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. Rapid compaction during RNA folding

    NASA Astrophysics Data System (ADS)

    Russell, Rick; Millett, Ian S.; Tate, Mark W.; Kwok, Lisa W.; Nakatani, Bradley; Gruner, Sol M.; Mochrie, Simon G. J.; Pande, Vijay; Doniach, Sebastian; Herschlag, Daniel; Pollack, Lois

    2002-04-01

    We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a time window of more than five orders of magnitude. A substantial phase of compaction is observed on the low millisecond timescale, and the overall compaction and global shape changes are largely complete within one second, earlier than any known tertiary contacts are formed. This finding indicates that the RNA forms a nonspecifically collapsed intermediate and then searches for its tertiary contacts within a highly restricted subset of conformational space. The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding.

  6. Lightweight, Compact, Long Range Camera Design

    NASA Astrophysics Data System (ADS)

    Shafer, Donald V.

    1983-08-01

    The model 700 camera is the latest in a 30-year series of LOROP cameras developed by McDonnell Douglas Astronautics Company (MDAC) and their predecessor companies. The design achieves minimum size and weight and is optimized for low-contrast performance. The optical system includes a 66-inch focal length, f/5.6, apochromatic lens and three folding mirrors imaging on a 4.5-inch square format. A three-axis active stabilization system provides the capability for long exposure time and, hence, fine grain films can be used. The optical path forms a figure "4" behind the lens. In front of the lens is a 45° pointing mirror. This folded configuration contributed greatly to the lightweight and compact design. This sequential autocycle frame camera has three modes of operation with one, two, and three step positions to provide a choice of swath widths within the range of lateral coverage. The magazine/shutter assembly rotates in relationship with the pointing mirror and aircraft drift angle to maintain film format alignment with the flight path. The entire camera is angular rate stabilized in roll, pitch, and yaw. It also employs a lightweight, electro-magnetically damped, low-natural-frequency spring suspension for passive isolation from aircraft vibration inputs. The combined film transport and forward motion compensation (FMC) mechanism, which is operated by a single motor, is contained in a magazine that can, depending on accessibility which is installation dependent, be changed in flight. The design also stresses thermal control, focus control, structural stiffness, and maintainability. The camera is operated from a remote control panel. This paper describes the leading particulars and features of the camera as related to weight and configuration.

  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, 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.

  9. 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.

  10. Nonlocal interactions stabilize compact folding intermediates in reduced unfolded bovine pancreatic trypsin inhibitor.

    PubMed

    Gottfried, D S; Haas, E

    1992-12-15

    To further our understanding of the protein folding process, it is desirable to examine the structural intermediates (equilibrium and kinetic) that are populated between the statistical coil state and the folded molecule. X-ray crystallography and NMR structural studies are unable to determine long-range distances in proteins under denaturing solution conditions. Nonradiative (Förster) energy transfer, however, has been shown to be a spectroscopic ruler for the measurement of distance distributions and diffusion between selected sites in proteins under a range of different solution conditions. The distributions of distances between a donor probe at the N-terminal residue and an acceptor attached to one of the four lysine residues (15, 26, 41, 46) of reduced and unfolded (in 6 M guanidine hydrochloride and 20 mM dithiothreitol) bovine pancreatic trypsin inhibitor (BPTI) were measured as a function of temperature. Even in strong denaturant and reducing agent, BPTI does not exist as a statistical coil polypeptide. It appears that nonlocal (long-range) interactions are already beginning to "fold" the protein toward a more compact, native conformation. As the temperature is increased under these conditions, hydrophobic interactions lead to an even more compact structure consistent with the predictions of phase diagrams for globular proteins. PMID:1281424

  11. 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.

  12. 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.

  13. Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments.

    PubMed

    Morrison, Greg; Hyeon, Changbong; Hinczewski, Michael; Thirumalai, D

    2011-04-01

    We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (P(fold)=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that P(fold) is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles. PMID:21517423

  14. Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments

    NASA Astrophysics Data System (ADS)

    Morrison, Greg; Hyeon, Changbong; Hinczewski, Michael; Thirumalai, D.

    2011-04-01

    We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (Pfold=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that Pfold is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles.

  15. 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.

  16. A dual chamber Gregorian subreflector system for compact range applications

    NASA Astrophysics Data System (ADS)

    Pistorius, Carl W. I.; Clerici, Giancarlo C.; Burnside, Walter D.

    1989-03-01

    A dual-chamber compact range configuration is proposed wherein the main reflector and target zone are located in the main chamber and an oversized Gregorian subreflector and associated feed assemblies in the other. The chambers are isolated by an absorber fence except for a small coupling aperture which is used to transmit signals between them. The absorber fence prevents diffraction by the subreflector and spillover by the feed from illuminating the main reflector and target zone. System performance is analyzed with and without the absorber fence to show how the coupling aperture should be shaped to minimize diffractions.

  17. A dual chamber Gregorian subreflector system for compact range applications

    NASA Technical Reports Server (NTRS)

    Pistorius, Carl W. I.; Clerici, Giancarlo C.; Burnside, Walter D.

    1989-01-01

    A dual-chamber compact range configuration is proposed wherein the main reflector and target zone are located in the main chamber and an oversized Gregorian subreflector and associated feed assemblies in the other. The chambers are isolated by an absorber fence except for a small coupling aperture which is used to transmit signals between them. The absorber fence prevents diffraction by the subreflector and spillover by the feed from illuminating the main reflector and target zone. System performance is analyzed with and without the absorber fence to show how the coupling aperture should be shaped to minimize diffractions.

  18. Interconnection of salt-induced hydrophobic compaction and secondary structure formation depends on solution conditions: revisiting early events of protein folding at single molecule resolution.

    PubMed

    Haldar, Shubhasis; Chattopadhyay, Krishnananda

    2012-03-30

    What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea.

  19. Nonlocal interactions stabilize long range loops in the initial folding intermediates of reduced bovine pancreatic trypsin inhibitor.

    PubMed

    Ittah, V; Haas, E

    1995-04-01

    A search for the topology of the chain folding of reduced bovine pancreatic trypsin inhibitor (BPTI), in unfolded and partially folded states, was done by means of time resolved dynamic nonradiative excitation energy transfer (ET) measurements. Four double labeled BPTI derivatives were used in which the donor was attached to the N-terminal arginine residue and the acceptor was specifically attached to one of the lysine residues. The four derivatives form a series of labeled backbone segments of increasing length spanning the full lengths of the BPTI chain: 15, 26, 41, and 46 residues. The intramolecular segmental end-to-end distance (EED) distributions were determined for all the derivatives by global analysis of the decay curves of both the donor and the acceptor in the reduced state, in low (0.5 M) guanidinium chloride (GuHCl) concentrations at pH 3.6 and 2.1 (R and A states, respectively). The results show that, in the partial folding conditions of low GuHCl concentration, reduced BPTI is in a compact state, but in this state the polypeptide chain is not in a condensed statistical coil conformation. Two distinct subpopulations were found for the four intramolecular EED distributions. One subpopulation was compact, with native-like EED distribution, while the second was unfolded. The pairs of sites, residues 1 and 26 and residues 1 and 46, showed close proximity in the dominant subpopulation. These contacts form two loops (probably collapsed): one consists of the first 26 residues, and the second comprises the full length of the chain from the N- to the C-terminal segments, which is in fact made up to two shorter loops (1-26 and 27-46). The N-terminal 15 residue segment was relaxed into statistical coil-like non-native conformation, in contrast to its extended conformation in the native state. The effect of temperature in the range of 2-60 degrees C was small; the folded subpopulations were stable over this range. These results show that in BPTI the compact

  20. Range estimation of cetaceans with compact volumetric arrays.

    PubMed

    Zimmer, Walter M X

    2013-09-01

    Passive acoustic monitoring is the method of choice to detect whales and dolphins that are acoustically active and to monitor their underwater behavior. The NATO Science and Technology Organization Centre for Maritime Research and Experimentation has recently implemented a compact passive acoustic monitor (CPAM), consisting of three arrays of two hydrophones each that are combined in a fixed three-dimensional arrangement and that may be towed at depths of more than 100 m. With its volumetric configuration, the CPAM is capable of estimating the three-dimensional direction vector of arriving sounds and under certain conditions on relative geometry between the whale and hydrophone array, the CPAM may also estimate the range to echolocating animals. Basic ranging methods assume constant sound speed and apply straightforward geometry to obtain depth and distance to the sound source. Alternatively, ray-tracing based methods may be employed to integrate the information provided by real sound speed profiles. Both ranging methods combine measurements of sound arrival angles and surface reflection delays and are easily implemented in real-time applications, whereby one could promote the ray-tracing approach as the preferred method because it may integrate real sound speed profiles. PMID:23968058

  1. 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.

  2. Sumoylated Human Histone H4 Prevents Chromatin Compaction by Inhibiting Long-range Internucleosomal Interactions*

    PubMed Central

    Dhall, Abhinav; Wei, Sijie; Fierz, Beat; Woodcock, Christopher L.; Lee, Tae-Hee; Chatterjee, Champak

    2014-01-01

    The structure of eukaryotic chromatin directly influences gene function, and is regulated by chemical modifications of the core histone proteins. Modification of the human histone H4 N-terminal tail region by the small ubiquitin-like modifier protein, SUMO-3, is associated with transcription repression. However, the direct effect of sumoylation on chromatin structure and function remains unknown. Therefore, we employed a disulfide-directed strategy to generate H4 homogenously and site-specifically sumoylated at Lys-12 (suH4ss). Chromatin compaction and oligomerization assays with nucleosomal arrays containing suH4ss established that SUMO-3 inhibits array folding and higher order oligomerization, which underlie chromatin fiber formation. Moreover, the effect of sumoylation differed from that of acetylation, and could be recapitulated with the structurally similar protein ubiquitin. Mechanistic studies at the level of single nucleosomes revealed that, unlike acetylation, the effect of SUMO-3 arises from the attenuation of long-range internucleosomal interactions more than from the destabilization of a compacted dinucleosome state. Altogether, our results present the first insight on the direct structural effects of histone H4 sumoylation and reveal a novel mechanism by which SUMO-3 inhibits chromatin compaction. PMID:25294883

  3. Ester-linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation - possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold.

    PubMed

    Eichenberger, Andreas P; Smith, Lorna J; van Gunsteren, Wilfred F

    2012-01-01

    Prediction and understanding of the folding and stability of the 3D structure of proteins is still a challenge. The different atomic interactions, such as non polar contacts and hydrogen bonding, are known but their exact relative weights and roles when contributing to protein folding and stability are not identified. Initiated by a previous molecular dynamics simulation of fully ester-linked hen egg white lysozyme (HEWL), which showed a more compact fold of the ester-linked molecule compared to the native one, three variants of this protein are analyzed in the present study. These are 129-residue native HEWL, partly ester-linked HEWL, in which only 34 peptide linkages that are not involved in the helical or β-strand parts of native HEWL were replaced by ester linkages, and fully (126 residues) ester-linked HEWL. Native and partly ester-linked HEWL showed comparable behaviour, whereas fully ester-linked HEWL could not maintain the native secondary structure of HEWL in the simulation and adopted a more compact fold. The conformational changes were analyzed by comparing simulation averaged values of quantities that can be measured by NMR, such as (1)H-(15)N backbone order parameters, residual dipolar couplings, proton-proton NOE distances and (3)J-couplings with the corresponding values derived from experimental NMR data for native HEWL. The information content of the latter appeared to be insufficient to detect the local conformational rearrangements upon esterification of the loop regions of the protein. For fully ester-linked HEWL, a significantly reduced agreement was observed. Upon esterification, the backbone-side chain and side chain-side chain hydrogen-bonding pattern of HEWL changes to maintain its compactness and thus the structural stability of the ester-linked lysozymes. PMID:22093234

  4. Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops

    PubMed Central

    Paslawski, Wojciech; Lillelund, Ove K.; Kristensen, Julie Veje; Schafer, Nicholas P.; Baker, Rosanna P.; Urban, Sinisa; Otzen, Daniel E.

    2015-01-01

    Despite the ubiquity of helical membrane proteins in nature and their pharmacological importance, the mechanisms guiding their folding remain unclear. We performed kinetic folding and unfolding experiments on 69 mutants (engineered every 2–3 residues throughout the 178-residue transmembrane domain) of GlpG, a membrane-embedded rhomboid protease from Escherichia coli. The only clustering of significantly positive ϕ-values occurs at the cytosolic termini of transmembrane helices 1 and 2, which we identify as a compact nucleus. The three loops flanking these helices show a preponderance of negative ϕ-values, which are sometimes taken to be indicative of nonnative interactions in the transition state. Mutations in transmembrane helices 3–6 yielded predominantly ϕ-values near zero, indicating that this part of the protein has denatured-state–level structure in the transition state. We propose that loops 1–3 undergo conformational rearrangements to position the folding nucleus correctly, which then drives folding of the rest of the domain. A compact N-terminal nucleus is consistent with the vectorial nature of cotranslational membrane insertion found in vivo. The origin of the interactions in the transition state that lead to a large number of negative ϕ-values remains to be elucidated. PMID:26056273

  5. Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops.

    PubMed

    Paslawski, Wojciech; Lillelund, Ove K; Kristensen, Julie Veje; Schafer, Nicholas P; Baker, Rosanna P; Urban, Sinisa; Otzen, Daniel E

    2015-06-30

    Despite the ubiquity of helical membrane proteins in nature and their pharmacological importance, the mechanisms guiding their folding remain unclear. We performed kinetic folding and unfolding experiments on 69 mutants (engineered every 2-3 residues throughout the 178-residue transmembrane domain) of GlpG, a membrane-embedded rhomboid protease from Escherichia coli. The only clustering of significantly positive ϕ-values occurs at the cytosolic termini of transmembrane helices 1 and 2, which we identify as a compact nucleus. The three loops flanking these helices show a preponderance of negative ϕ-values, which are sometimes taken to be indicative of nonnative interactions in the transition state. Mutations in transmembrane helices 3-6 yielded predominantly ϕ-values near zero, indicating that this part of the protein has denatured-state-level structure in the transition state. We propose that loops 1-3 undergo conformational rearrangements to position the folding nucleus correctly, which then drives folding of the rest of the domain. A compact N-terminal nucleus is consistent with the vectorial nature of cotranslational membrane insertion found in vivo. The origin of the interactions in the transition state that lead to a large number of negative ϕ-values remains to be elucidated.

  6. Evolution and Dynamics of a Fold-Thrust Belt: The Sulaiman Range of Pakistan

    NASA Astrophysics Data System (ADS)

    Reynolds, K.; Copley, A.; Hussain, E.

    2014-12-01

    Plan-view curvature of geological structures and range-front topography has long been a recognized and debated feature of both ancient and active fold-thrust belts. As part of the largest active mountain range on Earth, much of the body of work surrounding this topic has focused on the Tibetan Plateau. A lack of published data, extremely limited geodetic coverage and difficulty of access mean there have been relatively few studies of the western part of the India-Asia collision zone, where the Himalaya curve to the southwest into the lobate fold-thrust belts of Pakistan. The widest of these, the Sulaiman Range, forms a strongly curved lobe with ~300km across-strike width. We present observations and models of the Sulaiman Range of western Pakistan that shed new light on the evolution and deformation of fold-thrust belts. Earthquake source inversions show that the seismic deformation in the range is concentrated in the thick pile of sediments overlying the underthrusting lithosphere of the Indian subcontinent. The slip vectors of the earthquakes vary in strike around the margin of the range, in tandem with the shape of the topography, suggesting that gravitational driving forces arising from the topography play an important role in governing the deformation of the region. Numerical models suggest that the active deformation, and extreme plan-view curvature of the range, are governed by the presence of weak sediments in a pre-existing basin on the underthrusting Indian plate. These sediments affect the stress-state in the over-riding mountain range and allow for the rapid propagation of the nose of the range and the development of extreme curvature and laterally-varying surface gradients.

  7. 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.

  8. 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

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

    PubMed

    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

  10. 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.

  11. Folding of the four-helix bundle FF domain from a compact on-pathway intermediate state is governed predominantly by water motion.

    PubMed

    Sekhar, Ashok; Vallurupalli, Pramodh; Kay, Lewis E

    2012-11-20

    Friction plays a critical role in protein folding. Frictional forces originating from random solvent and protein fluctuations both retard motion along the folding pathway and activate protein molecules to cross free energy barriers. Studies of friction thus may provide insights into the driving forces underlying protein conformational dynamics. However, the molecular origin of friction in protein folding remains poorly understood because, with the exception of the native conformer, there generally is little detailed structural information on the other states participating in the folding process. Here, we study the folding of the four-helix bundle FF domain that proceeds via a transiently formed, sparsely populated compact on-pathway folding intermediate whose structure was elucidated previously. Because the intermediate is stabilized by both native and nonnative interactions, friction in the folding transition between intermediate and folded states is expected to arise from intrachain reorganization in the protein. However, the viscosity dependencies of rates of folding from or unfolding to the intermediate, as established by relaxation dispersion NMR spectroscopy, clearly indicate that contributions from internal friction are small relative to those from solvent, so solvent frictional forces drive the folding process. Our results emphasize the importance of solvent dynamics in mediating the interconversion between protein configurations, even those that are highly compact, and in equilibrium folding/unfolding fluctuations in general.

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

    NASA Astrophysics Data System (ADS)

    Reynolds, Kirsty; Copley, Alex; Hussain, Ekbal

    2015-05-01

    We present observations and models of the Sulaiman Range of western Pakistan that shed new light on the evolution and deformation of fold-thrust belts. Earthquake source inversions show that the seismic deformation in the range is concentrated in the thick pile of sediments overlying the underthrusting lithosphere of the Indian subcontinent. The slip vectors of the earthquakes vary in strike around the margin of the range, in tandem with the shape of the topography, suggesting that gravitational driving forces arising from the topography play an important role in governing the deformation of the region. Numerical models suggest that the active deformation, and the extreme plan-view curvature of the range, are governed by the presence of weak sediments in a pre-existing basin on the underthrusting Indian Plate. These sediments affect the stress-state in the over-riding mountain range and allow for the rapid propagation of the nose of the range and the development of extreme curvature and laterally varying surface gradients.

  13. 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.

  14. Relative Quantitation of Neuropeptides over a Thousand-fold Concentration Range

    NASA Astrophysics Data System (ADS)

    Hou, Xiaowen; Xie, Fang; Sweedler, Jonathan V.

    2012-12-01

    Neuropeptides are essential cell-to-cell signaling molecules that influence diverse regulatory and behavioral functions within biological systems. Differing in their amino acid sequences and post-translational modifications, hundreds of neuropeptides are produced via a series of enzymatic processing steps, and their levels vary with location, time, and physiological condition. Due to their wide range of endogenous concentrations and inherent chemical complexity, using mass spectrometry (MS) to accurately quantify changes in peptide levels can be challenging. Here we evaluate three different MS systems for their ability to accurately measure neuropeptide levels: capillary liquid chromatography-electrospray ionization-ion trap (CapLC-ESI-IT) MS, ultraperformance liquid chromatography-electrospray ionization-quadrupole-time-of-flight (UPLC-LC-ESI-Q-TOF) MS, and matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) MS. Specifically, eight sample mixtures composed of five neuropeptide standards, with four technical replicates of each, were labeled with H4/D4-succinic anhydride, followed by relative peptide quantitation using the three MS platforms. For these samples, the CapLC-ESI-IT MS platform offered the most robust ability to accurately quantify peptides over a concentration range of 1200-fold, although it required larger sample sizes than the other two platforms. Both the UPLC-ESI-Q-TOF MS and the MALDI-TOF MS systems had lower limits of quantification, with the MALDI-TOF having the lowest. By implementing several data acquisition schemes and optimizing the data analysis approaches, we were able to accurately quantify peptides over a three orders of magnitude concentration range using either the UPLC or MALDI-TOF platforms. Overall these results increase our understanding of both the capabilities and limits of using MS-based approaches to measure peptides.

  15. Laramide sedimentation, folding, and faulting in southern Wind River Range, Wyoming

    SciTech Connect

    Steidtmann, J.R.; McGee, L.C.; Middleton, L.

    1983-08-01

    Surface observations along the southern margin of the Wind River Range in Fremont County, Wyoming, indicate that early motion along the Wind River and Continental faults controlled depositional patterns and lithologic characteristics of the local syntectonic sediments, and that the latest motion on a segment of the Wind River fault between Oregon and Pacific buttes folded some of these same sediments into a monocline. The stratigraphic sequence exposed in the monocline consists (in ascending order) of a lower distal fan or alluvial plain unit (main body of the Wasatch Formation), a lake margin unit (Tipton Tongue of the Green River Formation), a fluvial and deltaic sandbody (Tipton Sandstone), and an alluvial fan unit (Cathedral Bluffs Tongue of the Wasatch Formation). Tectonic implications of these interpretations are: (1) early motion on the Wind River fault controlled the margin of Eocene Lake Gosiute and generated a distal sediment source to the east; (2) late early Eocene uplift of the north side of the Continental fault provided a proximal source for pegmatitic and granitic boulders to the north; (3) last motion on the Wind River fault was latest early Eocene or earliest middle Eocene between Oregon and Pacific buttes; (4) the Wind River fault consists of several segments which moved separately rather than as one, long continuous zone of concurrent faulting; (5) while the Wind River Range was being thrust to the southwest it may have been uncoupled from the basins to the south by a zone of transcurrent faulting; (6) Pliocene or younger recurrent motion along the Continental fault was opposite to that in the Eocene.

  16. 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.

  17. 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.

  18. 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

  19. An Integrated Compact Unit for Wide Range Micro-Newton Force Measurement

    NASA Astrophysics Data System (ADS)

    Akanda, M. A. Salam; Tohmyoh, Hironori; Saka, Masumi

    Wide range compact sensor is preferably sought for force sensing in testing of micro objects or local area of macro objects with the observation of high resolution microscope. This paper presents the design and development of an integrated passive cantilever type force sensing unit with the specificities of range variation, interchangeability of components and compact size by incorporating with cantilever, probe and a capacitive sensor for measurement of large range micro-newton forces in wide scope of application. In the design, the tactile force at the probe perpendicularly attached to the cantilever is converted as cantilever deflection, which is measured by the capacitive sensor. In connection to a tiny capacitive sensor a compatible cantilever with double-beam structure is considered. Cantilever length variation facility is incorporated in the unit for obtaining different force measurement ranges by using the same cantilever. Characterization of the cantilever is performed against a standard load cell. The force resolution with a typical cantilever is estimated as 10 nN. The elastic property of human hair is efficiently determined by testing with the combination of a digital microscope and the developed sensor system. The utility of the unit for different resolution/range by the interchangeability of cantilevers is also demonstrated. Experimental results show that this integrated force sensing unit achieves good sensitivity and linearity, and wide measurement range.

  20. 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.

  1. 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.

  2. 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.

  3. Compact range reflector analysis using the plane wave spectrum approach with an adjustable sampling rate

    NASA Astrophysics Data System (ADS)

    McKay, James P.; Rahmat-Samii, Yahya

    1991-06-01

    An improved method for determining the test zone field of compact range reflectors is presented. The plane wave spectrum (PWS) approach is used to obtain the test zone field from knowledge of the reflector aperture field distribution. The method is particularly well suited to the analysis of reflectors with a linearly serrated rim for reduced edge diffraction. Computation of the PWS of the reflector aperture field is facilitated by a closed-form expression for the Fourier transform of a polygonal window function. Inverse transformation in the test zone region is accomplished using a fast Fourier transform (FFT) algorithm with a properly adjusted sampling rate (which is a function of both the reflector size and the distance from the reflector). The method is validated by comparison with results obtained using surface current and aperture field integration techniques. The performance of several serrated reflectors is evaluated in order to observe the effects of edge diffraction on the test zone fields.

  4. 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

  5. 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.

  6. 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.

  7. Compact short-pulse laser for near-field range-gated imaging

    NASA Astrophysics Data System (ADS)

    Zutavern, Fred J.; Helgeson, Wesley D.; Loubriel, Guillermo M.; Yates, George J.; Gallegos, Robert A.; McDonald, Thomas E., Jr.

    1997-05-01

    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 100 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 and high gain, PCSS-driven LDAs developed at Sandia National Laboratories. 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.

  8. Use of a compact range approach to evaluate rf and dual-mode missiles

    NASA Astrophysics Data System (ADS)

    Willis, Kenneth E.; Weiss, Yosef

    2000-07-01

    This paper describes a hardware-in-the-loop (HWIL) system developed for testing Radio Frequency (RF), Infra-Red (IR), and Dual-Mode missile seekers. The system consists of a unique hydraulic five-axis (three seeker axes plus two target axes) Flight Motion Table (FMT), an off-axis parabolic reflector, and electronics required to generate the signals to the RF feeds. RF energy that simulates the target is fed into the reflector from three orthogonal feeds mounted on the inner target axis, at the focal point area of the parabolic reflector. The parabolic reflector, together with the three RF feeds (the Compact Range), effectively produces a far-field image of the target. Both FMT target axis motion and electronic control of the RF beams (deflection) modify the simulated line-of-sight target angles. Multiple targets, glint, multi-path, ECM, and clutter can be introduced electronically. To evaluate dual-mode seekers, the center section of the parabolic reflector is replaced with an IR- transparent, but RF-reflective section. An IR scene projector mounts to the FMT target axes, with its image focused on the intersection of the FMT seeker axes. The system eliminates the need for a large anechoic chamber and 'Target Wall' or target motion system used with conventional HWIL systems. This reduces acquisition and operating costs of the facility.

  9. 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.

  10. 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.

  11. 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.

  12. 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 degrees to 90 degrees 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

  13. New main reflector, subreflector and dual chamber concepts for compact range applications

    NASA Technical Reports Server (NTRS)

    Pistorius, C. W. I.; Burnside, W. D.

    1987-01-01

    A compact range is a facility used for the measurement of antenna radiation and target scattering problems. Most presently available parabolic reflectors do not produce ideal uniform plane waves in the target zone. Design improvements are suggested to reduce the amplitude taper, ripple and cross polarization errors. The ripple caused by diffractions from the reflector edges can be reduced by adding blended rolled edges and shaping the edge contour. Since the reflected edge continues smoothly from the parabola onto the rolled surface, rather than being abruptly terminated, the discontinuity in the reflected field is reduced which results in weaker diffracted fields. This is done by blending the rolled edges from the parabola into an ellipse. An algorithm which enables one to design optimum blended rolled edges was developed that is based on an analysis of the continuity of the surface radius of curvature and its derivatives across the junction. Futhermore, a concave edge contour results in a divergent diffracted ray pattern and hence less stray energy in the target zone. Design equations for three-dimensional reflectors are given. Various examples were analyzed using a new physical optics method which eliminates the effects of the false scattering centers on the incident shadow boundaries. A Gregorian subreflector system, in which both the subreflector and feed axes are tilted, results in a substantial reduction in the amplitude taper and cross polarization errors. A dual chamber configuration is proposed to eliminate the effects of diffraction from the subreflector and spillover from the feed. A computationally efficient technique, based on ray tracing and aperture integration, was developed to analyze the scattering from a lossy dielectric slab with a wedge termination.

  14. Petrology and provenance of modern sands from Cascade Range Forearc and Canadian Rocky Mountain fold-thrust belt

    SciTech Connect

    Kretchmer, A.G.; Ingersoll, R.V.

    1987-05-01

    The Cascade Range volcanic arc and forearc, and the Canadian Rocky Mountain fold-thrust belt represent the two sides of a continental margin arc-trench system. Sands from these areas show clear compositional differences. The most significant discriminating parameters are volcanic lithic grains, metamorphic lithic grains, plagioclase-to-feldspar ratio, and quartz. Variable sediment composition is also evident within each setting. Cascade sands are volcaniclastic and have high plagioclase-to-feldspar ratios. They divide into three categories (volcanic arc, alluvial forearc, and coastal forearc) that differ in their lithic contents and plagioclase-to-feldspar ratios. These changes reflect the attrition of volcanic lithics with distance from the arc and the input of recycled sediment and subduction-complex lithologies. Rocky Mountain sands are sedimenticlastic. They are of two types, a miogeocline-shelf provenance and a clastic-wedge provenance. These linear belts differ in clastic-carbonate content, plagioclase-to-feldspar ratio, and quartz content. The compositional differences reflect interstratified petrofacies of fold-thrust belts. Just as they can use detrital modes of modern sands to characterize provenance and tectonic setting, modes of ancient sandstones help up to recognize provenance terranes and reconstruct paleotectonic settings.

  15. 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

  16. 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

  17. 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.

  18. Anatomy of a volcanic district in a carbonate fold-and-thrust belt: the northern Volsci Range (Italy)

    NASA Astrophysics Data System (ADS)

    Cardello, Giovanni Luca; Consorti, Lorenzo; Di Filippo, Michele

    2015-04-01

    The Volsci Range is a carbonate fold-and-thrust belt crossed by important normal faults in places associated with explosive volcanic deposits and hydrothermal ongoing activity within a moderately active seismic area (e.g., Latina earthquake 2012, Mw=3.8). Though distribution of volcanites is known, origin, volume and field characterization of a previously unstudied volcanic district is far to be addressed and it is the topic of this work. Several monogenic phreatomagmatic vents occur at the edges of the chain and within its backbone. The most relevant ones are characterized at the base by well welded to zeolitized tuffs, followed either by incoherent tuffs or by surges (e.g., Patrica, Valvisciolo) and locally by lavas (i.e., Giuliano di Roma, Pofi, Terracina) and finally by late Quaternary slope deposits. Most explosive units are largely composed by local Mesozoic platform carbonate litic clasts, showing different degrees of rounding and decarbonation. Micropalaeontology and facies analysis confirm that clasts are not older than late Jurassic and not younger than Cenomanian (Upper part of the Ostracoda and Miliolidae biozone). Therefore considering the stratigraphy beneath the vent points, litics could come from depths of about 400-600 meters. Juvenile litics of different composition, accretionary lapilli and the above mention carbonate litic clasts testify for a complex conduct composition and for the rupture of the carbonatic aquifer during eruption. Right at the southern slope of the Lepini Mounts (northern Volsci Range), as detected from the analysis of the n-2 residual gravity anomalies, monogenic circular vents (tuff rings) occur buried under Quaternary deposits or are just barely cropping out as necks (Doganella di Ninfa). Further south, despite the occurrence of pyroclastic deposits in boreholes, thickness and shape of volcanic deposits below the Pontina Plain is still unconstrained, providing a challenge for further geophysical studies. However, the

  19. 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).

  20. 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.

  1. Beam-based measurements of long-range transverse wakefields in the Compact Linear Collider main-linac accelerating structure

    NASA Astrophysics Data System (ADS)

    Zha, Hao; Latina, Andrea; Grudiev, Alexej; De Michele, Giovanni; Solodko, Anastasiya; Wuensch, Walter; Schulte, Daniel; Adli, Erik; Lipkowitz, Nate; Yocky, Gerald S.

    2016-01-01

    The baseline design of CLIC (Compact Linear Collider) uses X-band accelerating structures for its main linacs. In order to maintain beam stability in multibunch operation, long-range transverse wakefields must be suppressed by 2 orders of magnitude between successive bunches, which are separated in time by 0.5 ns. Such strong wakefield suppression is achieved by equipping every accelerating structure cell with four damping waveguides terminated with individual rf loads. A beam-based experiment to directly measure the effectiveness of this long-range transverse wakefield and benchmark simulations was made in the FACET test facility at SLAC using a prototype CLIC accelerating structure. The experiment showed good agreement with the simulations and a strong suppression of the wakefields with an unprecedented minimum resolution of 0.1 V /(pC mm m ) .

  2. 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.

  3. 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

  4. Design of transmission-type phase holograms for a compact radar-cross-section measurement range at 650 GHz.

    PubMed

    Noponen, Eero; Tamminen, Aleksi; Vaaja, Matti

    2007-07-10

    A design formalism is presented for transmission-type phase holograms for use in a submillimeter-wave compact radar-cross-section (RCS) measurement range. The design method is based on rigorous electromagnetic grating theory combined with conventional hologram synthesis. Hologram structures consisting of a curved groove pattern on a 320 mmx280 mm Teflon plate are designed to transform an incoming spherical wave at 650 GHz into an output wave generating a 100 mm diameter planar field region (quiet zone) at a distance of 1 m. The reconstructed quiet-zone field is evaluated by a numerical simulation method. The uniformity of the quiet-zone field is further improved by reoptimizing the goal field. Measurement results are given for a test hologram fabricated on Teflon.

  5. Ca-Dependent Folding of Human Calumenin.

    PubMed

    Mazzorana, Marco; Hussain, Rohanah; Sorensen, Thomas

    2016-01-01

    Human calumenin (hCALU) is a six EF-hand protein belonging to the CREC family. As other members of the family, it is localized in the secretory pathway and regulates the activity of SERCA2a and of the ryanodine receptor in the endoplasmic reticulum (ER). We have studied the effects of Ca2+ binding to the protein and found it to attain a more compact structure upon ion binding. Circular Dichroism (CD) measurements suggest a major rearrangement of the protein secondary structure, which reversibly switches from disordered at low Ca2+ concentrations to predominantly alpha-helical when Ca2+ is added. SAXS experiments confirm the transition from an unfolded to a compact structure, which matches the structural prediction of a trilobal fold. Overall our experiments suggest that calumenin is a Ca2+ sensor, which folds into a compact structure, capable of interacting with its molecular partners, when Ca2+ concentration within the ER reaches the millimolar range. PMID:26991433

  6. Ca-Dependent Folding of Human Calumenin

    PubMed Central

    Mazzorana, Marco; Hussain, Rohanah; Sorensen, Thomas

    2016-01-01

    Human calumenin (hCALU) is a six EF-hand protein belonging to the CREC family. As other members of the family, it is localized in the secretory pathway and regulates the activity of SERCA2a and of the ryanodine receptor in the endoplasmic reticulum (ER). We have studied the effects of Ca2+ binding to the protein and found it to attain a more compact structure upon ion binding. Circular Dichroism (CD) measurements suggest a major rearrangement of the protein secondary structure, which reversibly switches from disordered at low Ca2+ concentrations to predominantly alpha-helical when Ca2+ is added. SAXS experiments confirm the transition from an unfolded to a compact structure, which matches the structural prediction of a trilobal fold. Overall our experiments suggest that calumenin is a Ca2+ sensor, which folds into a compact structure, capable of interacting with its molecular partners, when Ca2+ concentration within the ER reaches the millimolar range. PMID:26991433

  7. 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.

  8. 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

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

    SciTech Connect

    Wallace, W.K.; Hanks, C.L. )

    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.

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

    NASA Astrophysics Data System (ADS)

    Zhang, Xingyu; Chakravarty, Swapnajit; Chung, Chi-Jui; Pan, Zeyu; Yan, Hai; Chen, Ray T.

    2015-11-01

    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.

  11. 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.

  12. 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. PMID:26660188

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

    SciTech Connect

    Borgia, A. ); Burr, J. ); Montero, W.; Morales, L.D. ); Alvarado, G.E. )

    1990-08-30

    Long sublinear ridges and related scarps located at the base of large volcanic structures are frequently interpreted as normal faults associated with extensional regional stress. In contrast, the ridges bordering the Central Costa Rica volcanic range (CCRVR) are the topographic expression of hanging wall asymmetric angular anticlines overlying low-angle thrust faults at the base of the range. These faults formed by gravitational failure and slumping of the flanks of the range due to the weight of the volcanic edifices and were perhaps triggered by the intrusion of magma over the past 20,000 years. These anticlines are hypothesized to occur along the base of the volcano, where the thrust faults ramp up toward the sea bottom. Ridges and scarps between 2,000 and 5,000 m below sea level are interpreted as the topographic expression of these folds. The authors further suggest that the scarps of the CCRVR and valid scaled terrestrial analogs of the perimeter scarp of the Martian volcano Olympus Mons. They suggest that the crust below Olympus Mons has failed under the load of the volcano, triggering the radial slumping of the flanks of the volcano on basal thrusts. The thrusting would have, in turn, formed the anticlinal ridges and scarps that surround the edifice. The thrust faults may extend all the way to the base of the Martian crust (about 40 km), and they may have been active until almost the end of the volcanic activity. They suggest that gravitational failure and slumping of the flanks of volcanoes is a process common to most large volcanic edifices. In the CCRVR this slumping of the flanks is a slow intermittent process, but it could evolve to rapid massive avalanching leading to catastrophic eruptions. Thus monitoring of uplift and displacement of the folds related to the slump tectonics could become an additional effective method for mitigating volcanic hazards.

  14. 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.

  15. 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.

  16. 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

  17. Folding by Design

    NASA Astrophysics Data System (ADS)

    Dodd, Paul; Damasceno, Pablo; Glotzer, Sharon

    2014-03-01

    A form of self-assembly, ``self-folding'' presents an alternative approach to the creation of reconfigurable, responsive materials with applications ranging from robotics to drug design. However, the complexity of interactions present in biological and engineered systems that undergo folding makes it challenging to isolate the main factors controlling their assembly and dis-assembly. Here we use computer simulations of simple, minimalistic self-foldable structures and investigate their stochastic folding process. By dynamically accessing all the states that lead to, or inhibit, successful folding, we show that the mechanisms by which general stochastic systems can achieve their ``native'' structures can be identified and used to design rules for optimized folding propensity. Research supported by the National Science Foundation, Emerging Frontiers in Research and Innovation Award # EFRI-1240264.

  18. 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.

  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. Is there an en route folding intermediate for Cold shock proteins?

    PubMed

    Huang, Lei; Shakhnovich, Eugene I

    2012-05-01

    Cold shock proteins (Csps) play an important role in cold shock response of a diverse number of organisms ranging from bacteria to humans. Numerous studies of the Csp from various species showed that a two-state folding mechanism is conserved and the transition state (TS) appears to be very compact. However, the atomic details of the folding mechanism of Csp remain unclear. This study presents the folding mechanism of Csp in atomic detail using an all-atom Go model-based simulations. Our simulations predict that there may exist an en route intermediate, in which β strands 1-2-3 are well ordered and the contacts between β1 and β4 are almost developed. Such an intermediate might be too unstable to be detected in the previous fluorescence energy transfer experiments. The transition state ensemble has been determined from the P(fold) analysis and the TS appears even more compact than the intermediate state.

  1. 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.

  2. 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.

  3. Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element

    PubMed Central

    Majumder, Kinjal; Koues, Olivia I.; Chan, Elizabeth A.W.; Kyle, Katherine E.; Horowitz, Julie E.; Yang-Iott, Katherine; Bassing, Craig H.; Taniuchi, Ichiro; Krangel, Michael S.

    2015-01-01

    Gene regulation relies on dynamic changes in three-dimensional chromatin conformation, which are shaped by composite regulatory and architectural elements. However, mechanisms that govern such conformational switches within chromosomal domains remain unknown. We identify a novel mechanism by which cis-elements promote long-range interactions, inducing conformational changes critical for diversification of the TCRβ antigen receptor locus (Tcrb). Association between distal Vβ gene segments and the highly expressed DβJβ clusters, termed the recombination center (RC), is independent of enhancer function and recruitment of V(D)J recombinase. Instead, we find that tissue-specific folding of Tcrb relies on two distinct architectural elements located upstream of the RC. The first, a CTCF-containing element, directly tethers distal portions of the Vβ array to the RC. The second element is a chromatin barrier that protects the tether from hyperactive RC chromatin. When the second element is removed, active RC chromatin spreads upstream, forcing the tether to serve as a new barrier. Acquisition of barrier function by the CTCF element disrupts contacts between distal Vβ gene segments and significantly alters Tcrb repertoires. Our findings reveal a separation of function for RC-flanking regions, in which anchors for long-range recombination must be cordoned off from hyperactive RC landscapes by chromatin barriers. PMID:25512470

  4. 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.

  5. Single Mutations in the VP2 300 Loop Region of the Three-Fold Spike of the Carnivore Parvovirus Capsid Can Determine Host Range

    PubMed Central

    Organtini, Lindsey J.; Zhang, Sheng; Hafenstein, Susan L.; Holmes, Edward C.

    2015-01-01

    ABSTRACT Sylvatic carnivores, such as raccoons, have recently been recognized as important hosts in the evolution of canine parvovirus (CPV), a pandemic pathogen of domestic dogs. Although viruses from raccoons do not efficiently bind the dog transferrin receptor (TfR) or infect dog cells, a single mutation changing an aspartic acid to a glycine at capsid (VP2) position 300 in the prototype raccoon CPV allows dog cell infection. Because VP2 position 300 exhibits extensive amino acid variation among the carnivore parvoviruses, we further investigated its role in determining host range by analyzing its diversity and evolution in nature and by creating a comprehensive set of VP2 position 300 mutants in infectious clones. Notably, some position 300 residues rendered CPV noninfectious for dog, but not cat or fox, cells. Changes of adjacent residues (residues 299 and 301) were also observed often after cell culture passage in different hosts, and some of the mutations mimicked changes seen in viruses recovered from natural infections of alternative hosts, suggesting that compensatory mutations were selected to accommodate the new residue at position 300. Analysis of the TfRs of carnivore hosts used in the experimental evolution studies demonstrated that their glycosylation patterns varied, including a glycan present only on the domestic dog TfR that dictates susceptibility to parvoviruses. Overall, there were significant differences in the abilities of viruses with alternative position 300 residues to bind TfRs and infect different carnivore hosts, demonstrating that the process of infection is highly host dependent and that VP2 position 300 is a key determinant of host range. IMPORTANCE Although the emergence and pandemic spread of canine parvovirus (CPV) are well documented, the carnivore hosts and evolutionary pathways involved in its emergence remain enigmatic. We recently demonstrated that a region in the capsid structure of CPV, centered around VP2 position 300

  6. The 27 February 1997 Sibi double-earthquake (Mw 6.9, 6.7) in the Sulaiman range of Pakistan - implications for the tectonics of fold-and-thrust belts and for earthquake triggering mechanisms

    NASA Astrophysics Data System (ADS)

    Nissen, E.; Craig, T. J.; McMullan, K.; Parsons, B. E.; Rickerby, A.; Wright, T. J.

    2011-12-01

    The Sulaiman mountains form an arcuate fold-and-thrust belt which accommodates oblique shortening between the Indian and Eurasian plates in western Pakistan. Despite being an important component of the India-Eurasia collision zone, little is known about the active tectonics of the range. The Mw ~7 Sibi earthquake of 27 February 1997 was the largest event to strike the Sulaiman mountains in the past eighty years, and provides an excellent opportunity to investigate the regional style of deformation. A pair of radar interferograms constructed from descending-track ERS-2 data reveals two distinct areas containing coseismic surface displacements, spaced ~50 km apart. We model these displacements to yield source parameters for the two sub-events. The larger (Mw 6.9) north-western sub-event occurred on a buried, S-dipping reverse fault, with slip confined to depths of between ~10 km and ~20 km. The elongate pattern of surface deformation lies oblique to the trend of local surface anticlines, suggesting that the fault responsible for this sub-event is disconnected from surface folding, possibly by a weak decollement. The smaller (Mw 6.7) south-eastern sub-event also involved reverse slip on a buried, S-dipping fault, but slip here reached shallower depths of ~4 km. Here, coseismic uplift is concentrated along a prominent surface anticline, which we interpret as a fault-propagation fold whose growth is driven by slip on the underlying thrust. These results suggest that (1) detachment folding and forced folding both contribute towards shortening of the Sulaiman mountains, (2) the range contains active S-dipping reverse faults despite the overall southwards propagation of thrusting, and (3) earthquakes can be generated within the thick sedimentary cover and are not restricted to the underlying basement. Finally, we merge the spatial information provided by InSAR with temporal constraints from seismic body-waveform modelling to investigate possible mechanisms for the

  7. Concordant Exploration of the Kinetics of RNA Folding from Global and Local Perspectives

    SciTech Connect

    Kwok,L.; Scherbakova, I.; Lamb, J.; Park, H.; Andresen, K.; Smith, H.; Brenowitz, M.; Pollack, L.

    2006-01-01

    Time-resolved small-angle X-ray scattering (SAXS) with millisecond time-resolution reveals two discrete phases of global compaction upon Mg{sup 2+}-mediated folding of the Tetrahymena thermophila ribozyme. Electrostatic relaxation of the RNA occurs rapidly and dominates the first phase of compaction during which the observed radius of gyration (R{sub g}) decreases from 75 Angstroms to 55 Angstroms. A further decrease in R{sub g} to 45 Angstroms occurs in a well-defined second phase. An analysis of mutant ribozymes shows that the latter phase depends upon the formation of long-range tertiary contacts within the P4-P6 domain of the ribozyme; disruption of the three remaining long-range contacts linking the peripheral helices has no effect on the 55-45 Angstroms compaction transition. A better understanding of the role of specific tertiary contacts in compaction was obtained by concordant time-resolved hydroxyl radical ({center_dot}OH) analyses that report local changes in the solvent accessibility of the RNA backbone. Comparison of the global and local measures of folding shows that formation of a subset of native tertiary contacts (i.e. those defining the ribozyme core) can occur within a highly compact ensemble whose R{sub g} is close to that of the fully folded ribozyme. Analyses of additional ribozyme mutants and reaction conditions establish the generality of the rapid formation of a partially collapsed state with little to no detectable tertiary structure. These studies directly link global RNA compaction with formation of tertiary structure as the molecule acquires its biologically active structure, and underscore the strong dependence on salt of both local and global measures of folding kinetics.

  8. 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.

  9. 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)

  10. Periodic folding of viscous sheets

    NASA Astrophysics Data System (ADS)

    Ribe, Neil M.

    2003-09-01

    The periodic folding of a sheet of viscous fluid falling upon a rigid surface is a common fluid mechanical instability that occurs in contexts ranging from food processing to geophysics. Asymptotic thin-layer equations for the combined stretching-bending deformation of a two-dimensional sheet are solved numerically to determine the folding frequency as a function of the sheet’s initial thickness, the pouring speed, the height of fall, and the fluid properties. As the buoyancy increases, the system bifurcates from “forced” folding driven kinematically by fluid extrusion to “free” folding in which viscous resistance to bending is balanced by buoyancy. The systematics of the numerically predicted folding frequency are in good agreement with laboratory experiments.

  11. 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

  12. An Alternative Approach to Protein Folding

    PubMed Central

    Kang, Yeona; Fortmann, Charles M.

    2013-01-01

    A diffusion theory-based, all-physical ab initio protein folding simulation is described and applied. The model is based upon the drift and diffusion of protein substructures relative to one another in the multiple energy fields present. Without templates or statistical inputs, the simulations were run at physiologic and ambient temperatures (including pH). Around 100 protein secondary structures were surveyed, and twenty tertiary structures were determined. Greater than 70% of the secondary core structures with over 80% alpha helices were correctly identified on protein ranging from 30 to 200 amino-acid sequence. The drift-diffusion model predicted tertiary structures with RMSD values in the 3–5 Angstroms range for proteins ranging 30 to 150 amino acids. These predictions are among the best for an all ab initio protein simulation. Simulations could be run entirely on a desktop computer in minutes; however, more accurate tertiary structures were obtained using molecular dynamic energy relaxation. The drift-diffusion model generated realistic energy versus time traces. Rapid secondary structures followed by a slow compacting towards lower energy tertiary structures occurred after an initial incubation period in agreement with observations. PMID:24078920

  13. Atomic-level description of ubiquitin folding

    PubMed Central

    Piana, Stefano; Lindorff-Larsen, Kresten; Shaw, David E.

    2013-01-01

    Equilibrium molecular dynamics simulations, in which proteins spontaneously and repeatedly fold and unfold, have recently been used to help elucidate the mechanistic principles that underlie the folding of fast-folding proteins. The extent to which the conclusions drawn from the analysis of such proteins, which fold on the microsecond timescale, apply to the millisecond or slower folding of naturally occurring proteins is, however, unclear. As a first attempt to address this outstanding issue, we examine here the folding of ubiquitin, a 76-residue-long protein found in all eukaryotes that is known experimentally to fold on a millisecond timescale. Ubiquitin folding has been the subject of many experimental studies, but its slow folding rate has made it difficult to observe and characterize the folding process through all-atom molecular dynamics simulations. Here we determine the mechanism, thermodynamics, and kinetics of ubiquitin folding through equilibrium atomistic simulations. The picture emerging from the simulations is in agreement with a view of ubiquitin folding suggested from previous experiments. Our findings related to the folding of ubiquitin are also consistent, for the most part, with the folding principles derived from the simulation of fast-folding proteins, suggesting that these principles may be applicable to a wider range of proteins. PMID:23503848

  14. Cotranslational protein folding on the ribosome monitored in real time.

    PubMed

    Holtkamp, Wolf; Kokic, Goran; Jäger, Marcus; Mittelstaet, Joerg; Komar, Anton A; Rodnina, Marina V

    2015-11-27

    Protein domains can fold into stable tertiary structures while they are synthesized on the ribosome. We used a high-performance, reconstituted in vitro translation system to investigate the folding of a small five-helix protein domain-the N-terminal domain of Escherichia coli N5-glutamine methyltransferase HemK-in real time. Our observations show that cotranslational folding of the protein, which folds autonomously and rapidly in solution, proceeds through a compact, non-native conformation that forms within the peptide tunnel of the ribosome. The compact state rearranges into a native-like structure immediately after the full domain sequence has emerged from the ribosome. Both folding transitions are rate-limited by translation, allowing for quasi-equilibrium sampling of the conformational space restricted by the ribosome. Cotranslational folding may be typical of small, intrinsically rapidly folding protein domains. PMID:26612953

  15. 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.

  16. 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

  17. Progress in fold recognition.

    PubMed

    Flöckner, H; Braxenthaler, M; Lackner, P; Jaritz, M; Ortner, M; Sippl, M J

    1995-11-01

    The prediction experiment reveals that fold recognition has become a powerful tool in structural biology. We applied our fold recognition technique to 13 target sequences. In two cases, replication terminating protein and prosequence of subtilisin, the predicted structures are very similar to the experimentally determined folds. For the first time, in a public blind test, the unknown structures of proteins have been predicted ahead of experiment to an accuracy approaching molecular detail. In two other cases the approximate folds have been predicted correctly. According to the assessors there were 12 recognizable folds among the target proteins. In our postprediction analysis we find that in 7 cases our fold recognition technique is successful. In several of the remaining cases the predicted folds have interesting features in common with the experimental results. We present our procedure, discuss the results, and comment on several fundamental and technical problems encountered in fold recognition.

  18. Let Them Fold

    ERIC Educational Resources Information Center

    Grant, Nicholas; Tobin, Alexander

    1972-01-01

    Directions are given for seven activities involving the folding of paper strips to illustrate geometric concepts. Properties of pentagons, triangles, hexagons, and Mobius bands resulting from the various foldings are discussed. (DT)

  19. Ureilite compaction

    NASA Astrophysics Data System (ADS)

    Walker, D.; Agee, C. B.

    1988-03-01

    Ureilite meteorites show the simple mineralogy and compact recrystallized textures of adcumulate rock or melting residues. A certain amount of controversy exists about whether they are in fact adcumulate rocks or melting residues and about the nature of the precursor liquid or solid assemblage. The authors undertook a limited experimental study which made possible the evaluation of the potential of the thermal migration mechanism (diffusion on a saturation gradient) for forming ureilite-like aggregates from carbonaceous chondrite precursors. They find that the process can produce compact recrystallized aggregates of silicate crystals which do resemble the ureilities and other interstitial-liquid-free adcumulate rocks in texture.

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

    NASA Astrophysics Data System (ADS)

    Taylor, Mark; Paul, Wolfgang; Binder, Kurt

    2009-04-01

    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.

  1. 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.

  2. Spatially confined folding of chromatin in the interphase nucleus

    PubMed Central

    Mateos-Langerak, Julio; Bohn, Manfred; de Leeuw, Wim; Giromus, Osdilly; Manders, Erik M. M.; Verschure, Pernette J.; Indemans, Mireille H. G.; Gierman, Hinco J.; Heermann, Dieter W.; van Driel, Roel; Goetze, Sandra

    2009-01-01

    Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a satisfactory explanation of experimental data. In particularly, they ignore that each chromosome occupies a confined space, i.e., the chromosome territory. Here, we present a polymer model that is able to describe key properties of chromatin over length scales ranging from 0.5 to 75 Mb. This random loop (RL) model assumes a self-avoiding random walk folding of the polymer backbone and defines a probability P for 2 monomers to interact, creating loops of a broad size range. Model predictions are compared with systematic measurements of chromatin folding of the q-arms of chromosomes 1 and 11. The RL model can explain our observed data and suggests that on the tens-of-megabases length scale P is small, i.e., 10–30 loops per 100 Mb. This is sufficient to enforce folding inside the confined space of a chromosome territory. On the 0.5- to 3-Mb length scale chromatin compaction differs in different subchromosomal domains. This aspect of chromatin structure is incorporated in the RL model by introducing heterogeneity along the fiber contour length due to different local looping probabilities. The RL model creates a quantitative and predictive framework for the identification of nuclear components that are responsible for chromatin–chromatin interactions and determine the 3-dimensional organization of the chromatin fiber. PMID:19234129

  3. A technique for extending by ˜103 the dynamic range of compact proton spectrometers for diagnosing ICF implosions on the National Ignition Facility and OMEGAa)

    NASA Astrophysics Data System (ADS)

    Sio, H.; Séguin, F. H.; Frenje, J. A.; Gatu Johnson, M.; Zylstra, A. B.; Rinderknecht, H. G.; Rosenberg, M. J.; Li, C. K.; Petrasso, R. D.

    2014-11-01

    Wedge Range Filter (WRF) proton spectrometers are routinely used on OMEGA and the NIF for diagnosing ρR and ρR asymmetries in direct- and indirect-drive implosions of D3He-, D2-, and DT-gas-filled capsules. By measuring the optical opacity distribution in CR-39 due to proton tracks in high-yield applications, as opposed to counting individual tracks, WRF dynamic range can be extended by 102 for obtaining the spectral shape, and by 103 for mean energy (ρR) measurement, corresponding to proton fluences of 108 and 109 cm-2, respectively. Using this new technique, ρR asymmetries can be measured during both shock and compression burn (proton yield ˜108 and ˜1012, respectively) in 2-shock National Ignition Facility implosions with the standard WRF accuracy of ±˜10 mg/cm2.

  4. Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions

    PubMed Central

    Haldar, Shubhasis; Chattopadhyay, Krishnananda

    2012-01-01

    What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea. PMID:22303014

  5. A technique for extending by ∼10{sup 3} the dynamic range of compact proton spectrometers for diagnosing ICF implosions on the National Ignition Facility and OMEGA

    SciTech Connect

    Sio, H. Séguin, F. H.; Frenje, J. A.; Gatu Johnson, M.; Zylstra, A. B.; Rinderknecht, H. G.; Rosenberg, M. J.; Li, C. K.; Petrasso, R. D.

    2014-11-15

    Wedge Range Filter (WRF) proton spectrometers are routinely used on OMEGA and the NIF for diagnosing ρR and ρR asymmetries in direct- and indirect-drive implosions of D{sup 3}He-, D{sub 2}-, and DT-gas-filled capsules. By measuring the optical opacity distribution in CR-39 due to proton tracks in high-yield applications, as opposed to counting individual tracks, WRF dynamic range can be extended by 10{sup 2} for obtaining the spectral shape, and by 10{sup 3} for mean energy (ρR) measurement, corresponding to proton fluences of 10{sup 8} and 10{sup 9} cm{sup −2}, respectively. Using this new technique, ρR asymmetries can be measured during both shock and compression burn (proton yield ∼10{sup 8} and ∼10{sup 12}, respectively) in 2-shock National Ignition Facility implosions with the standard WRF accuracy of ±∼10 mg/cm{sup 2}.

  6. 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).

  7. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2012-10-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold distribution procedure. The fold distribution provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of change in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Distribution, Proposal 12778, as Cycle 19.

  8. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2010-09-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Analysis {11863} during Cycle 17.

  9. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2009-07-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Analysis {10035} during Cycle 12.

  10. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2013-10-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold distribution procedure. The fold distribution provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of change in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Distribution, Proposal 13149, as Cycle 20.

  11. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2011-10-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Analysis, Proposal 12416, as Cycle 18.

  12. 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

  13. 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. PMID:19937658

  14. Properties of dynamically compacted WIPP salt

    SciTech Connect

    Brodsky, N.S.; Hansen, F.D.; Pfeifle, T.W.

    1996-07-01

    Dynamic compaction of mine-run salt is being investigated for the Waste Isolation Pilot Plant (WIPP), where compacted salt is being considered for repository sealing applications. One large-scale and two intermediate-scale dynamic compaction demonstrations were conducted. Initial fractional densities of the compacted salt range form 0.85 to 0.90, and permeabilities vary. Dynamically-compacted specimens were further consolidated in the laboratory by application of hydrostatic pressure. Permeability as a function of density was determined, and consolidation microprocesses were studied. Experimental results, in conjunction with modeling results, indicate that the compacted salt will function as a viable seal material.

  15. 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.

  16. Probing the cytochrome c' folding landscape.

    PubMed

    Pletneva, Ekaterina V; Zhao, Ziqing; Kimura, Tetsunari; Petrova, Krastina V; Gray, Harry B; Winkler, Jay R

    2007-11-01

    The folding kinetics of R. palustris cytochrome c' (cyt c') have been monitored by heme absorption and native Trp72 fluorescence at pH 5. The Trp72 fluorescence burst signal suggests early compaction of the polypeptide ensemble. Analysis of heme transient absorption spectra reveals deviations from two-state behavior, including a prominent slow phase that is accelerated by the prolyl isomerase cyclophilin. A nonnative proline configuration (Pro21) likely interferes with the formation of the helical bundle surrounding the heme.

  17. Designing the structure and folding pathway of modular topological bionanostructures.

    PubMed

    Ljubetič, A; Drobnak, I; Gradišar, H; Jerala, R

    2016-04-18

    Polypeptides and polynucleotides are programmable natural polymers whose linear sequence can be easily designed and synthesized by the cellular transcription/translation machinery. Nature primarily uses proteins as the molecular machines and nucleic acids as the medium for the manipulation of heritable information. A protein's tertiary structure and function is defined by multiple cooperative weak long-range interactions that have been optimized through evolution. DNA nanotechnology uses orthogonal pairwise interacting modules of complementary nucleic acids as a strategy to construct defined complex 3D structures. A similar approach has recently been applied to protein design, using orthogonal dimerizing coiled-coil segments as interacting modules. When concatenated into a single polypeptide chain, they self-assemble into the 3D structure defined by the topology of interacting modules within the chain. This approach allows the construction of geometric polypeptide scaffolds, bypassing the folding problem of compact proteins by relying on decoupled pairwise interactions. However, the folding pathway still needs to be optimized in order to allow rapid self-assembly under physiological conditions. Again the modularity of designed topological structures can be used to define the rules that guide the folding pathway of long polymers, such as DNA, based on the stability and topology of connected building modules. This approach opens the way towards incorporation of designed foldamers in biological systems and their functionalization. PMID:27001947

  18. Mathematics Through Paper Folding.

    ERIC Educational Resources Information Center

    Olson, Alton T.

    This booklet is a revised edition of Donovan Johnson's "Paper Folding for the Mathematics Class" (ED 077 711). It begins with directions for folding basic constructions such as as a straight line, the line perpendicular to a given line passing through a given point, and the bisector of an angle. Subsequent chapters cover concepts related to…

  19. 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.

  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. 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.

  3. Protein Folding and Misfolding on Surfaces

    PubMed Central

    Stefani, Massimo

    2008-01-01

    Protein folding, misfolding and aggregation, as well as the way misfolded and aggregated proteins affects cell viability are emerging as key themes in molecular and structural biology and in molecular medicine. Recent advances in the knowledge of the biophysical basis of protein folding have led to propose the energy landscape theory which provides a consistent framework to better understand how a protein folds rapidly and efficiently to the compact, biologically active structure. The increased knowledge on protein folding has highlighted its strict relation to protein misfolding and aggregation, either process being in close competition with the other, both relying on the same physicochemical basis. The theory has also provided information to better understand the structural and environmental factors affecting protein folding resulting in protein misfolding and aggregation into ordered or disordered polymeric assemblies. Among these, particular importance is given to the effects of surfaces. The latter, in some cases make possible rapid and efficient protein folding but most often recruit proteins/peptides increasing their local concentration thus favouring misfolding and accelerating the rate of nucleation. It is also emerging that surfaces can modify the path of protein misfolding and aggregation generating oligomers and polymers structurally different from those arising in the bulk solution and endowed with different physical properties and cytotoxicities. PMID:19330090

  4. NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2009-07-01

    The performance of MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS SMOV as proposal 13555 {visit 5}.

  5. Semiempirical prediction of protein folds

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel; Colubri, Andrés; Appignanesi, Gustavo

    2001-08-01

    We introduce a semiempirical approach to predict ab initio expeditious pathways and native backbone geometries of proteins that fold under in vitro renaturation conditions. The algorithm is engineered to incorporate a discrete codification of local steric hindrances that constrain the movements of the peptide backbone throughout the folding process. Thus, the torsional state of the chain is assumed to be conditioned by the fact that hopping from one basin of attraction to another in the Ramachandran map (local potential energy surface) of each residue is energetically more costly than the search for a specific (Φ, Ψ) torsional state within a single basin. A combinatorial procedure is introduced to evaluate coarsely defined torsional states of the chain defined ``modulo basins'' and translate them into meaningful patterns of long range interactions. Thus, an algorithm for structure prediction is designed based on the fact that local contributions to the potential energy may be subsumed into time-evolving conformational constraints defining sets of restricted backbone geometries whereupon the patterns of nonbonded interactions are constructed. The predictive power of the algorithm is assessed by (a) computing ab initio folding pathways for mammalian ubiquitin that ultimately yield a stable structural pattern reproducing all of its native features, (b) determining the nucleating event that triggers the hydrophobic collapse of the chain, and (c) comparing coarse predictions of the stable folds of moderately large proteins (N~100) with structural information extracted from the protein data bank.

  6. Unified compaction curve model for tensile strength of tablets made by roller compaction and direct compression.

    PubMed

    Farber, Leon; Hapgood, Karen P; Michaels, James N; Fu, Xi-Young; Meyer, Robert; Johnson, Mary-Ann; Li, Feng

    2008-01-01

    A model that describes the relationship between roller-compaction conditions and tablet strength is proposed. The model assumes that compaction is cumulative during roller compaction and subsequent granule compaction, and compact strength (ribbon and tablet) is generated irreversibly as if strength is controlled by plastic deformation of primary particles only. Roller-compaction is treated as a compaction step where the macroscopic ribbon strength is subsequently destroyed in milling. This loss in strength is irreversible and tablets compressed from the resulting granulation are weaker than those compressed by direct compression at the same compression force. Roller-compacted ribbons were produced at a range of roll forces for three formulations and subsequently milled and compacted into tablets. Once the total compaction history is taken in account, the compaction behavior of the uncompacted blends and the roller-compacted granules ultimately follow a single master compaction curve--a unified compaction curve (UCC). The model successfully described the compaction behavior of DC grade starch and formulations of lactose monohydrate with 50% or more microcrystalline cellulose, and may be more generally applicable to systems containing significant proportions of any plastically deforming material, including MCC and starch. PMID:17689211

  7. 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

  8. Folding without charges

    PubMed Central

    Kurnik, Martin; Hedberg, Linda; Danielsson, Jens; Oliveberg, Mikael

    2012-01-01

    Surface charges of proteins have in several cases been found to function as “structural gatekeepers,” which avoid unwanted interactions by negative design, for example, in the control of protein aggregation and binding. The question is then if side-chain charges, due to their desolvation penalties, play a corresponding role in protein folding by avoiding competing, misfolded traps? To find out, we removed all 32 side-chain charges from the 101-residue protein S6 from Thermus thermophilus. The results show that the charge-depleted S6 variant not only retains its native structure and cooperative folding transition, but folds also faster than the wild-type protein. In addition, charge removal unleashes pronounced aggregation on longer timescales. S6 provides thus an example where the bias toward native contacts of a naturally evolved protein sequence is independent of charges, and point at a fundamental difference in the codes for folding and intermolecular interaction: specificity in folding is governed primarily by hydrophobic packing and hydrogen bonding, whereas solubility and binding relies critically on the interplay of side-chain charges. PMID:22454493

  9. Folded supersymmetry with a twist

    DOE PAGESBeta

    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. 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

  10. 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.

  11. 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.

  12. Ceramic powder compaction

    SciTech Connect

    Glass, S.J.; Ewsuk, K.G.; Mahoney, F.M.

    1995-12-31

    With the objective of developing a predictive model for ceramic powder compaction we have investigated methods for characterizing density gradients in ceramic powder compacts, reviewed and compared existing compaction models, conducted compaction experiments on a spray dried alumina powder, and conducted mechanical tests and compaction experiments on model granular materials. Die filling and particle packing, and the behavior of individual granules play an important role in determining compaction behavior and should be incorporated into realistic compaction models. These results support the use of discrete element modeling techniques and statistical mechanics principals to develop a comprehensive model for compaction, something that should be achievable with computers with parallel processing capabilities.

  13. 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…

  14. 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.

  15. Domains in folding of model proteins.

    PubMed Central

    Abkevich, V. I.; Gutin, A. M.; Shakhnovich, E. I.

    1995-01-01

    By means of Monte Carlo simulation, we investigated the equilibrium between folded and unfolded states of lattice model proteins. The amino acid sequences were designed to have pronounced energy minimum target conformations of different length and shape. For short fully compact (36-mer) proteins, the all-or-none transition from the unfolded state to the native state was observed. This was not always the case for longer proteins. Among 12 designed sequences with the native structure of a fully compact 48-mer, a simple all-or-none transition was observed in only three cases. For the other nine sequences, three states of behavior-the native, denatured, and intermediate states-were found. The contiguous part of the native structure (domain) was conserved in the intermediate state, whereas the remaining part was completely unfolded and structureless. These parts melted separately from each other. PMID:7549881

  16. Geometry and wetting of capillary folding.

    PubMed

    Péraud, Jean-Philippe; Lauga, Eric

    2014-04-01

    Capillary forces are involved in a variety of natural phenomena, ranging from droplet breakup to the physics of clouds. The forces from surface tension can also be exploited in industrial applications provided the length scales involved are small enough. Recent experimental investigations showed how to take advantage of capillarity to fold planar structures into three-dimensional configurations by selectively melting polymeric hinges joining otherwise rigid shapes. In this paper we use theoretical calculations to quantify the role of geometry and fluid wetting on the final folded state. Considering folding in two and three dimensions, studying both hydrophilic and hydrophobic situations with possible contact-angle hysteresis, and addressing the shapes to be folded to be successively infinite, finite, curved, kinked, and elastic, we are able to derive an overview of the geometrical parameter space available for capillary folding.

  17. Visualizing chaperone-assisted protein folding.

    PubMed

    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 C A

    2016-07-01

    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. 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 new 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 Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone. PMID:27239796

  18. 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.

  19. 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.

  20. Lighted, Folding Inspection Mirror

    NASA Technical Reports Server (NTRS)

    Roepe, Brian E.

    1991-01-01

    Compact, inexpensive tool used in place of expensive borescopes. Shortens inspection/photographing process. Includes two small metal or glass mirrors hinged together. Two 3-V light bulbs attached along edges of one mirror and connected to battery of two cells. Inserted into narrow opening of clevis or tand, and surface viewed and photographed in opposite mirror. Useful in assembly of segments of solid rocket motors as well as in postflight assessment, engineering evaluation, and refurbishment. Also applied in general to inspection and photographing of inner sealing surfaces to which access difficult.

  1. Freeform lens collimating spectrum-folded Hadamard transform near-infrared spectrometer

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoduo; Liu, Hua; Juschkin, Larissa; Li, Yunpeng; Xu, Jialin; Quan, Xiangqian; Lu, Zhenwu

    2016-12-01

    A novel Hadamard transform spectrometer collimated by a freeform lens has been designed, which doubles the working spectral range while the spectral resolution is maintained. The freeform lens is designed to redistribute the broadband spectra of the source from 800 nm to 2400 nm into two collimated beams with different wavelengths and different tilting angles, to achieve the folding of spectra on the digital micro-mirror devices (DMD). It is constructed by solving two partial differential equations. The grating diffraction efficiency of the two split beams are more uniform and higher compared with the traditional method. The simulation results show that the bandwidth of the spectrometer is doubled and the spectral resolution is better than 10 nm. The optical system becomes more compact, and the energy efficiency is improved by 11.98% by folding the spectra with one freeform lens and one grating.

  2. Oxidative folding: recent developments.

    PubMed

    Szarka, András; Bánhegyi, Gábor

    2011-10-01

    Disulfide bond formation in proteins is an effective tool of both structure stabilization and redox regulation. The prokaryotic periplasm and the endoplasmic reticulum of eukaryotes were long considered as the only compartments for enzyme mediated formation of stable disulfide bonds. Recently, the mitochondrial intermembrane space has emerged as the third protein-oxidizing compartment. The classic view on the mechanism of oxidative folding in the endoplasmic reticulum has also been reshaped by new observations. Moreover, besides the structure stabilizing function, reversible disulfide bridge formation in some proteins of the endoplasmic reticulum, seems to play a regulatory role. This review briefly summarizes the present knowledge of the redox systems supporting oxidative folding, emphasizing recent developments. PMID:25962043

  3. 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

  4. 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)

  5. 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.

  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. 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

  8. 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.

  9. 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

  10. Folding of Pollen Grains

    NASA Astrophysics Data System (ADS)

    Katifori, Eleni; Alben, Silas; Cerda, Enrique; Nelson, David; Dumais, Jacques

    2008-03-01

    At dehiscence, which occurs when the anther reaches maturity and opens, pollen grains dehydrate and their volume is reduced. The pollen wall deforms to accommodate the volume loss, and the deformation pathway depends on the initial turgid pollen grain geometry and the mechanical properties of the pollen wall. We demonstrate, using both experimental and theoretical approaches, that the design of the apertures (areas on the pollen wall where the stretching and the bending modulus are reduced) is critical for controlling the folding pattern, and ensures the pollen grain viability. An excellent fit to the experiments is obtained using a discretized version of the theory of thin elastic shells.

  11. 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. PMID:25107533

  12. Single-Molecule Studies of the Im7 Folding Landscape

    PubMed Central

    Pugh, Sara D.; Gell, Christopher; Smith, D. Alastair; Radford, Sheena E.; Brockwell, David J.

    2010-01-01

    Under appropriate conditions, the four-helical Im7 (immunity protein 7) folds from an ensemble of unfolded conformers to a highly compact native state via an on-pathway intermediate. Here, we investigate the unfolded, intermediate, and native states populated during folding using diffusion single-pair fluorescence resonance energy transfer by measuring the efficiency of energy transfer (or proximity or P ratio) between pairs of fluorophores introduced into the side chains of cysteine residues placed in the center of helices 1 and 4, 1 and 3, or 2 and 4. We show that while the native states of each variant give rise to a single narrow distribution with high P values, the distributions of the intermediates trapped at equilibrium (denoted Ieqm) are fitted by two Gaussian distributions. Modulation of the folding conditions from those that stabilize the intermediate to those that destabilize the intermediate enabled the distribution of lower P value to be assigned to the population of the unfolded ensemble in equilibrium with the intermediate state. The reduced stability of the Ieqm variants allowed analysis of the effect of denaturant concentration on the compaction and breadth of the unfolded state ensemble to be quantified from 0 to 6 M urea. Significant compaction is observed as the concentration of urea is decreased in both the presence and absence of sodium sulfate, as previously reported for a variety of proteins. In the presence of Na2SO4 in 0 M urea, the P value of the unfolded state ensemble approaches that of the native state. Concurrent with compaction, the ensemble displays increased peak width of P values, possibly reflecting a reduction in the rate of conformational exchange among iso-energetic unfolded, but compact conformations. The results provide new insights into the initial stages of folding of Im7 and suggest that the unfolded state is highly conformationally constrained at the outset of folding. PMID:20211187

  13. Single-molecule studies of the Im7 folding landscape.

    PubMed

    Pugh, Sara D; Gell, Christopher; Smith, D Alastair; Radford, Sheena E; Brockwell, David J

    2010-04-23

    Under appropriate conditions, the four-helical Im7 (immunity protein 7) folds from an ensemble of unfolded conformers to a highly compact native state via an on-pathway intermediate. Here, we investigate the unfolded, intermediate, and native states populated during folding using diffusion single-pair fluorescence resonance energy transfer by measuring the efficiency of energy transfer (or proximity or P ratio) between pairs of fluorophores introduced into the side chains of cysteine residues placed in the center of helices 1 and 4, 1 and 3, or 2 and 4. We show that while the native states of each variant give rise to a single narrow distribution with high P values, the distributions of the intermediates trapped at equilibrium (denoted I(eqm)) are fitted by two Gaussian distributions. Modulation of the folding conditions from those that stabilize the intermediate to those that destabilize the intermediate enabled the distribution of lower P value to be assigned to the population of the unfolded ensemble in equilibrium with the intermediate state. The reduced stability of the I(eqm) variants allowed analysis of the effect of denaturant concentration on the compaction and breadth of the unfolded state ensemble to be quantified from 0 to 6 M urea. Significant compaction is observed as the concentration of urea is decreased in both the presence and absence of sodium sulfate, as previously reported for a variety of proteins. In the presence of Na(2)SO(4) in 0 M urea, the P value of the unfolded state ensemble approaches that of the native state. Concurrent with compaction, the ensemble displays increased peak width of P values, possibly reflecting a reduction in the rate of conformational exchange among iso-energetic unfolded, but compact conformations. The results provide new insights into the initial stages of folding of Im7 and suggest that the unfolded state is highly conformationally constrained at the outset of folding.

  14. Improved Method of Design for Folding Inflatable Shells

    NASA Technical Reports Server (NTRS)

    Johnson, Christopher J.

    2009-01-01

    An improved method of designing complexly shaped inflatable shells to be assembled from gores was conceived for original application to the inflatable outer shell of a developmental habitable spacecraft module having a cylindrical mid-length section with toroidal end caps. The method is also applicable to inflatable shells of various shapes for terrestrial use. The method addresses problems associated with the assembly, folding, transport, and deployment of inflatable shells that may comprise multiple layers and have complex shapes that can include such doubly curved surfaces as toroids and spheres. One particularly difficult problem is that of mathematically defining fold lines on a gore pattern in a double- curvature region. Moreover, because the fold lines in a double-curvature region tend to be curved, there is a practical problem of how to implement the folds. Another problem is that of modifying the basic gore shapes and sizes for the various layers so that when they are folded as part of the integral structure, they do not mechanically interfere with each other at the fold lines. Heretofore, it has been a common practice to design an inflatable shell to be assembled in the deployed configuration, without regard for the need to fold it into compact form. Typically, the result has been that folding has been a difficult, time-consuming process resulting in a An improved method of designing complexly shaped inflatable shells to be assembled from gores was conceived for original application to the inflatable outer shell of a developmental habitable spacecraft module having a cylindrical mid-length section with toroidal end caps. The method is also applicable to inflatable shells of various shapes for terrestrial use. The method addresses problems associated with the assembly, folding, transport, and deployment of inflatable shells that may comprise multiple layers and have complex shapes that can include such doubly curved surfaces as toroids and spheres. One

  15. Folded waveguide coupler for ion cyclotron heating

    SciTech Connect

    Owens, T.L.; Chen, G.L.

    1986-01-01

    A new type of waveguide coupler for plasma heating in the ion cyclotron range of frequencies is described. The coupler consists of a series of interleaved metallic vanes within a rectangular enclosure analogous to a wide rectangular waveguide that has been ''folded'' several times. At the mouth of the coupler, a plate is attached which contains coupling apertures in each fold or every other fold of the waveguide, depending upon the wavenumber spectrum desired. This plate serves primarily as a wave field polarizer that converts coupler fields to the polarization of the fast magnetosonic wave within the plasma. Theoretical estimates indicate that the folded waveguide is capable of high-efficiency, multimegawatt operation into a plasma. Bench tests have verified the predicted field structure within the waveguide in preparation for high-power tests on the Radio Frequency Test Facility at the Oak Ridge National Laboratory.

  16. 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.

  17. 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.

  18. Folded pendulum tiltmeter

    NASA Astrophysics Data System (ADS)

    Wu, Shuchao; Fan, Shuhua; Luo, Jun; Hsu, Houtse

    2002-05-01

    The application of the folded pendulum (FP) as a tiltmeter is proposed and some features of it have been studied both theoretically and experimentally. First, FP could have a quite low resonance frequency due to its mechanical structure. The period of our prototype FP is 6.2 s and the amplification factor is about 100. Second, FP is not sensitive to the environmental temperature variation but seriously affected by the temperature gradient. The experiment with a temperature gradient modulation shows that the static equilibrium position of the FP will change by 2.5 μrad if the temperature difference between the horizontal platform and the base of the FP is 0.1 °C. With a prototype FP, we have observed obvious tilt tides, and the calibration result shows that the resolution of the FP is about 1.2 nrad.

  19. 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.

  20. Experimental investigation of protein folding and misfolding.

    PubMed

    Dobson, Christopher M

    2004-09-01

    Newly synthesised proteins need to fold, often to intricate and close-packed structures, in order to function. The underlying mechanism by which this complex process takes place both in vitro and in vivo is now becoming understood, at least in general terms, as a result of the application of a wide range of biophysical and computational methods used in combination with the techniques of biochemistry and protein engineering. It is increasingly apparent, however, that folding is not only crucial for generating biological activity, but that it is also coupled to a wide range of processes within the cell, ranging from the trafficking of proteins to specific organelles to the regulation of cell growth and differentiation. Not surprisingly, therefore, the failure of proteins to fold appropriately, or to remain correctly folded, is associated with a large number of cellular malfunctions that give rise to disease. Misfolding, and its consequences such as aggregation, can be investigated by extending the types of techniques used to study the normal folding process. Application of these techniques is enabling the development of a unified description of the interconversion and regulation of the different conformational states available to proteins in living systems. Such a description proves a generic basis for understanding the fundamental links between protein misfolding and its associated clinical disorders, such as Alzheimer's disease and Type II diabetes, and for exploring novel therapeutic strategies directed at their prevention and treatment on a rational basis.

  1. 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.

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Schmalholz, S. M.; Podladchikov, Y. Y.; Burg, J.-P.

    2002-01-01

    We show that folding of a non-Newtonian layer resting on a homogeneous Newtonian matrix with finite thickness under influence of gravity can occur by three modes: (1) matrix-controlled folding, dependent on the effective viscosity contrast between layer and matrix, (2) gravity-controlled folding, dependent on the Argand number (the ratio of the stress caused by gravity to the stress caused by shortening), and (3) detachment folding, dependent on the ratio of matrix thickness to layer thickness. We construct a phase diagram that defines the transitions between each of the three folding modes. Our priority is transparency of the analytical derivations (e.g., thin-plate versus thick-plate approximations), which permits complete classification of the folding modes involving a minimum number of dimensionless parameters. Accuracy and sensitivity of the analytical results to model assumptions are investigated. In particular, depth dependence of matrix rheology is only important for folding over a narrow range of material parameters. In contrast, strong depth dependence of the viscosity of the folding layer limits applicability of ductile rheology and leads to a viscoelastic transition. Our theory is applied to estimate the effective thickness of the folded central Asian upper crust using the ratio of topographic wavelength to Moho depth. Phase diagrams based on geometrical parameters show that gravity does not significantly control folding in the Jura and the Zagros Mountains but does control folding in central Asia. Applicability conditions of viscous and thin sheet models for large-scale lithospheric deformation, derived in terms of the Argand number, have implications for the plate-like style of planetary tectonics.

  5. Protein folding in the ER.

    SciTech Connect

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

    1999-10-01

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

  6. Mouse Embryo Compaction.

    PubMed

    White, M D; Bissiere, S; Alvarez, Y D; Plachta, N

    2016-01-01

    Compaction is a critical first morphological event in the preimplantation development of the mammalian embryo. Characterized by the transformation of the embryo from a loose cluster of spherical cells into a tightly packed mass, compaction is a key step in the establishment of the first tissue-like structures of the embryo. Although early investigation of the mechanisms driving compaction implicated changes in cell-cell adhesion, recent work has identified essential roles for cortical tension and a compaction-specific class of filopodia. During the transition from 8 to 16 cells, as the embryo is compacting, it must also make fundamental decisions regarding cell position, polarity, and fate. Understanding how these and other processes are integrated with compaction requires further investigation. Emerging imaging-based techniques that enable quantitative analysis from the level of cell-cell interactions down to the level of individual regulatory molecules will provide a greater understanding of how compaction shapes the early mammalian embryo. PMID:27475854

  7. A New Heuristic Algorithm for Protein Folding in the HP Model.

    PubMed

    Traykov, Metodi; Angelov, Slav; Yanev, Nicola

    2016-08-01

    This article presents an efficient heuristic for protein folding. The protein folding problem is to predict the compact three-dimensional structure of a protein based on its amino acid sequence. The focus is on an original integer programming model derived from a platform used for Contact Map Overlap problem.

  8. Evolutionary optimization of protein folding.

    PubMed

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

    2013-01-01

    Nature has shaped the make up of proteins since their appearance, [Formula: see text]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 [Formula: see text]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. Reversible DNA compaction.

    PubMed

    González-Pérez, Alfredo

    2014-01-01

    In this review we summarize and discuss the different methods we can use to achieve reversible DNA compaction in vitro. Reversible DNA compaction is a natural process that occurs in living cells and viruses. As a result these process long sequences of DNA can be concentrated in a small volume (compacted) to be decompacted only when the information carried by the DNA is needed. In the current work we review the main artificial compacting agents looking at their suitability for decompaction. The different approaches used for decompaction are strongly influenced by the nature of the compacting agent that determines the mechanism of compaction. We focus our discussion on two main artificial compacting agents: multivalent cations and cationic surfactants that are the best known compacting agents. The reversibility of the process can be achieved by adding chemicals like divalent cations, alcohols, anionic surfactants, cyclodextrins or by changing the chemical nature of the compacting agents via pH modifications, light induced conformation changes or by redox-reactions. We stress the relevance of electrostatic interactions and self-assembly as a main approach in order to tune up the DNA conformation in order to create an on-off switch allowing a transition between coil and compact states. The recent advances to control DNA conformation in vitro, by means of molecular self-assembly, result in a better understanding of the fundamental aspects involved in the DNA behavior in vivo and serve of invaluable inspiration for the development of potential biomedical applications. PMID:24444152

  10. 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

    2013-10-01

    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.

  11. Early Events in RNA Folding

    NASA Astrophysics Data System (ADS)

    Thirumalai, D.; Lee, Namkyung; Woodson, Sarah A.; Klimov, Dk

    2001-10-01

    We describe a conceptual framework for understanding the way large RNA molecules fold based on the notion that their free-energy landscape is rugged. A key prediction of our theory is that RNA folding can be described by the kinetic partitioning mechanism (KPM). According to KPM a small fraction of molecules folds rapidly to the native state whereas the remaining fraction is kinetically trapped in a low free-energy non-native state. This model provides a unified description of the way RNA and proteins fold. Single-molecule experiments on Tetrahymena ribozyme, which directly validate our theory, are analyzed using KPM. We also describe the earliest events that occur on microsecond time scales in RNA folding. These must involve collapse of RNA molecules that are mediated by counterion-condensation. Estimates of time scales for the initial events in RNA folding are provided for the Tetrahymena ribozyme.

  12. Kinetic Intermediates in RNA Folding

    NASA Astrophysics Data System (ADS)

    Zarrinkar, Patrick P.; Williamson, James R.

    1994-08-01

    The folding pathways of large, highly structured RNA molecules are largely unexplored. Insight into both the kinetics of folding and the presence of intermediates was provided in a study of the Mg2+-induced folding of the Tetrahymena ribozyme by hybridization of complementary oligodeoxynucleotide probes. This RNA folds via a complex mechanism involving both Mg2+-dependent and Mg2+-independent steps. A hierarchical model for the folding pathway is proposed in which formation of one helical domain (P4-P6) precedes that of a second helical domain (P3-P7). The overall rate-limiting step is formation of P3-P7, and takes place with an observed rate constant of 0.72 ± 0.14 minute-1. The folding mechanism of large RNAs appears similar to that of many multidomain proteins in that formation of independently stable substructures precedes their association into the final conformation.

  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. Physical experiments of transpressional folding

    NASA Astrophysics Data System (ADS)

    Tikoff, Basil; Peterson, Karl

    1998-06-01

    In order to understand the process of folding in obliquely convergent settings, we formed folds within a shear box capable of creating homogeneous transpressional deformations. Folds were created in a single layer of stiff mixed plasticine and silicone that overlay a Newtonian silicone, for a variety of plate convergence angles. As small amplitude folds became visible, they were parallel to the long axis of the horizontal finite strain ellipse. With increasing deformation, the fold hinges rotated parallel with the long axis of the horizontal finite strain ellipse for all angles of convergence. This parallelism indicates that fold hinges, once formed, rotate with the horizontal strain ellipse rather than as material lines. The experiments highlight several interesting effects of transpression dynamics. The fold hinges initiate parallel to either ṡ1 or ṡ2 and are parallel to either S1 or S2 with increasing deformation. Neither infinitesimal strain (stress) nor finite strain is resolvable solely from fold geometry. Further, the net amount of contraction determined by folding across the zone was overestimated in all cases except pure contraction. This effect is obvious for the case of wrenching, where folding implies that the zone contracts if elongation parallel to the fold hinge is not considered. Therefore, attempts to balance cross-sections in transpressional zones will tend to overestimate contraction unless the wrench component of deformation is addressed. This result is validated by applying the modeling results in folding in central California adjacent to the San Andreas fault, where cross-section balancing indicates higher amounts of contraction than predicted by plate motion.

  15. COS NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2010-09-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS MAMA Fold Analysis {11891} during Cycle 17.

  16. COS NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2012-10-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS MAMA Fold Analysis {12723} during Cycle 19.

  17. Folding superfunnel to describe cooperative folding of interacting proteins.

    PubMed

    Smeller, László

    2016-07-01

    This paper proposes a generalization of the well-known folding funnel concept of proteins. In the funnel model the polypeptide chain is treated as an individual object not interacting with other proteins. Since biological systems are considerably crowded, protein-protein interaction is a fundamental feature during the life cycle of proteins. The folding superfunnel proposed here describes the folding process of interacting proteins in various situations. The first example discussed is the folding of the freshly synthesized protein with the aid of chaperones. Another important aspect of protein-protein interactions is the folding of the recently characterized intrinsically disordered proteins, where binding to target proteins plays a crucial role in the completion of the folding process. The third scenario where the folding superfunnel is used is the formation of aggregates from destabilized proteins, which is an important factor in case of several conformational diseases. The folding superfunnel constructed here with the minimal assumption about the interaction potential explains all three cases mentioned above. Proteins 2016; 84:1009-1016. © 2016 Wiley Periodicals, Inc.

  18. 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

  19. Protein folding under confinement: A role for solvent

    PubMed Central

    Lucent, Del; Vishal, V.; Pande, Vijay S.

    2007-01-01

    Although most experimental and theoretical studies of protein folding involve proteins in vitro, the effects of spatial confinement may complicate protein folding in vivo. In this study, we examine the folding dynamics of villin (a small fast folding protein) with explicit solvent confined to an inert nanopore. We have calculated the probability of folding before unfolding (Pfold) under various confinement regimes. Using Pfold correlation techniques, we observed two competing effects. Confining protein alone promotes folding by destabilizing the unfolded state. In contrast, confining both protein and solvent gives rise to a solvent-mediated effect that destabilizes the native state. When both protein and solvent are confined we see unfolding to a compact unfolded state different from the unfolded state seen in bulk. Thus, we demonstrate that the confinement of solvent has a significant impact on protein kinetics and thermodynamics. We conclude with a discussion of the implications of these results for folding in confined environments such as the chaperonin cavity in vivo. PMID:17563390

  20. Mechanics of tissue compaction.

    PubMed

    Turlier, Hervé; Maître, Jean-Léon

    2015-12-01

    During embryonic development, tissues deform by a succession and combination of morphogenetic processes. Tissue compaction is the morphogenetic process by which a tissue adopts a tighter structure. Recent studies characterized the respective roles of cells' adhesive and contractile properties in tissue compaction. In this review, we formalize the mechanical and molecular principles of tissue compaction and we analyze through the prism of this framework several morphogenetic events: the compaction of the early mouse embryo, the formation of the fly retina, the segmentation of somites and the separation of germ layers during gastrulation.

  1. 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

  2. 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

  3. Structural Bridges through Fold Space.

    PubMed

    Edwards, Hannah; Deane, Charlotte M

    2015-09-01

    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.

  4. Novel sequences propel familiar folds.

    PubMed

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  5. 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…

  6. COS NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2013-10-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as Cycle 20 proposal 13128.

  7. Multidimensional theory of protein folding

    NASA Astrophysics Data System (ADS)

    Itoh, Kazuhito; Sasai, Masaki

    2009-04-01

    Theory of multidimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in terms of cooperativity within individual regions and interactions among multiple regions and thus obtained classification is used to analyze the folding process of several example proteins. Ribosomal protein S6, src-SH3 domain, CheY, barnase, and BBL domain are analyzed with the two-dimensional representation by using a structure-based Hamiltonian model. The extension to the higher dimensional representation leads to the finer description of the folding process. Barnase, NtrC, and an ankyrin repeat protein are examined with the three-dimensional representation. The multidimensional representation allows us to directly address questions on folding pathways, intermediates, and transition states.

  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. Generation of buckle folds in Naga fold thrust belt, north-east India

    NASA Astrophysics Data System (ADS)

    Saha, B.; Dietl, C.

    2009-04-01

    of the layer. The experiments are performed in a low stress and low temperature environment (ambient temperature being room temperature). The models produce a spectrum of fold shapes ranging from tight asymmetric to gentle. The folds generate initially as gentle folds with rounded hinges in the thick incompetent mica layers and box folds in the thin incompetent mica layers. Thrusts develop and grow by intersecting the existing fold limbs. With incremental compression, the folds become tighter. The thin mica layer is more affected by thrusting than the thicker layer. Our models have a clear advantage of using mixed layer models (sand + mica) over that of pure sand models, because mica accommodates the applied stress both by folding and thrusting. The pure sand models fail to reflect the subtle competence contrast and thus the buckle folds though they excellently simulate the upper crustal layer deformation through thrusting. From our experiments we infer that the difference in fold and thrust morphology is governed by the interplay of two main factors; namely: degree of competence contrast and thickness of competent unit. High mechanical anisotropy give rise to box folds with steep straight limbs, horizontal hinge and conjugate axial planes when the competent unit is a thick one; whereas comparatively low mechanical anisotropy generates rounded buckle fold when the competent unit is a thin one. The geometry of the buckle folds in the NFTB are in good agreement with our experimentally produced buckle folds. The competence contrast throughout the belt has been consistent, only minor variations of sand-shale content have been observed. The competence contrast remaining more or less constant throughout the region, the variable thickness of the stratigraphic units plays a significant role in determining the fold shape. The thicker incompetent units give rise to rounded tight folds and the thinner ones to open box shaped folds, both modified by simultaneously or later

  10. 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.

  11. Folding Myoglobin within a Sol-Gel Glass: Protein Folding Constrained to a Small Volume

    PubMed Central

    Peterson, Eric S.; Leonard, Emma F.; Foulke, Jocelyn A.; Oliff, Matthew C.; Salisbury, Rosanne D.; Kim, David Y.

    2008-01-01

    The unfolding and refolding reaction of myoglobin was examined in solution and within a porous silica sol-gel glass. The sol-gel pores constrain the protein to a volume that is the same size and shape as the folded native state accompanied by a few layers of water solvation. Denaturants such as low pH buffers can be diffused through the gel pores to the protein to initiate unfolding and refolding. Acid-induced unfolding was hindered by the steric constraints imposed by the gel pores such that more denaturing conditions were required within the gel than in solution to create the unfolded state. No new folding intermediates were observed. Refolding of myoglobin was not complete in millimolar pH 7 buffer alone. Addition of 25% glycerol to the pH 7 buffer resulted in nearly complete refolding, and the use of 1 M phosphate buffer resulted in complete refolding. The role of this cosolvent and salt in disrupting the ordered water surrounding the protein within the gel is discussed in light of the Hofmeister series and entropic trapping via a diminished hydrophobic effect within the gel. These results are consistent with the premises of folding models in which secondary and tertiary structures are considered to form within a compact conformation of the protein backbone. PMID:18339762

  12. Fast events in protein folding

    SciTech Connect

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

    1996-04-01

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

  13. 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.

  14. Compaction properties of isomalt.

    PubMed

    Bolhuis, Gerad K; Engelhart, Jeffrey J P; Eissens, Anko C

    2009-08-01

    Although other polyols have been described extensively as filler-binders in direct compaction of tablets, the polyol isomalt is rather unknown as pharmaceutical excipient, in spite of its description in all the main pharmacopoeias. In this paper the compaction properties of different types of ispomalt were studied. The types used were the standard product sieved isomalt, milled isomalt and two types of agglomerated isomalt with a different ratio between 6-O-alpha-d-glucopyranosyl-d-sorbitol (GPS) and 1-O-alpha-d-glucopyranosyl-d-mannitol dihydrate (GPM). Powder flow properties, specific surface area and densities of the different types were investigated. Compactibility was investigated by compression of the tablets on a compaction simulator, simulating the compression on high-speed tabletting machines. Lubricant sensitivity was measured by compressing unlubricated tablets and tablets lubricated with 1% magnesium stearate on an instrumented hydraulic press. Sieved isomalt had excellent flow properties but the compactibility was found to be poor whereas the lubricant sensitivity was high. Milling resulted in both a strong increase in compactibility as an effect of the higher surface area for bonding and a decrease in lubricant sensitivity as an effect of the higher surface area to be coated with magnesium stearate. However, the flow properties of milled isomalt were too bad for use as filler-binder in direct compaction. Just as could be expected, agglomeration of milled isomalt by fluid bed agglomeration improved flowability. The good compaction properties and the low lubricant sensitivity were maintained. This effect is caused by an early fragmentation of the agglomerated material during the compaction process, producing clean, lubricant-free particles and a high surface for bonding. The different GPS/GPM ratios of the agglomerated isomalt types studied had no significant effect on the compaction properties. PMID:19327398

  15. 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.

  16. Peptide folding in the presence of interacting protein crowders

    NASA Astrophysics Data System (ADS)

    Bille, Anna; Mohanty, Sandipan; Irbäck, Anders

    2016-05-01

    Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotatable side-chains, whereas the peptides are free to fold and unfold. In the simulations, the crowder proteins tend to distort the trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depends on the crowder type. Due to a sticky patch on its surface, BPTI causes larger changes than GB1 in the melting properties of the peptides. The observed effects on the peptides stem largely from attractive and specific interactions with the crowder surfaces, and differ from those seen in reference simulations with purely steric crowder particles.

  17. Folding analysis of the most complex Stevedore's protein knot.

    PubMed

    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

  18. Rise of the Helix from a Collapsed Globule during the Folding of Monellin.

    PubMed

    Goluguri, Rama Reddy; Udgaonkar, Jayant B

    2015-09-01

    Early kinetic intermediates observed during the folding of many proteins are invariably compact and appear to possess some secondary structure. Consequently, it has been difficult to understand whether compaction drives secondary structure formation or secondary structure formation facilitates compaction during folding. In this study of the folding of single-chain monellin, it is shown that a kinetic molten globule (MG) is populated at 2 ms of folding. Far-UV circular dichroism (CD) measurements show that the kinetic MG is devoid of any helical structure even under the most stabilizing folding conditions. Multisite fluorescence resonance energy transfer (FRET) measurements show that the kinetic MG is compact with different segments having contracted to different extents. It is shown that the sequence segment that goes on to form the sole helix in the native protein is fully collapsed in the kinetic MG. This segment expands to accommodate the helix as the kinetic MG folds further to the native state, while other segments of the protein contract. Helix formation starting from the kinetic MG is shown to occur in multiple kinetic steps, whether measured by far-UV CD or by FRET. PMID:26258844

  19. 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.

  20. 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.

  1. Electrochemistry of folded graphene edges.

    PubMed

    Ambrosi, Adriano; Bonanni, Alessandra; Pumera, Martin

    2011-05-01

    There is enormous interest in the investigation of electron transfer rates at the edges of graphene due to possible energy storage and sensing applications. While electrochemistry at the edges and the basal plane of graphene has been studied in the past, the new frontier is the electrochemistry of folded graphene edges. Here we describe the electrochemistry of folded graphene edges and compare it to that of open graphene edges. The materials were characterized in detail by high-resolution transmission electron microscopy, Raman spectroscopy, high-resolution X-ray photoelectron spectroscopy, electrochemical impedance spectroscopy and cyclic voltammetry. We found that the heterogeneous electron transfer rate is significantly lower on folded graphene edges compared to open edge sites for ferro/ferricyanide, and that electrochemical properties of open edges offer lower potential detection of biomarkers than the folded ones. It is apparent, therefore, that for sensing and biosensing applications the folded edges are less active than open edges, which should then be preferred for such applications. As folded edges are the product of thermal treatment of multilayer graphene, such thermal procedures should be avoided when fabricating graphene for electrochemical applications.

  2. Self-folding graphene-polymer bilayers

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    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.

  3. 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.

  4. Late Quaternary folding of coral reef terraces, Barbados

    NASA Astrophysics Data System (ADS)

    Taylor, Frederick W.; Mann, Paul

    1991-02-01

    Uplifted late Ouaternary coral reefs on the island of Barbados record folding of the emergent crest of the Lesser Antilles accretionary prism (Barbados Ridge complex) since ca. 1 Ma. Three northeast striking folds are defined by systematic changes in altitudes in the crest of First High Cliff, a mostly constructional reef terrace about 125 ka, and Second High Cliff, a partially erosional reef terrace about 500 ka. The folds have wavelengths of 6 to 8 km and fold axes extend about 10 km. The largest anticline rises to the northeast, where it has been breached by erosion exposing highly deformed Eocene to lower Miocene rocks of the Scotland District. Uplift rates based on heights of the last interglacial First High Cliff range from 0.07 to 0.44 mm/yr. Quaternary folding on Barbados indicates that the crest of the accretionary prism continues to be an active fold belt undergoing northwestsoutheast shortening.

  5. 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.

  6. 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.

  7. 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.

  8. Compact turbidity meter

    NASA Technical Reports Server (NTRS)

    Hirschberg, J. G.

    1979-01-01

    Proposed monitor that detects back-reflected infrared radiation makes in situ turbidity measurements of lakes, streams, and other bodies of water. Monitor is compact, works well in daylight as at night, and is easily operated in rough seas.

  9. 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.

  10. Compaction Waves in Granular HMX

    SciTech Connect

    E. Kober; R. Menikoff

    1999-01-01

    Piston driven compaction waves in granular HMX are simulated with a two-dimensional continuum mechanics code in which individual grains are resolved. The constitutive properties of the grains are modeled with a hydrostatic pressure and a simple elastic-plastic model for the shear stress. Parameters are chosen to correspond to inert HMX. For a tightly packed random grain distribution (with initial porosity of 19%) we varied the piston velocity to obtain weak partly compacted waves and stronger fully compacted waves. The average stress and wave speed are compatible with the porous Hugoniot locus for uni- axial strain. However, the heterogeneities give rise to stress concentrations, which lead to localized plastic flow. For weak waves, plastic deformation is the dominant dissipative mechanism and leads to dispersed waves that spread out in time. In addition to dispersion, the granular heterogeneities give rise to subgrain spatial variation in the thermodynamic variables. The peaks in the temperature fluctuations, known as hot spots, are in the range such that they are the critical factor for initiation sensitivity.

  11. Folding of a large protein at high structural resolution

    PubMed Central

    Walters, Benjamin T.; Mayne, Leland; Hinshaw, James R.; Sosnick, Tobin R.; Englander, S. Walter

    2013-01-01

    Kinetic folding of the large two-domain maltose binding protein (MBP; 370 residues) was studied at high structural resolution by an advanced hydrogen-exchange pulse-labeling mass-spectrometry method (HX MS). Dilution into folding conditions initiates a fast molecular collapse into a polyglobular conformation (<20 ms), determined by various methods including small angle X-ray scattering. The compaction produces a structurally heterogeneous state with widespread low-level HX protection and spectroscopic signals that match the equilibrium melting posttransition-state baseline. In a much slower step (7-s time constant), all of the MBP molecules, although initially heterogeneously structured, form the same distinct helix plus sheet folding intermediate with the same time constant. The intermediate is composed of segments that are distant in the MBP sequence but adjacent in the native protein where they close the longest residue-to-residue contact. Segments that are most HX protected in the early molecular collapse do not contribute to the initial intermediate, whereas the segments that do participate are among the less protected. The 7-s intermediate persists through the rest of the folding process. It contains the sites of three previously reported destabilizing mutations that greatly slow folding. These results indicate that the intermediate is an obligatory step on the MBP folding pathway. MBP then folds to the native state on a longer time scale (∼100 s), suggestively in more than one step, the first of which forms structure adjacent to the 7-s intermediate. These results add a large protein to the list of proteins known to fold through distinct native-like intermediates in distinct pathways. PMID:24191053

  12. Capability enhancement in compact digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Qu, Weijuan; Wen, Yongfu; Wang, Zhaomin; Yang, Fang; Asundi, Anand

    2015-03-01

    A compact reflection digital holographic microscopy (DHM) system integrated with the light source and optical interferometer is developed for 3D topographic characterization and real-time dynamic inspection for Microelectromechanical systems (MEMS). Capability enhancement methods in lateral resolution, axial resolving range and large field of view for the compact DHM system are presented. To enhance the lateral resolution, the numerical aperture of a reflection DHM system is analyzed and optimum designed. To enhance the axial resolving range, dual wavelengths are used to extend the measuring range. To enable the large field of view, stitching of the measurement results is developed in the user-friendly software. Results from surfaces structures on silicon wafer, micro-optics on fused silica and dynamic inspection of MEMS structures demonstrate applications of this compact reflection digital holographic microscope for technical inspection in material science.

  13. Foreland basins and fold belts

    SciTech Connect

    Macqueen, R.W.; Leckie, D.A. )

    1992-01-01

    The papers in this book describe six foreland basins and fold belts in terms of their regional setting, stratigraphy, tectonics, and structure, and their oil and gas systems. All of the basins show general similarities, but each differs significantly in detail from the others, posing something of a problem in terms of arriving at a 'typical' foreland basin and fold belt. Some are major hydrocarbon producers; others are not. The major characteristics of the six foreland basins and fold belts are summarized in Tables 1 through 5, which provide a convenient means of comparing and contrasting these basins and their hydrocarbon resources. The Western Canada foreland basin and fold belt serves as the type example for several reasons. These include: its setting and clear relationship to a major orogene of Mesozoic-Cenozoic age; the fact that it is uncomplicated by later overprinting, segmentation, or cover rocks unlike the Ouachita, Eastern Venezuela, and U.S. Rocky Mountain foreland basins and fold belts); the fact that there is a large volume of publicly available data on the basin and an active exploration and research community; and the fact that it has reasonable oil and gas reserves in a well-defined stratigraphic framework.

  14. New charged anisotropic compact models

    NASA Astrophysics Data System (ADS)

    Kileba Matondo, D.; Maharaj, S. D.

    2016-07-01

    We find new exact solutions to the Einstein-Maxwell field equations which are relevant in the description of highly compact stellar objects. The relativistic star is charged and anisotropic with a quark equation of state. Exact solutions of the field equations are found in terms of elementary functions. It is interesting to note that we regain earlier quark models with uncharged and charged matter distributions. A physical analysis indicates that the matter distributions are well behaved and regular throughout the stellar structure. A range of stellar masses are generated for particular parameter values in the electric field. In particular the observed mass for a binary pulsar is regained.

  15. 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.

  16. 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.

  17. Current Understanding and Future Directions for Vocal Fold Mechanobiology

    PubMed Central

    Li, Nicole Y.K.; Heris, Hossein K.; Mongeau, Luc

    2013-01-01

    The vocal folds, which are located in the larynx, are the main organ of voice production for human communication. The vocal folds are under continuous biomechanical stress similar to other mechanically active organs, such as the heart, lungs, tendons and muscles. During speech and singing, the vocal folds oscillate at frequencies ranging from 20 Hz to 3 kHz with amplitudes of a few millimeters. The biomechanical stress associated with accumulated phonation is believed to alter vocal fold cell activity and tissue structure in many ways. Excessive phonatory stress can damage tissue structure and induce a cell-mediated inflammatory response, resulting in a pathological vocal fold lesion. On the other hand, phonatory stress is one major factor in the maturation of the vocal folds into a specialized tri-layer structure. One specific form of vocal fold oscillation, which involves low impact and large amplitude excursion, is prescribed therapeutically for patients with mild vocal fold injuries. Although biomechanical forces affect vocal fold physiology and pathology, there is little understanding of how mechanical forces regulate these processes at the cellular and molecular level. Research into vocal fold mechanobiology has burgeoned over the past several years. Vocal fold bioreactors are being developed in several laboratories to provide a biomimic environment that allows the systematic manipulation of physical and biological factors on the cells of interest in vitro. Computer models have been used to simulate the integrated response of cells and proteins as a function of phonation stress. The purpose of this paper is to review current research on the mechanobiology of the vocal folds as it relates to growth, pathogenesis and treatment as well as to propose specific research directions that will advance our understanding of this subject. PMID:24812638

  18. 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.

  19. Quantum theory on protein folding

    NASA Astrophysics Data System (ADS)

    Luo, LiaoFu

    2014-03-01

    The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds and stretching-bending vibrations the molecular torsion has the lowest energy and can be looked as the slow variable of the system. Simultaneously, from the multi-minima property of torsion potential the local conformational states are well defined. Following the idea that the slow variables slave the fast ones and using the nonadiabaticity operator method we deduce the Hamiltonian describing conformational change. It is shown that the influence of fast variables on the macromolecule can fully be taken into account through a phase transformation of slow variable wave function. Starting from the conformation-transition Hamiltonian the nonradiative matrix element was calculated and a general formulas for protein folding rate was deduced. The analytical form of the formula was utilized to study the temperature dependence of protein folding rate and the curious non-Arrhenius temperature relation was interpreted. By using temperature dependence data the multi-torsion correlation was studied. The decoherence time of quantum torsion state is estimated. The proposed folding rate formula gives a unifying approach for the study of a large class problems of biological conformational change.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23700314

  1. 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.

  2. 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

  3. A technique for extending by ~103 the dynamic range of compact proton spectrometers for diagnosing ICF implosions on the National Ignition Facility and OMEGAa)

    SciTech Connect

    Sio, H.; Séguin, F. H.; Frenje, J. A.; Gatu Johnson, M.; Zylstra, A. B.; Rinderknecht, H. G.; Rosenberg, M. J.; Li, C. K.; Petrasso, R. D.

    2014-11-01

    Wedge Range Filter (WRF) proton spectrometers are routinely used on OMEGA and the NIF for diagnosing ρR and ρR asymmetries in direct- and indirect-drive implosions of D3He-, D2-, and DT-gas-filled capsules. By measuring the optical opacity distribution in CR-39 due to proton tracks in high-yield applications, as opposed to counting individual tracks, WRF dynamic range can be extended by 102 for obtaining the spectral shape, and by 103 for mean energy (ρR) measurement, corresponding to proton fluences of 108 and 109 cm-2, respectively. Finally, using this new technique, ρR asymmetries can be measured during both shock and compression burn (proton yield ~108 and ~1012, respectively) in 2-shock National Ignition Facility implosions with the standard WRF accuracy of ±~10 mg/cm2.

  4. 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.

  5. 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

  6. The radius of gyration of an apomyoglobin folding intermediate

    SciTech Connect

    Eliezer, D.; Jennings, P.A.; Wright, P.E.

    1995-10-20

    Apomyoglobin (apoMb) forms a stable compact partially folded state under acidic conditions. This {open_quotes}molten globule{close_quotes} intermediate is slightly expanded relative to the native form of the protein, with a radius of gyration (R{sub g}) of 23 ({plus_minus} 2) {Angstrom} versus 19 ({plus_minus}) {Angstrom}, and shows stable secondary structure in the A,G, and H helices. We demonstrated recently, with the use of stopped-flow circular dichroism and pulse-labeling hydrogen exchange measurements, that the earliest detectable intermediate (formed with 6 ms) in the apoMb kinetic refolding pathway closely resembles the equilibrium molten globule state populated under acid conditions. A key question remained as to how compact this kinetic intermediate is compared to the equilibrium and native states. The cooperative unfolding of the kinetic intermediate and the significant protection from amide proton exchange (as compared to corresponding isolated peptides in solution) led us to propose that the kinetic intermediate is also compact. Such a proposal could best be verified by direct determination of the size of the protein as it folds, but measurements of this nature were not feasible at the time. Newly developed improvements in time-resolved small angle x-ray scattering (SAXS) experiments allow direct measurement of the time-dependent change of R{sub g} of a protein as it folds in the millisecond to second time frame. We initiated studies of the refolding of apoMb using this technique, under conditions similar to those employed in our previous work. SAXS data collected during the first 100 ms after initiation of the refolding reaction are shown. 11 refs., 2 figs.

  7. 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

  8. Energy landscape in protein folding and unfolding.

    PubMed

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

    2016-03-22

    We use (1)H 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 < T < 365 K and following different trajectories along the protein energy surface, we observe that the hydrophilic (the amide NH) and hydrophobic (methyl CH3 and methine CH) peptide groups evolve and exhibit different behaviors. We also discuss the role of water and hydrogen bonding in the protein configurational stability.

  9. Predicting pore pressure in active fold-thrust systems: An empirical model for the deepwater Sabah foldbelt

    NASA Astrophysics Data System (ADS)

    Couzens-Schultz, Brent A.; Azbel, Konstantin

    2014-12-01

    Measurements related to mudrock (shale and siltstone) porosity such as acoustic velocity, density or electrical resistivity, have traditionally been used to predict pore pressures in extensional stress settings. The underlying assumption is that burial and vertical effective stress (VES), which is the overburden minus the pore pressure, controls the compaction of these rocks through porosity loss. The dataset presented here compares VES and acoustic velocity of similar composition mudrocks in both an extensional and a compressional stress setting. In the extensional stress environment, the mudrocks follow a typical compaction trend with a porosity loss and increase in acoustic velocity that can be related to VES. In an active fold-thrust belt, the compressive stresses further reduce the porosity and increase the acoustic velocity of the mudrocks. First a layer-parallel shortening compacts sediments beyond what is observed for the VES. This additional compaction is further enhanced near thrust faults and in anticlinal forelimbs, presumably due to additional shear stress in these areas. The mudrocks located in folds that are buried by additional sedimentation do not compact again until the tectonic compaction is overridden by enough new burial. After that, the mudrocks follow the observed extensional setting compaction trend. In the fold-thrust belt, the observed reduction in porosity by stresses other than burial leads to an under-prediction of pore pressure using traditional methods. To account for this, we present a correction that can be applied to the acoustic velocity (or porosity) using two parameters: (a) proximity to thrust faults and anticlinal forelimbs and (b) the amount of burial after fold formation. With these corrections, the extensional velocity-VES compaction trend can be used to accurately predict pore pressure within the active fold-thrust belt. The correction is calibrated with well data and is empirical. None-the-less, it is a first step toward

  10. 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

  11. Mechanics, Structure and Dynamics of Metaphase Chromosome Folding

    NASA Astrophysics Data System (ADS)

    Marko, John F.

    2014-03-01

    During cell division, eukaryote chromosomes are restructured from a relatively dispersed interphase form, into a relatively compact folded metaphase form. I will discuss experiments aimed at analyzing the folding scheme of metaphase chromosomes, where mechanical response and biochemical perturbation are used as tools for diagnosing structure. Experiments with nucleases reveal that the continuity of the metaphase chromosome depends on DNA, i.e., that the metaphase chromosome can be considered to be a ``chromatin gel.'' Experiments with topoisomerases indicate that chromatin entanglements play an appreciable role in determining chromosome mechanical properties, suggesting that they may play a structural role. We further show that perturbation of condensin complexes dramatically changes metaphase chromosome mechanics. Finally we report results of fluorescence visualization of distributions of condensin I and II along metaphase chromosomes. Supported by NSF Grants MCB-1022117 and DMR-1206868, and by NIH Grants 1U54CA143869-01, 1U54HD076188 and 1R01GM105847-01.

  12. Nonuniform chain collapse during early stages of staphylococcal nuclease folding detected by fluorescence resonance energy transfer and ultrarapid mixing methods

    PubMed Central

    Mizukami, Takuya; Xu, Ming; Cheng, Hong; Roder, Heinrich; Maki, Kosuke

    2013-01-01

    The development of tertiary structure during folding of staphylococcal nuclease (SNase) was studied by time-resolved fluorescence resonance energy transfer measured using continuous- and stopped-flow techniques. Variants of this two-domain protein containing intradomain and interdomain fluorescence donor/acceptor pairs (Trp and Cys-linked fluorophore or quencher) were prepared to probe the intradomain and interdomain structural evolution accompanying SNase folding. The intra-domain donor/acceptor pairs are within the β-barrel domain (Trp27/Cys64 and Trp27/Cys97) and the interdomain pair is between the α-helical domain and the β-barrel domain (Trp140/Cys64). Time-resolved energy transfer efficiency accompanying folding and unfolding at different urea concentrations was measured over a time range from 30 μs to ∼10 s. Information on average donor/acceptor distances at different stages of the folding process was obtained by using a quantitative kinetic modeling approach. The average distance for the donor/acceptor pairs in the β-barrel domain decreases to nearly native values whereas that of the interdomain donor/acceptor pairs remains unchanged in the earliest intermediate (<500 μs of refolding). This indicates a rapid nonuniform collapse resulting in an ensemble of heterogeneous conformations in which the central region of the β-barrel domain is well developed while the C-terminal α-helical domain remains disordered. The distance between Trp140 and Cys64 decreases to native values on the 100-ms time scale, indicating that the α-helical domain docks onto the preformed β-barrel at a late stage of the folding. In addition, the unfolded state is found to be more compact under native conditions, suggesting that changes in solvent conditions may induce a nonspecific hydrophobic collapse. PMID:23904284

  13. Steric constraints as folding coadjuvant

    NASA Astrophysics Data System (ADS)

    Tarragó, M. E.; Rocha, Luiz F.; Dasilva, R. A.; Caliri, A.

    2003-03-01

    Through the analyses of the Miyazawa-Jernigan matrix it has been shown that the hydrophobic effect generates the dominant driving force for protein folding. By using both lattice and off-lattice models, it is shown that hydrophobic-type potentials are indeed efficient in inducing the chain through nativelike configurations, but they fail to provide sufficient stability so as to keep the chain in the native state. However, through comparative Monte Carlo simulations, it is shown that hydrophobic potentials and steric constraints are two basic ingredients for the folding process. Specifically, it is shown that suitable pairwise steric constraints introduce strong changes on the configurational activity, whose main consequence is a huge increase in the overall stability condition of the native state; detailed analysis of the effects of steric constraints on the heat capacity and configurational activity are provided. The present results support the view that the folding problem of globular proteins can be approached as a process in which the mechanism to reach the native conformation and the requirements for the globule stability are uncoupled.

  14. 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.

  15. 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…

  16. 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.

  17. Compact ultradense matter impactors.

    PubMed

    Rafelski, Johann; Labun, Lance; Birrell, Jeremiah

    2013-03-15

    We study interactions of meteorlike compact ultradense objects (CUDO), having nuclear or greater density, with Earth and other rocky bodies in the Solar System as a possible source of information about novel forms of matter. We study the energy loss in CUDO puncture of the body and discuss differences between regular matter and CUDO impacts.

  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. All complete intersection Calabi-Yau four-folds

    NASA Astrophysics Data System (ADS)

    Gray, James; Haupt, Alexander S.; Lukas, Andre

    2013-07-01

    We present an exhaustive, constructive, classification of the Calabi-Yau four-folds which can be described as complete intersections in products of projective spaces. A comprehensive list of 921,497 configuration matrices which represent all topologically distinct types of complete intersection Calabi-Yau four-folds is provided and can be downloaded from http://www-thphys.physics.ox.ac.uk/projects/CalabiYau/Cicy4folds/index.html. The manifolds have non-negative Euler characteristics in the range 0 ≤ χ ≤ 2610. This data set will be of use in a wide range of physical and mathematical applications. Nearly all of these four-folds are elliptically fibered and are thus of interest for F-theory model building.

  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. Time resolved small angle x-ray scattering studies of macromolecular folding

    NASA Astrophysics Data System (ADS)

    Kwok, Lisa; Smith, Heather; Sandy, Alec; Pollack, Lois

    2005-03-01

    Large biological molecules like proteins and RNA, carry out their functions by folding to well-defined three-dimensional structures. We are interested in the physical interactions that direct this self-assembly process. By combining microfabricated rapid mixers with synchrotron x-ray scattering, we have gained insight into the earliest steps of folding of the Tetrahymena ribozyme, a model for large RNAs. Previous work has shown that the first folding step involves electrostatic relaxation of the molecule. We will discuss a recent series of experiments that identify the tertiary contacts that form from within this compact state.

  2. 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…

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

    PubMed Central

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

    2009-01-01

    Abstract The mutant Tyr22Trp/Glu33Tyr/Gly46Ala/Gly48Ala of λ repressor fragment λ6−85 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 ∼4.5 μs for this fast folder. PMID:19580767

  4. Mechanical compaction in Bleurswiller sandstone: effective pressure law and compaction localization

    NASA Astrophysics Data System (ADS)

    Baud, Patrick; Reuschlé, Thierry; Ji, Yuntao; Wong, Teng-fong

    2016-04-01

    We performed a systematic investigation of mechanical compaction and strain localization in Bleurswiller sandstone of 24% porosity. 70 conventional triaxial compression experiments were performed at confining pressures up to 200 MPa and pore pressures ranging from 5 to 100 MPa. Our new data show that the effective pressure principle can be applied in both the brittle faulting and cataclastic flow regimes, with an effective pressure coefficient close to but somewhat less than 1. Under relatively high confinement, the samples typically fail by development of compaction bands. X-ray computed tomography (CT) was used to resolve preexisting porosity clusters, as well as the initiation and propagation of the compaction bands in deformed samples. Synthesis of the CT and microstructural data indicates that there is no casual relation between collapse of the porosity clusters in Bleurswiller sandstone and nucleation of the compaction bands. Instead, the collapsed porosity clusters may represent barriers for the propagation of compaction localization, rendering the compaction bands to propagate along relatively tortuous paths so as to avoid the porosity clusters. The diffuse and tortuous geometry of compaction bands results in permeability reduction that is significantly lower than that associated with compaction band formation in other porous sandstones. Our data confirm that Bleurswiller sandstone stands out as the only porous sandstone associated with a compactive cap that is linear, and our CT and microstructural observation show that it is intimately related to collapse of the porosity clusters. We demonstrate that the anomalous linear caps and their slopes are in agreement with a micromechanical model based on the collapse of a spherical pore embedded in an elastic-plastic matrix that obeys the Coulomb failure criterion.

  5. 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.

  6. Progress in Compact Toroid Experiments

    SciTech Connect

    Dolan, Thomas James

    2002-09-01

    The term "compact toroids" as used here means spherical tokamaks, spheromaks, and field reversed configurations, but not reversed field pinches. There are about 17 compact toroid experiments under construction or operating, with approximate parameters listed in Table 1.

  7. 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.

  8. Compact submanifolds supporting singular interactions

    SciTech Connect

    Kaynak, Burak Tevfik Teoman Turgut, O.

    2013-12-15

    A quantum particle moving under the influence of singular interactions on embedded surfaces furnish an interesting example from the spectral point of view. In these problems, the possible occurrence of a bound-state is perhaps the most important aspect. Such systems can be introduced as quadratic forms and generically they do not require renormalization. Yet an alternative path through the resolvent is also beneficial to study various properties. In the present work, we address these issues for compact surfaces embedded in a class of ambient manifolds. We discover that there is an exact bound state solution written in terms of the heat kernel of the ambient manifold for a range of coupling strengths. Moreover, we develop techniques to estimate bounds on the ground state energy when several surfaces, each of which admits a bound state solution, coexist. -- Highlights: •Schrödinger operator with singular interactions supported on compact submanifolds. •Exact bound-state solution in terms of the heat kernel of the ambient manifold. •Generalization of the variational approach to a collection of submanifolds. •Existence of a lower bound for a unique ground state energy.

  9. 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

  10. Folding of a Cyclin Box

    PubMed Central

    Chemes, Lucía B.; Noval, María G.; Sánchez, Ignacio E.; de Prat-Gay, Gonzalo

    2013-01-01

    The retinoblastoma tumor suppressor (Rb) controls the proliferation, differentiation, and survival of cells in most eukaryotes with a role in the fate of stem cells. Its inactivation by mutation or oncogenic viruses is required for cellular transformation and eventually carcinogenesis. The high conservation of the Rb cyclin fold prompted us to investigate the link between conformational stability and ligand binding properties of the RbAB pocket domain. RbAB unfolding presents a three-state transition involving cooperative secondary and tertiary structure changes and a partially folded intermediate that can oligomerize. The first transition corresponds to unfolding of the metastable B subdomain containing the binding site for the LXCXE motif present in cellular and viral targets, and the second transition corresponds to the stable A subdomain. The low thermodynamic stability of RbAB translates into a propensity to rapidly oligomerize and aggregate at 37 °C (T50 = 28 min) that is suppressed by human papillomavirus E7 and E2F peptide ligands, suggesting that Rb is likely stabilized in vivo through binding to target proteins. We propose that marginal stability and associated oligomerization may be conserved for function as a “hub” protein, allowing the formation of multiprotein complexes, which could constitute a robust mechanism to retain its cell cycle regulatory role throughout evolution. Decreased stability and oligomerization are shared with the p53 tumor suppressor, suggesting a link between folding and function in these two essential cell regulators that are inactivated in most cancers and operate within multitarget signaling pathways. PMID:23632018

  11. 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

  12. 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.

  13. Compact torsatron reactors

    SciTech Connect

    Lyon, J.F.; Carreras, B.A.; Lynch, V.E.; Tolliver, J.S.; Sviatoslavsky, I.N.

    1988-05-01

    Low-aspect-ratio torsatron configurations could lead to compact stellarator reactors with R/sub 0/ = 8--11m, roughly one-half to one-third the size of more conventional stellarator reactor designs. Minimum-size torsatron reactors are found using various assumptions. Their size is relatively insensitive to the choice of the conductor parameters and depends mostly on geometrical constraints. The smallest size is obtained by eliminating the tritium breeding blanket under the helical winding on the inboard side and by reducing the radial depth of the superconducting coil. Engineering design issues and reactor performance are examined for three examples to illustrate the feasibility of this approach for compact reactors and for a medium-size (R/sub 0/ approx. = 4 m,/bar a/ /approx lt/ 1 m) copper-coil ignition experiment. 26 refs., 11 figs., 7 tabs.

  14. 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.

  15. Super-Compact Laser

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Microcosm, Inc. produced the portable Farfield-2 laser for field applications that require high power pulsed illumination. The compact design was conceived through research at Goddard Space Flight Center on laser instruments for space missions to carry out geoscience studies of Earth. An exclusive license to the key NASA patent for the compact laser design was assigned to Microcosm. The FarField-2 is ideal for field applications, has low power consumption, does not need water cooling or gas supplies, and produces nearly ideal beam quality. The properties of the laser also make it effective over long distances, which is one reason why NASA developed the technology for laser altimeters that can be toted aboard spacecraft. Applications for the FarField-2 include medicine, biology, and materials science and processing, as well as diamond marking, semiconductor line-cutting, chromosome surgery, and fluorescence microscopy.

  16. Learning Protein Folding Energy Functions

    PubMed Central

    Guan, Wei; Ozakin, Arkadas; Gray, Alexander; Borreguero, Jose; Pandit, Shashi; Jagielska, Anna; Wroblewska, Liliana; Skolnick, Jeffrey

    2014-01-01

    A critical open problem in ab initio protein folding is protein energy function design, which pertains to defining the energy of protein conformations in a way that makes folding most efficient and reliable. In this paper, we address this issue as a weight optimization problem and utilize a machine learning approach, learning-to-rank, to solve this problem. We investigate the ranking-via-classification approach, especially the RankingSVM method and compare it with the state-of-the-art approach to the problem using the MINUIT optimization package. To maintain the physicality of the results, we impose non-negativity constraints on the weights. For this we develop two efficient non-negative support vector machine (NNSVM) methods, derived from L2-norm SVM and L1-norm SVMs, respectively. We demonstrate an energy function which maintains the correct ordering with respect to structure dissimilarity to the native state more often, is more efficient and reliable for learning on large protein sets, and is qualitatively superior to the current state-of-the-art energy function. PMID:25311546

  17. 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.

  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. A compact versatile femtosecond spectrometer

    NASA Astrophysics Data System (ADS)

    Nagarajan, V.; Johnson, E.; Schellenberg, P.; Parson, W.; Windeler, R.

    2002-12-01

    A compact apparatus for femtosecond pump-probe experiments is described. The apparatus is based on a cavity-dumped titanium:sapphire laser. Probe pulses are generated by focusing weak (˜1 nJ) pulses into a microstructure fiber that produces broadband continuum pulses with high efficiency. With the pump pulses compressed and probe pulses uncompressed, the rise time of the pump-probe signals is <100 fs. The 830 nm pump pulses are also frequency doubled to generate light for excitation at 415 nm. The versatility of the spectrometer is demonstrated by exciting molecules at either 830 or 415 nm, and probing at wavelengths ranging from 500 to 950 nm. Some results on the green fluorescent protein are presented.

  20. 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.

  1. 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.

  2. Misplaced helix slows down ultrafast pressure-jump protein folding.

    PubMed

    Prigozhin, Maxim B; Liu, Yanxin; Wirth, Anna Jean; Kapoor, Shobhna; Winter, Roland; Schulten, Klaus; Gruebele, Martin

    2013-05-14

    Using a newly developed microsecond pressure-jump apparatus, we monitor the refolding kinetics of the helix-stabilized five-helix bundle protein λ*YA, the Y22W/Q33Y/G46,48A mutant of λ-repressor fragment 6-85, from 3 μs to 5 ms after a 1,200-bar P-drop. In addition to a microsecond phase, we observe a slower 1.4-ms phase during refolding to the native state. Unlike temperature denaturation, pressure denaturation produces a highly reversible helix-coil-rich state. This difference highlights the importance of the denatured initial condition in folding experiments and leads us to assign a compact nonnative helical trap as the reason for slower P-jump-induced refolding. To complement the experiments, we performed over 50 μs of all-atom molecular dynamics P-drop refolding simulations with four different force fields. Two of the force fields yield compact nonnative states with misplaced α-helix content within a few microseconds of the P-drop. Our overall conclusion from experiment and simulation is that the pressure-denatured state of λ*YA contains mainly residual helix and little β-sheet; following a fast P-drop, at least some λ*YA forms misplaced helical structure within microseconds. We hypothesize that nonnative helix at helix-turn interfaces traps the protein in compact nonnative conformations. These traps delay the folding of at least some of the population for 1.4 ms en route to the native state. Based on molecular dynamics, we predict specific mutations at the helix-turn interfaces that should speed up refolding from the pressure-denatured state, if this hypothesis is correct. PMID:23620522

  3. Mechanisms for folding of high-grade rocks in extensional tectonic settings

    NASA Astrophysics Data System (ADS)

    Harris, Lyal B.; Koyi, Hemin A.; Fossen, Haakon

    2002-11-01

    This review of structures developed in extensional high-grade terrains, combined with results of centrifuge analogue modelling, illustrates the range of fold styles and mechanisms for folding of amphibolite to granulite facies rocks during rifting or the collapse of a thrust-thickened orogen. Several extensional fold mechanisms (such as folding within detachment shear zones) are similar to those in contractional settings. The metamorphic P- T- t path, and not fold style or mode of formation, is therefore required to determine the tectonic setting in which some folds developed. Other mechanisms such as rollover above and folding between listric normal shear zones, and folding due to isostatic adjustments during crustal thinning, are unique to extensional tectonic settings. Several mechanisms for folding during crustal extension produce structures that could easily be misinterpreted as implying regional contraction and hence lead to errors in their tectonic interpretation. It is shown that isoclinal recumbent folds refolded by open, upright folds may develop during regional extension in the deep crust. Folds with a thrust sense of asymmetry can develop due to high shear strains within an extensional detachment, or from enhanced back-rotation of layers between normal shear zones. During back-rotation folding, layers rotated into the shortening field undergo further buckle folding, and all may rotate towards orthogonality to the maximum shortening direction. This mechanism explains the presence of many transposed folds, folds with axial planar pegmatites and folds with opposite vergence in extensional terrains. Examples of folds in high-grade rocks interpreted as forming during regional extension included in this paper are from the Grenville Province of Canada, Norwegian Caledonides, Albany Mobile Belt and Leeuwin Complex of Western Australia, Ruby Mountains in the Basin and Range Province of Nevada, the Atâ Sund area of Greenland, the Napier Complex of Enderby Land

  4. Effect of fold structures on seismic anisotropy in continental crust

    NASA Astrophysics Data System (ADS)

    Song, W. J.; Vel, S. S.; Johnson, S. E.; Okaya, D.

    2012-04-01

    Tectonic deformation and metamorphism in the middle and lower crust can produce and modify seismic anisotropy owing to the development of micro-scale fabrics including crystallographic preferred orientation and large-scale structures such as folds, domes, faults and shear zones. Although the impact of the microfabrics on seismic anisotropy is well known via petrophysical or thin-section-based measurements, there have been few studies on how the macro-scale structures affect seismic responses. In this study, we investigate the influence of types and limb angles of cylindrical fold structures on seismic anisotropy through tensor manipulation. To calculate the velocity of seismic waves propagating through the fold structures, the elastic stiffness tensor in the Christoffel equation is substituted by geological effective media (GEM) of the folds. Here the Voigt averaging method is used in computing the GEM stiffness analytically or numerically. In this case, the GEM (C*) is decomposed into the product of a structural geometry operator (SGO) and stiffness of a representative rock that makes up the fold (Crep); C* = SGO - Crep. SGO is an operator that reorients Crep at each point of the fold with respect to a geographical reference frame and averages the reoriented stiffnesses. As an example of the representative rock stiffness, we take the stiffness tensor of the Haast schist of South Island, New Zealand (Okaya & Christensen, 2002), which has intrinsic P-wave anisotropy (AVP) of 12.7% and S1-wave anisotropy (AVS1) of 16.5%. While the rock is hexagonal in symmetry, the calculated GEM for the fold structures range between hexagonal to orthorhombic symmetry, depending on limb angle. The common types of folds are described via power or trigonometric functions: cuspate, chevron, sinusoidal, parabolic and box folds. Our results include the velocity behavior with respect to limb angle and incident angle on specific planes of the folds as well as the seismic anisotropy as a

  5. 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

  6. Paper Folding for the Mathematics Class.

    ERIC Educational Resources Information Center

    Johnson, Donovan A.

    Directions are given for folding paper to show geometric figures and relationships. Topics covered are folding the basic constructions, geometric concepts concerning triangles and quadrilaterals, circle relationships, products and factors, polygon constructions, symmetry, conic sections, and recreations. (DT)

  7. The parallel universe of RNA folding.

    PubMed

    Batey, R T; Doudna, J A

    1998-05-01

    How do large RNA molecules find their active conformations among a universe of possible structures? Two recent studies reveal that RNA folding is a rapid and ordered process, with surprising similarities to protein folding mechanisms.

  8. 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.

  9. 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.

  10. 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)

  11. 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)

  12. Compact Q-balls

    NASA Astrophysics Data System (ADS)

    Bazeia, D.; Losano, L.; Marques, M. A.; Menezes, R.; da Rocha, R.

    2016-07-01

    In this work we deal with non-topological solutions of the Q-ball type in two space-time dimensions, in models described by a single complex scalar field that engenders global symmetry. The main novelty is the presence of stable Q-balls solutions that live in a compact interval of the real line and appear from a family of models controlled by two distinct parameters. We find analytical solutions and study their charge and energy, and show how to control the parameters to make the Q-balls classically and quantum mechanically stable.

  13. Compact Plasma Accelerator

    NASA Technical Reports Server (NTRS)

    Foster, John E.

    2004-01-01

    A plasma accelerator has been conceived for both material-processing and spacecraft-propulsion applications. This accelerator generates and accelerates ions within a very small volume. Because of its compactness, this accelerator could be nearly ideal for primary or station-keeping propulsion for spacecraft having masses between 1 and 20 kg. Because this accelerator is designed to generate beams of ions having energies between 50 and 200 eV, it could also be used for surface modification or activation of thin films.

  14. Compact LINAC for deuterons

    SciTech Connect

    Kurennoy, S S; O' Hara, J F; Rybarcyk, L J

    2008-01-01

    We are developing a compact deuteron-beam accelerator up to the deuteron energy of a few MeV based on room-temperature inter-digital H-mode (IH) accelerating structures with the transverse beam focusing using permanent-magnet quadrupoles (PMQ). Combining electromagnetic 3-D modeling with beam dynamics simulations and thermal-stress analysis, we show that IHPMQ structures provide very efficient and practical accelerators for light-ion beams of considerable currents at the beam velocities around a few percent of the speed of light. IH-structures with PMQ focusing following a short RFQ can also be beneficial in the front end of ion linacs.

  15. 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.

  16. 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)

  17. 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…

  18. Surgical revision of the upper eyelid fold.

    PubMed

    Cies, W A; Baylis, H I

    1975-12-01

    We performed surgery on 107 patients primarily with blepharoptosis and eyelid fold abnormalities, between 1973 and 1974. Production of an eyelid fold at the time of an initial blepharoptosis procedure should be a primary goal. Lack of a distinct symmetrical upper eyelid fold constituted a cosmetic blemish and necessitated revision.

  19. 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

  20. 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

  1. 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.

  2. A compact SADM family

    NASA Astrophysics Data System (ADS)

    Barbet, Vincent; Le Quintrec, Cyrille; Jeandot, Xavier; Chaix, Alain; Grain, Eric; Roux, Jerome

    2005-07-01

    Alcatel Space has developed a new SADM family driven by cost, modularity, mass and performances. The modularity concept is based on separating the rotation drive function from the electrical transfer function. The drive actuator has been designed for various applications where pointing and reliability is needed. It can be associated with high dissipative rotary devices (SA collectors, RF joints..). The design goal was to minimize the number of parts in order to reach the most simple and compact mechanism. Mass reduction was achieved by reducing as much as possible the load path between the Solar Array interface and the spacecraft interface. Following these guidelines, the drive actuator was developed and qualified on ATV SADM (part od Alcatel Space Solar Array Drive Sub System for ATV). Further more a high power integrated collector was qualified inside the SADM for Geo-stationary telecom satellite (SPACEBUS platforms). Fine thermal and mechanical modeling was necessary to predict SADM behaviors for the numerous thermal environments over the missions (steady and transient cases). These modeling were well correlated through mechanical and thermal balances qualification tests. The challenging approach of thermal dissipation in a compact design leads to a family of 3 SADM capabilities form 2kW up to 15kW per SADM weighing less than 4.5 kg each.

  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. Compaction of Titanium Powders

    NASA Astrophysics Data System (ADS)

    Gerdemann, Stephen J.; Jablonski, Paul D.

    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 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.

  5. Quark matter and fermionic dark matter compact stars

    NASA Astrophysics Data System (ADS)

    Samanta, Chhanda; Mukhopadhyay, Somenath; Basu, Devasish Narayan

    2016-03-01

    Compact stars, made of quark matter and fermionic dark matter with arbitrary masses and interaction strengths, are studied by solving the Tolman-Oppenheimer-Volkoff equation of general relativity. The mass-radius relation for quark matter compact stars is obtained from the MIT bag model equation of state (EoS) with thin crust for different bag constants. The EoS of non-self-annihilating dark matter for an interacting Fermi gas with dark matter particle of 1-100 GeV mass is studied. For sufficiently strong interactions, the maximum stable mass of compact stars and its radius are controlled by the parameter of the interaction, both increasing linearly with the interaction strength. The mass-radius relation for compact stars made of strongly interacting fermions shows that the radius remains approximately constant for a wide range of compact stars.

  6. 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

  7. 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

  8. The fracture network, a proxy for mesoscale deformation: Constraints on layer parallel shortening history from the Malargüe fold and thrust belt, Argentina

    NASA Astrophysics Data System (ADS)

    Branellec, M.; Callot, J. P.; Nivière, B.; Ringenbach, J. C.

    2015-04-01

    An analysis was performed of the fracture networks in the N-S trending thick-skinned Malargüe fold and thrust belt (MFTB). A total of 2000 planar structures including joints and veins were measured in different structural domains ranging from surficial thin-skinned systems detached in the cover to large-scale structures such as basement-cored folds. The investigated stratigraphic section ranges from the Middle Jurassic (Cuyo Group) to the Paleocene (Malargüe Group), including sandstones, siltstones, shales, and limestones. Four main fracture sets are identified trending, E-W, NW-SE, NE-SW, and N-S. The abutting relationships provide a reliable chronology between the four fracture sets which are ubiquitously found in the MFTB throughout the various structural domains. Due to this observation, we assume the fracture signal to be regional and developed in response to both large-scale processes and folding. In particular, based on a fold test and the characteristics of data dispersion, the fracture sets I, II, and III exhibit a prefolding origin, while set IV shows a synfolding origin. A regional interpretation of the various fractures is proposed, involving several stages of fracture formation from compaction to folding, including prefolding layer parallel shortening. The fracture signal yields useful insights about the structural history of the MFTB and the spatiotemporal evolution of the foreland tectonic regime since Late Cretaceous times. We then place the various identified fracture sets into the known pattern of geodynamic evolution since the Late Cretaceous.

  9. 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.

  10. 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.

  11. Vocal fold ion transport and mucin expression following acrolein exposure.

    PubMed

    Levendoski, Elizabeth Erickson; Sivasankar, M Preeti

    2014-05-01

    The vocal fold epithelium is exposed to inhaled particulates including pollutants during breathing in everyday environments. Yet, our understanding of the effects of pollutants on vocal fold epithelial function is extremely limited. The objective of this study was to investigate the effect of the pollutant acrolein on two vocal fold epithelial mechanisms: ion transport and mucin (MUC) synthesis. These mechanisms were chosen as each plays a critical role in vocal defense and in maintaining surface hydration which is necessary for optimal voice production. Healthy, native porcine vocal folds (N = 85) were excised and exposed to an acrolein or sham challenge. A 60-min acrolein, but not sham challenge significantly reduced ion transport and inhibited cyclic adenosine monophosphate-dependent, increases in ion transport. Decreases in ion transport were associated with reduced sodium absorption. Within the same timeline, no significant acrolein-induced changes in MUC gene or protein expression were observed. These results improve our understanding of the effects of acrolein on key vocal fold epithelial functions and inform the development of future investigations that seek to elucidate the impact of a wide range of pollutant exposures on vocal fold health.

  12. Viral Capsid Proteins Are Segregated in Structural Fold Space

    PubMed Central

    Cheng, Shanshan; Brooks, Charles L.

    2013-01-01

    Viral capsid proteins assemble into large, symmetrical architectures that are not found in complexes formed by their cellular counterparts. Given the prevalence of the signature jelly-roll topology in viral capsid proteins, we are interested in whether these functionally unique capsid proteins are also structurally unique in terms of folds. To explore this question, we applied a structure-alignment based clustering of all protein chains in VIPERdb filtered at 40% sequence identity to identify distinct capsid folds, and compared the cluster medoids with a non-redundant subset of protein domains in the SCOP database, not including the viral capsid entries. This comparison, using Template Modeling (TM)-score, identified 2078 structural “relatives” of capsid proteins from the non-capsid set, covering altogether 210 folds following the definition in SCOP. The statistical significance of the 210 folds shared by two sets of the same sizes, estimated from 10,000 permutation tests, is less than 0.0001, which is an upper bound on the p-value. We thus conclude that viral capsid proteins are segregated in structural fold space. Our result provides novel insight on how structural folds of capsid proteins, as opposed to their surface chemistry, might be constrained during evolution by requirement of the assembled cage-like architecture. Also importantly, our work highlights a guiding principle for virus-based nanoplatform design in a wide range of biomedical applications and materials science. PMID:23408879

  13. Folding of apocytochrome c induced by the interaction with negatively charged lipid micelles proceeds via a collapsed intermediate state.

    PubMed Central

    Rankin, S. E.; Watts, A.; Roder, H.; Pinheiro, T. J.

    1999-01-01

    Unfolded apocytochrome c acquires an alpha-helical conformation upon interaction with lipid. Folding kinetic results below and above the lipid's CMC, together with energy transfer measurements of lipid bound states, and salt-induced compact states in solution, show that the folding transition of apocytochrome c from the unfolded state in solution to a lipid-inserted helical conformation proceeds via a collapsed intermediate state (I(C)). This initial compact state is driven by a hydrophobic collapse of the polypeptide chain in the absence of the heme group and may represent a heme-free analogue of an early compact intermediate detected on the folding pathway of cytochrome c in solution. Insertion into the lipid phase occurs via an unfolding step of I(C) through a more extended state associated with the membrane surface (I(S)). While I(C) appears to be as compact as salt-induced compact states in solution with substantial alpha-helix content, the final lipid-inserted state (Hmic) is as compact as the unfolded state in solution at pH 5 and has an alpha-helix content which resembles that of native cytochrome c. PMID:10048331

  14. 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.

  15. Geomorphology and fold growth, southern Tunisia.

    NASA Astrophysics Data System (ADS)

    Ahamadi, R.; Mercier, E.; Ouali, J.; van Vliet-Lanoë, B.; Mansy, J. L.; Launeau, P.; Rekis, F.

    2003-04-01

    At the northern edge of the Gafsa basin, a fold belt, the Metlaoui chain mostly rised from the Upper Miocene till today [1]. This region, endoreic since the Oligocene, is for lithologic and climate reasons a good laboratory to test various theories concerning fold growth. The origin of the fold belt is link to a main detachment level at the base of the Jurassic series (seismic profiles). The folding is facilitate with few strong calcareous beds by the dominance of soft lithologic series. This enhances the sliding along secondary detachment levels. Geomorphological, hydrological and chronological arguments prove that the folds mostly deformed as a "fault propagation fold" [2]. Furthermore, detailed field observations validate several features first observed by modelling of "fault propagation fold": 1) the stability of the roof of the fold, 2) the propagation of a knock-fold in front of the fold, disturbing the shape of pediments [3] and 3) the backward migration and extent of the backslope of the fold, in association with a backward migration of the depot centre of the syntectonic sedimentation. [1] Outtani, F., B. Addoum, E. Mercier, D. Frizon de Lamotte, J. Andrieux, Tectonophysics, 249, 233-248, 1995. [2] Suppe, J., and D.A. Medwedeff, , Eclogae geol. Helv., 83(3), 409-454, 1990. [3] Rafini S. and E. Mercier (2002). Sedimentary Geology, 146, 75-89

  16. 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.)

  17. 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.

  18. Sheath fold development around slip surfaces subject to general shear

    NASA Astrophysics Data System (ADS)

    Adamuszek, Marta; Senderak, Barbara; Dabrowski, Marcin

    2016-04-01

    Sheath folds are cone-shaped structures, which typically develop in high-strain shear zones in a variety of geological settings. When observed in the cross-sections perpendicular to the shear direction, sheath folds display characteristic elliptical closed contours. The aspect ratio of the outermost closed contour is commonly used for the classification and quantitative analysis. Alsop and Holdsworth (2006) showed that the outermost aspect ratio observed in the natural sheath folds varies between 1 and 7. Previous work on sheath folds development around slip surfaces focused on simple shear deformation (Reber et al., 2013). The aspect ratio developing under such conditions exhibits values larger than the ones observed in nature. Therefore, we investigate sheath fold development around slip surfaces under general shear conditions, in which a shortening component acts in the direction parallel to the shearing plane and perpendicular to the simple shear direction. In our models, the out-of-plane shortening is accommodated by 1) extension in the shear direction only or by 2) uniform extension perpendicular to the shortening direction (dilation). On one hand, the pure shear deformation leads to a decrease of the aspect ratio of the outermost closed contour of the developed sheath folds. On the other hand, it also modifies the slip surface size and orientation, which promotes development of sheath folds with larger aspect ratios. The numerical simulations show that the latter effect is minor and, for the two tested scenarios, we generate sheath folds with the aspect ratios of the outermost ellipse that favourably compare to the range observed in nature.

  19. Gas cooking range

    SciTech Connect

    Narang, R.K.; Narang, K.

    1984-02-14

    An energy-efficient gas cooking range features an oven section with improved heat circulation and air preheat, a compact oven/broiler burner, a smoke-free drip pan, an efficient piloted ignition, flame-containing rangetop burner rings, and a small, portable oven that can be supported on the burner rings. Panels spaced away from the oven walls and circulation fans provide very effective air flow within the oven. A gas shutoff valve automatically controls the discharge of heated gases from the oven so that they are discharged only when combustion is occurring.

  20. Microsecond Rearrangements of Hydrophobic Clusters in an Initially Collapsed Globule Prime Structure Formation during the Folding of a Small Protein.

    PubMed

    Goluguri, Rama Reddy; Udgaonkar, Jayant B

    2016-07-31

    Determining how polypeptide chain collapse initiates structure formation during protein folding is a long standing goal. It has been challenging to characterize experimentally the dynamics of the polypeptide chain, which lead to the formation of a compact kinetic molten globule (MG) in about a millisecond. In this study, the sub-millisecond events that occur early during the folding of monellin from the guanidine hydrochloride-unfolded state have been characterized using multiple fluorescence and fluorescence resonance energy transfer probes. The kinetic MG is shown to form in a noncooperative manner from the unfolded (U) state as a result of at least three different processes happening during the first millisecond of folding. Initial chain compaction completes within the first 37μs, and further compaction occurs only after structure formation commences at a few milliseconds of folding. The transient nonnative and native-like hydrophobic clusters with side chains of certain residues buried form during the initial chain collapse and the nonnative clusters quickly disassemble. Subsequently, partial chain desolvation occurs, leading to the formation of a kinetic MG. The initial chain compaction and subsequent chain rearrangement appear to be barrierless processes. The two structural rearrangements within the collapsed globule appear to prime the protein for the actual folding transition. PMID:27370109

  1. Conformational landscape of cytochrome c folding studied by microsecond-resolved small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Akiyama, Shuji; Takahashi, Satoshi; Kimura, Tetsunari; Ishimori, Koichiro; Morishima, Isao; Nishikawa, Yukihiro; Fujisawa, Tetsuro

    2002-02-01

    To investigate protein folding dynamics in terms of compactness, we developed a continuous-flow mixing device to make small-angle x-ray scattering measurements with the time resolution of 160 μs and characterized the radius of gyration (Rg) of two folding intermediates of cytochrome c (cyt c). The early intermediate possesses 20 Å of Rg, which is smaller by 4 Å than that of the acid-unfolded state. The Rg of the later intermediate is ≈18 Å, which is close to that of the molten globule state. Considering the α-helix content (fH) of the intermediates, we clarified the folding pathway of cyt c on the conformational landscape defined by Rg and fH. Cyt c folding proceeds with a collapse around a specific region of the protein followed by a cooperative acquisition of secondary structures and compactness.

  2. Metal tube can be folded for compact stowage, is self-erecting

    NASA Technical Reports Server (NTRS)

    1966-01-01

    Metal tube configuration reduces the section modulus to that of a thin plate, thus permitting the section to be bent into a coil for stowage in limited space without destructive yielding of the material. It is readily released to serve as a rigid fluid transportation conduit or structural member.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Multipurpose Compact Spectrometric Unit

    NASA Astrophysics Data System (ADS)

    Bočarov, Viktor; Čermák, Pavel; Mamedov, Fadahat; Štekl, Ivan

    2009-11-01

    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.

  9. 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.

  10. 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.

  11. 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.

  12. Compact reactor design automation

    NASA Technical Reports Server (NTRS)

    Nassersharif, Bahram; Gaeta, Michael J.

    1991-01-01

    A conceptual compact reactor design automation experiment was performed using the real-time expert system G2. The purpose of this experiment was to investigate the utility of an expert system in design; in particular, reactor design. The experiment consisted of the automation and integration of two design phases: reactor neutronic design and fuel pin design. The utility of this approach is shown using simple examples of formulating rules to ensure design parameter consistency between the two design phases. The ability of G2 to communicate with external programs even across networks provides the system with the capability of supplementing the knowledge processing features with conventional canned programs with possible applications for realistic iterative design tools.

  13. 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.

  14. 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

  15. Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a β -hairpin peptide

    NASA Astrophysics Data System (ADS)

    Daidone, Isabella; Zanetti-Polzi, Laura; Thukral, Lipi; Alekozai, Emal M.; Amadei, Andrea

    2016-08-01

    A theoretical-computational approach is presented to characterize the temperature-dependent thermodynamics of protein folding. Making use of the Quasi-Gaussian Entropy (QGE) theory and temperature exchanged molecular dynamics (TREMD) simulations, a complete picture of the folding thermodynamics can be obtained. The strategy is applied to analyze the folding thermodynamics of a β -hairpin peptide, Peptide 1, the folding process of which was experimentally characterized by means of infrared spectroscopy. The results provided by the approach here presented very well reproduce the experimental results, showing that the methodology can be successfully utilized to investigate the thermodynamics of folding processes in a wide temperature range.

  16. Compaction-based VLSI layout

    SciTech Connect

    Xiong, Xiao-Ming.

    1989-01-01

    Generally speaking, a compaction based VLSI layout system consists of two major parts: (1) a symbolic editor which maintains explicit connectivity and structural information about the circuit; (2) a compactor which translates the high level description of a circuit to the detailed layout needed for fabrication and tries to make as compact a layout as Possible without violating any design rules. Instead of developing a complete compaction based VLSI layout system, this thesis presents some theoretical concepts and several new compaction techniques, such as scan line based approach, which can either cooperate with a symbolic editor to form a layout system or work as a post-process step to improve the results obtained by an existing layout system. Also, some compaction related problems are solved and proposed. Based on the special property of channel routing, the author presents a geometric method for channel compaction. For a given channel routing topology, the minimum channel height is always achieved with the incorporation of sliding contacts and automatically inserting necessary jogs. The geometric compaction approach is then generalized and applied to compact the entire VLSI chip at the building-block level. With a systematic way of automatic jog insertion, he proves that under the given layout topology and design rules, the lower bound of one dimensional compaction with automatic jog insertion is achieved by the geometric compaction algorithm. A new simultaneous two-dimensional compaction algorithm is developed primarily for placement refinement of building-block layout. The algorithm is based on a set of defined graph operations on a mixed adjacency graph for a given placement. The mixed-adjacency graph can be updated efficiently if the placement is represented by tiles in the geometric domain.

  17. Meta-analysis of published transcriptional and translational fold changes reveals a preference for low-fold inductions.

    PubMed

    Wren, Jonathan D; Conway, Tyrrell

    2006-01-01

    The goals of this study were to gain a better quantitative understanding of the dynamic range of transcriptional and translational response observed in biological systems and to examine the reporting of regulatory events for trends and biases. A straightforward pattern-matching routine extracted 3,408 independent observations regarding transcriptional fold-changes and 1,125 regarding translational fold-changes from over 15 million MEDLINE abstracts. Approximately 95% of reported changes were > or =2-fold. Further, the historical trend of reporting individual fold-changes is declining in favor of high-throughput methods for transcription but not translation. Where it was possible to compare the average fold-changes in transcription and translation for the same gene/product (203 examples), approximately 53% were a < or =2-fold difference, suggesting a loose tendency for the two to be coupled in magnitude. We found also that approximately three-fourths of reported regulatory events have been at the transcriptional level. The frequency distribution appears to be normally distributed and peaks near 2-fold, suggesting that nature selects for a low-energy solution to regulatory responses. Because high-throughput technologies ordinarily sacrifice measurement quality for quantity, this also suggests that many regulatory events may not be reliably detectable by such technologies. Text mining of regulatory events and responses provides additional information incorporable into microarray analysis, such as prior fold-change observations and flagging genes that are regulated post-transcription. All extracted regulation and response patterns can be downloaded at the following website: www.ou.edu/microarray/ oumcf/Meta_analysis.xls.

  18. 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

  19. Reduced alphabet for protein folding prediction.

    PubMed

    Huang, Jitao T; Wang, Titi; Huang, Shanran R; Li, Xin

    2015-04-01

    What are the key building blocks that would have been needed to construct complex protein folds? This is an important issue for understanding protein folding mechanism and guiding de novo protein design. Twenty naturally occurring amino acids and eight secondary structures consist of a 28-letter alphabet to determine folding kinetics and mechanism. Here we predict folding kinetic rates of proteins from many reduced alphabets. We find that a reduced alphabet of 10 letters achieves good correlation with folding rates, close to the one achieved by full 28-letter alphabet. Many other reduced alphabets are not significantly correlated to folding rates. The finding suggests that not all amino acids and secondary structures are equally important for protein folding. The foldable sequence of a protein could be designed using at least 10 folding units, which can either promote or inhibit protein folding. Reducing alphabet cardinality without losing key folding kinetic information opens the door to potentially faster machine learning and data mining applications in protein structure prediction, sequence alignment and protein design.

  20. Some aspects of vocal fold bowing.

    PubMed

    Tanaka, S; Hirano, M; Chijiwa, K

    1994-05-01

    Bowing of the vocal fold frequently occurs in patients with vocal fold paralysis (VFP), those with sulcus vocalis, and those who have had laser surgery. Additionally, there are vocal folds that present bowing with no noticeable organic lesion. For the purpose of investigating the causes and mechanisms of vocal fold bowing, consecutive fiberscopic videorecordings of 127 patients with VFP, 33 with sulcus vocalis, 33 with laser surgery, and 33 with dysphonia having no clinically noticeable organic lesion were reviewed. Sixty-nine percent of the paralyzed vocal folds had bowing, and the occurrence of bowing was significantly related to the activity of the thyroarytenoid muscle as measured by electromyography. The cricothyroid activity had no significant relationship to vocal fold bowing. All vocal folds with sulcus presented with bowing. Thirty-five percent of the vocal folds that had had laser surgery had bowing. The extent of tissue removal was closely related to the occurrence of bowing. Twelve cases with no organic lesion had vocal fold bowing. Of these 12 patients, 8 were male and 9 were older than 60 years. Some aging process in the mucosa was presumed to be the cause of the bowing in this age group of patients without clinically noticeable organic lesions. Causes of vocal fold bowing in the younger group of patients without organic lesions were not determined in this study.

  1. Some aspects of vocal fold bowing.

    PubMed

    Tanaka, S; Hirano, M; Chijiwa, K

    1994-05-01

    Bowing of the vocal fold frequently occurs in patients with vocal fold paralysis (VFP), those with sulcus vocalis, and those who have had laser surgery. Additionally, there are vocal folds that present bowing with no noticeable organic lesion. For the purpose of investigating the causes and mechanisms of vocal fold bowing, consecutive fiberscopic videorecordings of 127 patients with VFP, 33 with sulcus vocalis, 33 with laser surgery, and 33 with dysphonia having no clinically noticeable organic lesion were reviewed. Sixty-nine percent of the paralyzed vocal folds had bowing, and the occurrence of bowing was significantly related to the activity of the thyroarytenoid muscle as measured by electromyography. The cricothyroid activity had no significant relationship to vocal fold bowing. All vocal folds with sulcus presented with bowing. Thirty-five percent of the vocal folds that had had laser surgery had bowing. The extent of tissue removal was closely related to the occurrence of bowing. Twelve cases with no organic lesion had vocal fold bowing. Of these 12 patients, 8 were male and 9 were older than 60 years. Some aging process in the mucosa was presumed to be the cause of the bowing in this age group of patients without clinically noticeable organic lesions. Causes of vocal fold bowing in the younger group of patients without organic lesions were not determined in this study. PMID:8179251

  2. 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.

  3. 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.

  4. 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.

  5. Protein folding at atomic resolution: analysis of autonomously folding supersecondary structure motifs by nuclear magnetic resonance.

    PubMed

    Sborgi, Lorenzo; Verma, Abhinav; Sadqi, Mourad; de Alba, Eva; Muñoz, Victor

    2013-01-01

    The study of protein folding has been conventionally hampered by the assumption that all single-domain proteins fold by an all-or-none process (two-state folding) that makes it impossible to resolve folding mechanisms experimentally. Here we describe an experimental method for the thermodynamic analysis of protein folding at atomic resolution using nuclear magnetic resonance (NMR). The method is specifically developed for the study of small proteins that fold autonomously into basic supersecondary structure motifs, and that do so in the sub-millisecond timescale (folding archetypes). From the NMR experiments we obtain hundreds of atomic unfolding curves that are subsequently analyzed leading to the determination of the characteristic network of folding interactions. The application of this approach to a comprehensive catalog of elementary folding archetypes holds the promise of becoming the first experimental approach capable of unraveling the basic rules connecting protein structure and folding mechanism. PMID:22987355

  6. 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.

  7. 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

  8. A Compaction Model for Highly Porous Silica Powder.

    NASA Astrophysics Data System (ADS)

    Church, P. D.; Tsembelis, K.

    2005-07-01

    This paper describes research to develop an equation of state to describe the behaviour of a highly porous silica powder. It shows that whilst molecular modelling techniques can be readily applied to develop a description of a compact material the description of the compaction process is more problematic. An empirical model, based upon the Lennard-Jones potential, has been shown to be capable of describing the compaction process observed in simple experiments. This development and application of the model in the Eulerian hydrocode GRIM to reproduce experimental plate impact data over a wide range of impact velocities is described and the results compared with experimental data.

  9. Compact designer TALENs for efficient genome engineering

    PubMed Central

    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. PMID:23612303

  10. Compost improves compacted urban soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Urban construction sites usually result in compacted soils that limit infiltration and root growth. The purpose of this study was to determine if compost, aeration, and/or prairie grasses can remediate a site setup as a simulated post-construction site (compacted). Five years after establishing the ...

  11. The Meaning of a Compact

    ERIC Educational Resources Information Center

    Wasescha, Anna

    2016-01-01

    To mark the 30th anniversary of "Campus Compact," leaders from across the network came together in the summer of 2015 to reaffirm a shared commitment to the public purposes of higher education. Campus Compact's 30th Anniversary Action Statement of Presidents and Chancellors is the product of that collective endeavor. In signing the…

  12. On the universe of protein folds.

    PubMed

    Kolodny, Rachel; Pereyaslavets, Leonid; Samson, Abraham O; Levitt, Michael

    2013-01-01

    In the fifty years since the first atomic structure of a protein was revealed, tens of thousands of additional structures have been solved. Like all objects in biology, proteins structures show common patterns that seem to define family relationships. Classification of proteins structures, which started in the 1970s with about a dozen structures, has continued with increasing enthusiasm, leading to two main fold classifications, SCOP and CATH, as well as many additional databases. Classification is complicated by deciding what constitutes a domain, the fundamental unit of structure. Also difficult is deciding when two given structures are similar. Like all of biology, fold classification is beset by exceptions to all rules. Thus, the perspectives of protein fold space that the fold classifications offer differ from each other. In spite of these ambiguities, fold classifications are useful for prediction of structure and function. Studying the characteristics of fold space can shed light on protein evolution and the physical laws that govern protein behavior.

  13. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect

    Zheng, Zhongzhou; Sosnick, Tobin R.

    2010-05-25

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

  14. Protein vivisection reveals elusive intermediates in folding.

    PubMed

    Zheng, Zhongzhou; Sosnick, Tobin R

    2010-04-01

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu-->Glu(-)) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the beta5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  15. 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

  16. Acquired retinal folds in the cat.

    PubMed

    MacMillan, A D

    1976-06-01

    Retinal folds were found in 5 cats. The apparent cause of the folding was varied: in 1 cat the folds appeared after a localized retinal detachment; in 2 cats the condition accompanied other intraocular abnormalities associated with feline infectious peritonitis; 1 cat had active keratitis, and the retinal changes were thought to have been injury related; and 1 cat, bilaterally affected, had chronic glomerulonephritis. PMID:945253

  17. COS Side 2 NUV MAMA Fold Test

    NASA Astrophysics Data System (ADS)

    Bacinski, John

    2013-10-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS MAMA Fold Analysis {13128} during Cycle 20.This proposal is an exact duplication of nominal COS MAMA Fold Analysis {proposal 13128, Cycle 20}. Any changes 13128 or subsequent cycle submissions should be reflected in this proposal and vice versa.

  18. Microwave-enhanced folding and denaturation of globular proteins

    NASA Astrophysics Data System (ADS)

    Bohr, Henrik; Bohr, Jakob

    2000-04-01

    It is shown that microwave irradiation can affect the kinetics of the folding process of some globular proteins, especially β-lactoglobulin. At low temperature the folding from the cold denatured phase of the protein is enhanced, while at a higher temperature the denaturation of the protein from its folded state is enhanced. In the latter case, a negative temperature gradient is needed for the denaturation process, suggesting that the effects of the microwaves are nonthermal. This supports the notion that coherent topological excitations can exist in proteins. The application of microwaves hold promises for a wide range of biotechnological applications, such as protein synthesis, protein aggregation, etc., and may have implications for biological systems as well.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. A compact acoustic recorder

    NASA Astrophysics Data System (ADS)

    Stein, Ronald

    1989-09-01

    The design and operation of a portable compact acoustic recorder is discussed. Designed to be used in arctic conditions for applications that require portable equipment, the device is configured to fit into a lightweight briefcase. It will operate for eight hours at -40 F with heat provided by a hot water bottle. It has proven to be an effective scientific tool in the measurement of underwater acoustic signals in arctic experiments. It has also been used successfully in warmer climates, e.g., in recording acoustic signals from small boats with no ac power. The acoustic recorder's cost is moderate since it is based on a Sony Walkman Professional (WM-D6C) tape recorder playback unit. A speaker and battery assembly and a hydrophone interface electronic assembly complete the system electronics. The interface assembly supplies a number of functions, including a calibration tone generator, an audio amplifier, and a hydrophone interface. Calibrated acoustic recordings can be made by comparing the calibration tone amplitude with the acoustic signal amplitude. The distortion of the recording is minimized by using a high quality, consumer tape recorder.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36

    NASA Astrophysics Data System (ADS)

    Mukherjee, Arnab; Bagchi, Biman

    2003-03-01

    We explore the correlation between the energy landscape and topology in the folding of a model protein (chicken villin headpiece HP-36) by using a force-field which incorporates the effects of water through a hydropathy scale and the role of helical propensity of amino acids through a nonlocal harmonic potential. Each amino acid is represented by one side chain atom which is attached to the backbone Cα atom. Sizes and interactions of all the side chain residues are different and depend on the hydrophobicity of a particular amino acid, whereas helical propensities are incorporated in the interaction of Cα atoms. Simulations have been carried out by quenching from a fixed high temperature to two different low temperatures for many initial random configurations. The simulated structures resemble the real native state rather closely, with the root mean square deviation of the best structure being 4.5 Å. Moreover, the structure shows both the helices and bends at the appropriate positions of the model protein. The simplified model allows the study of energy landscape and also of the correlation between energy landscape with the dynamics of folding and topology. The initial part of folding is very fast, followed by two distinct slow stages, with the last stage being certainly the rate determining of the folding process. The initial fast dynamics is primarily due to hydrophobic collapse. The very slow last stage of folding is accompanied by a significant and sharp increase in the relative contact order parameter but relatively small decrease in energy. Analysis of the time dependence of the formation of the individual contact pairs show rich and complicated dynamics, where some contacts wait for a long time to form. This seems to suggest that the slow late stage folding is due to long range contact formation and also that the free energy barrier is entropic in origin. Results have been correlated with the theories of protein folding.

  10. Simultaneous Alignment and Folding of Protein Sequences

    PubMed Central

    Waldispühl, Jérôme; O'Donnell, Charles W.; Will, Sebastian; Devadas, Srinivas; Backofen, Rolf

    2014-01-01

    Abstract Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments, partiFold-Align significantly outperforms state-of-the-art pairwise and multiple sequence alignment tools in the most difficult low-sequence homology case. It also improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families (partiFold-Align is available at http://partifold.csail.mit.edu/). PMID:24766258

  11. 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

  12. 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.

  13. Folding Polyominoes from One Level to Two

    ERIC Educational Resources Information Center

    Frederickson, Greg N.

    2011-01-01

    For any given polyomino, is it possible to cut it into pieces and then hinge the pieces, so that the polyomino folds up into a similar version of itself but two levels thick? While we don't know how to do this for every polyomino, the article does show how to cut, hinge, and fold polyominoes from several infinite classes, providing an…

  14. CFTR Folding Consortium: Methods Available for Studies of CFTR Folding and Correction

    PubMed Central

    Peters, Kathryn W.; Okiyoneda, Tsukasa; Balch, William E.; Braakman, Ineke; Brodsky, Jeffrey L.; Guggino, William B.; Penland, Christopher M.; Pollard, Harvey B.; Sorscher, Eric J.; Skach, William R.; Thomas, Philip J.; Lukacs, Gergely L.; Frizzell, Raymond A.

    2012-01-01

    The CFTR Folding Consortium (CFC) was formed in 2004 under the auspices of the Cystic Fibrosis Foundation and its drug discovery and development affiliate, CFF Therapeutics. A primary goal of the CFC is the development and distribution of reagents and assay methods designed to better understand the mechanistic basis of mutant CFTR misfolding and to identify targets whose manipulation may correct CFTR folding defects. As such, reagents available from the CFC primarily target wild-type CFTR NBD1 and its common variant, F508del, and they include antibodies, cell lines, constructs, and proteins. These reagents are summarized here, and two protocols are described for the detection of cell surface CFTR: (a) an assay of the density of expressed HA-tagged CFTR by ELISA and (b) the generation and use of an antibody to CFTR’s first extracellular loop for the detection of endogenous CFTR. Finally, we highlight a systematic collection of assays, the CFC Roadmap, which is being used to assess the cellular locus and mechanism of mutant CFTR correction. The Roadmap queries CFTR structure–function relations at levels ranging from purified protein to well-differentiated human airway primary cultures. PMID:21547742

  15. 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

  16. Fast, Approximate Kinetics of RNA Folding

    PubMed Central

    Senter, Evan

    2015-01-01

    Abstract In this article, we introduce the software suite Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure S of a given RNA sequence has base pair distance x (resp. y) from reference structure A (resp. B), Hermes computes the exact kinetics of folding from A to B in this coarse-grained model. In particular, Hermes computes the mean first passage time from the transition probability matrix by using matrix inversion, and also computes the equilibrium time from the rate matrix by using spectral decomposition. Due to the model granularity and the speed of Hermes, it is capable of determining secondary structure refolding kinetics for large RNA sequences, beyond the range of other methods. Comparative benchmarking of Hermes with other methods indicates that Hermes provides refolding kinetics of accuracy suitable for use in the computational design of RNA, an important area of synthetic biology. Source code and documentation for Hermes are available. PMID:25684201

  17. 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.

  18. Similarities between protein folding and granular jamming

    PubMed Central

    Jose, Prasanth P; Andricioaei, Ioan

    2012-01-01

    Grains and glasses, widely different materials, arrest their motions upon decreasing temperature and external load, respectively, in common ways, leading to a universal jamming phase diagram conjecture. However, unified theories are lacking, mainly because of the disparate nature of the particle interactions. Here we demonstrate that folded proteins exhibit signatures common to both glassiness and jamming by using temperature- and force-unfolding molecular dynamics simulations. Upon folding, proteins develop a peak in the interatomic force distributions that falls on a universal curve with experimentally measured forces on jammed grains and droplets. Dynamical signatures are found as a dramatic slowdown of stress relaxation upon folding. Together with granular similarities, folding is tied not just to the jamming transition, but a more nuanced picture of anisotropy, preparation protocol and internal interactions emerges. Results have implications for designing stable polymers and can open avenues to link protein folding to jamming theory. PMID:23093180

  19. Prediction of sound from human vocal folds

    NASA Astrophysics Data System (ADS)

    Bodony, Daniel; Luo, Haoxiang; Mittal, Rajat

    2007-11-01

    The creation of voiced sounds in humans depends on the flow-induced vibration of the vocal folds within the larynx. The vocal folds, which are a complex structural system of cartilage and tissue, create an oscillatory ``glottal jet'' whose harmonic content partially determines the tone of the speech. In this work we will discuss the process of sound generation in the laynx by combining a fully coupled two-dimensional fluid-structure simulation of the incompressible flow field in the vicinity of the vocal folds to an acoustic analogy description of the sound field. The structural dynamics of the vocal folds are based on physically realistic properties and are coupled to the motion of the fluid via an immersed boundary method. Relationships between the sound produced and the vocal fold dynamics will be discussed.

  20. 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.

  1. 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.

  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. The robustness and innovability of protein folds.

    PubMed

    Tóth-Petróczy, Agnes; Tawfik, Dan S

    2014-06-01

    Assignment of protein folds to functions indicates that >60% of folds carry out one or two enzymatic functions, while few folds, for example, the TIM-barrel and Rossmann folds, exhibit hundreds. Are there structural features that make a fold amenable to functional innovation (innovability)? Do these features relate to robustness--the ability to readily accumulate sequence changes? We discuss several hypotheses regarding the relationship between the architecture of a protein and its evolutionary potential. We describe how, in a seemingly paradoxical manner, opposite properties, such as high stability and rigidity versus conformational plasticity and structural order versus disorder, promote robustness and/or innovability. We hypothesize that polarity--differentiation and low connectivity between a protein's scaffold and its active-site--is a key prerequisite for innovability.

  4. Landscapes with megabasins: Polyamorphism in liquids and biopolymers and the role of nucleation in folding and folding diseases

    NASA Astrophysics Data System (ADS)

    Angell, C. A.

    1997-02-01

    We show how energy landscape concepts can rationalize the observations on glassforming liquids over the whole range of behavior, strong to fragile. In particular, we show how the existence of landscapes with both strong and fragile megabasins can provide a basis for understanding the nature of quasi-first-order transitions between amorphous states such as those observed to occur in the glassy states of “strong” glassformers. We show how this propensity originates in the liquid state and then emphasize the analogy provided, at the mesoscopic level, by the folding transition in proteins. Recognition that the folding transition is an equilibrium first-order transition between polyamorphic forms of a complex system implies recognition of the need for a nucleation step in the process. When nucleated phase transitions are kinetically retarded, their probability can be influenced by time-temperature history and by the presence of nucleating agents. Nucleation events are statistically rare in mesoscopic systems, hence the ability to fold rapidly should require special features in the folding molecular structure or the presence of nucleating agents. We propose that the unwanted folding events leading to pathogenic forms of certain proteins (prions) can be stimulated by nucleating agents, which thus may be the unidentified infectious agents in “mad cow” disease and related maladies.

  5. Comparison of Different TMAO Force Fields and Their Impact on the Folding Equilibrium of a Hydrophobic Polymer.

    PubMed

    Rodríguez-Ropero, Francisco; Rötzscher, Philipp; van der Vegt, Nico F A

    2016-09-01

    Trimethylamine N-oxide (TMAO) is a protective osmolyte able to preserve protein folded states in the presence of denaturants like urea and under extreme thermodynamic conditions of high pressure and temperature. The current understanding posits that TMAO exerts its stabilizing effect on proteins by preferential exclusion from the macromolecular hydration shell. Additionally, TMAO is also known to favor the folding of hydrophobic polymers. In this latter case, theoretical and experimental studies support a scenario in which TMAO directly interacts with the macromolecule. While atomistic simulations may potentially elucidate the precise TMAO-induced stabilization mechanism, the comparative accuracy of the different TMAO force field models available in the literature remains elusive. Herein, we compare four different TMAO models, study their structural hydration properties, and validate the models against experimental osmotic coefficients and air-water surface tension data over a broad range of TMAO concentrations. The models were furthermore applied to study the effect of TMAO on the folding equilibrium of a generic hydrophobic polymer in aqueous solution. Interestingly, we find that TMAO increasingly stabilizes the compact globular state of the polymer up to approximately 1 M TMAO, while in turn destabilizing it with further increase in TMAO concentration. Hence, TMAO acts as a stabilizing osmolyte or as a denaturant depending on the TMAO concentration of the solution. TMAO-induced stabilization up to 1 M is accompanied by positive preferential TMAO binding and with an increase in the chain configurational entropy, which is reduced at concentrations higher than 1 M. These results are qualitatively independent of the TMAO force field. PMID:27482971

  6. Compact Grism Spectrometer

    NASA Astrophysics Data System (ADS)

    Teare, S. W.

    2003-05-01

    Many observatories and instrument builders are retrofitting visible and near-infrared spectrometers into their existing imaging cameras. Camera designs that reimage the focal plane and have the optical filters located in a pseudo collimated beam are ideal candidates for the addition of a spectrometer. One device commonly used as the dispersing element for such spectrometers is a grism. The traditional grism is constructed from a prism that has had a diffraction grating applied on one surface. The objective of such a design is to use the prism wedge angle to select the desired "in-line" or "zero-deviation" wavelength that passes through on axis. The grating on the surface of the prism provides much of the dispersion for the spectrometer. A grism can also be used in a "constant-dispersion" design which provides an almost linear spatial scale across the spectrum. In this paper we provide an overview of the development of a grism spectrometer for use in a near infrared camera and demonstrate that a compact grism spectrometer can be developed on a very modest budget that can be afforded at almost any facility. The grism design was prototyped using visible light and then a final device was constructed which provides partial coverage in the near infrared I, J, H and K astronomical bands using the appropriate band pass filter for order sorting. The near infrared grism presented here provides a spectral resolution of about 650 and velocity resolution of about 450 km/s. The design of this grism relied on a computer code called Xspect, developed by the author, to determine the various critical parameters of the grism. This work was supported by a small equipment grant from NASA and administered by the AAS.

  7. Compact Holographic Data Storage

    NASA Astrophysics Data System (ADS)

    Chao, T. H.; Reyes, G. F.; Zhou, H.

    2001-01-01

    NASA's future missions would require massive high-speed onboard data storage capability to Space Science missions. For Space Science, such as the Europa Lander mission, the onboard data storage requirements would be focused on maximizing the spacecraft's ability to survive fault conditions (i.e., no loss in stored science data when spacecraft enters the 'safe mode') and autonomously recover from them during NASA's long-life and deep space missions. This would require the development of non-volatile memory. In order to survive in the stringent environment during space exploration missions, onboard memory requirements would also include: (1) survive a high radiation environment (1 Mrad), (2) operate effectively and efficiently for a very long time (10 years), and (3) sustain at least a billion write cycles. Therefore, memory technologies requirements of NASA's Earth Science and Space Science missions are large capacity, non-volatility, high-transfer rate, high radiation resistance, high storage density, and high power efficiency. JPL, under current sponsorship from NASA Space Science and Earth Science Programs, is developing a high-density, nonvolatile and rad-hard Compact Holographic Data Storage (CHDS) system to enable large-capacity, high-speed, low power consumption, and read/write of data in a space environment. The entire read/write operation will be controlled with electrooptic mechanism without any moving parts. This CHDS will consist of laser diodes, photorefractive crystal, spatial light modulator, photodetector array, and I/O electronic interface. In operation, pages of information would be recorded and retrieved with random access and high-speed. The nonvolatile, rad-hard characteristics of the holographic memory will provide a revolutionary memory technology meeting the high radiation challenge facing the Europa Lander mission. Additional information is contained in the original extended abstract.

  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. Compact and large depth of field image scanner for auto document feeder with compound eye system

    NASA Astrophysics Data System (ADS)

    Kawano, Hiroyuki; Okamoto, Tatsuki; Matsuzawa, Taku; Nakajima, Hajime; Makita, Junko; Toyoda, Yoshitaka; Funakura, Tetsuo; Nakanishi, Takahito; Kunieda, Tatsuya; Minobe, Tadashi

    2013-03-01

    We designed a compact and large depth of field image scanner targeted for auto document feeders (ADF) by using a compound eye system design with plural optical units in which the ray paths are folded by a reflective optics. Though we have previously proposed the principle concept, we advance the design using a free-form surface mirror to reduce the F-number for less illumination energy and to shrink its optical track width to 40 mm. We achieved large depth of field (DOF) of 1.2 mm, defined as a range exceeding 30% modulation transfer function (MTF) at 300 dpi, which is about twice as large as a conventional gradient index (GRIN) lens array contact image sensor (CIS). The aperture stop has a rectangular-shaped aperture, where one side length is as large as 4.0mm for collecting much light, and another side length is as small as 1.88mm for avoiding interference of folded ray paths.

  10. 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

  11. 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.

  12. 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)

  13. 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.

  14. MESOSCALE SIMULATIONS OF POWDER COMPACTION

    SciTech Connect

    Lomov, Ilya; Fujino, Don; Antoun, Tarabay; Liu, Benjamin

    2009-12-28

    Mesoscale 3D simulations of shock compaction of metal and ceramic powders have been performed with an Eulerian hydrocode GEODYN. The approach was validated by simulating a well-characterized shock compaction experiment of a porous ductile metal. Simulation results using the Steinberg material model and handbook values for solid 2024 aluminum showed good agreement with experimental compaction curves and wave profiles. Brittle ceramic materials are not as well studied as metals, so a simple material model for solid ceramic (tungsten carbide) has been calibrated to match experimental compaction curves. Direct simulations of gas gun experiments with ceramic powders have been performed and showed good agreement with experimental data. The numerical shock wave profile has same character and thickness as that measured experimentally using VISAR. The numerical results show reshock states above the single-shock Hugoniot line as observed in experiments. We found that for good quantitative agreement with experiments 3D simulations are essential.

  15. Mesoscale Simulations of Powder Compaction

    NASA Astrophysics Data System (ADS)

    Lomov, Ilya.; Fujino, Don; Antoun, Tarabay; Liu, Benjamin

    2009-12-01

    Mesoscale 3D simulations of shock compaction of metal and ceramic powders have been performed with an Eulerian hydrocode GEODYN. The approach was validated by simulating a well-characterized shock compaction experiment of a porous ductile metal. Simulation results using the Steinberg material model and handbook values for solid 2024 aluminum showed good agreement with experimental compaction curves and wave profiles. Brittle ceramic materials are not as well studied as metals, so a simple material model for solid ceramic (tungsten carbide) has been calibrated to match experimental compaction curves. Direct simulations of gas gun experiments with ceramic powders have been performed and showed good agreement with experimental data. The numerical shock wave profile has same character and thickness as that measured experimentally using VISAR. The numerical results show reshock states above the single-shock Hugoniot line as observed in experiments. We found that for good quantitative agreement with experiments 3D simulations are essential.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Dynamics of an Ultrafast Folding Subdomain in the Context of a Larger Protein Fold

    PubMed Central

    Davis, Caitlin M.; Dyer, R. Brian

    2014-01-01

    Small fast folding subdomains with low contact order have been postulated to facilitate the folding of larger proteins. We have tested this idea by determining how the fastest folding linear β-hairpin, CLN025, which folds on the nanosecond time scale, folds within the context of a two-hairpin WW domain system, which folds on the microsecond time scale. The folding of the wild type FBP28 WW domain was compared to constructs in which each of the loops was replaced by CLN025. A combination of FTIR spectroscopy and laser-induced temperature-jump coupled with infrared spectroscopy was used to probe changes in the peptide backbone. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding bands assigned in the amide I region. The folding rate of the CLN025 β-hairpin is unchanged within the larger protein. Insertion of the β-hairpin into the second loop results in an overall stabilization of the WW domain and a relaxation lifetime five times faster than the parent WW domain. In both mutants, folding is initiated in the turns and the β-sheets form last. These results demonstrate that fast folding subdomains can be used to speed the folding of more complex proteins, and that the folding dynamics of the subdomain is unchanged within the context of the larger protein. PMID:24320936

  1. Effects of Folding on Metalloprotein Active Sites

    NASA Astrophysics Data System (ADS)

    Winkler, Jay R.; Wittung-Stafshede, Pernilla; Leckner, Johan; Malmstrom, Bo G.; Gray, Harry B.

    1997-04-01

    Experimental data for the unfolding of cytochrome c and azurin by guanidinium chloride (GuHCl) are used to construct free-energy diagrams for the folding of the oxidized and reduced proteins. With cytochrome c, the driving force for folding the reduced protein is larger than that for the oxidized form. Both the oxidized and the reduced folded forms of yeast cytochrome c are less stable than the corresponding states of the horse protein. Due to the covalent attachment of the heme and its fixed tetragonal coordination geometry, cytochrome c folding can be described by a two-state model. A thermodynamic cycle leads to an expression for the difference in self-exchange reorganization energies for the folded and unfolded proteins. The reorganization energy for electron exchange in the folded protein is approximately 0.5 eV smaller than that for a heme in aqueous solution. The finding that reduced azurin unfolds at lower GuHCl concentrations than the oxidized protein suggests that the coordination structure of copper is different in oxidized and reduced unfolded states: it is likely that the geometry of CuI in the unfolded protein is linear or trigonal, whereas CuII prefers to be tetragonal. The evidence indicates that protein folding lowers the azurin reorganization energy by roughly 1.7 eV relative to an aqueous Cu(1,10-phenanthroline)2{}2+/+ reference system.

  2. 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.

  3. Folding pathways of the Tetrahymena ribozyme.

    PubMed

    Mitchell, David; Russell, Rick

    2014-06-12

    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.

  4. 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

  5. Compact Optoelectronic Compass

    NASA Technical Reports Server (NTRS)

    Christian, Carl

    2004-01-01

    A compact optoelectronic sensor unit measures the apparent motion of the Sun across the sky. The data acquired by this chip are processed in an external processor to estimate the relative orientation of the axis of rotation of the Earth. Hence, the combination of this chip and the external processor finds the direction of true North relative to the chip: in other words, the combination acts as a solar compass. If the compass is further combined with a clock, then the combination can be used to establish a threeaxis inertial coordinate system. If, in addition, an auxiliary sensor measures the local vertical direction, then the resulting system can determine the geographic position. This chip and the software used in the processor are based mostly on the same design and operation as those of the unit described in Micro Sun Sensor for Spacecraft (NPO-30867) elsewhere in this issue of NASA Tech Briefs. Like the unit described in that article, this unit includes a small multiple-pinhole camera comprising a micromachined mask containing a rectangular array of microscopic pinholes mounted a short distance in front of an image detector of the active-pixel sensor (APS) type (see figure). Further as in the other unit, the digitized output of the APS in this chip is processed to compute the centroids of the pinhole Sun images on the APS. Then the direction to the Sun, relative to the compass chip, is computed from the positions of the centroids (just like a sundial). In the operation of this chip, one is interested not only in the instantaneous direction to the Sun but also in the apparent path traced out by the direction to the Sun as a result of rotation of the Earth during an observation interval (during which the Sun sensor must remain stationary with respect to the Earth). The apparent path of the Sun across the sky is projected on a sphere. The axis of rotation of the Earth lies at the center of the projected circle on the sphere surface. Hence, true North (not magnetic

  6. 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.

    2016-10-01

    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 LIGO-detectable compact object binary mergers. Recent simulations of compact binary evolution suggest 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 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.

  7. 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

  8. Osteochondrodysplasia in three Scottish Fold cats.

    PubMed

    Chang, Jinhwa; Jung, Joohyun; Oh, Sunkyoung; Lee, Sungok; Kim, Gyeongmin; Kim, Haksang; Kweon, Ohkyeong; Yoon, Junghee; Choi, Mincheol

    2007-09-01

    This report explains typical radiographic features of Scottish Fold osteochondrodysplasia. Three Scottish Fold cats suffering from lameness were referred to the Veterinary Medical Teaching Hospital, Seoul National University, Korea. Based on the breed predisposition, history, clinical signs, physical examination, and radiographic findings, Scottish Fold osteochondrodysplasia was confirmed in three cases. Radiographic changes mainly included exostosis and secondary arthritis around affected joint lesions, and defective conformation in the phalanges and caudal vertebrae. The oral chondroprotective agents such as glucosamine and chondroitin sulfate make the patients alleviate their pain without adverse effects. PMID:17679781

  9. 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).

  10. Network measures for protein folding state discrimination.

    PubMed

    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

  11. Alternative wavelengths for laser ranging

    NASA Technical Reports Server (NTRS)

    Hamal, Karel

    1993-01-01

    The following are considered to be necessary to accomplish multicolor laser ranging: the nature of the atmospheric dispersion and absorption, the satellite/lunar/ground retro-array characteristics, and ground/satellite ranging machine performance. The energy balance and jitter budget have to be considered as well. It is concluded that the existing satellite/laser retroreflectors seem inadequate for future experiments. The Raman Stokes/Anti-Stokes (0.68/0.43 micron) plus solid state detector appear to be promising instrumentation that satisfy the ground/satellite and satellite/ground ranging machine requirements on the precision, compactness, and data processing.

  12. Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

    PubMed Central

    Chahine, Jorge; Oliveira, Ronaldo J.; Leite, Vitor B. P.; Wang, Jin

    2007-01-01

    We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively. PMID:17804812

  13. 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.

  14. Analysis of NSWC quasi-static compaction data for porous beds of ball powder, melamine, and Teflon, using structural compaction model

    SciTech Connect

    Weston, A.M.; Lee, E.L.

    1983-04-06

    A structural compaction model is used to correlate NSWC quasi-static compaction data on porous beds of six (6) different materials, i.e., four (4) ball powders, melamine, and Teflon. Initial densities of the porous beds ranged from 44 percent solid theoretical maximum density (TMD) to 70 percent TMD. Maximum compacted densities were about 90 percent TMD except for Teflon which was compacted to approximately 98 percent TMD. Pressures calculated by the model, plotted as a function of percent TMD, agree well with the NSWC data.

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

    PubMed

    Tu, Liwei; Khanna, Pooja; Deutsch, Carol

    2014-01-01

    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.

  16. Transmembrane Segments Form Tertiary Hairpins in the Folding Vestibule of the Ribosome.

    PubMed Central

    Tu, LiWei; Khanna, Pooja; Deutsch, Carol

    2013-01-01

    Folding of membrane proteins begins in the ribosome as the peptide is elongated. During this process, the nascent peptide navigates along 100 Å 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. PMID:24055377

  17. An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters.

    PubMed

    Sun, Tianjun; Lin, Feng-Hsu; Campbell, Robert L; Allingham, John S; Davies, Peter L

    2014-02-14

    When polypeptide chains fold into a protein, hydrophobic groups are compacted in the center with exclusion of water. We report the crystal structure of an alanine-rich antifreeze protein that retains ~400 waters in its core. The putative ice-binding residues of this dimeric, four-helix bundle protein point inwards and coordinate the interior waters into two intersecting polypentagonal networks. The bundle makes minimal protein contacts between helices, but is stabilized by anchoring to the semi-clathrate water monolayers through backbone carbonyl groups in the protein interior. The ordered waters extend outwards to the protein surface and likely are involved in ice binding. This protein fold supports both the anchored-clathrate water mechanism of antifreeze protein adsorption to ice and the water-expulsion mechanism of protein folding.

  18. 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.

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

    PubMed

    Tu, Liwei; Khanna, Pooja; Deutsch, Carol

    2014-01-01

    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. PMID:24055377

  20. Directional Oscillations, Concentrations, and Compensated Compactness via Microlocal Compactness Forms

    NASA Astrophysics Data System (ADS)

    Rindler, Filip

    2015-01-01

    This work introduces microlocal compactness forms (MCFs) as a new tool to study oscillations and concentrations in L p -bounded sequences of functions. Decisively, MCFs retain information about the location, value distribution, and direction of oscillations and concentrations, thus extending at the same time the theories of (generalized) Young measures and H-measures. In L p -spaces oscillations and concentrations precisely discriminate between weak and strong compactness, and thus MCFs allow one to quantify the difference in compactness. The definition of MCFs involves a Fourier variable, whereby differential constraints on the functions in the sequence can also be investigated easily—a distinct advantage over Young measure theory. Furthermore, pointwise restrictions are reflected in the MCF as well, paving the way for applications to Tartar's framework of compensated compactness; consequently, we establish a new weak-to-strong compactness theorem in a "geometric" way. After developing several aspects of the abstract theory, we consider three applications; for lamination microstructures, the hierarchy of oscillations is reflected in the MCF. The directional information retained in an MCF is harnessed in the relaxation theory for anisotropic integral functionals. Finally, we indicate how the theory pertains to the study of propagation of singularities in certain systems of PDEs. The proofs combine measure theory, Young measures, and harmonic analysis.

  1. 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

  2. Probing Protein Fluctuations, Folding and Misfolding at Single-molecule Resolution

    NASA Astrophysics Data System (ADS)

    Deniz, Ashok

    2010-03-01

    The conformational fluctuations and folding of proteins are key for their function in cells and organisms. Conversely, misfolding and aggregation can cause disease, although amyloids with functional significance are also being identified. To better understand these aspects of protein biophysics, we utilize single-molecule fluorescence and complementary methods to directly study complex protein dynamics, structural distributions, and conformational transitions. In one example, we used these methods to investigate disorder and disorder-to-order transitions in intrinsically disordered proteins (IDPs). IDPs are an interesting class of proteins which are relatively unstructured in isolation, but can often fold by interacting with binding partners. These complex systems are increasingly found to play major roles in biology and disease. In one case, we used a combination of single-molecule FRET (smFRET), coincidence and correlation analyses to probe the native structural features of a yeast protein Sup35, whose amyloid state is believed to be used in a beneficial context in yeast. We find that the monomeric protein populates a compact and rapidly fluctuating ensemble of conformations. In another case, we studied the binding-coupled folding of the IDP alpha-synuclein, whose misfolding and aggregation have been linked to Parkinson's disease. Single-molecule measurements directly revealed a complex multi-state folding landscape for this protein. Observations of a transient folding intermediate using microfluidic mixing, and links to misfolding and aggregation will also be discussed. Our results highlight single-molecule methodology that is broadly applicable to map protein folding and misfolding landscapes.

  3. Flexible Momentum Compaction Return Arcs for RLAs

    SciTech Connect

    Trbojevic, Dejan; Bogacz, Alex; Bogacz, Slawomir; Bogacz, Alex; Bogacz, Slawomir; Johnson, Rolland; Popovic, Milorad

    2008-07-01

    Neutrino Factories and Muon Colliders require rapid acceleration of short-lived muons to multi-GeV and TeV energies. A Recirculating Linear Accelerator (RLA) that uses a single Linac and teardrop return arcs can provide exceptionally fast and economical acceleration to the extent that the focusing range of the RLA quadrupoles allows each muon to pass several times through each high-gradient cavity and the cost of the return arcs is appropriate. Flexible Momentum Compaction (FMC) lattice designs for the teardrop return arcs provide sufficient momentum acceptance to allow multiple passes of each sign of muon in one string of magnets to improve cost-effectiveness.

  4. 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.

  5. 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.

  6. 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.

  7. Dew-driven folding of insect wings

    NASA Astrophysics Data System (ADS)

    Dickerson, Andrew; Beadles, Sam; Clement, Courtney; Hu, David

    2013-11-01

    Small insect wings fold into tacos when exposed to dewfall or fog for extended times. Such shapes are tightly held together and require great force or long evaporation times for the wings to unfold. In this experimental investigation, we use time-lapse and high-speed videography on a mosquito wing exposed to fog to characterize the folding process from a flat wing to a taco. We observe a taco is formed through a series of processes involving wing bending, unbending, and subsequent tight folding of the wing following the sliding of the drop off the wing. We use a simplified 2D model to determine the forces coalescing drops exert on the wing, and present folding-resistant design suggestions for micro-aerial vehicle wings.

  8. 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.

  9. Reinke Edema: Watch For Vocal Fold Cysts.

    PubMed

    Tüzüner, Arzu; Demirci, Sule; Yavanoglu, Ahmet; Kurkcuoglu, Melih; Arslan, Necmi

    2015-06-01

    Reinke edema is one of the common cause of dysphonia middle-aged population, and severe thickening of vocal folds require surgical treatment. Smoking plays a major role on etiology. Vocal fold cysts are also benign lesions and vocal trauma blamed for acquired cysts. We would like to present 3 cases with vocal fold cyst related with Reinke edema. First case had a subepidermal epidermoid cyst with Reinke edema, which could be easily observed before surgery during laryngostroboscopy. Second case had a mucous retention cyst into the edematous Reinke tissue, which was detected during surgical intervention, and third case had a epidermoid cyst that occurred 2 months after before microlaryngeal operation regarding Reinke edema reduction. These 3 cases revealed that surgical management of Reinke edema needs a careful dissection and close follow-up after surgery for presence of vocal fold cysts.

  10. Monster Mash: Protein Folding Gone Wrong

    MedlinePlus

    ... Articles | Inside Life Science Home Page Monster Mash: Protein Folding Gone Wrong By Joseph Piergrossi Posted October 31, 2013 In this image, globs of misfolded proteins called amyloid plaques (blobs) are found outside neurons ( ...

  11. Unexplained Profound Hypoglycemia After Vocal Fold Lipoinjection.

    PubMed

    Modanlou, Shohreh; Marie Giglio, Nicole; Carroll, Thomas; Pancaro, Carlo

    2016-02-01

    Vocal fold injection is used for the management of glottal incompetence from various causes. The procedure is well tolerated and has few reported complications. We present a case of a 66-year-old man with long-lasting hoarseness secondary to vocal fold atrophy, who underwent an uneventful bilateral vocal fold injection with autologous fat. While in the recovery area, he experienced profuse sweating approximately 30 minutes after the surgical procedure. His blood glucose value was measured at 24 mg/dL, and plasmatic insulin level was 246 mU/L. To our knowledge, this is the first reported case of a systemic side effect after vocal fold lipoinjection. PMID:26491839

  12. 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.

  13. Cellular Mechanisms of Membrane Protein Folding

    PubMed Central

    Skach, William R.

    2010-01-01

    The membrane protein folding problem can be articulated by two central questions. How is protein topology established by selective peptide transport to opposite sides of the cellular membrane? And how are transmembrane segments inserted, integrated and folded within the lipid bilayer? In eukaryotes, this process usually takes place in the endoplasmic reticulum (ER) coincident with protein synthesis, and is facilitated by the translating Ribosome and the Sec61 Translocon Complex (RTC). At its core, the RTC forms a dynamic pathway through which the elongating nascent polypeptide moves as it is delivered into cytosolic, lumenal and lipid compartments. This perspective will focus on emerging evidence that the RTC functions as a protein folding machine that restricts conformational space by establishing transmembrane topology and yet provides a permissive environment that enables nascent transmembrane domains to efficiently progress down their folding energy landscape. PMID:19491932

  14. Kinetic Analysis of Protein Folding Lattice Models

    NASA Astrophysics Data System (ADS)

    Chen, Hu; Zhou, Xin; Liaw, Chih Young; Koh, Chan Ghee

    Based on two-dimensional square lattice models of proteins, the relation between folding time and temperature is studied by Monte Carlo simulation. The results can be represented by a kinetic model with three states — random coil, molten globule, and native state. The folding process is composed of nonspecific collapse and final searching for the native state. At high temperature, it is easy to escape from local traps in the folding process. With decreasing temperature, because of the trapping in local traps, the final searching speed decreases. Then the folding shows chevron rollover. Through the analysis of the fitted parameters of the kinetic model, it is found that the main difference between the energy landscapes of the HP model and the Go model is that the number of local minima of the Go model is less than that of the HP model.

  15. Hsp70 biases the folding pathways of client proteins.

    PubMed

    Sekhar, Ashok; Rosenzweig, Rina; Bouvignies, Guillaume; Kay, Lewis E

    2016-05-17

    The 70-kDa heat shock protein (Hsp70) family of chaperones bind cognate substrates to perform a variety of different processes that are integral to cellular homeostasis. Although detailed structural information is available on the chaperone, the structural features of folding competent substrates in the bound form have not been well characterized. Here we use paramagnetic relaxation enhancement (PRE) NMR spectroscopy to probe the existence of long-range interactions in one such folding competent substrate, human telomere repeat binding factor (hTRF1), which is bound to DnaK in a globally unfolded conformation. We show that DnaK binding modifies the energy landscape of the substrate by removing long-range interactions that are otherwise present in the unbound, unfolded conformation of hTRF1. Because the unfolded state of hTRF1 is only marginally populated and transiently formed, it is inaccessible to standard NMR approaches. We therefore developed a (1)H-based CEST experiment that allows measurement of PREs in sparse states, reporting on transiently sampled conformations. Our results suggest that DnaK binding can significantly bias the folding pathway of client substrates such that secondary structure forms first, followed by the development of longer-range contacts between more distal parts of the protein. PMID:27140645

  16. 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

  17. [Surgery of benign vocal fold lesions].

    PubMed

    Olthoff, A

    2016-09-01

    Surgical treatment of benign vocal fold lesions can be indicated for clinical or functional reasons. The principles of phonosurgery have to be maintained in either case. The appropriate phonosurgical technique depends on the type of vocal fold lesion. Depending on the findings, phonosurgery aims to maintain or improve voice quality. The evaluation of clinical and functional results includes indirect laryngoscopy, videostroboscopy, and voice analysis. PMID:27552826

  18. On a smooth quintic 4-fold

    SciTech Connect

    Cheltsov, I A

    2000-10-31

    The birational geometry of an arbitrary smooth quintic 4-fold is studied using the properties of log pairs. As a result, a new proof of its birational rigidity is given and all birational maps of a smooth quintic 4-fold into fibrations with general fibre of Kodaira dimension zero are described. In the Addendum similar results are obtained for all smooth hypersurfaces of degree n in P{sup n} in the case of n equal to 6, 7, or 8.

  19. 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

  20. Muscular Anatomy of the Human Ventricular Folds

    PubMed Central

    Moon, Jerald; Alipour, Fariborz

    2013-01-01

    Objective The purpose of this study was to better understand the muscular anatomy of the ventricular folds (VF) to help improve biomechanical modeling of phonation and to better understand the role of these muscles during phonatory and non-phonatory tasks. Method Four human larynges were decalcified and sectioned coronally from the posterior to anterior using a CryoJane tape transfer system, and stained using Massons trichrome. The total and relative area of muscles observed in each section were calculated and used for characterizing muscle distribution within the ventricular folds. Results The ventricular folds of the larynges contained anteriorly coursing thyroarytenoid and ventricularis muscle fibers lying in the lower half of the VF posteriorly, with some ventricularis muscle evident in the upper and lateral portion of the fold more anteriorly. Very little muscle tissue was observed in the medial half of the fold, and the anterior half of the VF was largely devoid of any muscle tissue. All four VF’s contained muscle bundles coursing superiorly and medially through the upper half of the fold toward the lateral margin of the epiglottis. Conclusions While variability in expression was evident, the well-defined thyroarytenoid muscle was readily apparent lateral to the arytenoid cartilage in all specimens. PMID:24224399

  1. Structural Characteristics of Novel Protein Folds

    PubMed Central

    Fernandez-Fuentes, Narcis; Dybas, Joseph M.; Fiser, Andras

    2010-01-01

    Folds are the basic building blocks of protein structures. Understanding the emergence of novel protein folds is an important step towards understanding the rules governing the evolution of protein structure and function and for developing tools for protein structure modeling and design. We explored the frequency of occurrences of an exhaustively classified library of supersecondary structural elements (Smotifs), in protein structures, in order to identify features that would define a fold as novel compared to previously known structures. We found that a surprisingly small set of Smotifs is sufficient to describe all known folds. Furthermore, novel folds do not require novel Smotifs, but rather are a new combination of existing ones. Novel folds can be typified by the inclusion of a relatively higher number of rarely occurring Smotifs in their structures and, to a lesser extent, by a novel topological combination of commonly occurring Smotifs. When investigating the structural features of Smotifs, we found that the top 10% of most frequent ones have a higher fraction of internal contacts, while some of the most rare motifs are larger, and contain a longer loop region. PMID:20421995

  2. 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.

  3. "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.

  4. Theoretical consideration of the flow behavior in oscillating vocal fold.

    PubMed

    Deguchi, Shinji; Hyakutake, Toru

    2009-05-11

    Self-excited oscillation of the vocal folds produces a source sound of the human voiced speech. The mechanism of the self-excitation remains elusive partly because characteristics of the flow in rapidly oscillating vocal folds are unclear. This paper deals with theoretical considerations of the flow behavior in oscillating constriction based on general flow equations. The cause-and-effect relationships between time-varying glottal width and physical variables such as glottal pressure, velocity, and volume flow are analytically derived as functions of oscillatory frequency through perturbation analysis. The result shows that the unsteady effect due to convective acceleration of vocal fold wall-induced flow becomes comparable in magnitude to the Bernoulli effect at a high but physiological frequency of phonation. Consequently, a phase difference between the vocal fold motion and glottal pressure appears, enabling self-excited oscillation. The phase-lead of the pressure compared to wall motion is described as a monotonically increasing function of the Strouhal number. The above two effects essentially play the dominant role in the glottal flow. These explicit descriptions containing flow-related variables are useful for understanding of the glottal aerodynamics particularly at high frequency range of the falsetto voice register. PMID:19269641

  5. Wrinkles and folds in a compressed granular raft

    NASA Astrophysics Data System (ADS)

    Jambon-Puillet, Etienne; Josserand, Christophe; Protiere, Suzie

    Wrinkles and folds occur in a wide variety of situations, we find them in Nature but also in man-made products. They typically appear when a thin sheet bound to a foundation is compressed. Here we demonstrate that particle ladden interfaces, despite being made of discrete very hard particles, can form wrinkles and folds like a soft elastic solid. We call granular raft a close packed monolayer of heavy, athermal particles at the interface between two fluids. We use beads of different materials with diameters ranging from 30 μm to 0 . 8 mm dispersed at a planar oil/water interface. Upon uniaxial compression the raft buckles out of plane like a soft elastic solid and forms a periodic wrinkling pattern, then the deformation localizes in a large unique fold/crease. This behavior is reminiscent of a compressed elastic sheet floating on water. We will highlight similarities and differences between the mechanical properties of our discrete heavy granular raft and a continuous elastic floating film. Finally we will show how elasticity and gravity contribute to rationalize the original shape of the fold we observe.

  6. Folding simulations of alanine-based peptides with lysine residues.

    PubMed Central

    Sung, S S

    1995-01-01

    The folding of short alanine-based peptides with different numbers of lysine residues is simulated at constant temperature (274 K) using the rigid-element Monte Carlo method. The solvent-referenced potential has prevented the multiple-minima problem in helix folding. From various initial structures, the peptides with three lysine residues fold into helix-dominated conformations with the calculated average helicity in the range of 60-80%. The peptide with six lysine residues shows only 8-14% helicity. These results agree well with experimental observations. The intramolecular electrostatic interaction of the charged lysine side chains and their electrostatic hydration destabilize the helical conformations of the peptide with six lysine residues, whereas these effects on the peptides with three lysine residues are small. The simulations provide insight into the helix-folding mechanism, including the beta-bend intermediate in helix initiation, the (i, i + 3) hydrogen bonds, the asymmetrical helix propagation, and the asymmetrical helicities in the N- and C-terminal regions. These findings are consistent with previous studies. PMID:7756550

  7. 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.

  8. Compaction and segregation of sister chromatids via active loop extrusion

    PubMed Central

    Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, Leonid

    2016-01-01

    The mechanism by which chromatids and chromosomes are segregated during mitosis and meiosis is a major puzzle of biology and biophysics. Using polymer simulations of chromosome dynamics, we show that a single mechanism of loop extrusion by condensins can robustly compact, segregate and disentangle chromosomes, arriving at individualized chromatids with morphology observed in vivo. Our model resolves the paradox of topological simplification concomitant with chromosome 'condensation', and explains how enzymes a few nanometers in size are able to control chromosome geometry and topology at micron length scales. We suggest that loop extrusion is a universal mechanism of genome folding that mediates functional interactions during interphase and compacts chromosomes during mitosis. DOI: http://dx.doi.org/10.7554/eLife.14864.001 PMID:27192037

  9. 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.

  10. 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

  11. Blue ellipticals in compact groups

    NASA Technical Reports Server (NTRS)

    Zepf, Stephen E.; Whitmore, Bradley C.

    1990-01-01

    By studying galaxies in compact groups, the authors examine the hypothesis that mergers of spiral galaxies make elliptical galaxies. The authors combine dynamical models of the merger-rich compact group environment with stellar evolution models and predict that roughly 15 percent of compact group ellipticals should be 0.15 mag bluer in B - R color than normal ellipticals. The published colors of these galaxies suggest the existence of this predicted blue population, but a normal distribution with large random errors can not be ruled out based on these data alone. However, the authors have new ultraviolet blue visual data which confirm the blue color of the two ellipticals with blue B - R colors for which they have their own colors. This confirmation of a population of blue ellipticals indicates that interactions are occurring in compact groups, but a blue color in one index alone does not require that these ellipticals are recent products of the merger of two spirals. The authors demonstrate how optical spectroscopy in the blue may distinguish between a true spiral + spiral merger and the swallowing of a gas-rich system by an already formed elliptical. The authors also show that the sum of the luminosity of the galaxies in each group is consistent with the hypothesis that the final stage in the evolution of compact group is an elliptical galaxy.

  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. Adapted to Roar: Functional Morphology of Tiger and Lion Vocal Folds

    PubMed Central

    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. PMID:22073246

  14. Folding patterns and shape optimization using SMA-based self-folding laminates

    NASA Astrophysics Data System (ADS)

    Peraza-Hernandez, Edwin A.; Frei, Katherine R.; Hartl, Darren J.; Lagoudas, Dimitris C.

    2014-03-01

    Origami engineering, a discipline encompassing the creation of practical three-dimensional structures from two- dimensional entities via folding operations, has the potential to impact multiple fields of manufacturing and design. In some circumstances, it may be practical to have self-folding capabilities instead of creating folds by external manipulations (as in morphing structures in outer space or on the ocean floor). This paper considers the use of a self-folding laminate composite consisting of two outer layers of thermally actuated shape memory alloy (SMA) wire meshes separated by an inner compliant insulating layer. Methods for designing folding patterns and determining temperature fields to obtain desired shapes and behaviors are proposed. Sheets composed of the self-folding laminate are modeled via finite element analysis (FEA) and the proposed methods are implemented to test their capabilities. One method uses a previously developed and freely available software called Freeform Origami for folding pattern design. The second method entails the use of optimization to determine the localized activation temperatures required to obtain desired shapes or to perform specific functions. The proposed methods are demonstrated to be applicable for the design of folding patterns and determination of activation temperatures for the self-folding laminate by showing successful examples of their implementation. This exploratory study provides new tools that can be integrated into the design framework of self-folding origami structures.

  15. Evolution of stress and strain during 3D folding: application to orthogonal fracture systems in folded turbidites, SW Portugal

    NASA Astrophysics Data System (ADS)

    Reber, J. E.; Schmalholz, S. M.; Lechmann, S. M.

    2009-04-01

    and a viscous rheology. The stress and strain tensor components are calculated at each numerical nodal point. The stress and strain fields are visualized through ellipses and ellipsoids which are calculated using the eigenvalues of the respective tensors. The shortest main axis represents the direction of the smallest stress σ3 and the longest main axis represents the direction of the largest stress σ1. To generate two orthogonal fracture systems in the fold limbs we expect a relatively rapid change of the stress field in the fold limbs during folding. With a relatively slow change of the stress field we would expect to see more than two fracture systems with a wide range of fracture orientation which we did not observe in the field. The preliminary 2D results show, as expected, a sudden flip of the main axes of the stress ellipse which corresponds to a change from limb-parallel compression to extension. For the 3D model we expect similar results and we will investigate the impact of different deformation boundary conditions on the evolution of the 3D stress and strain fields.

  16. Cellular folding pathway of a metastable serpin.

    PubMed

    Chandrasekhar, Kshama; Ke, Haiping; Wang, Ning; Goodwin, Theresa; Gierasch, Lila M; Gershenson, Anne; Hebert, Daniel N

    2016-06-01

    Although proteins generally fold to their thermodynamically most stable state, some metastable proteins populate higher free energy states. Conformational changes from metastable higher free energy states to lower free energy states with greater stability can then generate the work required to perform physiologically important functions. However, how metastable proteins fold to these higher free energy states in the cell and avoid more stable but inactive conformations is poorly understood. The serpin family of metastable protease inhibitors uses large conformational changes that are downhill in free energy to inhibit target proteases by pulling apart the protease active site. The serpin antithrombin III (ATIII) targets thrombin and other proteases involved in blood coagulation, and ATIII misfolding can thus lead to thrombosis and other diseases. ATIII has three disulfide bonds, two near the N terminus and one near the C terminus. Our studies of ATIII in-cell folding reveal a surprising, biased order of disulfide bond formation, with early formation of the C-terminal disulfide, before formation of the N-terminal disulfides, critical for folding to the active, metastable state. Early folding of the predominantly β-sheet ATIII domain in this two-domain protein constrains the reactive center loop (RCL), which contains the protease-binding site, ensuring that the RCL remains accessible. N-linked glycans and carbohydrate-binding molecular chaperones contribute to the efficient folding and secretion of functional ATIII. The inability of a number of disease-associated ATIII variants to navigate the folding reaction helps to explain their disease phenotypes. PMID:27222580

  17. Compact orthogonal NMR field sensor

    SciTech Connect

    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.

  18. Compaction Stress in Fine Powders

    SciTech Connect

    Hurd, A.J.; Kenkre, V.M.; Pease, E.A.; Scott, J.E.

    1999-04-01

    A vexing feature in granular materials compaction is density extrema interior to a compacted shape. Such inhomogeneities can lead to weaknesses and loss of dimensional control in ceramic parts, unpredictable dissolution of pharmaceuticals, and undesirable stress concentration in load-bearing soil. As an example, the centerline density in a cylindrical compact often does not decrease monotonically from the pressure source but exhibits local maxima and minima. Two lines of thought in the literature predict, respectively, diffusive and wavelike propagation of stress. Here, a general memory function approach has been formulated that unifies these previous treatments as special cases; by analyzing a convenient intermediate case, the telegrapher's equation, one sees that local density maxima arise via semidiffusive stress waves reflecting from the die walls and adding constructively at the centerline.

  19. A Two-step Mechanism for the Folding of Actin by the Yeast Cytosolic Chaperonin

    PubMed Central

    Stuart, Sarah F.; Leatherbarrow, Robin J.; Willison, Keith R.

    2011-01-01

    Actin requires the chaperonin containing TCP1 (CCT), a hexadecameric ATPase essential for cell viability in eukaryotes, to fold to its native state. Following binding of unfolded actin to CCT, the cavity of the chaperone closes and actin is folded and released in an ATP-dependent folding cycle. In yeast, CCT forms a ternary complex with the phosducin-like protein PLP2p to fold actin, and together they can return nascent or chemically denatured actin to its native state in a pure in vitro folding assay. The complexity of the CCT-actin system makes the study of the actin folding mechanism technically challenging. We have established a novel spectroscopic assay through selectively labeling the C terminus of yeast actin with acrylodan and observe significant changes in the acrylodan fluorescence emission spectrum as actin is chemically unfolded and then refolded by the chaperonin. The variation in the polarity of the environment surrounding the fluorescent probe during the unfolding/folding processes has allowed us to monitor actin as it folds on CCT. The rate of actin folding at a range of temperatures and ATP concentrations has been determined for both wild type CCT and a mutant CCT, CCT4anc2, defective in folding actin in vivo. Binding of the non-hydrolysable ATP analog adenosine 5′-(β,γ-imino)triphosphate to the ternary complex leads to 3-fold faster release of actin from CCT following addition of ATP, suggesting a two-step folding process with a conformational change occurring upon closure of the cavity and a subsequent final folding step involving packing of the C terminus to the native-like state. PMID:21056978

  20. 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.

  1. Generating folded protein structures with a lattice chain growth algorithm

    NASA Astrophysics Data System (ADS)

    Gan, Hin Hark; Tropsha, Alexander; Schlick, Tamar

    2000-10-01

    We present a new application of the chain growth algorithm to lattice generation of protein structure and thermodynamics. Given the difficulty of ab initio protein structure prediction, this approach provides an alternative to current folding algorithms. The chain growth algorithm, unlike Metropolis folding algorithms, generates independent protein structures to achieve rapid and efficient exploration of configurational space. It is a modified version of the Rosenbluth algorithm where the chain growth transition probability is a normalized Boltzmann factor; it was previously applied only to simple polymers and protein models with two residue types. The independent protein configurations, generated segment-by-segment on a refined cubic lattice, are based on a single interaction site for each amino acid and a statistical interaction energy derived by Miyazawa and Jernigan. We examine for several proteins the algorithm's ability to produce nativelike folds and its effectiveness for calculating protein thermodynamics. Thermal transition profiles associated with the internal energy, entropy, and radius of gyration show characteristic folding/unfolding transitions and provide evidence for unfolding via partially unfolded (molten-globule) states. From the configurational ensembles, the protein structures with the lowest distance root-mean-square deviations (dRMSD) vary between 2.2 to 3.8 Å, a range comparable to results of an exhaustive enumeration search. Though the ensemble-averaged dRMSD values are about 1.5 to 2 Å larger, the lowest dRMSD structures have similar overall folds to the native proteins. These results demonstrate that the chain growth algorithm is a viable alternative to protein simulations using the whole chain.

  2. 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.

  3. 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.

  4. Estimation of vocal fold plane in 3D CT images for diagnosis of vocal fold abnormalities.

    PubMed

    Hewavitharanage, Sajini; Gubbi, Jayavardhana; Thyagarajan, Dominic; Lau, Ken; Palaniswami, Marimuthu

    2015-01-01

    Vocal folds are the key body structures that are responsible for phonation and regulating air movement into and out of lungs. Various vocal fold disorders may seriously impact the quality of life. When diagnosing vocal fold disorders, CT of the neck is the commonly used imaging method. However, vocal folds do not align with the normal axial plane of a neck and the plane containing vocal cords and arytenoids does vary during phonation. It is therefore important to generate an algorithm for detecting the actual plane containing vocal folds. In this paper, we propose a method to automatically estimate the vocal fold plane using vertebral column and anterior commissure localization. Gray-level thresholding, connected component analysis, rule based segmentation and unsupervised k-means clustering were used in the proposed algorithm. The anterior commissure segmentation method achieved an accuracy of 85%, a good estimate of the expert assessment. PMID:26736949

  5. A compact holographic optical tweezers instrument

    NASA Astrophysics Data System (ADS)

    Gibson, G. M.; Bowman, R. W.; Linnenberger, A.; Dienerowitz, M.; Phillips, D. B.; Carberry, D. M.; Miles, M. J.; Padgett, M. J.

    2012-11-01

    Holographic optical tweezers have found many applications including the construction of complex micron-scale 3D structures and the control of tools and probes for position, force, and viscosity measurement. We have developed a compact, stable, holographic optical tweezers instrument which can be easily transported and is compatible with a wide range of microscopy techniques, making it a valuable tool for collaborative research. The instrument measures approximately 30×30×35 cm and is designed around a custom inverted microscope, incorporating a fibre laser operating at 1070 nm. We designed the control software to be easily accessible for the non-specialist, and have further improved its ease of use with a multi-touch iPad interface. A high-speed camera allows multiple trapped objects to be tracked simultaneously. We demonstrate that the compact instrument is stable to 0.5 nm for a 10 s measurement time by plotting the Allan variance of the measured position of a trapped 2 μm silica bead. We also present a range of objects that have been successfully manipulated.

  6. Compact hybrid particulate collector

    SciTech Connect

    Chang, R.

    1991-06-18

    This paper describes a method for removing particulates from flue gas. It comprises: flowing the flue gas through an electrostatic precipitator for removing 90-99% of the particulates, and for imparting a residual electric charge on remaining particulates exhausted from the electrostatic precipitator ins aid flue gas; maintaining the residual electric charge on the remaining particulates while flowing the flue gas through a barrier filter placed downstream of the electrostatic precipitator at a high filtration velocity in the range of from 4.06-20.32 centimeters per second (8-40 feet per minute), the barrier filter collecting the charged particulates exhausted from the electrostatic precipitator in the flue gas before the residual electric charge substantially dissipates.

  7. Computational and theoretical methods for protein folding.

    PubMed

    Compiani, Mario; Capriotti, Emidio

    2013-12-01

    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.

  8. 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

  9. 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.

  10. 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).

  11. Nonlinear Models for Protein Folding and Function

    NASA Astrophysics Data System (ADS)

    Cruzeiro, L.

    Earlier a specific kinetic process for reproducible protein folding was proposed according to which the nascent chain is helical and the first step in in vivo protein folding is the bending of the initial helix at specific amino acid sites. Here the theoretical feasibility of this kinetic process is tested. To that end, two proteins, one belonging to the mainly α class and the other belonging to the α/β class, are selected and targeted molecular dynamics is applied to generate folding pathways for those two proteins, starting from two well defined initial conformations: a fully extended and a α-helical conformation. Not only are the native states closer to an initial helical structure for both proteins but also the pathways from the α-helical initial conformation to the native state have lower potential energy than the pathways that start from the fully extended conformation. For the α/β protein, 30% (40%) of the pathways from an initial α-helix (fully extended) structure lead to unentangled native folds, a success rate that can be increased to 85% by the introduction of a putative intermediate structure. These results lend support to the kinetic process proposed and open up a new direction in which to look for a solution to the protein folding problem. The chapter ends with a section that emphasizes the formal similarities between the dynamics quantum vibrational excited states in proteins and electrons in nonlinear lattices.

  12. Towards a systematic classification of protein folds

    NASA Astrophysics Data System (ADS)

    Lindgård, Per-Anker; Bohr, Henrik

    1997-10-01

    A lattice model Hamiltonian is suggested for protein structures that can explain the division into structural fold classes during the folding process. Proteins are described by chains of secondary structure elements, with the hinges in between being the important degrees of freedom. The protein structures are given a unique name, which simultaneously represent a linear string of physical coupling constants describing hinge spin interactions. We have defined a metric and a precise distance measure between the fold classes. An automated procedure is constructed in which any protein structure in the usual protein data base coordinate format can be transformed into the proposed chain representation. Taking into account hydrophobic forces we have found a mechanism for the formation of domains with a unique fold containing predicted magic numbers \\{4,6,9,12,16,18,...\\} of secondary structures and multiples of these domains. It is shown that the same magic numbers are robust and occur as well for packing on other nonclosed packed lattices. We have performed a statistical analysis of available protein structures and found agreement with the predicted preferred abundances of proteins with a predicted magic number of secondary structures. Thermodynamic arguments for the increased abundance and a phase diagram for the folding scenario are given. This includes an intermediate high symmetry phase, the parent structures, between the molten globule and the native states. We have made an exhaustive enumeration of dense lattice animals on a cubic lattice for acceptance number Z=4 and Z=5 up to 36 vertices.

  13. 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…

  14. Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome

    PubMed Central

    Elcock, Adrian H

    2006-01-01

    Although molecular simulation methods have yielded valuable insights into mechanistic aspects of protein refolding in vitro, they have up to now not been used to model the folding of proteins as they are actually synthesized by the ribosome. To address this issue, we report here simulation studies of three model proteins: chymotrypsin inhibitor 2 (CI2), barnase, and Semliki forest virus protein (SFVP), and directly compare their folding during ribosome-mediated synthesis with their refolding from random, denatured conformations. To calibrate the methodology, simulations are first compared with in vitro data on the folding stabilities of N-terminal fragments of CI2 and barnase; the simulations reproduce the fact that both the stability and thermal folding cooperativity increase as fragments increase in length. Coupled simulations of synthesis and folding for the same two proteins are then described, showing that both fold essentially post-translationally, with mechanisms effectively identical to those for refolding. In both cases, confinement of the nascent polypeptide chain within the ribosome tunnel does not appear to promote significant formation of native structure during synthesis; there are however clear indications that the formation of structure within the nascent chain is sensitive to location within the ribosome tunnel, being subject to both gain and loss as the chain lengthens. Interestingly, simulations in which CI2 is artificially stabilized show a pronounced tendency to become trapped within the tunnel in partially folded conformations: non-cooperative folding, therefore, appears in the simulations to exert a detrimental effect on the rate at which fully folded conformations are formed. Finally, simulations of the two-domain protease module of SFVP, which experimentally folds cotranslationally, indicate that for multi-domain proteins, ribosome-mediated folding may follow different pathways from those taken during refolding. Taken together, these

  15. 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

  16. 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

  17. Influence of the ventricular folds on a voice source with specified vocal fold motion1

    PubMed Central

    McGowan, Richard S.; Howe, Michael S.

    2010-01-01

    The unsteady drag on the vocal folds is the major source of sound during voiced speech. The drag force is caused by vortex shedding from the vocal folds. The influence of the ventricular folds (i.e., the “false” vocal folds that protrude into the vocal tract a short distance downstream of the glottis) on the drag and the voice source are examined in this paper by means of a theoretical model involving vortex sheets in a two-dimensional geometry. The effect of the ventricular folds on the output acoustic pressure is found to be small when the movement of the vocal folds is prescribed. It is argued that the effect remains small when fluid-structure interactions account for vocal fold movement. These conclusions can be justified mathematically when the characteristic time scale for change in the velocity of the glottal jet is large compared to the time it takes for a vortex disturbance to be convected through the vocal fold and ventricular fold region. PMID:20329852

  18. 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.

  19. Thermal conductance modulator based on folded graphene nanoribbons

    SciTech Connect

    Ouyang, Tao; Chen, Yuanping; Xie, Yuee; Stocks, George Malcolm; Zhong, Jianxin

    2011-01-01

    Based on folded graphene nanoribbons, we report a thermal conductance modulator which performs analogous operations as the rheostat in electronic circuits. This fundamental device can controllably and reversibly modulate the thermal conductance by varying the geometric structures and its tuning range can be up to 40% of the conductance of unfolded nanoribbons ( 1 nm wide and 7 15 nm long). Under this modulation, the conductance shows a linearly dependence on the folded angle, while undergoes a transition with the variation of the inter-layer distance. This primary thermal device may have great potential applications for phononic circuits and nanoscale thermal management. VC2011 American Institute of Physics. [doi:10.1063/1.3665184

  20. 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

  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. Globular Protein Folding In Vitro and In Vivo.

    PubMed

    Gruebele, Martin; Dave, Kapil; Sukenik, Shahar

    2016-07-01

    In vitro, computational, and theoretical studies of protein folding have converged to paint a rich and complex energy landscape. This landscape is sensitively modulated by environmental conditions and subject to evolutionary pressure on protein function. Of these environments, none is more complex than the cell itself, where proteins function in the cytosol, in membranes, and in different compartments. A wide variety of kinetic and thermodynamics experiments, ranging from single-molecule studies to jump kinetics and from nuclear magnetic resonance to imaging on the microscope, have elucidated how protein energy landscapes facilitate folding and how they are subject to evolutionary constraints and environmental perturbation. Here we review some recent developments in the field and refer the reader to some original work and additional reviews that cover this broad topic in protein science. PMID:27391927

  3. 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

  4. 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

  5. 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

  6. 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.

  7. Kinetics of Peptide Folding in Lipid Membranes

    PubMed Central

    Oh, Kwang-Im; Smith-Dupont, Kathryn B.; Markiewicz, Beatrice N.; Gai, Feng

    2015-01-01

    Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments. PMID:25808575

  8. Stretching and folding in finite time.

    PubMed

    Ma, Tian; Ouellette, Nicholas T; Bollt, Erik M

    2016-02-01

    Complex flows mix efficiently, and this process can be understood by considering the stretching and folding of material volumes. Although many metrics have been devised to characterize stretching, fewer are able to capture folding in a quantitative way in spatiotemporally variable flows. Here, we extend our previous methods based on the finite-time curving of fluid-element trajectories to nonzero scales and show that this finite-scale finite-time curvature contains information about both stretching and folding. We compare this metric to the more commonly used finite-time Lyapunov exponent and illustrate our methods using experimental flow-field data from a quasi-two-dimensional laboratory flow. Our new analysis tools add to the growing set of Lagrangian methods for characterizing mixing in complex, aperiodic fluid flows.

  9. Exact folded-band chaotic oscillator

    NASA Astrophysics Data System (ADS)

    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.

  10. Effects of Knots on Protein Folding Properties

    PubMed Central

    Soler, Miguel A.; Faísca, Patrícia F. N.

    2013-01-01

    This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin) can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation. PMID:24023962

  11. Ontogeny of the mouse vocal fold epithelium

    PubMed Central

    Lungova, Vlasta; Verheyden, Jamie M.; Herriges, John; Sun, Xin; Thibeault, Susan L.

    2015-01-01

    This investigation provides the first systematic determination of the cellular and molecular progression of vocal fold (VF) epithelium development in a murine model. We define five principal developmental events that constitute the progression from VF initiation in the embryonic anterior foregut tube to fully differentiated and functional adult tissue. These developmental events include (1) the initiation of the larynx and vocal folds with apposition of the lateral walls of the primitive laryngopharynx (embryonic (E) day 10.5); (2) the establishment of the epithelial lamina with fusion of the lateral walls of the primitive laryngopharynx (E11.5); (3) the epithelial lamina recanalization and separation of VFs (E13.5–18.5); (4) the stratification of the vocal folds (E13.5–18.5); and (5) the maturation of vocal fold epithelium (postnatal stages). The illustration of these morphogenetic events is substantiated by dynamic changes in cell proliferation and apoptosis, as well as the expression pattern of key transcription factors, FOXA2, SOX2 and NKX2-1 that specify and pattern the foregut endoderm. Furthermore, we documented the gradual conversion of VF epithelial cells from simple precursors expressing cytokeratins 8 and 18 in the embryo into mature stratified epithelial cells also expressing cytokeratins 5 and 14 in the adult. Interestingly, in the adult, cytokeratins 5 and 14 appear to be expressed in all cell layers in the VF, in contrast to their preferential localization to the basal cell layer in surrounding epithelium. To begin investigating the role of signaling molecules in vocal fold development, we characterized the expression pattern of SHH pathway genes, and how loss of Shh affects vocal fold development in the mutant. This study defines the cellular and molecular context and serves as the necessary foundation for future functional investigations of VF formation. PMID:25601450

  12. 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.

  13. 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.

  14. 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.

  15. Circular permutant GFP insertion folding reporters

    SciTech Connect

    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.

  16. Circular permutant GFP insertion folding reporters

    SciTech Connect

    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.

  17. Prions and protein-folding diseases.

    PubMed

    Norrby, E

    2011-07-01

    Prions represent a group of proteins with a unique capacity to fold into different conformations. One isoform is rich in beta-pleated sheets and can aggregate into amyloid that may be pathogenic. This abnormal form propagates itself by imposing its confirmation on the homologous normal host cell protein. Pathogenic prions have been shown to cause lethal neurodegenerative diseases in humans and animals. These diseases are sometimes infectious and hence referred to as transmissible spongiform encephalopathies. In the present review, the remarkable evolution of the heterodox prion concept is summarized. The origin of this phenomenon is based on information transfer between homologous proteins, without the involvement of nucleic acid-encoded mechanisms. Historically, kuru and Creutzfeldt-Jakob disease (CJD) were the first infectious prion diseases to be identified in man. It was their relationship to scrapie in sheep and experimental rodents that allowed an unravelling of the particular molecular mechanism that underlie the disease process. Transmission between humans has been documented to have occurred in particular contexts, including ritual cannibalism, iatrogenic transmission because of pituitary gland-derived growth hormone or the use in neurosurgical procedures of dura mater from cadavers, and the temporary use of a prion-contaminated protein-rich feed for cows. The latter caused a major outbreak of bovine spongiform encephalopathy, which spread to man by human consumption of contaminated meat, causing approximately 200 cases of variant CJD. All these epidemics now appear to be over because of measures taken to curtail further spread of prions. Recent studies have shown that the mechanism of protein aggregation may apply to a wider range of diseases in and possibly also outside the brain, some of which are relatively common such as Alzheimer's and Parkinson's diseases. Furthermore, it has become apparent that the phenomenon of prion aggregation may have a wider

  18. Compact 3D flash lidar video cameras and applications

    NASA Astrophysics Data System (ADS)

    Stettner, Roger

    2010-04-01

    The theory and operation of Advanced Scientific Concepts, Inc.'s (ASC) latest compact 3D Flash LIDAR Video Cameras (3D FLVCs) and a growing number of technical problems and solutions are discussed. The solutions range from space shuttle docking, planetary entry, decent and landing, surveillance, autonomous and manned ground vehicle navigation and 3D imaging through particle obscurants.

  19. Compact Circuit Preprocesses Accelerometer Output

    NASA Technical Reports Server (NTRS)

    Bozeman, Richard J., Jr.

    1993-01-01

    Compact electronic circuit transfers dc power to, and preprocesses ac output of, accelerometer and associated preamplifier. Incorporated into accelerometer case during initial fabrication or retrofit onto commercial accelerometer. Made of commercial integrated circuits and other conventional components; made smaller by use of micrologic and surface-mount technology.

  20. Generalized high order compact methods.

    SciTech Connect

    Spotz, William F.; Kominiarczuk, Jakub

    2010-09-01

    The fundamental ideas of the high order compact method are combined with the generalized finite difference method. The result is a finite difference method that works on unstructured, nonuniform grids, and is more accurate than one would classically expect from the number of grid points employed.

  1. 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.

  2. Mesoscale Simulations of Power Compaction

    SciTech Connect

    Lomov, I; Fujino, D; Antoun, T; Liu, B

    2009-08-06

    Mesoscale 3D simulations of metal and ceramic powder compaction in shock waves have been performed with an Eulerian hydrocode GEODYN. The approach was validated by simulating shock compaction of porous well-characterized ductile metal using Steinberg material model. Results of the simulations with handbook values for parameters of solid 2024 aluminum have good agreement with experimental compaction curves and wave profiles. Brittle ceramic materials are not so well studied as metals, so material model for ceramic (tungsten carbide) has been fitted to shock compression experiments of non-porous samples and further calibrated to match experimental compaction curves. Direct simulations of gas gun experiments with ceramic powder have been performed and showed good agreement with experimental data. Numerical shock wave profile has same character and thickness as measured with VISAR. Numerical results show reshock states above the single-shock Hugoniot line also observed in experiments. They found that to receive good quantitative agreement with experiment it is essential to perform 3D simulations.

  3. Mesoscale simulations of powder compaction

    NASA Astrophysics Data System (ADS)

    Lomov, Ilya; Antoun, Tarabay; Liu, Benjamin

    2009-06-01

    Mesoscale 3D simulations of metal and ceramic powder compaction in shock waves have been performed with an Eulerian hydrocode GEODYN. The approach was validated by simulating shock compaction of porous well-characterized ductile metal using Steinberg material model. Results of the simulations with handbook values for parameters of solid 2024 aluminum have good agreement with experimental compaction curves and wave profiles. Brittle ceramic materials are not so well studied as metals, so material model for ceramic (tungsten carbide) has been fitted to shock compression experiments of non-porous samples and further calibrated to experimental match compaction curves. Direct simulations of gas gun experiments with ceramic powder have been performed and showed good agreement with experimental data. Numerical shock wave profile has same character and thickness as measured with VISAR. Numerical results show evidence of hard-to-explain reshock states above the single-shock Hugoniot line, which have also been observed in the experiments. We found that to receive good quantitative agreement with experiment it is essential to perform 3D simulations, since 2D results tend to underpredict stress levels for high-porosity powders regardless of material properties. We developed a process to extract macroscale information for the simulation which can be directly used in calibration of continuum model for heterogeneous media.

  4. Gradual Folding of an Off-Pathway Molten Globule Detected at the Single-Molecule Level.

    PubMed

    Lindhoud, Simon; Pirchi, Menahem; Westphal, Adrie H; Haran, Gilad; van Mierlo, Carlo P M

    2015-09-25

    Molten globules (MGs) are compact, partially folded intermediates that are transiently present during folding of many proteins. These intermediates reside on or off the folding pathway to native protein. Conformational evolution during folding of off-pathway MGs is largely unexplored. Here, we characterize the denaturant-dependent structure of apoflavodoxin's off-pathway MG. Using single-molecule fluorescence resonance energy transfer (smFRET), we follow conversion of unfolded species into MG down to denaturant concentrations that favor formation of native protein. Under strongly denaturing conditions, fluorescence resonance energy transfer histograms show a single peak, arising from unfolded protein. The smFRET efficiency distribution shifts to higher value upon decreasing denaturant concentration because the MG folds. Strikingly, upon approaching native conditions, the fluorescence resonance energy transfer efficiency of the MG rises above that of native protein. Thus, smFRET exposes the misfolded nature of apoflavodoxin's off-pathway MG. We show that conversion of unfolded into MG protein is a gradual, second-order-like process that simultaneously involves separate regions within the polypeptide. PMID:26163276

  5. Continuous Cropping Systems Reduce Near-Surface Maximum Compaction in No-Till Soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Because of increased concerns over compaction in NT soils, it is important to assess how continuous cropping systems influence risks of soil compaction across a range of soils and NT management systems. We quantified differences in maximum bulk density (BDmax) and critical water content (CWC) by the...

  6. 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…

  7. 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

  8. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    NASA Astrophysics Data System (ADS)

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-09-01

    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.

  9. 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

    2015-01-01

    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

  10. 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.

  11. Statistical Mechanical Model for pH-Induced Protein Folding: Application to Apomyoglobin.

    PubMed

    Mizukami, Takuya; Sakuma, Yosuke; Maki, Kosuke

    2016-09-01

    Despite the major role of pH in protein folding and stability, a quantitative understanding of the pH-induced protein folding mechanism remains elusive. Two conventional models, the Monod-Wyman-Changeux and Linderstrøm-Lang smeared charge models, respectively, have been used to analyze the formation/disruption of specific native structures and fluctuating non-native states. However, there are only a few models that can represent the overall kinetic events of folding/unfolding independent of the properties of relevant molecular species, which has hampered the efforts to systematically analyze pH-induced folding. Here, we constructed a statistical mechanical model that incorporates the protonation mechanism of conventional models along with a combined manual search and least-squares fitting procedure, which was used to investigate the folding of horse apomyoglobin over a wide pH range (2.2-6.7), with a time window ranging from ∼40 μs to ∼100 s, using continuous-/stopped-flow fluorescence at 8 °C. Quantitative analysis assuming a five-state sequential scheme indicated that (1) pH-induced folding/unfolding is represented by both specific binding and Coulombic interactions; (2) kinetic folding/unfolding intermediates share kinetic mechanisms with the equilibrium intermediate, indicating their equivalence; and (3) native-like properties are acquired successively during folding by intermediates and in transition states. This model could also be applied to a variety of association/dissociation processes. PMID:27491483

  12. Multiple contact network is a key determinant to protein folding rates.

    PubMed

    Gromiha, M Michael

    2009-04-01

    Understanding the relationship between amino acid sequences and folding rates of proteins is an important task in computational and molecular biology. It has been shown that topological parameters, contact order, long-range order, and total contact distance relate well with protein folding rates. In this work, we have systematically analyzed the influence of amino acid residues that form multiple contacts in protein structures to folding rates of proteins. We observed an inverse relationship between the number of residues with multiple contacts and protein folding rates. Further analysis indicates that multiple contacts are influenced by hydrophobic residues, whereas the role is minimal between the residues that are capable of forming hydrogen bonds. The propensity of multiple contacts forming residues showed that aromatic and hydrophobic residues are dominant in two-state proteins, whereas the polar residues Ser and Thr are also preferred ones in three-state proteins. In addition, multiple contact forming residues are interconnected with each other through contact networks in protein structures. The comparison between slow and fast folding proteins demonstrated the presence of more multiple contact forming residues in slow folding proteins with a limit of 4-6 contacts/residue. These results have been reflected in amino acid sequences in the form of short-, medium-, and long-range contacts, which could discriminate slow and fast folding proteins with an accuracy of 96% using a 5-fold cross-validation method.

  13. Effect of grain size distribution on the development of compaction localization in porous sandstone

    NASA Astrophysics Data System (ADS)

    Cheung, Cecilia S. N.; Baud, Patrick; Wong, Teng-fong

    2012-11-01

    Compaction bands are strain localization structures that are relatively impermeable and can act as barriers to fluid flow in reservoirs. Laboratory studies have shown that discrete compaction bands develop in several sandstones with porosities of 22-25%, at stress states in the transitional regime between brittle faulting and cataclastic flow. To identify the microstructural parameters that influence compaction band formation, we conducted a systematic study of mechanical deformation, failure mode and microstructural evolution in Bleurswiller and Boise sandstones, of similar porosity (˜25%) and mineralogy but different sorting. Discrete compaction bands were observed to develop over a wide range of pressure in the Bleurswiller sandstone that has a relatively uniform grain size distribution. In contrast, compaction localization was not observed in the poorly sorted Boise sandstone. Our results demonstrate that grain size distribution exerts important influence on compaction band development, in agreement with recently published data from Valley of Fire and Buckskin Gulch, as well as numerical studies.

  14. Fold in Origami and Unfold Math

    ERIC Educational Resources Information Center

    Georgeson, Joseph

    2011-01-01

    Students enjoy origami and like making everything from paper cranes to footballs out of small, colorful squares of paper. They can invent their own shapes and are intrigued by the polyhedrons that they can construct. Paper folding is fun, but where is the math? Unless teachers develop lessons that address mathematical objectives, origami could be…

  15. Role of cofactors in metalloprotein folding.

    PubMed

    Wilson, Corey J; Apiyo, David; Wittung-Stafshede, Pernilla

    2004-01-01

    Metals are commonly found as natural constituents of proteins. Since many such metals can interact specifically with their corresponding unfolded proteins in vitro , cofactor-binding prior to polypeptide folding may be a biological path to active metalloproteins. By interacting with the unfolded polypeptide, the metal may create local structure that initiates and directs the polypeptide-folding process. Here, we review recent literature that addresses the involvement of metals in protein-folding reactions in vitro . To date, the best characterized systems are simple one such as blue-copper proteins, heme-binding proteins, iron-sulfur-cluster proteins and synthetic metallopeptides. Taken together, the available data demonstrates that metals can play diverse roles: it is clear that many cofactors bind before polypeptide folding and influence the reaction; yet, some do not bind until a well-structured active site is formed. The significance of characterizing the effects of metals on protein conformational changes is underscored by the many human diseases that are directly linked to anomalous protein-metal interactions.

  16. Folded-path optical analysis gas cell

    DOEpatents

    Carangelo, Robert M.; Wright, David D.

    1995-01-01

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

  17. Hydroxyapatite surface-induced peptide folding.

    PubMed

    Capriotti, Lisa A; Beebe, Thomas P; Schneider, Joel P

    2007-04-25

    Herein, we describe the design and surface-binding characterization of a de novo designed peptide, JAK1, which undergoes surface-induced folding at the hydroxyapatite (HA)-solution interface. JAK1 is designed to be unstructured in buffered saline solution, yet undergo HA-induced folding that is largely governed by the periodic positioning of gamma-carboxyglutamic acid (Gla) residues within the primary sequence of the peptide. Circular dichroism (CD) spectroscopy and analytical ultracentrifugation indicate that the peptide remains unfolded and monomeric in solution under normal physiological conditions; however, CD spectroscopy indicates that in the presence of hydroxyapatite, the peptide avidly binds to the mineral surface adopting a helical structure. Adsorption isotherms indicate nearly quantitative surface coverage and Kd = 310 nM for the peptide-surface binding event. X-ray photoelectron spectroscopy (XPS) coupled with the adsorption isotherm data suggests that JAK1 binds to HA, forming a self-limiting monolayer. This study demonstrates the feasibility of using HA surfaces to trigger the intramolecular folding of designed peptides and represents the initial stages of defining the design rules that allow HA-induced peptide folding.

  18. How do metal ions direct ribozyme folding?

    NASA Astrophysics Data System (ADS)

    Denesyuk, Natalia A.; Thirumalai, D.

    2015-10-01

    Ribozymes, which carry out phosphoryl-transfer reactions, often require Mg2+ ions for catalytic activity. The correct folding of the active site and ribozyme tertiary structure is also regulated by metal ions in a manner that is not fully understood. Here we employ coarse-grained molecular simulations to show that individual structural elements of the group I ribozyme from the bacterium Azoarcus form spontaneously in the unfolded ribozyme even at very low Mg2+ concentrations, and are transiently stabilized by the coordination of Mg2+ ions to specific nucleotides. However, competition for scarce Mg2+ and topological constraints that arise from chain connectivity prevent the complete folding of the ribozyme. A much higher Mg2+ concentration is required for complete folding of the ribozyme and stabilization of the active site. When Mg2+ is replaced by Ca2+ the ribozyme folds, but the active site remains unstable. Our results suggest that group I ribozymes utilize the same interactions with specific metal ligands for both structural stability and chemical activity.

  19. Hydroxyapatite surface-induced peptide folding.

    PubMed

    Capriotti, Lisa A; Beebe, Thomas P; Schneider, Joel P

    2007-04-25

    Herein, we describe the design and surface-binding characterization of a de novo designed peptide, JAK1, which undergoes surface-induced folding at the hydroxyapatite (HA)-solution interface. JAK1 is designed to be unstructured in buffered saline solution, yet undergo HA-induced folding that is largely governed by the periodic positioning of gamma-carboxyglutamic acid (Gla) residues within the primary sequence of the peptide. Circular dichroism (CD) spectroscopy and analytical ultracentrifugation indicate that the peptide remains unfolded and monomeric in solution under normal physiological conditions; however, CD spectroscopy indicates that in the presence of hydroxyapatite, the peptide avidly binds to the mineral surface adopting a helical structure. Adsorption isotherms indicate nearly quantitative surface coverage and Kd = 310 nM for the peptide-surface binding event. X-ray photoelectron spectroscopy (XPS) coupled with the adsorption isotherm data suggests that JAK1 binds to HA, forming a self-limiting monolayer. This study demonstrates the feasibility of using HA surfaces to trigger the intramolecular folding of designed peptides and represents the initial stages of defining the design rules that allow HA-induced peptide folding. PMID:17397165

  20. Folded-path optical analysis gas cell

    DOEpatents

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

    1995-08-08

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