curvature, and temperature, and delineate an effective phase diagram between folded and unfolded states. We find that while overall curvature is reduced, in addition to torsional and self-adhesive energy barriers, a local increase in curvature results in the largest impedance to unfolding. PMID:24252156

  16. The early folding kinetics of apomyoglobin.

    PubMed Central

    Pappu, R. V.; Weaver, D. L.

    1998-01-01

    The folding pathway of apomyoglobin has been experimentally shown to have early kinetic intermediates involving the A, B, G, and H helices. The earliest detected kinetic events occur on a ns to micros time scale. We show that the early folding kinetics of apomyoglobin may be understood as the association of nascent helices through a network of diffusion-collision-coalescence steps G + H <--> GH + A <--> AGH + B <--> ABGH obtained by solving the diffusion-collision model in a chemical kinetics approximation. Our reproduction of the experimental results indicates that the model is a useful way to analyze folding data. One prediction from our fit is that the nascent A and H helices should be relatively more helix-like before coalescence than the other apomyoglobin helices. PMID:9521125

  17. Transversal Clifford gates on folded surface codes

    NASA Astrophysics Data System (ADS)

    Moussa, Jonathan E.

    2016-10-01

    Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surface codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. The specific application of these codes to universal quantum computation based on qubit fusion is also discussed.

  18. Microbial Manipulation of the Amyloid Fold

    PubMed Central

    DePas, William H.

    2012-01-01

    Microbial biofilms are encased in a protein, DNA and polysaccharide matrix that protects the community, promotes interactions with the environment, and helps cells to adhere together. The protein component of these matrices is often a remarkably stable, β-sheet-rich polymer called amyloid. Amyloids form ordered, self-templating fibers that are highly aggregative, making them a valuable biofilm component. Some eukaryotic proteins inappropriately adopt the amyloid fold and these misfolded protein aggregates disrupt normal cellular proteostasis, which can cause significant cytotoxicity. Indeed, until recently amyloids were considered solely the result of protein misfolding. However, research over the past decade has revealed how various organisms have capitalized on the amyloid fold by developing sophisticated biogenesis pathways that coordinate gene expression, protein folding, and secretion so that amyloid-related toxicities are minimized. How microbes manipulate amyloids, by augmenting their advantageous properties and by reducing their undesirable properties, will be the subject of this review. PMID:23108148

  19. Learning To Fold Proteins Using Energy Landscape Theory

    PubMed Central

    Schafer, N.P.; Kim, B.L.; Zheng, W.; Wolynes, P.G.

    2014-01-01

    This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy landscape theory of protein folding. We also present a review of the results of the AMH/AMC/AMW/AWSEM family of coarse-grained molecular dynamics protein folding models to illustrate the points covered in the first part of the article. Accurate coarse-grained structure prediction models can be used to investigate a wide range of conceptual and mechanistic issues outside of protein structure prediction; specifically, the paper concludes by reviewing how AWSEM has in recent years been able to elucidate questions related to the unusual kinetic behavior of artificially designed proteins, multidomain protein misfolding, and the initial stages of protein aggregation. PMID:25308991

  20. Two-mirror optical system with a small fold mirror

    NASA Astrophysics Data System (ADS)

    Liu, Xinping; Li, Yingcai; Yang, Jianfeng

    1998-09-01

    A new configuration of two-mirror optical system with a small fold mirror is presented in this paper. Consisting of a concave (positive power) primary mirror followed by a small flat mirror, a concave (positive power) secondary mirror, four lenses and a beam splitter, it gives the excellent image quality. A 1.5-m EFL, F/10 system of the upper configuration is designed over the 4 degree(s) field angle and 0.50 approximately 0.70 micrometers wavelength range. The aberrations have been highly corrected and the distortion is less than 0.3% over the field. The obscuration could be minimized by reducing primary radius of curvature and avoiding the spider that holds the small fold mirror.

  1. New approach to folding with the Coulomb wave function

    SciTech Connect

    Blokhintsev, L. D.; Savin, D. A.; Kadyrov, A. S.; Mukhamedzhanov, A. M.

    2015-05-15

    Due to the long-range character of the Coulomb interaction theoretical description of low-energy nuclear reactions with charged particles still remains a formidable task. One way of dealing with the problem in an integral-equation approach is to employ a screened Coulomb potential. A general approach without screening requires folding of kernels of the integral equations with the Coulomb wave. A new method of folding a function with the Coulomb partial waves is presented. The partial-wave Coulomb function both in the configuration and momentum representations is written in the form of separable series. Each term of the series is represented as a product of a factor depending only on the Coulomb parameter and a function depending on the spatial variable in the configuration space and the momentum variable if the momentum representation is used. Using a trial function, the method is demonstrated to be efficient and reliable.

  2. Gap engineering in strained fold-like armchair graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Torres, V.; León, C.; Faria, D.; Latgé, A.

    2017-01-01

    Strained fold-like deformations on armchair graphene nanoribbons (AGNRs) can be properly engineered in experimental setups, and could lead to a controlling tool for gaps and transport properties. Here, we analyze the electronic properties of folded AGNRs relating to the electronic responses and the mechanical deformation. An important and universal parameter for the gap engineering is the ribbon percent-width variation, i.e., the difference between the deformed and undeformed ribbon widths. AGNRs band gap can be tuned mechanically in a well-defined bounded range of energy values, eventually leading to a metallic system. This characteristic provides a controllable degree of freedom that allows manipulation of electronic currents. We show that the numerical results are analytically predicted by solving the Dirac equation for the strained system.

  3. Raytheon's next generation compact inline cryocooler architecture

    SciTech Connect

    Schaefer, B. R.; Bellis, L.; Ellis, M. J.; Conrad, T.

    2014-01-29

    Since the 1970s, Raytheon has developed, built, tested and integrated high performance cryocoolers. Our versatile designs for single and multi-stage cryocoolers provide reliable operation for temperatures from 10 to 200 Kelvin with power levels ranging from 50 W to nearly 600 W. These advanced cryocoolers incorporate clearance seals, flexure suspensions, hermetic housings and dynamic balancing to provide long service life and reliable operation in all relevant environments. Today, sensors face a multitude of cryocooler integration challenges such as exported disturbance, efficiency, scalability, maturity, and cost. As a result, cryocooler selection is application dependent, oftentimes requiring extensive trade studies to determine the most suitable architecture. To optimally meet the needs of next generation passive IR sensors, the Compact Inline Raytheon Stirling 1-Stage (CI-RS1), Compact Inline Raytheon Single Stage Pulse Tube (CI-RP1) and Compact Inline Raytheon Hybrid Stirling/Pulse Tube 2-Stage (CI-RSP2) cryocoolers are being developed to satisfy this suite of requirements. This lightweight, compact, efficient, low vibration cryocooler combines proven 1-stage (RS1 or RP1) and 2-stage (RSP2) cold-head architectures with an inventive set of warm-end mechanisms into a single cooler module, allowing the moving mechanisms for the compressor and the Stirling displacer to be consolidated onto a common axis and in a common working volume. The CI cryocooler is a significant departure from the current Stirling cryocoolers in which the compressor mechanisms are remote from the Stirling displacer mechanism. Placing all of the mechanisms in a single volume and on a single axis provides benefits in terms of package size (30% reduction), mass (30% reduction), thermodynamic efficiency (>20% improvement) and exported vibration performance (≤25 mN peak in all three orthogonal axes at frequencies from 1 to 500 Hz). The main benefit of axial symmetry is that proven balancing

  4. Raytheon's next generation compact inline cryocooler architecture

    NASA Astrophysics Data System (ADS)

    Schaefer, B. R.; Bellis, L.; Ellis, M. J.; Conrad, T.

    2014-01-01

    Since the 1970s, Raytheon has developed, built, tested and integrated high performance cryocoolers. Our versatile designs for single and multi-stage cryocoolers provide reliable operation for temperatures from 10 to 200 Kelvin with power levels ranging from 50 W to nearly 600 W. These advanced cryocoolers incorporate clearance seals, flexure suspensions, hermetic housings and dynamic balancing to provide long service life and reliable operation in all relevant environments. Today, sensors face a multitude of cryocooler integration challenges such as exported disturbance, efficiency, scalability, maturity, and cost. As a result, cryocooler selection is application dependent, oftentimes requiring extensive trade studies to determine the most suitable architecture. To optimally meet the needs of next generation passive IR sensors, the Compact Inline Raytheon Stirling 1-Stage (CI-RS1), Compact Inline Raytheon Single Stage Pulse Tube (CI-RP1) and Compact Inline Raytheon Hybrid Stirling/Pulse Tube 2-Stage (CI-RSP2) cryocoolers are being developed to satisfy this suite of requirements. This lightweight, compact, efficient, low vibration cryocooler combines proven 1-stage (RS1 or RP1) and 2-stage (RSP2) cold-head architectures with an inventive set of warm-end mechanisms into a single cooler module, allowing the moving mechanisms for the compressor and the Stirling displacer to be consolidated onto a common axis and in a common working volume. The CI cryocooler is a significant departure from the current Stirling cryocoolers in which the compressor mechanisms are remote from the Stirling displacer mechanism. Placing all of the mechanisms in a single volume and on a single axis provides benefits in terms of package size (30% reduction), mass (30% reduction), thermodynamic efficiency (>20% improvement) and exported vibration performance (≤25 mN peak in all three orthogonal axes at frequencies from 1 to 500 Hz). The main benefit of axial symmetry is that proven balancing

  5. Dynamic Hysteresis in Compacted Magnetic Nanoparticles

    NASA Astrophysics Data System (ADS)

    Chowdary, Krishna M.

    The frequency and temperature dependent magnetic response of a bulk soft magnetic nanocomposite made by compacting Fe10Co 90 nanoparticles was measured and modeled. Electron microscopy and x-ray diffraction were used to characterize the size, composition, and structure of the nanoparticles and nanocomposite. Polyol synthesis was used to produce 200 nm particles with average grain size 20 nm and large superparamagnetic fraction. The nanoparticles were consolidated to 90% theoretical density by plasma pressure compaction. The compacted nanoparticles retained the 20 nm average grain size and large superparamagnetic fraction. The nanocomposite resistivity was more than three times that of the bulk alloy. Vibrating sample and SQUID-MPMS magnetometers were used for low frequency magnetic measurements of the nanoparticles and nanocomposite. Compaction reduced the coercivity from 175 Oe to 8 Oe and the effective anisotropy from 124 x 10 3 ergs/cc to 7.9 x 103 ergs/cc. These reductions were caused by increased exchange coupling between surface nanograins, consistent with predictions from the Random Anisotropy model. Varying degrees of exchange coupling existed within the nanocomposite, contributing to a distribution of energy barriers. A permeameter was used for frequency dependent magnetic measurements on a toroid cut from the nanocomposite. Complex permeability, coercivity, and power loss were extracted from dynamic minor hysteresis loops measured over a range of temperatures (77 K - 873 K) and frequencies (0.1 kHz - 100 kHz). The real and imaginary parts of the complex permeability spectrum showed asymmetries consistent with a distribution of energy barriers and high damping. When the complex permeability, power loss, and coercivity were scaled relative to the peak frequency of the imaginary permeability, all fell on universal curves. Various microscopic and macroscopic models for the complex permeability were investigated. The complex permeability was successfully fit

  6. Compaction of Norphlet sandstones, Rankin County, Mississippi

    SciTech Connect

    McBride, E.F.

    1987-09-01

    Fabric and porosity changes resulting from compaction were studied in sandstones from three cores sampled at depths between 15,900 and 22,500 ft. Point counts of 30 thin sections indicate that 0.4% of the rock volume was lost by ductile grain deformation and 3% by pressure solution at both grain contacts and at widely spaced stylolites. Pre-cement porosities of eolian sandstone range from 27 to 35% (mean = 29%), indicating that a total of from 10 to 18% porosity (mean = 16%) was lost by compaction (assuming 45% initial porosity). The difference between the total porosity loss and the sum of the other two processes is assumed to be the porosity lost by grain rearrangement (mean = 12.6%). The amount of pressure solution at grain contacts for each well is independent of depth, temperature, and amount of both quartz cement and total cement. Stylolites transect both grains and cements, which indicates they formed late in the diagenetic sequence. Silica released by pressure solution at quartz grain contacts could not be the sole source and was probably not even the major source of quartz cement in the formation, because cementation by quartz preceded the episode of strong pressure solution. In addition, the volume of silica released by pressure solution appears to have been inadequate to provide the volume of quartz cement present.

  7. Pyroflow Compact: The next generation CFB boiler

    SciTech Connect

    Darling, S.L.

    1995-12-31

    CFB technology is the modern way to burn coal and other solid fuels. This technology was specifically developed to address today`s needs for fuel flexibility and low emissions. The low furnace temperatures characteristic of CFB technology provide for (a) low NO{sub x} emissions, (b) low SO{sub 2} emissions via simple furnace limestone injection and (c) the ability to fire a wide range of fuels because slagging is avoided. Lack of pulverizers and stack gas scrubbers results in a simple design with low maintenance costs and high availability. Ahlstrom, responsible for many innovations in CFB technology, has recently developed an improved CFB boiler design called the Pyroflow Compact. This new design retains all the benefits of the proven AHLSTROM PYROFLOW{reg_sign}CFB boiler while providing many advantages. This paper will describe the design features of the new Pyroflow Compact design, the advantages of this new design, operating experience, an up-to-date list of projects and Ahlstrom`s future plans for the new design.

  8. Computational analysis of hydrogenated graphyne folding

    NASA Astrophysics Data System (ADS)

    Lenear, Christopher; Becton, Matthew; Wang, Xianqiao

    2016-02-01

    This letter employs molecular mechanics simulations to analyze the geometric changes of foreign-atom-doped graphyne. Simulation results show that higher the density of dopant and the greater area covered by the dopant correlates to a greater folding angle of the graphyne sheet. Compared to graphene, graphyne folding could prove to be more effective for various nanodevices based on its unique band gap, especially when doped, and its tunable interactions with and absorption of foreign molecules. Therefore, our findings may offer unique perspectives into the development of novel graphyne-based nanodevices and stimulate the community's research interest in graphene-related origami.

  9. FOLD LENS FLUX ANOMALIES: A GEOMETRIC APPROACH

    SciTech Connect

    Goldberg, David M.; Chessey, Mary K.; Harris, Wendy B.; Richards, Gordon T.

    2010-06-01

    We develop a new approach for studying flux anomalies in quadruply imaged fold lens systems. We show that in the absence of substructure, microlensing, or differential absorption, the expected flux ratios of a fold pair can be tightly constrained using only geometric arguments. We apply this technique to 11 known quadruple lens systems in the radio and infrared and compare our estimates to the Monte Carlo based results of Keeton et al. We show that a robust estimate for a flux ratio from a smoothly varying potential can be found, and at long wavelengths those lenses deviating from this ratio almost certainly contain significant substructure.

  10. Fold Lens Flux Anomalies: A Geometric Approach

    NASA Astrophysics Data System (ADS)

    Goldberg, David M.; Chessey, Mary K.; Harris, Wendy B.; Richards, Gordon T.

    2010-06-01

    We develop a new approach for studying flux anomalies in quadruply imaged fold lens systems. We show that in the absence of substructure, microlensing, or differential absorption, the expected flux ratios of a fold pair can be tightly constrained using only geometric arguments. We apply this technique to 11 known quadruple lens systems in the radio and infrared and compare our estimates to the Monte Carlo based results of Keeton et al. We show that a robust estimate for a flux ratio from a smoothly varying potential can be found, and at long wavelengths those lenses deviating from this ratio almost certainly contain significant substructure.

  11. Circular permutant GFP insertion folding reporters

    SciTech Connect

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16

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

  12. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2008-06-24

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

  13. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12

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

  14. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2011-06-14

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

  15. The lack of large compact symmetric objects

    NASA Astrophysics Data System (ADS)

    Augusto, P.

    2009-02-01

    In recent years, `baby' (< 103 yr) and `young' (103-105 yr) radio galaxies have been found and classified, although their numbers are still small (tens). Also, they have many different names, depending on the type of survey and scientific context in which they were found: compact steep spectrum sources (CSS), giga-Hertz peaked spectrum sources (GPS) and compact-medium symmetric objects (C-MSO). The latter have the radio galaxy structure more obvious and correspond to the `babies' (CSOs; < 1 kpc) and `young' (MSOs; 1-15 kpc) radio galaxies. The log-size distribution of CSOs shows a sharp drop at 0.3 kpc. This trend continues through flat-spectrum MSOs (over the full 1-15 kpc size range). In order to find out if this lack of large CSOs and flat-spectrum MSOs is due to poor sampling (lack of surveys that probe efficiently the 0.3-15 kpc size range) and/or has physical meaning (e.g. if the lobes of CSOs expand as they grow and age, they might become CSSs, `disappearing' from the flat-spectrum MSO statistics), we have built a sample of 157 flat-spectrum radio sources with structure on ˜0.3-15 kpc scales. We are using new, archived and published data to produce and inspect hundreds of multi-frequency multi-instrument maps and models. We have already found 13 new secure CSO/MSOs. We expect to uncover ˜30-40 new CSOs and MSOs, most on the 0.3-15 kpc size range, when our project is complete.

  16. Invariant distributions on compact homogeneous spaces

    SciTech Connect

    Gorbatsevich, V V

    2013-12-31

    In this paper, we study distributions on compact homogeneous spaces, including invariant distributions and also distributions admitting a sub-Riemannian structure. We first consider distributions of dimension 1 and 2 on compact homogeneous spaces. After this, we study the cases of compact homogeneous spaces of dimension 2, 3, and 4 in detail. Invariant distributions on simply connected compact homogeneous spaces are also treated. Bibliography: 18 titles.

  17. Modulation of folding energy landscape by charge-charge interactions: linking experiments with computational modeling.

    PubMed

    Tzul, Franco O; Schweiker, Katrina L; Makhatadze, George I

    2015-01-20

    The kinetics of folding-unfolding of a structurally diverse set of four proteins optimized for thermodynamic stability by rational redesign of surface charge-charge interactions is characterized experimentally. The folding rates are faster for designed variants compared with their wild-type proteins, whereas the unfolding rates are largely unaffected. A simple structure-based computational model, which incorporates the Debye-Hückel formalism for the electrostatics, was used and found to qualitatively recapitulate the experimental results. Analysis of the energy landscapes of the designed versus wild-type proteins indicates the differences in refolding rates may be correlated with the degree of frustration of their respective energy landscapes. Our simulations indicate that naturally occurring wild-type proteins have frustrated folding landscapes due to the surface electrostatics. Optimization of the surface electrostatics seems to remove some of that frustration, leading to enhanced formation of native-like contacts in the transition-state ensembles (TSE) and providing a less frustrated energy landscape between the unfolded and TS ensembles. Macroscopically, this results in faster folding rates. Furthermore, analyses of pairwise distances and radii of gyration suggest that the less frustrated energy landscapes for optimized variants are a result of more compact unfolded and TS ensembles. These findings from our modeling demonstrates that this simple model may be used to: (i) gain a detailed understanding of charge-charge interactions and their effects on modulating the energy landscape of protein folding and (ii) qualitatively predict the kinetic behavior of protein surface electrostatic interactions.

  18. Principles of protein folding--a perspective from simple exact models.

    PubMed Central

    Dill, K. A.; Bromberg, S.; Yue, K.; Fiebig, K. M.; Yee, D. P.; Thomas, P. D.; Chan, H. S.

    1995-01-01

    General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics--fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse. PMID:7613459

  19. Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy

    PubMed Central

    Jones, Kevin C.; Peng, Chunte Sam; Tokmakoff, Andrei

    2013-01-01

    We provide a time- and structure-resolved characterization of the folding of the heterogeneous β-hairpin peptide Tryptophan Zipper 2 (Trpzip2) using 2D IR spectroscopy. The amide I′ vibrations of three Trpzip2 isotopologues are used as a local probe of the midstrand contacts, β-turn, and overall β-sheet content. Our experiments distinguish between a folded state with a type I′ β-turn and a misfolded state with a bulged turn, providing evidence for distinct conformations of the peptide backbone. Transient 2D IR spectroscopy at 45 °C following a laser temperature jump tracks the nanosecond and microsecond kinetics of unfolding and the exchange between conformers. Hydrogen bonds to the peptide backbone are loosened rapidly compared with the 5-ns temperature jump. Subsequently, all relaxation kinetics are characterized by an observed 1.2 ± 0.2-μs exponential. Our time-dependent 2D IR spectra are explained in terms of folding of either native or nonnative contacts from a common compact disordered state. Conversion from the disordered state to the folded state is consistent with a zip-out folding mechanism. PMID:23382249

  20. Compact Reversed-Field Pinch Reactors (CRFPR): preliminary engineering considerations

    SciTech Connect

    Hagenson, R.L.; Krakowski, R.A.; Bathke, C.G.; Miller, R.L.; Embrechts, M.J.; Schnurr, N.M.; Battat, M.E.; LaBauve, R.J.; Davidson, J.W.

    1984-08-01

    The unique confinement physics of the Reversed-Field Pinch (RFP) projects to a compact, high-power-density fusion reactor that promises a significant reduction in the cost of electricity. The compact reactor also promises a factor-of-two reduction in the fraction of total cost devoted to the reactor plant equipment (i.e., fusion power core (FPC) plus support systems). In addition to operational and developmental benefits, these physically smaller systems can operate economically over a range of total power output. After giving an extended background and rationale for the compact fusion approaches, key FPC subsystems for the Compact RFP Reactor (CRFPR) are developed, designed, and integrated for a minimum-cost, 1000-MWe(net) system. Both the problems and promise of the compact, high-power-density fusion reactor are quantitatively evaluated on the basis of this conceptual design. The material presented in this report both forms a framework for a broader, more expanded conceptual design as well as suggests directions and emphases for related research and development.

  1. Dynamics of compact homogeneous universes

    SciTech Connect

    Tanimoto, M.; Koike, T.; Hosoya, A.

    1997-01-01

    A complete description of dynamics of compact locally homogeneous universes is given, which, in particular, includes explicit calculations of Teichm{umlt u}ller deformations and careful counting of dynamical degrees of freedom. We regard each of the universes as a simply connected four-dimensional space{endash}time with identifications by the action of a discrete subgroup of the isometry group. We then reduce the identifications defined by the space{endash}time isometries to ones in a homogeneous section, and find a condition that such spatial identifications must satisfy. This is essential for explicit construction of compact homogeneous universes. Some examples are demonstrated for Bianchi II, VI{sub 0}, VII{sub 0}, and I universal covers. {copyright} {ital 1997 American Institute of Physics.}

  2. Marginally compact hyperbranched polymer trees.

    PubMed

    Dolgushev, M; Wittmer, J P; Johner, A; Benzerara, O; Meyer, H; Baschnagel, J

    2017-03-29

    Assuming Gaussian chain statistics along the chain contour, we generate by means of a proper fractal generator hyperbranched polymer trees which are marginally compact. Static and dynamical properties, such as the radial intrachain pair density distribution ρpair(r) or the shear-stress relaxation modulus G(t), are investigated theoretically and by means of computer simulations. We emphasize that albeit the self-contact density diverges logarithmically with the total mass N, this effect becomes rapidly irrelevant with increasing spacer length S. In addition to this it is seen that the standard Rouse analysis must necessarily become inappropriate for compact objects for which the relaxation time τp of mode p must scale as τp ∼ (N/p)(5/3) rather than the usual square power law for linear chains.

  3. Compact portable diffraction moire interferometer

    DOEpatents

    Deason, Vance A.; Ward, Michael B.

    1989-01-01

    A compact and portable moire interferometer used to determine surface deformations of an object. The improved interferometer is comprised of a laser beam, optical and fiber optics devices coupling the beam to one or more evanescent wave splitters, and collimating lenses directing the split beam at one or more specimen gratings. Observation means including film and video cameras may be used to view and record the resultant fringe patterns.

  4. Compact portable diffraction moire interferometer

    DOEpatents

    Deason, V.A.; Ward, M.B.

    1988-05-23

    A compact and portable moire interferometer used to determine surface deformations of an object. The improved interferometer is comprised of a laser beam, optical and fiber optics devices coupling the beam to one or more evanescent wave splitters, and collimating lenses directing the split beam at one or more specimen gratings. Observations means including film and video cameras may be used to view and record the resultant fringe patterns. 7 figs.

  5. Compaction of Global Data Fields

    DTIC Science & Technology

    1990-05-01

    AD- A225 856 Naval Oceanographic and Technical Note 27 Atmospheric Research Laboratory May 1990 nC II FILF Copy Compaction of Global Data Fields A. H...IU 0 Ij P\\ I -’ as - -O - - YrŘ 5/ ii Ch Cc I 4" IIJ /1 1 att, 14 o c qu 0 in 64 low Ln u Ln U Ln LLJ KA E0 U-j u odd LD x 0 LL- cr - -1 Ap 0 Ln 00

  6. Compact magnetic energy storage module

    DOEpatents

    Prueitt, Melvin L.

    1994-01-01

    A superconducting compact magnetic energy storage module in which a plurality of superconducting toroids, each having a toroidally wound superconducting winding inside a poloidally wound superconducting winding, are stacked so that the flow of electricity in each toroidally wound superconducting winding is in a direction opposite from the direction of electrical flow in other contiguous superconducting toroids. This allows for minimal magnetic pollution outside of the module.

  7. Compact optical microfiber phase modulator.

    PubMed

    Zhang, Xueliang; Belal, M; Chen, G Y; Song, Zhangqi; Brambilla, G; Newson, T P

    2012-02-01

    A compact optical microfiber phase modulator with MHz bandwidth is presented. A micrometer-diameter microfiber is wound on a millimeter-diameter piezoelectric ceramic rod with two electrodes. When a voltage is applied to the piezoelectric ceramic, the rod is strained, leading to a phase change along the microfiber; because of the small size, the optical microfiber phase modulator can have as high as a few MHz bandwidth response.

  8. Nuclear Physics for Compact Stars

    SciTech Connect

    Baldo, M.

    2009-05-04

    A brief overview is given of the different lines of research developed under the INFN project 'Compact Stellar Objects and Dense Hadronic Matter' (acronym CT51). The emphasis of the project is on the structure of Neutron Stars (NS) and related objects. Starting from crust, the different Nuclear Physics problems are described which are encountered going inside a NS down to its inner core. The theoretical challenges and the observational inputs are discussed in some detail.

  9. COMB: Compact embedded object simulations

    NASA Astrophysics Data System (ADS)

    McEwen, Jason D.

    2016-06-01

    COMB supports the simulation on the sphere of compact objects embedded in a stochastic background process of specified power spectrum. Support is provided to add additional white noise and convolve with beam functions. Functionality to support functions defined on the sphere is provided by the S2 code (ascl:1606.008); HEALPix (ascl:1107.018) and CFITSIO (ascl:1010.001) are also required.

  10. Compact magnetic energy storage module

    DOEpatents

    Prueitt, M.L.

    1994-12-20

    A superconducting compact magnetic energy storage module in which a plurality of superconducting toroids, each having a toroidally wound superconducting winding inside a poloidally wound superconducting winding, are stacked so that the flow of electricity in each toroidally wound superconducting winding is in a direction opposite from the direction of electrical flow in other contiguous superconducting toroids. This allows for minimal magnetic pollution outside of the module. 4 figures.

  11. Compact planar microwave blocking filters

    NASA Technical Reports Server (NTRS)

    U-Yen, Kongpop (Inventor); Wollack, Edward J. (Inventor)

    2012-01-01

    A compact planar microwave blocking filter includes a dielectric substrate and a plurality of filter unit elements disposed on the substrate. The filter unit elements are interconnected in a symmetrical series cascade with filter unit elements being organized in the series based on physical size. In the filter, a first filter unit element of the plurality of filter unit elements includes a low impedance open-ended line configured to reduce the shunt capacitance of the filter.

  12. Structure and folding of the Tetrahymena telomerase RNA pseudoknot

    PubMed Central

    Cash, Darian D.; Feigon, Juli

    2017-01-01

    Telomerase maintains telomere length at the ends of linear chromosomes using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). An essential part of TER is the template/pseudoknot domain (t/PK) which includes the template, for adding telomeric repeats, template boundary element (TBE), and pseudoknot, enclosed in a circle by stem 1. The Tetrahymena telomerase holoenzyme catalytic core (p65-TER-TERT) was recently modeled in our 9 Å resolution cryo-electron microscopy map by fitting protein and TER domains, including a solution NMR structure of the Tetrahymena pseudoknot. Here, we describe in detail the structure and folding of the isolated pseudoknot, which forms a compact structure with major groove U•A-U and novel C•G-A+ base triples. Base substitutions that disrupt the base triples reduce telomerase activity in vitro. NMR studies also reveal that the pseudoknot does not form in the context of full-length TER in the absence of TERT, due to formation of a competing structure that sequesters pseudoknot residues. The residues around the TBE remain unpaired, potentially providing access by TERT to this high affinity binding site during an early step in TERT-TER assembly. A model for the assembly pathway of the catalytic core is proposed. PMID:27899638

  13. Self-folding polyhedra and analogies to biomolecular assembly

    NASA Astrophysics Data System (ADS)

    Pandey, Shivendra; Menon, Govind; Gracias, David

    2013-03-01

    We detail model studies aimed at uncovering design principles that govern the self-assembly of polyhedral structures from two-dimensional precursors using surface tension forces. For a given polyhedron, there are a very large number of two-dimensional precursor nets that can be utilized, and remarkably many of these will self-assemble but with varying yields. We uncovered design rules that suggest striking analogies to biomolecular assembly such as observed in proteins and viruses. For example our studies revealed that the compactness of two-dimensional nets determines the yield of self-folding polyhedra and that certain intermediates and pathways were preferred. Consequently, a search algorithm was implemented to screen the large numbers of nets (e.g. 2.3 million for the truncated octahedron) and find high-yielding precursors. This assembly process represents a model system that can be utilized to design and then visualize self-assembly processes. The model system, design rules and findings will be discussed.

  14. Compact Stellarator Path to DEMO

    NASA Astrophysics Data System (ADS)

    Lyon, J. F.

    2007-11-01

    Issues for a DEMO reactor are sustaining an ignited/high-Q plasma in steady state, avoiding disruptions and large variations in power flux to the wall, adequate confinement of thermal plasma and alpha-particles, control of a burning plasma, particle and power handling, etc. Compact stellarators have key advantages -- steady-state high-plasma-density operation without external current drive or disruptions, stability without a close conducting wall or active feedback systems, and low recirculating power -- in addition to moderate plasma aspect ratio, good confinement, and high-beta potential. The ARIES-CS study established that compact stellarators can be competitive with tokamaks as reactors. Many of the issues for a compact stellarator DEMO can be answered using results from large tokamaks, ITER D-T experiments and fusion materials, technology and component development programs, in addition to stellarators in operation, under construction or in development. However, a large next-generation stellarator will be needed to address some physics issues: size scaling and confinement at higher parameters, burning plasma issues, and operation with a strongly radiative divertor. Technology issues include simpler coils, structure, and divertor fabrication, and better cost information.

  15. Compaction with automatic jog introduction

    NASA Astrophysics Data System (ADS)

    Maley, F. M.

    1986-05-01

    This thesis presents an algorithm for one-dimensional compaction of VLSI layouts. It differs from older methods in treating wires not as objects to be moved, but as constraints on the positions of other circuit components. These constraints are determined for each wiring layer using the theory of planar routing. Assuming that the wiring layers can be treated independently, the algorithm minimizes the width of a layout, automatically inserting as many jogs in wires as necessary. It runs in time 0(n4) on input of size n. Several heuristics are suggested for improving the algorithm's practical performance. The compaction algorithm takes as input a data structure called a sketch, which explicitly distinguishes between flexible components (wires) and rigid components (modules). The algorithm first finds constraints on the positions of modules that ensure enough space is left for wires. Next, it solves the system of constraints by a standard graph-theoretic technique, obtaining a placement for the modules. It then relies on a single-layer router to restore the wires to each circuit layer. An efficient single-layer router is already known; it is able to minimize the length of every wire, though not the number of jogs. As given, the compaction algorithm applies only to a VLSI model that requires wires to run a rectilinear grid. This restriction is needed only because the theory of planar routing (and single-layer routers) has not yet been extended to other models.

  16. Fish larvae exploit edge vortices along their dorsal and ventral fin folds to propel themselves

    PubMed Central

    Müller, Ulrike K.; van Leeuwen, Johan L.

    2016-01-01

    Larvae of bony fish swim in the intermediate Reynolds number (Re) regime, using body- and caudal-fin undulation to propel themselves. They share a median fin fold that transforms into separate median fins as they grow into juveniles. The fin fold was suggested to be an adaption for locomotion in the intermediate Reynolds regime, but its fluid-dynamic role is still enigmatic. Using three-dimensional fluid-dynamic computations, we quantified the swimming trajectory from body-shape changes during cyclic swimming of larval fish. We predicted unsteady vortices around the upper and lower edges of the fin fold, and identified similar vortices around real larvae with particle image velocimetry. We show that thrust contributions on the body peak adjacent to the upper and lower edges of the fin fold where large left–right pressure differences occur in concert with the periodical generation and shedding of edge vortices. The fin fold enhances effective flow separation and drag-based thrust. Along the body, net thrust is generated in multiple zones posterior to the centre of mass. Counterfactual simulations exploring the effect of having a fin fold across a range of Reynolds numbers show that the fin fold helps larvae achieve high swimming speeds, yet requires high power. We conclude that propulsion in larval fish partly relies on unsteady high-intensity vortices along the upper and lower edges of the fin fold, providing a functional explanation for the omnipresence of the fin fold in bony-fish larvae. PMID:27009180

  17. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.

    PubMed

    Shimada, J; Kussell, E L; Shakhnovich, E I

    2001-04-20

    We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding, all side-chain and backbone torsions, and uses a Go potential. In this study, we focus on the 46 residue alpha/beta protein crambin and two of its structural components, the helix and helix hairpin. For a wide range of temperatures, we recorded multiple folding events of these three structures from random coils to native conformations that differ by less than 1 A C(alpha) dRMS from their crystal structure coordinates. The thermodynamics and kinetic mechanism of the helix-coil transition obtained from our simulation shows excellent agreement with currently available experimental and molecular dynamics data. Based on insights obtained from folding its smaller structural components, a possible folding mechanism for crambin is proposed. We observed that the folding occurs via a cooperative, first order-like process, and that many folding pathways to the native state exist. One particular sequence of events constitutes a "fast-folding" pathway where kinetic traps are avoided. At very low temperatures, a kinetic trap arising from the incorrect packing of side-chains was observed. These results demonstrate that folding to the native state can be observed in a reasonable amount of time on desktop computers even when an all-atom representation is used, provided the energetics sufficiently stabilize the native state.

  18. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    PubMed Central

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  19. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers.

    PubMed

    Mao, Yiqi; Yu, Kai; Isakov, Michael S; Wu, Jiangtao; Dunn, Martin L; Jerry Qi, H

    2015-09-08

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

  20. Fish larvae exploit edge vortices along their dorsal and ventral fin folds to propel themselves.

    PubMed

    Li, Gen; Müller, Ulrike K; van Leeuwen, Johan L; Liu, Hao

    2016-03-01

    Larvae of bony fish swim in the intermediate Reynolds number (Re) regime, using body- and caudal-fin undulation to propel themselves. They share a median fin fold that transforms into separate median fins as they grow into juveniles. The fin fold was suggested to be an adaption for locomotion in the intermediate Reynolds regime, but its fluid-dynamic role is still enigmatic. Using three-dimensional fluid-dynamic computations, we quantified the swimming trajectory from body-shape changes during cyclic swimming of larval fish. We predicted unsteady vortices around the upper and lower edges of the fin fold, and identified similar vortices around real larvae with particle image velocimetry. We show that thrust contributions on the body peak adjacent to the upper and lower edges of the fin fold where large left-right pressure differences occur in concert with the periodical generation and shedding of edge vortices. The fin fold enhances effective flow separation and drag-based thrust. Along the body, net thrust is generated in multiple zones posterior to the centre of mass. Counterfactual simulations exploring the effect of having a fin fold across a range of Reynolds numbers show that the fin fold helps larvae achieve high swimming speeds, yet requires high power. We conclude that propulsion in larval fish partly relies on unsteady high-intensity vortices along the upper and lower edges of the fin fold, providing a functional explanation for the omnipresence of the fin fold in bony-fish larvae.