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.

    1988-01-01

    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.

  8. Compact range for variable-zone measurements

    DOEpatents

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

    1987-02-27

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

  9. 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.

  10. Compact range test applications, phase 2

    NASA Astrophysics Data System (ADS)

    Davis, Francis L.

    1992-01-01

    Georgia Tech Research Institute (GTRI) has designed and fabricated a large outdoor Compact Antenna Range for the U.S. Army Electronic Proving Ground (USAEPG). This range enables USAEPG to test antenna systems of large ground vehicles or aircraft that weigh up to 70 tons and are up to 50 feet in size over a frequency range of 6 to 40 GHz. Ongoing investigation and study are being conducted to determine the compatibility and adaptability of this antenna pattern measurement range to measure other system parameters such as target return signals and system responses to specialized electromagnetic environments.

  11. 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

  12. 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.

  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. Folding of polymer chains with short-range binormal interactions

    NASA Astrophysics Data System (ADS)

    Craig, A.; Terentjev, E. M.

    2006-05-01

    We study the structure of chains which have anisotropic short-range contact interactions that depend on the alignment of the binormal vectors of chain segments. This represents a crude model of hydrogen bonding or 'stacking' interactions out of the plane of curvature. The polymers are treated as ribbon-like semi-flexible chains, where the plane of the ribbon is determined by the local binormal. We show that with dipole-dipole interactions between the binormals of contacting chain segments, mean-field theory predicts a first-order transition to a binormally aligned state. We describe the onset of this transition as a function of the temperature-dependent parameters that govern the chain stiffness and the strength of the binormal interaction, as well as the binormal alignment's coupling to chain collapse. We also examine a metastable state governing the folding kinetics. Finally, we discuss the possible mesoscopic structure of the aligned phase, and application of our model to secondary structure motifs like β-sheets and α-helices, as well as composite structures like β-(amyloid) fibrils.

  15. 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.

  16. Compact laser sources for laser designation, ranging and active imaging

    NASA Astrophysics Data System (ADS)

    Goldberg, Lew; Nettleton, John; Schilling, Brad; Trussel, Ward; Hays, Alan

    2007-04-01

    Recent advances in compact solid sate lasers for laser designation, eye-safe range finding and active imaging are described. Wide temperature operation of a compact Nd:YAG laser was achieved by end pumping and the use of multi-λ diode stacks. Such lasers enabled construction of fully operational 4.7 lb laser designator prototypes generating over 50 mJ at 10-20 Hz PRF. Output pulse energy in excess of 100 mJ was demonstrated in a breadboard version of the end-pumped laser. Eye-safe 1.5 μm lasers based on flash-pumped, low PRF, Monoblock lasers have enabled compact STORM laser range finders that have recently been put into production. To achieve higher optical and electrical efficiency needed for higher PRF operation, Monoblock lasers were end-pumped by a laser diode stack. Laser diode end-pumped Monoblock lasers were operated at 10-20 Hz PRF over a wide temperature range (-20 to +50 °C). Compared with bulk compact solid state lasers, fiber lasers are characterized by lower pulse energy, higher PRF's, shorter pulses and higher electrical efficiency. An example of fiber lasers suitable for LIDAR, and atmospheric measurement applications is described. Eye-safe, low intensity diode pumped solid state green warning laser developed for US Army checkpoint and convoy applications is also described.

  17. The ogive as a RCS compact range standard

    NASA Technical Reports Server (NTRS)

    Dominek, A.; Nguyen, T.

    1989-01-01

    E- and H-plane radar cross section (RCS) patterns at 4 and 10 GHz are provided (based upon moment method calculations) for a perfectly conducting ogive to be used as a compact range verification standard. The dimensions of the ogive are 36 in. and 9.546 in. long with half tip angles of 15 deg and 20 deg, respectively. Comparison between the calculations and measurements are also provided.

  18. 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.

  19. Design of blended rolled edges for compact range main reflectors

    NASA Technical Reports Server (NTRS)

    Ericksen, K. P.; Gupta, I. J.; Burnside, W. D.

    1988-01-01

    A procedure to design blended rolled edge terminations for arbitrary rim shape compact range main reflectors is presented. The reflector may be center-fed or offset-fed. The design procedure leads to a reflector which has a continuous and smooth surface. This procedure also ensures small diffracted fields from the junction between the paraboloid and the blended rolled edge while satisfying certain constraints regarding the maximum height of the reflector and minimum operating frequency of the system. The prescribed procedure is used to design several reflectors and the performance of these reflectors is presented.

  20. 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

  1. An aperture-matched compact range feed horn design

    NASA Technical Reports Server (NTRS)

    Heedy, D. J.; Burnside, W. D.

    1985-01-01

    The moment method and the uniform geometrical theory of diffraction are used to obtain two separate solutions for the E-plane far field pattern of an aperture-matched horn antenna. This particular horn antenna consists of a standard pyramidal horn with the following modifications: a rolled edge section attached to the aperture edges and a curved throat section. The resulting geometry provides significantly better performance in terms of the pattern, impedance, and frequency characteristics than normally obtainable. The moment method is used to calculate the E-plane pattern and voltage standing-wave ratio (VSWR) of the antenna. However, at higher frequencies, the moment method requires large amounts of computation time. On the other hand, the uniform geometrical theory of diffraction provides a quick and efficient high frequency solution for the E-plane field pattern. This procedure has been successfully applied to design a compact range feed horn.

  2. 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

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

    PubMed

    Ratnaparkhi, G S; Varadarajan, R

    2001-08-01

    Osmolytes stabilize proteins to thermal and chemical denaturation. We have studied the effects of the osmolytes sarcosine, betaine, trimethylamine-N-oxide, and taurine on the structure and stability of the protein.peptide complex RNase S using x-ray crystallography and titration calorimetry, respectively. The largest degree of stabilization is achieved with 6 m sarcosine, which increases the denaturation temperatures of RNase S and S pro by 24.6 and 17.4 degrees C, respectively, at pH 5 and protects both proteins against tryptic cleavage. Four crystal structures of RNase S in the presence of different osmolytes do not offer any evidence for osmolyte binding to the folded state of the protein or any perturbation in the water structure surrounding the protein. The degree of stabilization in 6 m sarcosine increases with temperature, ranging from -0.52 kcal mol(-1) at 20 degrees C to -5.4 kcal mol(-1) at 60 degrees C. The data support the thesis that osmolytes that stabilize proteins, do so by perturbing unfolded states, which change conformation to a compact, folding competent state in the presence of osmolyte. The increased stabilization thus results from a decrease in conformational entropy of the unfolded state. PMID:11373282

  4. 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.

  5. 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

  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. 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

  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. Optical design and development of near-range compact lidar

    NASA Astrophysics Data System (ADS)

    Shiina, Tatsuo

    2011-12-01

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

  10. 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.

  11. 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.

  12. Compact and low power thermo-optic switch using folded silicon waveguides.

    PubMed

    Densmore, Adam; Janz, Siegfried; Ma, Rubin; Schmid, Jens H; Xu, Dan-Xia; Delâge, André; Lapointe, Jean; Vachon, Martin; Cheben, Pavel

    2009-06-22

    By exploiting the small bend radius achievable using high-index-contrast silicon photonic wire waveguides, we demonstrate a new low power thermo-optic switch arranged in a dense, double spiral geometry. Such a design permits the waveguide length to be extended for increased phase shift, without the need for increased heated volume. This provides an effective means to reduce the power consumption of thermo-optic switches, as well as a compact geometry desirable for the development of switch arrays. A low switching power of 6.5 mW was obtained for a spiral-path Mach-Zehnder interferometer device having a 10% - 90% rise time of 14 micros. The switching power is shown to be reduced by more than 5 times compared to a Mach-Zehnder interferometer employing a conventional straight waveguide geometry. PMID:19550441

  13. 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. PMID:23129654

  14. 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.

  15. Folded multiple-capture: an architecture for high dynamic range disturbance-tolerant focal plane array

    NASA Astrophysics Data System (ADS)

    Kavusi, Sam; El Gamal, Abbas

    2004-08-01

    Earlier studies have shown that multiple capture can achieve high SNR, but cannot satisfy the high dynamic range (HDR) and high speed requirements of the Vertically-Integrated-Sensor-Array (VISA) project. Synchronous self-reset, on the other hand, can achieve these requirements, but suffers from poor SNR. Extended counting can achieve high dynamic range at high frame rate and with good SNR, but at the expense of high power consumption. The paper proposes a new HDR focal plane array architecture, denoted by folded-multiple capture (FMC), which by combining features of the synchronous self-reset and multiple capture schemes, can satisfy the VISA requirements at a fraction of the power dissipation and with more robustness to device variations than extended counting. The architecture is also capable of detecting subframe disturbances, e.g., due to laser jamming, and correcting for it.

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

    NASA Astrophysics Data System (ADS)

    Leitold, Christian; Dellago, Christoph

    2014-10-01

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

  17. Range-front deformation on the northern limb of the Manastash Anticline, Yakima Fold Belt, Washington

    NASA Astrophysics Data System (ADS)

    Ladinsky, T. C.; Kelsey, H. M.; Sherrod, B. L.; Pratt, T. L.

    2010-12-01

    The Manastash Ridge range front on the south edge of the Kittitas Valley near Ellensburg Washington is a prominent north-facing range front within the Yakima fold belt that hosts a suite of landforms that may reflect active faulting. Quaternary mapping on LiDAR imagery of the northern limb provides evidence for episodic uplift and/or base level lowering that may be associated with crustal shortening of the Manastash anticline. The geomorphic evolution of the Manastash front is preserved through terrace sequences and uplifted alluvial fan deposits. Abandoned terraces record prior positions of the Yakima River. Field verification of the LiDAR mapping corroborated a series of fan deposits that record periods of sedimentation from short, steep drainages issuing north off the Manastash range front. Subsequently, the fans were modified through erosion by the Yakima River. Therefore, terrace sequences locally are proximal to the mouths of the short, steep drainages. Field exposures indicate that the lower terraces are composed of alluvial fill, while higher terraces are incised into bedrock with a surficial cover. The sequence of Quaternary alluvial deposits and terraces suggest a minimum of three base level-lowering events adjacent to the Manastash front. From the lack of well developed loess cover on lowest terrace, we infer that the most recent base level lowering event was latest Pleistocene or Holocene. Abandoned terraces and fan deposits are consistent with the interpretation that the Manastash Ridge is translating upward relative to the Kittitas Valley. Each base level lowering event may be a manifestation of co-seismic slip on a blind fault underlying the range front. If such a blind fault is responsible for base level lowering, the sense of slip is unclear from abandoned terraces alone. However, bedrock exposures along Shushuskin Canyon, a valley that drains north out of the range front, exhibit a tight syncline within the northern limb of the anticline. This

  18. Modelling of the void space of tablets compacted over a range of pressures.

    PubMed

    Ridgway, C J; Ridgway, K; Matthews, G P

    1997-04-01

    A previously developed computer model, named Pore-Cor, has been used to simulate the changes in the void-space dimensions which occur during the compaction of tablets over a range of pressures. The tablets were made by mixing pharmaceutical grade crystalline lactose and an anti-inflammatory compound in the proportion 4:1. Compacts were made by placing a weighed amount of the mixed powder into a stainless-steel die and applying pressure with a hand-operated calibrated hydraulic press. Compacts were prepared at eight pressures over the hydraulic pressure range 1 to 8 ton in-2 (15.4-123.2 MPa) in 1 ton in-2 increments. Mercury-intrusion curves were measured for the eight samples by use of a porosimeter and the Pore-Cor package was then used to simulate the mercury-intrusion curves and generate void-space models of the correct porosity. The experimental and simulated characteristic throat diameter, the experimental and simulated porosity, and the simulated permeability of the tablets have all been shown to follow expected trends. The successful modelling of void-structure parameters, which are difficult or impossible to measure experimentally, opens the way to an improved understanding of the strength of compacts. PMID:9232534

  19. 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.

  20. 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.

  1. Long range correlations and folding angle with applications to α-helical proteins

    SciTech Connect

    Krokhotin, Andrey; Nicolis, Stam; Niemi, Antti J.

    2014-03-07

    The conformational complexity of chain-like macromolecules such as proteins and other linear polymers is much larger than that of point-like atoms and molecules. Unlike particles, chains can bend, twist, and even become knotted. Thus chains might also display a much richer phase structure. Unfortunately, it is not very easy to characterize the phase of a long chain. Essentially, the only known attribute is the radius of gyration. The way how it changes when the degree of polymerization becomes different, and how it evolves when the ambient temperature and solvent properties change, is commonly used to disclose the phase. But in any finite length chain there are corrections to scaling that complicate the detailed analysis of the phase structure. Here we introduce a quantity that we call the folding angle to identify and scrutinize the phase structure, as a complement to the radius of gyration. We argue for a mean-field level relationship between the folding angle and the scaling exponent in the radius of gyration. We then estimate the value of the folding angle in the case of crystallographic α-helical protein structures in the Protein Data Bank. We also show how the experimental value of the folding angle can be obtained computationally, using a semiclassical Born-Oppenheimer description of α-helical chiral chains.

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

    NASA Technical Reports Server (NTRS)

    Gupta, Inder J.; Burnside, Walter D.

    1989-01-01

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

  3. Compact MWIR zoom camera with 20:1 zoom range and automatic athermalization

    NASA Astrophysics Data System (ADS)

    Kim, Hyun S.; Kim, Chang W.; Hong, Seok-Min

    2002-07-01

    A compact mid-wavelength infrared zoom camera with a zoom range of 20:1 and automatic athermalization has been developed. The moving groups for a wide zoom range are only two lens groups and the loci of zoom are very simple, which allows easy access of optomechanical and electromechanical design. In addition, the microscanning technique was introduced to improve resolving power. We acquired increased resolving power of 7.6 cycles/mrad, superior to the original Nyquist frequency of 4.5 cycles/mrad. The temperature range, being -30 to +55 degree(s)C, in which the camera is to operate, is rather wide. The minimum resolvable temperature difference of the zoom camera is 0.3 degree(s)C at 6 cycles/mrad.

  4. 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.

  5. Compact and efficient nanosecond pulsed tuneable OPO in the mid-IR spectral range

    NASA Astrophysics Data System (ADS)

    Hellström, J.; Jänes, P.; Elgcrona, G.; Karlsson, H.

    2013-05-01

    A compact, robust and efficient nanosecond pulsed optical parametric oscillator (OPO) generating radiation in the mid- IR spectral range is reported. The OPO is based on periodically poled material for the efficient non-linear processes of up-converting 1064 nm radiation to 1538 and 3450 nm respectively. Pulsed emission exceeding 130 mW average power at the idler (3450 nm) with a total conversion efficiency of 30%, including both signal and idler, has been reached. The maximum pulse energy of the idler is 11 μJ, pulse duration around 4 ns and peak power close to 3 kW. The results are achieved for an optical pump power of 1.4 W at the entrance of the OPO and an electrical pump power of 14 W. The total size of the OPO device is only 125x70x45 mm3 (LxWxH) including the pump laser at 1064 nm. The idler output radiation is narrowed by spectral filtering to < 1.5nm and temperature tuneable over > 50 nm. The OPO has a robust design and withstands shocks up to 60g at 8 ms and the storage temperature is -20 °C to + 60 °C. The compact size and low power consumption make this OPO device suitable for many kinds of molecular spectroscopy applications in the areas of environmental monitoring and pollution control as well as in combustion physics and process control. Integration of the OPO source into compact equipment for Photo Acoustic Spectroscopy (PAS) allowing fast and highly sensitive detection of methane and ethanol at ppb-levels is also described.

  6. Development of a phase contrast imaging system based on a yttrium aluminum garnet laser with folded beam for observations of density fluctuations in compact helical system

    SciTech Connect

    Matsuo, K.; Uchida, N.; Kawakubo, M.; Iguchi, H.; Okamura, S.; Matsuoka, K.; Akiyama, T.

    2008-10-15

    A near-infrared laser phase contrast optical system incorporating a folded beam was developed in order to measure the distribution of density fluctuations in a high-temperature plasma. The coherent light source used was an yttrium aluminum garnet laser stabilized by a ring oscillator. The probe beam system separates and reflects the incident and exiting beams with a polarizer and a fully reflective mirror with a waveplate. This system was employed with a compact helical system to detect fluctuations at the plasma edge.

  7. Stray signal requirements for compact range reflectors based on RCS measurement errors

    NASA Technical Reports Server (NTRS)

    Lee, Teh-Hong; Burnside, Walter D.

    1991-01-01

    The authors present a performance criterion for compact range reflectors such that their edge diffracted stray signal levels meet a reasonable radar cross section (RCS) measurement error requirement. It is shown by example that one of the significant error sources is the diffracted fields emanating from the edges or junctions of the reflector. This measurement error is demonstrated by placing a diagonal square flat plate in the target zone and rotating it to appropriate angles. These angles are determined by bisecting the plane wave and stray signal directions. This results in a peak bistatic measurement of the edge diffracted stray signal. It is proposed that the diagonal flat plate be used to evaluate new reflector designs as well as existing systems. A reasonable stray signal performance level has been developed so that new reflector systems can be characterized in terms of an RCS measurement error requirement.

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

    NASA Technical Reports Server (NTRS)

    Gupta, Inder J.; Burnside, Walter D.

    1987-01-01

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

  9. The slow folding reaction of barstar: the core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain.

    PubMed

    Sridevi, K; Juneja, J; Bhuyan, A K; Krishnamoorthy, G; Udgaonkar, J B

    2000-09-15

    The slow folding of a single tryptophan-containing mutant of barstar has been studied in the presence of 2 M urea at 10 degrees C, using steady state and time-resolved fluorescence methods and far and near-UV CD measurements. The protein folds in two major phases: a fast phase, which is lost in the dead time of measurement during which the polypeptide collapses to a compact form, is followed by a slow observable phase. During the fast phase, the rotational correlation time of Trp53 increases from 2.2 ns to 7.2 ns, and its mean fluorescence lifetime increases from 2.3 ns to 3.4 ns. The fractional changes in steady-state fluorescence, far-UV CD, and near-UV CD signals, which are associated with the fast phase are, respectively, 36 %, 46 %, and 16 %. The product of the fast phase can bind the hydrophobic dye ANS. These observations together suggest that the folding intermediate accumulated at the end of the fast phase has: (a) about 20 % of the native-state secondary structure, (b) marginally formed or disordered tertiary structure, (c) a water-intruded and mobile protein interior; and (d) solvent-accessible patches of hydrophobic groups. Measurements of the anisotropy decay of Trp53 suggest that it undergoes two types of rotational motion in the intermediate: (i) fast (tau(r) approximately 1 ns) local motion of its indole side-chain, and (ii) a slower (tau(r) approximately 7.2 ns) motion corresponding to global tumbling of the entire protein molecule. The ability of the Trp53 side-chain to undergo fast local motion in the intermediate, but not in the fully folded protein where it is completely buried in the hydrophobic core, suggests that the core of the intermediate is still poorly packed. The global tumbling time of the fully folded protein is faster at 5.6 ns, suggesting that the volume of the intermediate is 25 % more than that of the fully folded protein. The rate of folding of this intermediate to the native state, measured by steady-state fluorescence, far

  10. 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.

  11. Compact laser transmitter delivering a long-range infrared beam aligned with a monitoring visible beam.

    PubMed

    Lee, Hong-Shik; Kim, Haeng-In; Lee, Sang-Shin

    2012-06-10

    A compact laser transmitter, which takes advantage of an optical subassembly module, was proposed and demonstrated, providing precisely aligned collinear IR and visible beams. The collimated IR beam acts as a long-range projectile for simulated combat, carrying an optical pulsed signal, whereas the visible beam plays the role of tracking the IR beam. The proposed laser transmitter utilizes IR (λ(1)=905 nm) and visible (λ(2)=660 nm) light sources, a fiber-optic collimator, and a beam combiner, which includes a wavelength division multiplexing (WDM) filter in conjunction with optical fiber. The device was built via the laser welding technique and then evaluated by investigating the characteristics of the generated light beams. The IR collimated beam produced had a Gaussian profile and a divergence angle of ~1.3 mrad, and the visible monitoring beam was appropriately collimated to be readily discernible in the vicinity of the transmitter. The two beams were highly aligned within an angle of 0.004 deg as anticipated. Finally, we performed a practical outdoor field test to assess the IR beam with the help of a receiver. An effective trajectory was observed ranging up to 660 m with an overall detectable beam width of ~60 cm. PMID:22695673

  12. Rapid Protein Global Fold Determination Using Ultrasparse Sampling, High-Dynamic Range Artifact Suppression, and Time-Shared NOESY

    PubMed Central

    Coggins, Brian E.; Werner-Allen, Jonathan W.; Yan, Anthony; Zhou, Pei

    2012-01-01

    In structural studies of large proteins by NMR, global fold determination plays an increasingly important role in providing a first look at a target’s topology and reducing assignment ambiguity in NOESY spectra of fully-protonated samples. In this work, we demonstrate the use of ultrasparse sampling, a new data processing algorithm, and a 4-D time-shared NOESY experiment (1) to collect all NOEs in 2H/13C/15N-labeled protein samples with selectively-protonated amide and ILV methyl groups at high resolution in only four days, and (2) to calculate global folds from this data using fully automated resonance assignment. The new algorithm, SCRUB, incorporates the CLEAN method for iterative artifact removal, but applies an additional level of iteration, permitting real signals to be distinguished from noise and allowing nearly all artifacts generated by real signals to be eliminated. In simulations with 1.2% of the data required by Nyquist sampling, SCRUB achieves a dynamic range over 10000:1 (250× better artifact suppression than CLEAN) and completely quantitative reproduction of signal intensities, volumes, and lineshapes. Applied to 4-D time-shared NOESY data, SCRUB processing dramatically reduces aliasing noise from strong diagonal signals, enabling the identification of weak NOE crosspeaks with intensities 100× less than diagonal signals. Nearly all of the expected peaks for interproton distances under 5 Å were observed. The practical benefit of this method is demonstrated with structure calculations for 23 kDa and 29 kDa test proteins using the automated assignment protocol of CYANA, in which unassigned 4-D time-shared NOESY peak lists produce accurate and well-converged global fold ensembles, whereas 3-D peak lists either fail to converge or produce significantly less accurate folds. The approach presented here succeeds with an order of magnitude less sampling than required by alternative methods for processing sparse 4-D data. PMID:22946863

  13. 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.

  14. Ultra-long-range symmetric plasmonic waveguide for high-density and compact photonic devices.

    PubMed

    Huang, Chia-Chien

    2013-12-01

    This study reports a symmetric hybrid plasmonic waveguide consisting of a cylindrical metal nanowire surrounded by low-index SiO₂ and high-index Si covered with SiO₂. The symmetric circumambience relative to the metal nanowire significantly facilitates the present design to minimize the energy attenuation resulting from Ohmic losses while retaining highly confined modes guided in the low-index nanoscale gaps between the metal nanowire and the high-index Si. The geometric dependence of the mode characteristics on the proposed structure is analyzed in detail, showing long propagation lengths beyond 10 mm with normalized mode areas on the order of 10⁻². In addition to enabling the building of long-range plasmonic circuit interconnects, the compactness and high-density integration of the proposed structure are examined by analyzing crosstalk in a directional coupler composed of two such waveguides and bending losses for a 90° bend. A relatively short coupling length of 1.16 μm is obtained at a center-to-center separation of 0.26 μm between adjacent waveguides. Increasing the separation to 1.65 μm could completely prevent coupling between waveguides. Power transmission exceeds 80% in the case of a 90° bend with small radius of curvature of 0.5 μm. Moreover, the dependence of spectral response on coupling length and the transmission of a 90° bend, ranging from telecom wavelengths of 1.40 to 1.65 μm, are investigated. Over a wide wavelength range, a strong coupling length dependence on wavelength and a high transmission for a 90° bend also make the proposed plasmonic waveguide promising for the realization of wavelength-selective components. PMID:24514506

  15. 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.

  16. 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.

  17. 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; Pereira de Araújo, Antônio F

    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. Proteins 2016; 84:515-531. © 2016 Wiley Periodicals, Inc. PMID:26815167

  18. 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

  19. 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

  20. Nuclear mass formula with a finite-range droplet model and a folded-Yukawa single-particle potential

    SciTech Connect

    Moeller, P.; Myers, W.D.; Swiatecki, W.J.; Treiner, J.

    1988-07-01

    We calculate ground-state masses for 4678 nuclei ranging from /sup 16/O to /sup 318/122 by use of a macroscopic-microscopic model, which incorporates several new features. For the macroscopic model we use the finite-range droplet model which we introduced in 1984. The microscopic contribution is taken from a calculation based on a folded-Yukawa single-particle potential. Some new features now incorporated are a new model for the average pairing strength and the solution of the microscopic pairing equations by use of the Lipkin-Nogami method with approximate particle number conservation. To estimate the parameters of the macroscopic model we use an approach that starts by defining the error of a mass formula in a rigorous way, which leads naturally to the use of experimental uncertainties and of the maximum-likelihood method to derive a set of equations for estimating the parameters and error of the theoretical model. By considering 1593 experimental masses from /sup 16/O to /sup 263/106 we estimate the error of the theoretical model to be 0.769 MeV. The model retains its accuracy far from stability and the values of the model parameters are very insensitive to details of the adjustment procedure. copyright 1988 Academic Press, Inc.

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

    PubMed Central

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

    2015-01-01

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

  2. 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.

  3. A billion-fold range in acidity for the solvent-exposed amides of Pyrococcus furiosus rubredoxin.

    PubMed

    Anderson, Janet S; Hernández, Griselda; Lemaster, David M

    2008-06-10

    The exchange rates of the static solvent-accessible amide hydrogens of Pyrococcus furiosus rubredoxin range from near the diffusion-limited rate to a billion-fold slower for the non-hydrogen-bonded Val 38 (eubacterial numbering). Hydrogen exchange directly monitors the kinetic acidity of the peptide nitrogen. Electrostatic solvation free energies were calculated by Poisson-Boltzmann methods for the individual peptide anions that form during the hydroxide-catalyzed exchange reaction to examine how well the predicted thermodynamic acidities match the experimentally determined kinetic acidities. With the exception of the Ile 12 amide, the differential exchange rate constant for each solvent-exposed amide proton that is not hydrogen bonded to a backbone carbonyl can be predicted within a factor of 6 (10 (0.78)) root-mean-square deviation (rmsd) using the CHARMM22 electrostatic parameter set and an internal dielectric value of 3. Under equivalent conditions, the PARSE parameter set yields a larger rmsd value of 1.28 pH units, while the AMBER parm99 parameter set resulted in a considerably poorer correlation. Either increasing the internal dielectric value to 4 or reducing it to a value of 2 significantly degrades the quality of the prediction. Assigning the excess charge of the peptide anion equally between the peptide nitrogen and the carbonyl oxygen also reduces the correlation to the experimental data. These continuum electrostatic calculations were further analyzed to characterize the specific structural elements that appear to be responsible for the wide range of peptide acidities observed for these solvent-exposed amides. The striking heterogeneity in the potential at sites along the protein-solvent interface should prove germane to the ongoing challenge of quantifying the contribution that electrostatic interactions make to the catalytic acceleration achieved by enzymes. PMID:18479148

  4. 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

  5. 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).

  6. Folded waveguide cavity coupler for ICRF heating

    SciTech Connect

    Owens, T.L.

    1986-01-01

    This paper introduces a new type of waveguide coupler for ion cyclotron range of frequencies (ICRF) heating which is an adaptation of a concept known as a ''folded waveguide'' reported by Barrow and Schaevitz in connection with low-frequency waveguide transmission systems. The basic idea involves ''folding'' a simple rectangular waveguide to form a more compact structure. Cutoff for the folded waveguide occurs when one-half of a free-space wavelength equals the path length around the ''folds'' of the structure. By adding a large number of folds, the path length around the folds can be made large, leading to very low cutoff frequencies relative to those for simple rectangular waveguides having comparable outside dimensions. Folded waveguide couplers are practical for frequencies as low as 60 MHz for some ports found on present-day experients.

  7. 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.

  8. 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.

  9. Compact multispectral continuous zoom camera for color and SWIR vision with integrated laser range finder

    NASA Astrophysics Data System (ADS)

    Hübner, M.; Gerken, M.; Achtner, Bertram; Kraus, M.; Münzberg, M.

    2014-06-01

    In an electro-optical sensor suite for long range surveillance tasks the optics for the visible (450nm - 700nm) and the SWIR spectral wavelength range (900nm - 1700 nm) are combined with the receiver optics of an integrated laser range finder (LRF) .The incoming signal from the observed scene and the returned laser pulse are collected within the common entrance aperture of the optics. The common front part of the optics is a broadband corrected lens design from 450 - 1700nm wavelength range. The visible spectrum is split up by a dichroic beam splitter and focused on a HDTV CMOS camera. The returned laser pulse is spatially separated from the scene signal by a special prism and focused on the laser receiver diode of the integrated LRF. The achromatic lens design has a zoom factor 14 and F#2.6 in the visible path. In the SWIR path the F-number is adapted to the corresponding chip dimensions . The alignment of the LRF with respect to the SWIR camera line of sight can be controlled by adjustable integrated wedges. The two images in the visible and the SWIR spectral range match in focus and field of view (FOV) over the full zoom range between 2° and 22° HFOV. The SWIR camera has a resolution of 640×512 pixels. The HDTV camera provides a resolution of 1920×1080. The design and the performance parameters of the multispectral sensor suite is discussed.

  10. 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 ) .

  11. 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

  12. 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. PMID:17579673

  13. 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

  14. A Fold Province in the Hinterland of the Sevier Orogenic Belt in Eastern Nevada: A Valley and Ridge in the Basin and Range

    NASA Astrophysics Data System (ADS)

    Long, S. P.

    2014-12-01

    The overprinting effects of Cenozoic extensional tectonism hinder analysis of the style, geometry, and timing of Cordilleran contractional deformation in the hinterland of the Sevier fold-thrust belt in Nevada. To address this problem, a 1:250,000-scale paleogeologic map of eastern Nevada, showing spatial distributions of Paleozoic-Mesozoic rocks exposed beneath a Paleogene unconformity, divided out at the formation scale, is integrated with maps of dip magnitude for Paleozoic-Mesozoic and Tertiary rocks, published sedimentary thickness records, and a published reconstruction of Basin and Range extension, in order to define and regionally-correlate thrust faults and folds, and estimate the pre-extensional amplitude, wavelength, and limb dips of folds. A new structural province, the Eastern Nevada fold belt (ENFB) is defined, and consists of a 100-150 km-wide region containing as many as five 1st-order, N-trending folds that can be traced for map distances between 100-250 km, have amplitudes between 2-4 km, wavelengths between 20-40 km, pre-extensional limb dips typically between 10-30˚, and deform rocks as young as Jurassic and Early Cretaceous. No regional-scale thrust faults or decollemont horizons breach modern exposure levels in the ENFB. ENFB folds are interpreted to have formed above a deep (≥10 km below the Paleogene unconformity), blind decollemont or shear zone, perhaps the westward projection of the master decollemont of the Sevier fold-thrust belt. Two additional structural provinces of the Sevier hinterland, the Central Nevada thrust belt (CNTB) and Western Utah thrust belt (WUTB), represent zones of N-striking, E-vergent thrust faults and folds that each accommodated ca. 10 km of shortening. Both thrust belts branch northward off of the Sevier thrust belt, and are interpreted to represent contemporary, interior components of the Sevier thrust system. The CNTB, WUTB, and the intervening ENFB collectively record low-magnitude (a few 10's of km) upper

  15. 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.

  16. 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

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

    PubMed Central

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

    2014-01-01

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

  18. 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.

  19. Hydrogen Bonds in Polymer Folding

    NASA Astrophysics Data System (ADS)

    Borg, Jesper; Jensen, Mogens H.; Sneppen, Kim; Tiana, Guido

    2001-02-01

    We studied the thermodynamics of a homopolymeric chain with both van der Waals and directed hydrogen bond interaction. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give rise to long-range order and to conformations displaying secondary structures. For compact polymers a transition is found between helix-rich states and low-entropy sheet-dominated states. The consequences of this transition for protein folding and, in particular, for the problem of prions are discussed.

  20. 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.

  1. Connecting Crustal Faults and Tectonics from Puget Sound across the Cascade Range to the Yakima Fold and Thrust Belt, Washington: Evidence from New High-Resolution Aeromagnetic Data

    NASA Astrophysics Data System (ADS)

    Blakely, R. J.; Sherrod, B. L.; Weaver, C. S.; Wells, R. E.

    2009-05-01

    A series of regional-scale faults in the Cascadia forearc, including the Tacoma, Seattle, and southern Whidbey Island faults, cuts the Puget Sound lowland in response to 6 mm/yr of north-south compression. The Cascadia backarc of Washington, on the other hand, currently migrates <3 mm/yr northeastward relative to stable North America (McCaffrey et al., 2007). The tectonic connection between these two regions has remained problematic in part because of the lack of clearly mapped faults across the Cascade Range. A new, high-resolution aeromagnetic survey of a portion of the Cascade Range and the Yakima fold and thrust belt offers a view of the tectonic connection between the forearc and backarc. The aeromagnetic survey was acquired in 2008 and includes the cities of Yakima and Ellensburg, Washington. Total-field intensity was measured at a nominal altitude of 250 m above terrain, along flight lines spaced 400 m apart, and along tie lines spaced 4 km apart. Upper crustal rocks in this region have diverse magnetic properties, ranging from highly magnetic rocks of the Miocene Columbia River Basalt Group (CRBG), with both normal and reverse polarities, to weakly magnetic sedimentary rocks of the Miocene Ellensburg Formation. These distinctive magnetic properties permit the mapping of important lithologies from their exposures to covered areas. High- gradient aeromagnetic lineaments correspond with mapped faults and folds of the CRBG and indicate where these structures extend beyond surface exposures. For example, a two-dimensional model of the northwest- striking Umtanum Ridge fault zone, based on the new aeromagnetic data and constrained by geologic mapping, consists of three thrust faults and associated folds that deform normal and reverse flows of the CRBG. In this model, Umtanum Ridge itself is viewed as a transpressional structure uplifted 1 to 2 km along northwest-striking thrust faults with opposing dip. Modeling indicates that these thrust faults penetrate

  2. Protein folding. Translational tuning optimizes nascent protein folding in cells.

    PubMed

    Kim, Soo Jung; Yoon, Jae Seok; Shishido, Hideki; Yang, Zhongying; Rooney, LeeAnn A; Barral, Jose M; Skach, William R

    2015-04-24

    In cells, biosynthetic machinery coordinates protein synthesis and folding to optimize efficiency and minimize off-pathway outcomes. However, it has been difficult to delineate experimentally the mechanisms responsible. Using fluorescence resonance energy transfer, we studied cotranslational folding of the first nucleotide-binding domain from the cystic fibrosis transmembrane conductance regulator. During synthesis, folding occurred discretely via sequential compaction of N-terminal, α-helical, and α/β-core subdomains. Moreover, the timing of these events was critical; premature α-subdomain folding prevented subsequent core formation. This process was facilitated by modulating intrinsic folding propensity in three distinct ways: delaying α-subdomain compaction, facilitating β-strand intercalation, and optimizing translation kinetics via codon usage. Thus, de novo folding is translationally tuned by an integrated cellular response that shapes the cotranslational folding landscape at critical stages of synthesis. PMID:25908822

  3. 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.

  4. Protein folds and protein folding

    PubMed Central

    Schaeffer, R. Dustin; Daggett, Valerie

    2011-01-01

    The classification of protein folds is necessarily based on the structural elements that distinguish domains. Classification of protein domains consists of two problems: the partition of structures into domains and the classification of domains into sets of similar structures (or folds). Although similar topologies may arise by convergent evolution, the similarity of their respective folding pathways is unknown. The discovery and the characterization of the majority of protein folds will be followed by a similar enumeration of available protein folding pathways. Consequently, understanding the intricacies of structural domains is necessary to understanding their collective folding pathways. We review the current state of the art in the field of protein domain classification and discuss methods for the systematic and comprehensive study of protein folding across protein fold space via atomistic molecular dynamics simulation. Finally, we discuss our large-scale Dynameomics project, which includes simulations of representatives of all autonomous protein folds. PMID:21051320

  5. 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.

  6. Tectonic and climatic influences on the deposition and preservation of Quaternary units along the range-front of the Manastash Anticline, Yakima Fold Belt, Washington

    NASA Astrophysics Data System (ADS)

    Ladinsky, T. C.; Kelsey, H. M.; Sherrod, B. L.; Mahan, S.; Pratt, T. L.; Blakely, R. J.

    2012-12-01

    Based on multiple independent data sets, we infer episodic base-level lowering of the Kittitas Valley relative to tributaries flowing northward off the Manastash Ridge range-front and within the neighboring Lower Yakima River Canyon of central Washington. Manastash Ridge is a southeast-striking anticline within the Yakima fold and thrust belt, which deforms the extensive Miocene Columbia River Basalt flows that cover the region. Understanding the roles of climate aggradation and degradation cycles in concurrence with tectonic faulting along Manastash Ridge suggests both have contributed to the landscape evolution of the southern Kittitas Valley and Manastash range-front. Previously described proglacial outwash terraces within the northern Kittitas Valley and Upper Yakima River Canyon document periods of aggradation followed by fluvial degradation and entrenchment due to alteration in hillslope sediment production and transport capacity related to glacial and interglacial conditions. Luminescence age determinations and tephrochronology for Manastash range-front Quaternary units yield preliminary timing for aggradation of alluvial units, which we correlate to the late Pleistocene (MIS Stage V) glacial-interglacial climate transition. Seismic-reflection imagery, LiDAR, aeromagnetic surveys, and field mapping of Quaternary deposits reveal fault scarp lineaments within the Manastash range-front, west of the canyon entrance. We suggest these scarps are related to a series of north-verging thrust faults accommodating growth of the Manastash anticline. These faults isolate and uplift fan complexes, each complex generated during climate conditions favorable to fan aggradation. Entrenched alluvial fan deposits along the rangefront, strath terrace sequences, coincident knickpoints within tributary longitudinal profiles, and fault scarp lineaments suggest uplift rates of 0.02 to 0.2 m/1000yrs.

  7. Chromosome Compaction by Active Loop Extrusion.

    PubMed

    Goloborodko, Anton; Marko, John F; Mirny, Leonid A

    2016-05-24

    During cell division, chromosomes are compacted in length by more than a 100-fold. A wide range of experiments demonstrated that in their compacted state, mammalian chromosomes form arrays of closely stacked consecutive ∼100 kb loops. The mechanism underlying the active process of chromosome compaction into a stack of loops is unknown. Here we test the hypothesis that chromosomes are compacted by enzymatic machines that actively extrude chromatin loops. When such loop-extruding factors (LEF) bind to chromosomes, they progressively bridge sites that are further away along the chromosome, thus extruding a loop. We demonstrate that collective action of LEFs leads to formation of a dynamic array of consecutive loops. Simulations and an analytically solved model identify two distinct steady states: a sparse state, where loops are highly dynamic but provide little compaction; and a dense state, where there are more stable loops and dramatic chromosome compaction. We find that human chromosomes operate at the border of the dense steady state. Our analysis also shows how the macroscopic characteristics of the loop array are determined by the microscopic properties of LEFs and their abundance. When the number of LEFs are used that match experimentally based estimates, the model can quantitatively reproduce the average loop length, the degree of compaction, and the general loop-array morphology of compact human chromosomes. Our study demonstrates that efficient chromosome compaction can be achieved solely by an active loop-extrusion process. PMID:27224481

  8. Truss Structure Could Be Folded For Transport

    NASA Technical Reports Server (NTRS)

    Theer, Douglas S.

    1996-01-01

    Proposed truss structure comprises cubical bays and folded for compactness during transport. When folded, truss 1/25.6 as long as when fully extended. Conceived for transport and deployment in outerspace, suitable for terrestrial structures that must be transported compactly and erected quickly.

  9. Transtensional folding

    NASA Astrophysics Data System (ADS)

    Fossen, Haakon; Teyssier, Christian; Whitney, Donna L.

    2014-05-01

    For now three decades transpression has dominated the concepts that underlie oblique tectonics, but in more recent years transtension has garnered much interest as a simple model that can be applied to shallow and deep crustal tectonics. One fundamental aspect that distinguishes transtension from transpression is that material lines in transtension rotate toward the direction of oblique divergence. Another point that may be less intuitive when thinking of transtension is that while transtensional strain involves shortening in the vertical direction, one of the horizontal axes is also a shortening axis, whatever the angle of divergence. It is the combination of these two shortening axes that leads to constrictional finite strain in transtension. The existence of a horizontal shortening strain axis implies that transtension offers the potential for folds of horizontal layers to form and then rotate toward the direction of oblique divergence. An investigation of transtensional folding using 3D strain modeling reveals that folding is more likely for simple shear dominated transtension (large wrench component). Transtensional folds can only accumulate a fixed amount of horizontal shortening and tightness that are prescribed by the angle of oblique divergence, regardless of finite strain. Transtensional folds are characterized by hinge-parallel stretching that exceeds that expected from pure wrenching. In addition, the magnitude of hinge-parallel stretching always exceeds hinge-perpendicular shortening, causing constrictional fabrics and hinge-parallel boudinage to develop. Because the dominant vertical strain axis is shortening, transtensional fold growth is generally suppressed, but when folds do develop their limbs enter the field of shortening, resulting in possible fold interference patterns akin to cascading folds. Application of these transtensional folding principles to regions of oblique rifting (i.e. Gulf of California) or exhumation of deep crust (i.e. Western

  10. 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

  11. Implementation of a k/k0 method to identify long-range structure in transition states during conformational folding/unfolding of proteins

    PubMed Central

    Pradeep, Lovy; Kurinov, Igor; Ealick, Steven E.; Scheraga, Harold A.

    2007-01-01

    Summary A previously-introduced kinetic-rate constant (k/k0) method, where k and k0 are the folding (unfolding) rate constants in the mutant and the wild-type forms, respectively, of a protein, has been applied to obtain qualitative information about structure in the transition state (TS) ensemble of bovine pancreatic ribonuclease A (RNase A) which contains four native disulfide bonds. The method compares the folding (unfolding) kinetics of two versions of RNase A, with and without a covalent crosslink (in the form of a fifth disulfide bond); the method tests whether the crosslinked residues are associated in the folding (unfolding) transition state of the non-crosslinked version. To confirm that the fifth disulfide bond has not introduced a significant structural perturbation, we solved the crystal structure of the V43C-R85C mutant to 1.6 Å resolution. Our findings suggest that residues Val 43 and Arg 85 are not associated in the folding (unfolding) TS ensemble of RNase A, and also that Ala 4 and Val 118 may form non-native contacts in the folding (unfolding) TS ensemble. PMID:17937908

  12. Implementation of a k/k(0) method to identify long-range structure in transition states during conformational folding/unfolding of proteins.

    PubMed

    Pradeep, Lovy; Kurinov, Igor; Ealick, Steven E; Scheraga, Harold A

    2007-10-01

    A previously introduced kinetic-rate constant (k/k(0)) method, where k and k(0) are the folding (unfolding) rate constants in the mutant and the wild-type forms, respectively, of a protein, has been applied to obtain qualitative information about structure in the transition state ensemble (TSE) of bovine pancreatic ribonuclease A (RNase A), which contains four native disulfide bonds. The method compares the folding (unfolding) kinetics of RNase A, with and without a covalent crosslink and tests whether the crosslinked residues are associated in the folding (unfolding) transition state (TS) of the noncrosslinked version. To confirm that the fifth disulfide bond has not introduced a significant structural perturbation, we solved the crystal structure of the V43C-R85C mutant to 1.6 A resolution. Our findings suggest that residues Val43 and Arg85 are not associated, and that residues Ala4 and Val118 may form nonnative contacts, in the folding (unfolding) TSE of RNase A. PMID:17937908

  13. 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. PMID:24664936

  14. Kinematics of constant arc length folding for different fold shapes

    NASA Astrophysics Data System (ADS)

    Ghassemi, Mohammad R.; Schmalholz, Stefan M.; Ghassemi, Ali R.

    2010-06-01

    Basic mathematical functions are applied for the two-dimensional geometrical and kinematical analysis of different fold shapes. Relationships between different fold parameters are established and related to the bulk shortening taking place during folding under upper crustal conditions. The bulk shortening taking place during constant arc length folding is mathematically related to the bulk shortening during homogenous pure shear using a particular aspect ratio, which is for folding the ratio of amplitude to half wavelength and for pure shear the ratio of vertical to horizontal length of the deformed, initially square body. The evolution of the fold aspect ratio with bulk shortening is similar for a wide range of fold shapes and indicates that the fold aspect ratio allows a good estimate of the bulk shortening. The change of the geometry of individual layers across a multilayer sequence in disharmonic folding indicates a specific kinematics of multilayer folding, referred to here as "wrap folding", which does not require significant flexural slip nor flexural flow. The kinematic analysis indicates that there is a critical value for constant arc length folding between shortening values of 30-40% (depending on the fold geometry). For shortening values smaller than the critical value limb rotation and fold amplitude growth are dominating. For shortening larger than this value, faulting, boudinage and foliation development are likely the dominating deformation process during continued shortening. The kinematical analysis of constant arc length folding can be used for estimating the bulk shortening taking place during multilayer folding which is an important component of the deformation of crustal rocks during the early history of shortening. The bulk shortening is estimated for a natural, multilayer detachment fold and the shortening estimates based on the kinematic analysis are compared and supported by numerical finite element simulations of multilayer detachment

  15. 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.

  16. [Design of a medical folding fridge].

    PubMed

    Sun, Jianjun; Wei, Jiancang; Wu, Taihu; Meng, Xingju

    2011-07-01

    This article introduces a design of a medical folding fridge, which consists of three major components, base, folding frame and insulated cover. The base has a cooling system. The frame and cover are expanded during normal use and folded during storage or transportation. The device is compact, durable, transportable and well environmental adaptable. The system design is proved proper and the temperature inside is reliable. It is very suitable for temperature sensitive supplies stored in the medical emergency field. PMID:22097750

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

  18. 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

  19. Compact sources for the generation of high-peak power wavelength-stabilized laser pulses in the picoseconds and nanoseconds ranges

    NASA Astrophysics Data System (ADS)

    Wenzel, H.; Klehr, A.; Schwertfeger, S.; Liero, A.; Hoffmann, Th.; Brox, O.; Thomas, M.; Erbert, G.; Tränkle, G.

    2012-03-01

    Diode lasers are ideally suited for the generation of optical pulses in the nanoseconds and picoseconds ranges by gainswitching, Q-switching or mode-locking. We have developed diode-laser based light sources where the pulses are spectrally stabilized and nearly-diffraction limited as required by many applications. Diffraction limited emission is achieved by a several microns wide ridge waveguide (RW), so that only the fundamental lateral mode should lase. Spectral stabilization is realized with a Bragg grating integrated into the semiconductor chip, resulting in distributed feedback (DFB) or distributed Bragg reflector (DBR) lasers. We obtained a peak power of 3.8W for 4ns long pulses using a gain-switched DFB laser and a peak power of more than 4W for 65ps long pulses using a three-section DBR laser. Higher peak powers of several tens of Watts can be reached by an amplification of the pulses with semiconductor optical amplifiers, which can be either monolithically or hybrid integrated with the master oscillators. We developed compact modules with a footprint of 4×5cm2 combining master oscillator, tapered power amplifier, beam-shaping optical elements and high-frequency electronics. In order to diminish the generation of amplified spontaneous emission between the pulses, the amplifier is modulated with short-pulses of high amplitude, too. Beyond the amplifier, we obtained a peak power of more than 10W for 4ns long pulses, a peak power of about 35W for 80ps long pulses and a peak power of 70W for 10ps long pulses at emission wavelengths around 1064nm.

  20. Adult Compacts.

    ERIC Educational Resources Information Center

    Further Education Unit, London (England).

    This bulletin focuses on adult compacts, three-way agreements among employers, potential employees, and trainers to provide the right kind of quality training to meet the employers' requirements. Part 1 is an executive summary of a report of the Adult Compacts Project, which studied three adult compacts in Birmingham and Loughborough, England, and…

  1. Folding of proteins with diverse folds.

    PubMed

    Mohanty, Sandipan; Hansmann, Ulrich H E

    2006-11-15

    Using parallel tempering simulations with high statistics, we investigate the folding and thermodynamic properties of three small proteins with distinct native folds: the all-helical 1RIJ, the all-sheet beta3s, and BBA5, which has a mixed helix-sheet fold. In all three cases, simulations with our energy function find the native structures as global minima in free energy at experimentally relevant temperatures. However, the folding process strongly differs for the three molecules, indicating that the folding mechanism is correlated with the form of the native structure. PMID:16950845

  2. Protein Folding in Confined and Crowded Environments

    PubMed Central

    Zhou, Huan-Xiang

    2007-01-01

    Confinement and crowding are two major factors that can potentially impact protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize proteins by over 10kBT but crowding has a very modest effect on stability. On the other hand, confinement and crowding are both predicted to favor conformations of the unfolded state which are compact, and consequently may increase the folding rate. These predictions are largely borne out by experimental studies of protein folding under confined and crowded conditions in the test tube. Protein folding in cellular environments is further complicated by interactions with surrounding surfaces and other factors. Concerted theoretical modeling and test-tube and in vivo experiments promise to elucidate the complexity of protein folding in cellular environments. PMID:17719556

  3. Peptide folding driven by Van der Waals interactions.

    PubMed

    Sung, Shen-Shu

    2015-09-01

    Contrary to the widespread view that hydrogen bonding and its entropy effect play a dominant role in protein folding, folding into helical and hairpin-like structures is observed in molecular dynamics (MD) simulations without hydrogen bonding in the peptide-solvent system. In the widely used point charge model, hydrogen bonding is calculated as part of the interaction between atomic partial charges. It is removed from these simulations by setting atomic charges of the peptide and water to zero. Because of the structural difference between the peptide and water, van der Waals (VDW) interactions favor peptide intramolecular interactions and are a major contributing factor to the structural compactness. These compact structures are amino acid sequence dependent and closely resemble standard secondary structures, as a consequence of VDW interactions and covalent bonding constraints. Hydrogen bonding is a short range interaction and it locks the approximate structure into the specific secondary structure when it is included in the simulation. In contrast to standard molecular simulations where the total energy is dominated by charge-charge interactions, these simulation results will give us a new view of the folding mechanism. PMID:26013298

  4. Understanding the folding rates and folding nuclei of globular proteins.

    PubMed

    Finkelstein, Alexei V; Ivankov, Dmitry N; Garbuzynskiy, Sergiy O; Galzitskaya, Oxana V

    2007-12-01

    The first part of this paper contains an overview of protein structures, their spontaneous formation ("folding"), and the thermodynamic and kinetic aspects of this phenomenon, as revealed by in vitro experiments. It is stressed that universal features of folding are observed near the point of thermodynamic equilibrium between the native and denatured states of the protein. Here the "two-state" ("denatured state" <--> "native state") transition proceeds without accumulation of metastable intermediates, but includes only the unstable "transition state". This state, which is the most unstable in the folding pathway, and its structured core (a "nucleus") are distinguished by their essential influence on the folding/unfolding kinetics. In the second part of the paper, a theory of protein folding rates and related phenomena is presented. First, it is shown that the protein size determines the range of a protein's folding rates in the vicinity of the point of thermodynamic equilibrium between the native and denatured states of the protein. Then, we present methods for calculating folding and unfolding rates of globular proteins from their sizes, stabilities and either 3D structures or amino acid sequences. Finally, we show that the same theory outlines the location of the protein folding nucleus (i.e., the structured part of the transition state) in reasonable agreement with experimental data. PMID:18220841

  5. Quantitative Morphology of Epithelial Folds.

    PubMed

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

    2016-01-01

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

  6. 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)

  7. Asymmetric hindwing foldings in rove beetles

    PubMed Central

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

    2014-01-01

    Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right–left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use. PMID:25368178

  8. Asymmetric hindwing foldings in rove beetles.

    PubMed

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

    2014-11-18

    Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use. PMID:25368178

  9. 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

  10. 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

  11. Stability and folding of the tumour suppressor protein p16.

    PubMed

    Tang, K S; Guralnick, B J; Wang, W K; Fersht, A R; Itzhaki, L S

    1999-01-29

    The tumour suppressor p16 is a member of the INK4 family of inhibi tors of the cyclin D-dependent kinases, CDK4 and CDK6, that are involved in the key growth control pathway of the eukaryotic cell cycle. The 156 amino acid residue protein is composed of four ankyrin repeats (a helix-turn-helix motif) that stack linearly as two four-helix bundles resulting in a non-globular, elongated molecule. The thermodynamic and kinetic properties of the folding of p16 are unusual. The protein has a very low free energy of unfolding, Delta GH-2O/D-N, of 3.1 kcal mol-1 at 25 degreesC. The rate-determining transition state of folding/unfolding is very compact (89% as compact as the native state). The other unusual feature is the very rapid rate of unfolding in the absence of denaturant of 0.8 s-1 at 25 degreesC. Thus, p16 has both thermodynamic and kinetic instability. These features may be essential for the regulatory function of the INK4 proteins and of other ankyrin-repeat-containing proteins that mediate a wide range of protein-protein interactions. The mechanisms of inactivation of p16 by eight cancer-associated mutations were dissected using a systematic method designed to probe the integrity of the secondary structure and the global fold. The structure and folding of p16 appear to be highly vulnerable to single point mutations, probably as a result of the protein's low stability. This vulnerability provides one explanation for the striking frequency of p16 mutations in tumours and in immortalised cell lines. PMID:9917418

  12. 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)

  13. Teaching polymers to fold

    SciTech Connect

    Judson, R.S. )

    1992-12-10

    A new method is presented for predicting folding pathways of polymers. The folding pathway is described as a generic program or sequence of logical steps of such a form that a computer can carry them out to produce a folded structure. A genetic (GA) is used to learn specific sequences or folding pathways that carry a denatured conformation into a target final conformation. The method is demonstrated on a model 2-dimensional polymer for which the global energy minimum is known. The GA learns a program that will fold a denatured polymer into its global energy minimum conformation. 27 refs., 4 figs.

  14. Mechanics of Curved Folds

    NASA Astrophysics Data System (ADS)

    Dias, Marcelo A.; Santangelo, Christian D.

    2011-03-01

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

  15. 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.

  16. Compact middle infrared zoom lens design

    NASA Astrophysics Data System (ADS)

    Zhang, Xuan-zhi; Jiao, Ming-yin; Luan, Yadong; Chang, Wei-jun; Sun, Ting

    2011-08-01

    A compact mid-wavelength infrared zoom camera with a zoom range of 15:1 and active athermalization has been developed. The moving groups for a wide zoom range are only two lens groups and moving machanisms of zoom are very simple, which allows easy access of opto-mechanical and electromechanical design. The final design adopts the configuration of reflective mirror fold, comprising of two mirrors and eleven refractive lenses made of two infrared materials such as germanium or silicon. The movement of the lens groups and the focal length of the system are smooth and continuous. The zoom lens has the advantages of simple structure, high image quality, simple moving lens groups, short zoom path and smooth zoom locus.

  17. A technique for extending by ∼10(3) the dynamic range of compact proton spectrometers for diagnosing ICF implosions on the National Ignition Facility and OMEGA.

    PubMed

    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 D(3)He-, 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 10(2) for obtaining the spectral shape, and by 10(3) for mean energy (ρR) measurement, corresponding to proton fluences of 10(8) and 10(9) cm(-2), respectively. Using this new technique, ρR asymmetries can be measured during both shock and compression burn (proton yield ∼10(8) and ∼10(12), respectively) in 2-shock National Ignition Facility implosions with the standard WRF accuracy of ±∼10 mg/cm(2). PMID:25430298

  18. 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}.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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).

  6. 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.

  7. Multiply folded graphene

    NASA Astrophysics Data System (ADS)

    Kim, Kwanpyo; Lee, Zonghoon; Malone, Brad D.; Chan, Kevin T.; Alemán, Benjamín; Regan, William; Gannett, Will; Crommie, M. F.; Cohen, Marvin L.; Zettl, A.

    2011-06-01

    The folding of paper, hide, and woven fabric has been used for millennia to achieve enhanced articulation, curvature, and visual appeal for intrinsically flat, two-dimensional materials. For graphene, an ideal two-dimensional material, folding may transform it to complex shapes with new and distinct properties. Here, we present experimental results that folded structures in graphene, termed grafold, exist, and their formations can be controlled by introducing anisotropic surface curvature during graphene synthesis or transfer processes. Using pseudopotential-density-functional-theory calculations, we also show that double folding modifies the electronic band structure of graphene. Furthermore, we demonstrate the intercalation of C60 into the grafolds. Intercalation or functionalization of the chemically reactive folds further expands grafold's mechanical, chemical, optical, and electronic diversity.

  8. Compact CFB: The next generation CFB boiler

    SciTech Connect

    Utt, J.

    1996-12-31

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

  9. Folding of a miniprotein with mixed fold.

    PubMed

    Mohanty, Sandipan; Hansmann, U H E

    2007-07-21

    Using the 28 residue betabetaalpha protein FSD-EY as a target system, we examine correction terms for the ECEPP/3 force field. We find an increased probability of formation of the native state at low temperatures resulting from a reduced propensity to form alpha helices and increased formation of beta sheets. Our analysis of the observed folding events suggests that the C-terminal helix of FSD-EY is much more stable than the N-terminal beta hairpin and forms first. The hydrophobic groups of the helix provide a template which promotes the formation of the beta hairpin that is never observed to form without the helix. PMID:17655464

  10. 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

  11. Compact magnetograph

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Chwastyk, Mateusz; Cieplak, Marek

    2015-07-01

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

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

    PubMed

    Chwastyk, Mateusz; Cieplak, Marek

    2015-07-28

    We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding. PMID:26233164

  14. 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.

  15. Fold interaction and wavelength selection in 3D models of multilayer detachment folding

    NASA Astrophysics Data System (ADS)

    Fernandez, Naiara; Kaus, Boris J. P.

    2014-09-01

    Many fold-and-thrust belts are dominated by folding and exhibit a fairly regular fold-spacing. Yet, in map-view, the aspect ratio of doubly-plunging anticlines varies considerably from very elongated, and sometimes slightly curved, cylindrical folds to nearly circular, dome-like structures. In addition, the fold spacing often varies significantly around an average value. So far, it remains unclear whether these features are consistent with a folding instability. Therefore, we here study the dynamics of multilayer detachment folding, process by which shortening can be accommodated in thin-skinned fold-and-thrust belts. We start by analysing the physics of this process by using both a semi-analytical thick plate theory and numerical simulations. Results show that several different folding modes occur, about half of which are affected by gravity and have a wavelength that depends on the background deformation rate. Non-dimensional expressions are derived that predict the dominant wavelength and growth rate of each of these folding modes and mechanical phase diagrams are presented that illustrate the applicability of each of the modes. Next, we perform 3D simulations and compare the results with those of 2D models and analytical theory. Both 2D and 3D numerical simulations have wavelengths that are in good agreement with the analytical predictions. In the high-resolution 3D simulations the lateral growth of folds is studied, in particular with respect to fold segment interactions and evolution of fold width-length aspect ratio. The numerical simulations show a number of similarities with the Fars region of the Zagros fold-and-thrust belt including a large range of fold aspect ratio and a normally distributed fold wavelength around a dominant one.

  16. Programmable matter by folding

    PubMed Central

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

    2010-01-01

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

  17. 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

  18. Folded supersymmetry with a twist

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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. These models remain minimally fine-tuned in light of LHC8 data and provide a range of both standard and exotic signatures accessible at LHC13.

  19. 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

  20. Synthesizing folded band chaos.

    PubMed

    Corron, Ned J; Hayes, Scott T; Pethel, Shawn D; Blakely, Jonathan N

    2007-04-01

    A randomly driven linear filter that synthesizes Lorenz-like, reverse-time chaos is shown also to produce Rössler-like folded band wave forms when driven using a different encoding of the random source. The relationship between the topological entropy of the random source, dissipation in the linear filter, and the positive Lyapunov exponent for the reverse-time wave form is exposed. The two drive encodings are viewed as grammar restrictions on a more general encoding that produces a chaotic superset encompassing both the Lorenz butterfly and Rössler folded band paradigms of nonlinear dynamics. PMID:17500950

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

    SciTech Connect

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

    2010-05-25

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

  2. 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. PMID:17905832

  3. Secondary structures in long compact polymers

    NASA Astrophysics Data System (ADS)

    Oberdorf, Richard; Ferguson, Allison; Jacobsen, Jesper L.; Kondev, Jané

    2006-11-01

    Compact polymers are self-avoiding random walks that visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform numerical calculations is generating a sufficiently large number of randomly sampled configurations. We present a Monte Carlo algorithm that uniformly samples compact polymer configurations in an efficient manner, allowing investigations of chains much longer than previously studied. Chain configurations generated by the algorithm are used to compute statistics of secondary structures in compact polymers. We determine the fraction of monomers participating in secondary structures, and show that it is self-averaging in the long-chain limit and strictly less than 1. Comparison with results for lattice models of open polymer chains shows that compact chains are significantly more likely to form secondary structure.

  4. Secondary structures in long compact polymers.

    PubMed

    Oberdorf, Richard; Ferguson, Allison; Jacobsen, Jesper L; Kondev, Jané

    2006-11-01

    Compact polymers are self-avoiding random walks that visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform numerical calculations is generating a sufficiently large number of randomly sampled configurations. We present a Monte Carlo algorithm that uniformly samples compact polymer configurations in an efficient manner, allowing investigations of chains much longer than previously studied. Chain configurations generated by the algorithm are used to compute statistics of secondary structures in compact polymers. We determine the fraction of monomers participating in secondary structures, and show that it is self-averaging in the long-chain limit and strictly less than 1. Comparison with results for lattice models of open polymer chains shows that compact chains are significantly more likely to form secondary structure. PMID:17279930

  5. 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

  6. 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.

  7. 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.

  8. Guiding the folding pathway of DNA origami

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  9. Compaction behavior of roller compacted ibuprofen.

    PubMed

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

    2008-06-01

    The effect of roller compaction pressure on the bulk compaction of roller compacted ibuprofen was investigated using instrumented rotary tablet press. Three different roller pressures were utilized to prepare granules and Heckel analysis, Walker analysis, compressibility, and tabletability were performed to derive densification, deformation, course of volume reduction and bonding phenomenon of different pressure roller compacted granules. Nominal single granule fracture strength was obtained by micro tensile testing. Heckel analysis indicated that granules prepared using lower pressure during roller compaction showed lower yield strength. The reduction in tabletability was observed for higher pressure roller compacted granules. The reduction in tabletability supports the results of granule size enlargement theory. Apart from the granule size enlargement theory, the available fines and relative fragmentation during compaction is responsible for higher bonding strength and provide larger areas for true particle contact at constant porosity for lower pressure roller compacted granules. Overall bulk compaction parameters indicated that granules prepared by lower roller compaction pressure were advantageous in terms of tabletability and densification. Overall results suggested that densification during roller compaction affects the particle level properties of specific surface area, nominal fracture strength, and compaction behavior. PMID:18280716

  10. Compact Reactor

    SciTech Connect

    Williams, Pharis E.

    2007-01-30

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

  11. 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.

  12. The uteroglobin fold.

    PubMed

    Callebaut, I; Poupon, A; Bally, R; Demaret, J P; Housset, D; Delettré, J; Hossenlopp, P; Mornon, J P

    2000-01-01

    Uteroglobin (UTG) forms a fascinating homodimeric structure that binds small- to medium-sized ligands through an internal hydrophobic cavity, located at the interface between the two monomers. Previous studies have shown that UTG fold is not limited to the UTG/CC10 family, whose sequence/structure relationships are highlighted here, but can be extended to the cap domain of Xanthobacter autotrophicus haloalkane dehalogenase. We show here that UTG fold is adopted by several other cap domains within the alpha/beta hydrolase family, making it a well-suited "geode" structure allowing it to sequester various hydrophobic molecules. Additionally, some data about a new crystal form of oxidized rabbit UTG are presented, completing previous structural studies, as well as results from molecular dynamics, suggesting an alternative way for the ligand to reach the internal cavity. PMID:11193783

  13. Compaction of ribosomal protein S6 by sucrose occurs only under native conditions.

    PubMed

    Chen, LuYang; Ferreira, José A B; Costa, Sílvia M B; Cabrita, Gonçalo J M; Otzen, Daniel E; Melo, Eduardo Pinho

    2006-02-21

    The effect of osmolyte sucrose on the stability and compaction of the folded and unfolded states of ribosomal protein S6 from Thermus thermophilus was analyzed. Confirming previous results obtained with sodium sulfate and trehalose, refolding stopped-flow measurements of S6 show that sucrose favors the conversion of the unfolded state ensemble to a highly compact structure (75% as compact as the folded state). This conversion occurs when the unfolded state is suddenly placed under native conditions and the compact state accumulates in a transient off-folding pathway. This effect of sucrose on the compaction of the unfolded state ensemble is counteracted by guanidinium hydrochloride. The compact state does not accumulate at higher guanidinium concentrations and the unfolded state ensemble does not display increased compaction in the presence of 6 M guanidinium as evaluated by collisional quenching of tryptophan fluorescence. In contrast, accessibility of the tryptophan residue of folded S6 above 1 M sucrose concentration decreased as a result of an increased compaction of the folded state. Unfolding stopped-flow measurements of S6 reflect this increased compaction of the folded state, but the unfolding pathway is not affected by sucrose. Compaction of folded and unfolded S6 induced by sucrose occurs under native conditions indicating that decreased protein conformational entropy significantly contributes to the mechanism of protein stabilization by osmolytes. PMID:16475807

  14. 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)

  15. 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.

  16. Chirality and protein folding

    NASA Astrophysics Data System (ADS)

    Kwiecinska, Joanna I.; Cieplak, Marek

    2005-05-01

    There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the root mean square deviation distance away from the native state. Another checks whether all native contacts are established, i.e. whether the interacting amino acids come closer than some characteristic distance. We use Go-like models of proteins and show that such simple criteria may prompt one to declare folding even though fragments of the resulting conformations have a wrong sense of chirality. We propose that a better condition of folding should augment the simple criteria with the requirement that most of the local values of the chirality should be nearly native. The kinetic discrepancy between the simple and compound criteria can be substantially reduced in the Go-like models by providing the Hamiltonian with a term which favours native values of the local chirality. We study the effects of this term as a function of its amplitude and compare it to other models such as ones with side groups and ones with angle-dependent potentials.

  17. Folding within seconds

    NASA Astrophysics Data System (ADS)

    Kenkmann, Thomas

    2002-03-01

    Hypervelocity impacts of cosmic projectiles larger than ˜200 m diameter are capable of forming complex craters on Earth. At these craters, shock loading, shock damage, and excavation flow are followed by a gravity-driven collapse of the deep transient cavity. Such impact structures are characterized by a central uplift, a flat crater floor, and a terraced crater rim. Collapse-induced deformation features, like folds and brittle fault zones, have many similarities to tectonic structures. Typical deformation patterns of complex terrestrial impact craters of 5 15 km diameter are compiled and analyzed with respect to their kinematic development. Unlike their tectonic counterparts, deformation structures are always the result of non-plane-strain deformation and are formed in a single event that takes place in seconds to minutes. To understand the high-strain-rate processes, the microstructure of an impact-induced fold of the Crooked Creek impact crater (˜7 km diameter), Missouri, United States, is investigated in detail. A period of 20 30 s at the most is determined for the collapse phase of this crater. The gross plastic deformation behavior of the fold is achieved by localized brittle deformation along millimeter- to centimeter-spaced fault zones, forming a network of veins. Shock damage has fractured ˜40% of grain boundaries. The onset of collapse and associated deformation started in rocks with a reduced cohesion and is friction controlled.

  18. Ab initio RNA folding.

    PubMed

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding. PMID:25993396

  19. 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.

  20. 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

  1. 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

  2. Information from folds: A review

    NASA Astrophysics Data System (ADS)

    Hudleston, Peter J.; Treagus, Susan H.

    2010-12-01

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

  3. Scaled-up in vitro experiments of vocal fold paralysis

    NASA Astrophysics Data System (ADS)

    Peterson, Keith; Wei, Timothy; Krane, Michael

    2006-11-01

    Vocal fold paralysis is the inability of either one, or both vocal folds to open and close properly. Digital Particle Image Velocimetry (DPIV) measurements were taken to further understand the consequences paralyzed vocal folds have on the fluid dynamics downstream of the vocal folds during human phonation. The experiments were taken in a free-stream water tunnel using a simplified scaled-up model of human vocal folds. The Reynolds and Strouhal numbers ranged from 4500 to 10000, and 0.01 to 0.04, respectively. Various configuration setups were tested to emulate several types of vocal fold paralyses. These configurations include unilateral vocal fold immobility (UVFI), bilateral vocal fold immobility (BVFI) and the vocal folds operating at different oscillating frequencies. Data from these different conditions will be compared with an eye toward understanding the critical dynamics associated with this class of disease.

  4. Peptide folding simulations.

    PubMed

    Gnanakaran, S; Nymeyer, Hugh; Portman, John; Sanbonmatsu, Kevin Y; García, Angel E

    2003-04-01

    Developments in the design of small peptides that mimic proteins in complexity, recent advances in nanosecond time-resolved spectroscopy methods to study peptides and the development of modern, highly parallel simulation algorithms have come together to give us a detailed picture of peptide folding dynamics. Two newly implemented simulation techniques, parallel replica dynamics and replica exchange molecular dynamics, can now describe directly from simulations the kinetics and thermodynamics of peptide formation, respectively. Given these developments, the simulation community now has the tools to verify and validate simulation protocols and models (forcefields). PMID:12727509

  5. 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

  6. 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.

  7. 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.

  8. Folds on Europa

    NASA Technical Reports Server (NTRS)

    2000-01-01

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

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

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

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

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

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

  9. 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.

  10. 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.

  11. VARIABLE MOMENTUM COMPACTION LATTICE STUDIES.

    SciTech Connect

    KRAMER,S.; MURPHY,J.B.

    1999-03-29

    The VUV storage ring at the National Synchrotron Light Source was used to study the impact of changes in the momentum compaction factors over a large range from positive to negative values. Changes in bunch length and synchrotron tune were measured versus current and RF parameters for these different lattices. By controlling both the first and second-order momentum compaction factors, a lattice was developed in which a pair of alpha buckets was created within the energy aperture of the vacuum chamber and beam was stored simultaneously in both buckets.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Gosavi, Shachi; Jennings, Pat; Onuchic, Jose

    2007-03-01

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

  15. The Effect of Internucleosomal Interaction on Folding of the Chromatin Fiber

    PubMed Central

    Stehr, René; Kepper, Nick; Rippe, Karsten; Wedemann, Gero

    2008-01-01

    The folding of the nucleosome chain into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The fiber conformation depends crucially on the interaction between individual nucleosomes. However, this parameter has not been accurately determined experimentally, and it is affected by posttranslational histone modifications and binding of chromosomal proteins. Here, the effect of different internucleosomal interaction strengths on the fiber conformation was investigated by Monte Carlo computer simulations. The fiber geometry was modeled to fit that of chicken erythrocyte chromatin, which has been examined in numerous experimental studies. In the Monte Carlo simulation, the nucleosome shape was described as an oblate spherocylinder, and a replica exchange protocol was developed to reach thermal equilibrium for a broad range of internucleosomal interaction energies. The simulations revealed the large impact of the nucleosome geometry and the nucleosome repeat length on the compaction of the chromatin fiber. At high internucleosomal interaction energies, a lateral self-association of distant fiber parts and an interdigitation of nucleosomes were apparent. These results identify key factors for the control of the compaction and higher order folding of the chromatin fiber. PMID:18658212

  16. 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.

  17. 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.

  18. 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. PMID:27153764

  19. Coherent topological phenomena in protein folding.

    PubMed

    Bohr, H; Brunak, S; Bohr, J

    1997-01-01

    A theory is presented for coherent topological phenomena in protein dynamics with implications for protein folding and stability. We discuss the relationship to the writhing number used in knot diagrams of DNA. The winding state defines a long-range order along the backbone of a protein with long-range excitations, 'wring' modes, that play an important role in protein denaturation and stability. Energy can be pumped into these excitations, either thermally or by an external force. PMID:9218961

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Limited cooperativity in protein folding.

    PubMed

    Muñoz, Victor; Campos, Luis A; Sadqi, Mourad

    2016-02-01

    Theory and simulations predict that the structural concert of protein folding reactions is relatively low. Experimentally, folding cooperativity has been difficult to study, but in recent years we have witnessed major advances. New analytical procedures in terms of conformational ensembles rather than discrete states, experimental techniques with improved time, structural, or single-molecule resolution, and combined thermodynamic and kinetic analysis of fast folding have contributed to demonstrate a general scenario of limited cooperativity in folding. Gradual structural disorder is already apparent on the unfolded and native states of slow, two-state folding proteins, and it greatly increases in magnitude for fast folding domains. These results demonstrate a direct link between how fast a single-domain protein folds and unfolds, and how cooperative (or structurally diverse) is its equilibrium unfolding process. Reducing cooperativity also destabilizes the native structure because it affects unfolding more than folding. We can thus define a continuous cooperativity scale that goes from the 'pliable' two-state character of slow folders to the gradual unfolding of one-state downhill, and eventually to intrinsically disordered proteins. The connection between gradual unfolding and intrinsic disorder is appealing because it suggests a conformational rheostat mechanism to explain the allosteric effects of folding coupled to binding. PMID:26845039

  6. Paradoxical Vocal Fold Movement (PVFM)

    MedlinePlus

    ... Careers Certification Publications Events Advocacy Continuing Education Practice Management Research Home / Information for the Public / Speech, Language and Swallowing / Disorders and Diseases Paradoxical Vocal Fold ...

  7. 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. PMID:27090200

  8. Chromatin Compaction Protects Genomic DNA from Radiation Damage

    PubMed Central

    Takata, Hideaki; Hanafusa, Tomo; Mori, Toshiaki; Shimura, Mari; Iida, Yutaka; Ishikawa, Kenichi; Yoshikawa, Kenichi; Yoshikawa, Yuko; Maeshima, Kazuhiro

    2013-01-01

    Genomic DNA is organized three-dimensionally in the nucleus, and is thought to form compact chromatin domains. Although chromatin compaction is known to be essential for mitosis, whether it confers other advantages, particularly in interphase cells, remains unknown. Here, we report that chromatin compaction protects genomic DNA from radiation damage. Using a newly developed solid-phase system, we found that the frequency of double-strand breaks (DSBs) in compact chromatin after ionizing irradiation was 5–50-fold lower than in decondensed chromatin. Since radical scavengers inhibited DSB induction in decondensed chromatin, condensed chromatin had a lower level of reactive radical generation after ionizing irradiation. We also found that chromatin compaction protects DNA from attack by chemical agents. Our findings suggest that genomic DNA compaction plays an important role in maintaining genomic integrity. PMID:24130727

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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…

  15. 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

  16. How do chaperonins fold protein?

    PubMed Central

    Motojima, Fumihiro

    2015-01-01

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

  17. Compaction behavior of isomalt after roll compaction.

    PubMed

    Quodbach, Julian; Mosig, Johanna; Kleinebudde, Peter

    2012-01-01

    The suitability of the new isomalt grade galenIQ™ 801 for dry granulation and following tableting is evaluated in this study. Isomalt alone, as well as a blend of equal parts with dibasic calcium phosphate, is roll compacted and tableted. Particle size distribution and flowability of the granules and friability and disintegration time of the tablets are determined. Tensile strength of tablets is related to the specific compaction force during roll compaction and the tableting force. In all cases, the tensile strength increases with raising tableting forces. The specific compaction force has a different influence. For isomalt alone the tensile strength is highest for tablets made from granules prepared at 2 kN/cm and 6 kN/cm and decreases at higher values, i.e., >10 kN/cm. Tensile strength of the blend tablets is almost one third lower compared to the strongest tablets of pure isomalt. Friability of pure isomalt tablets is above the limit. Disintegration time is longest when the tensile strength is at its maximum and decreases with higher porosity and lower tensile strengths. Isomalt proves to be suitable for tableting after roll compaction. Even though the capacity as a binder might not be as high as of other excipients, it is a further alternative for the formulation scientist. PMID:24300366

  18. Compaction Behavior of Isomalt after Roll Compaction

    PubMed Central

    Quodbach, Julian; Mosig, Johanna; Kleinebudde, Peter

    2012-01-01

    The suitability of the new isomalt grade galenIQ™ 801 for dry granulation and following tableting is evaluated in this study. Isomalt alone, as well as a blend of equal parts with dibasic calcium phosphate, is roll compacted and tableted. Particle size distribution and flowability of the granules and friability and disintegration time of the tablets are determined. Tensile strength of tablets is related to the specific compaction force during roll compaction and the tableting force. In all cases, the tensile strength increases with raising tableting forces. The specific compaction force has a different influence. For isomalt alone the tensile strength is highest for tablets made from granules prepared at 2 kN/cm and 6 kN/cm and decreases at higher values, i.e., >10 kN/cm. Tensile strength of the blend tablets is almost one third lower compared to the strongest tablets of pure isomalt. Friability of pure isomalt tablets is above the limit. Disintegration time is longest when the tensile strength is at its maximum and decreases with higher porosity and lower tensile strengths. Isomalt proves to be suitable for tableting after roll compaction. Even though the capacity as a binder might not be as high as of other excipients, it is a further alternative for the formulation scientist. PMID:24300366

  19. 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

  20. Structure based prediction of protein folding intermediates.

    PubMed

    Xie, D; Freire, E

    1994-09-01

    The complete unfolding of a protein involves the disruption of non-covalent intramolecular interactions within the protein and the subsequent hydration of the backbone and amino acid side-chains. The magnitude of the thermodynamic parameters associated with this process is known accurately for a growing number of globular proteins for which high-resolution structures are also available. The existence of this database of structural and thermodynamic information has facilitated the development of statistical procedures aimed at quantifying the relationships existing between protein structure and the thermodynamic parameters of folding/unfolding. Under some conditions proteins do not unfold completely, giving rise to states (commonly known as molten globules) in which the molecule retains some secondary structure and remains in a compact configuration after denaturation. This phenomenon is reflected in the thermodynamics of the process. Depending on the nature of the residual structure that exists after denaturation, the observed enthalpy, entropy and heat capacity changes will deviate in a particular and predictable way from the values expected for complete unfolding. For several proteins, these deviations have been shown to exhibit similar characteristics, suggesting that their equilibrium folding intermediates exhibit some common structural features. Employing empirically derived structure-energetic relationships, it is possible to identify in the native structure of the protein those regions with the higher probability of being structured in equilibrium partly folded states. In this work, a thermodynamic search algorithm aimed at identifying the structural determinants of the molten globule state has been applied to six globular proteins; alpha-lactalbumin, barnase, IIIGlc, interleukin-1 beta, phage T4 lysozyme and phage 434 repressor. Remarkably, the structural features of the predicted equilibrium intermediates coincide to a large extent with the known

  1. Scale invariant sheath folds in salt, sediments and shear zones

    NASA Astrophysics Data System (ADS)

    Alsop, G. I.; Holdsworth, R. E.; McCaffrey, K. J. W.

    2007-10-01

    Sheath folds are developed in a broad spectrum of geological environments in which material flow occurs, including gravity-driven surficial deformation in ignimbrites, unconsolidated sediments and salt, together with deeper level ductile shear zones in metamorphic rocks. This study represents the first geometric comparison of sheath folds in these different settings across a wide range of scales. Elliptical closures defining eye-folds represent ( y- z) cross sections through highly-curvilinear sheath folds. Our analysis of the published literature, coupled with field observations, reveals remarkably similar ellipticities ( R yz) for sheath folds in metamorphic shear zones ( R yz 4.23), salt ( R yz 4.29), sediment slumps ( R yz 4.34), glaciotectonites ( R yz 4.48), and ignimbrites ( R yz 4.34). Nested eye-folds across this range of materials ( N = 1800) reveal distinct and consistent differences in ellipticity from the outer- ( R yz) to the inner-most ( R y' z' ) elliptical "rings" of individual sheath folds. The variation in ratios from outer to inner rings ( R' = R yz/ R y' z' ) in gravity-driven surficial flows typically displays a relative increase in ellipticity to define cats-eye-folds ( R' < 1) similar to those observed during simple and general shear in metamorphic rocks. We show that sheath folds develop across a range of scales within these different environments, and display elliptical ratios ( R yz) that are remarkably constant ( R2 > 0.99) across 9 orders of magnitude (sheath y axes range from ˜0.1 mm to >75 km). Our findings lead us to conclude that the geometric properties of sheath folds are scale invariant and primarily controlled by the type and amount of strain, with R' also reflecting the rheological significance of layering associated with original buckle fold mechanisms. The scaling pattern of sheath folds reflects the length scales of the precursor buckle folds (and width of deformation zones) across a broad range of materials and

  2. Compact Doppler magnetograph

    NASA Astrophysics Data System (ADS)

    Ruzmaikin, Alexander; Moynihan, Philip I.; Vaughan, Arthur H.; Cacciani, Alessandro

    1998-11-01

    We designed a low-cost flight instrument that images the full solar disk through two narrow band filters at the red nd blue 'wings' of the solar potassium absorption line. The images are produced on a 1024 X 1024 charge-coupled device with a resolution of 2 arcsec per pixel. Four filtergrams taken in a very short time at both wings in the left and right states of circular polarization are used to yield a Dopplergram and a magnetogram simultaneously. The noise-equivalent velocity associated with each pixel is less than 3 m/s. The measured signal is linearly proportional to the velocity in the range +/- 4000 m/s. The range of magnetic fields is from 3 to 3000 Gauss. The optical system of the instrument is simple and easily aligned. With a pixel size of 12 micrometers , the effective focal length is 126 cm. A Raleigh resolution limit of 4 arcsec is achieved with a 5-cm entrance apertures, providing an f/25 focal ratio. The foreoptic is a two-component telephoto lens serving to limit the overall optical length to 89 cm or less. The mass of the instrument is 14 kg. the power required is less than 30 Watts. The Compact Doppler Magnetograph can be used in space mission with severe mass and power requirements. It can also be effectively used for ground-based observations: large telescope, dome or other observatory facilities are not required.

  3. 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.

  4. Compact ultraviolet laser

    NASA Astrophysics Data System (ADS)

    Baird, Brian Walter

    1997-09-01

    wavelength are presented. This work includes results for the highest cw output powers reported for NUV SHG output from a laser-pumped KTP PSW. In an important step towards demonstration of an URSL- pumped KTP PSW laser, fabrication methods and test results ate reported for half-symmetric, low magnification SQW AlGaAs URSLs emitting at 770 nm and designed for use as diode pump sources for hydrothermal KTP PSWs. These devices utilize a 200 /mu m × 500 /mu m active region profile and were focused-ion- beam micromachined to achieve a total resonator magnification of 2.9. The first demonstration of high brightness, single-longitudinal mode operation from a core grating URSL is reported. This dissertation concludes with results for the first demonstration of an URSL-pumped KTP waveguide laser. This compact ultraviolet laser represents a pioneering effort to take advantage of the high cw output powers available from high brightness URSLs to increase the SH output powers obtainable from diode-pumped nonlinear waveguide lasers and to extend the useful spectral range from these sources into the near ultraviolet.

  5. Folded fibre bus interconnects with distributed amplification

    NASA Astrophysics Data System (ADS)

    Lorenzo, Raul Hernandez; Urquhart, Paul; Lopez-Amo, Manuel

    1998-06-01

    An optical fibre network for application as an interconnect within major nodes is investigated theoretically. The network is configured as a folded bus in which the spine consists of erbium doped fibre to overcome the power division at the couplers. It is argued that high received powers with a narrow dynamic range can be obtained simultaneously with bit rates in the order of 10 Gbit/s and bit error rates of 10 -12 or less.

  6. 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.

  7. Peptide folding in the presence of interacting protein crowders.

    PubMed

    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. PMID:27155657

  8. 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

  9. 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

  10. ACOUSTIC COMPACTION LAYER DETECTION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The depth and strength of compacted layers in fields have been determined traditionally using the ASAE standardized cone penetrometer method. However, an on-the-go method would be much faster and much less labor intensive. The soil measurement system described here attempts to locate the compacted...

  11. 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.

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

    SciTech Connect

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

    2010-07-13

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

  13. 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.

  14. 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.

  15. 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.

  16. Dynamical compactness and sensitivity

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  17. Compact Proton Accelerator for Cancer Therapy

    SciTech Connect

    Chen, Y; Paul, A C

    2007-06-12

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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. Folding of a large protein at high structural resolution.

    PubMed

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

    2013-11-19

    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

  4. 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

  5. Nanoparticles of compacted DNA transfect postmitotic cells.

    PubMed

    Liu, Ge; Li, DeShan; Pasumarthy, Murali K; Kowalczyk, Tomasz H; Gedeon, Christopher R; Hyatt, Susannah L; Payne, Jennifer M; Miller, Timothy J; Brunovskis, Peter; Fink, Tamara L; Muhammad, Osman; Moen, Robert C; Hanson, Richard W; Cooper, Mark J

    2003-08-29

    Charge-neutral DNA nanoparticles have been developed in which single molecules of DNA are compacted to their minimal possible size. We speculated that the small size of these DNA nanoparticles may facilitate gene transfer in postmitotic cells, permitting nuclear uptake across the 25-nm nuclear membrane pore. To determine whether DNA nanoparticles can transfect nondividing cells, growth-arrested neuroblastoma and hepatoma cells were transfected with DNA/liposome mixtures encoding luciferase. In both models, growth-arrested cells were robustly transfected by compacted DNA (6,900-360-fold more than naked DNA). To evaluate mechanisms responsible for enhanced transfection, HuH-7 cells were microinjected with naked or compacted plasmids encoding enhanced green fluorescent protein. Cytoplasmic microinjection of DNA nanoparticles generated a approximately 10-fold improvement in transgene expression as compared with naked DNA; this enhancement was reversed by the nuclear pore inhibitor, wheat germ agglutinin. To determine the upper size limit for gene transfer, DNA nanoparticles of various sizes were microinjected into the cytoplasm. A marked decrease in transgene expression was observed as the minor ellipsoidal diameter approached 25 nm. In summary, suitably sized DNA nanoparticles productively transfect growth arrested cells by traversing the nuclear membrane pore. PMID:12807905

  6. Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models

    PubMed Central

    2014-01-01

    We have developed a hidden Markov model and optimization procedure for photon-based single-molecule FRET data, which takes into account the trace-dependent background intensities. This analysis technique reveals an unprecedented amount of detail in the folding kinetics of the Diels–Alderase ribozyme. We find a multitude of extended (low-FRET) and compact (high-FRET) states. Five states were consistently and independently identified in two FRET constructs and at three Mg2+ concentrations. Structures generally tend to become more compact upon addition of Mg2+. Some compact structures are observed to significantly depend on Mg2+ concentration, suggesting a tertiary fold stabilized by Mg2+ ions. One compact structure was observed to be Mg2+-independent, consistent with stabilization by tertiary Watson–Crick base pairing found in the folded Diels–Alderase structure. A hierarchy of time scales was discovered, including dynamics of 10 ms or faster, likely due to tertiary structure fluctuations, and slow dynamics on the seconds time scale, presumably associated with significant changes in secondary structure. The folding pathways proceed through a series of intermediate secondary structures. There exist both compact pathways and more complex ones, which display tertiary unfolding, then secondary refolding, and, subsequently, again tertiary refolding. PMID:24568646

  7. 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.

  8. 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.

  9. Dark compact planets

    NASA Astrophysics Data System (ADS)

    Tolos, Laura; Schaffner-Bielich, Jürgen

    2015-12-01

    We investigate compact objects formed by dark matter admixed with ordinary matter made of neutron-star matter and white-dwarf material. We consider non-self annihilating dark matter with an equation of state given by an interacting Fermi gas. We find new stable solutions, dark compact planets, with Earth-like masses and radii from a few Km to few hundred Km for weakly interacting dark matter which are stabilized by the mutual presence of dark matter and compact star matter. For the strongly interacting dark matter case, we obtain dark compact planets with Jupiter-like masses and radii of few hundred Km. These objects could be detected by observing exoplanets with unusually small radii. Moreover, we find that the recently observed 2 M⊙ pulsars set limits on the amount of dark matter inside neutron stars which is, at most, 1 0-6 M⊙ .

  10. Compact baby Skyrmions

    SciTech Connect

    Adam, C.; Klimas, P.; Sanchez-Guillen, J.; Wereszczynski, A.

    2009-11-15

    For the baby Skyrme model with a specific potential, compacton solutions, i.e., configurations with a compact support and parabolic approach to the vacuum, are derived. Specifically, in the nontopological sector, we find spinning Q-balls and Q-shells, as well as peakons. Moreover, we obtain compact baby skyrmions with nontrivial topological charge. All these solutions may form stable multisoliton configurations provided they are sufficiently separated.

  11. Thixoforming of Stellite Powder Compacts

    SciTech Connect

    Hogg, S. C.; Atkinson, H. V.; Kapranos, P.

    2007-04-07

    Thixoforming involves processing metallic alloys in the semi-solid state. The process requires the microstructure to be spheroidal when part-solid and part-liquid i.e. to consist of solid spheroids surrounded by liquid. The aim of this work was to investigate whether powder compacts can be used as feedstock for thixoforming and whether the consolidating pressure in the thixoformer can be used to remove porosity from the compact. The powder compacts were made from stellite 6 and stellite 21 alloys, cobalt-based alloys widely used for e.g. manufacturing prostheses. Isothermal heat treatments of small samples in the consolidated state showed the optimum thixoforming temperature to be in the range 1340 deg. C-1350 deg. C for both materials. The alloys were thixoformed into graphite dies and flowed easily to fill the die. Porosity in the thixoformed components was lower than in the starting material. Hardness values at various positions along the radius of the thixoformed demonstrator component were above the specification for both alloys.

  12. 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.

  13. Thixoforming of Stellite Powder Compacts

    NASA Astrophysics Data System (ADS)

    Hogg, S. C.; Atkinson, H. V.; Kapranos, P.

    2007-04-01

    Thixoforming involves processing metallic alloys in the semi-solid state. The process requires the microstructure to be spheroidal when part-solid and part-liquid i.e. to consist of solid spheroids surrounded by liquid. The aim of this work was to investigate whether powder compacts can be used as feedstock for thixoforming and whether the consolidating pressure in the thixoformer can be used to remove porosity from the compact. The powder compacts were made from stellite 6 and stellite 21 alloys, cobalt-based alloys widely used for e.g. manufacturing prostheses. Isothermal heat treatments of small samples in the consolidated state showed the optimum thixoforming temperature to be in the range 1340°C-1350°C for both materials. The alloys were thixoformed into graphite dies and flowed easily to fill the die. Porosity in the thixoformed components was lower than in the starting material. Hardness values at various positions along the radius of the thixoformed demonstrator component were above the specification for both alloys.

  14. 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. PMID:23700314

  15. Polymer principles and protein folding.

    PubMed Central

    Dill, K. A.

    1999-01-01

    This paper surveys the emerging role of statistical mechanics and polymer theory in protein folding. In the polymer perspective, the folding code is more a solvation code than a code of local phipsi propensities. The polymer perspective resolves two classic puzzles: (1) the Blind Watchmaker's Paradox that biological proteins could not have originated from random sequences, and (2) Levinthal's Paradox that the folded state of a protein cannot be found by random search. Both paradoxes are traditionally framed in terms of random unguided searches through vast spaces, and vastness is equated with impossibility. But both processes are partly guided. The searches are more akin to balls rolling down funnels than balls rolling aimlessly on flat surfaces. In both cases, the vastness of the search is largely irrelevant to the search time and success. These ideas are captured by energy and fitness landscapes. Energy landscapes give a language for bridging between microscopics and macroscopics, for relating folding kinetics to equilibrium fluctuations, and for developing new and faster computational search strategies. PMID:10386867

  16. Osmolyte solutions and protein folding

    PubMed Central

    Hu, Char Y; Roesgen, Joerg

    2009-01-01

    In this brief review we discuss the evolution of recent thought regarding the role and mechanism of osmolytes with respect to protein stability. Osmolytes are naturally occurring intracellular compounds that change the protein folding landscape. Contributions from experiments are considered in the context of current theory and simulation results. PMID:19960095

  17. Predicting RNA pseudoknot folding thermodynamics.

    PubMed

    Cao, Song; Chen, Shi-Jie

    2006-01-01

    Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease. PMID:16709732

  18. 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.

  19. 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.

  20. 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

  1. Metagratings for Diffraction Based, Compact, Holographic Imaging

    NASA Astrophysics Data System (ADS)

    Inampudi, Sandeep; Podolskiy, Viktor; Multiscale Electromagnetics Group Team

    2013-03-01

    Recent developments in semiconductor technology brought to life a new generation of highly-compact visible-frequency cameras. Unfortunately, straight forward extension of this progress to low-frequency domains (such as mid-IR imaging) is impossible since the pixel size at these frequencies is limited by free-space diffraction limit. Here we present an approach to realize highly-compact imaging systems at lower frequencies. Our approach takes advantage of high refractive index of materials commonly utilized in semiconductor detectors of mid-IR radiation, accompanied by metagratings, structures with engineered diffraction properties, to achieve a 10-fold reduction in the pixel size. In contrast to conventional refraction-based imaging, the approach essentially produces a digital hologram - a 2D projection of the 3D optical field, enabling a post-imaging ``refocusing'' of the picture. The perspectives of numerical recovery of the optical field and the stability of such recovery are discussed.

  2. Homogeneous Crystal Nucleation: To Fold or Not to Fold?

    NASA Astrophysics Data System (ADS)

    Crist, Buckley

    2007-03-01

    Recent simulations and related theories have addressed interesting aspects of homogeneous nucleation of polymer crystals in very dilute solutions; embryos and very small crystals are composed of folded chains. At the same time there has been renewed activity with experimental studies of homogeneous nucleation in molten polymers, either with dispersed droplets or with microphase-separated block copolymers. Compared to dilute solutions, melts offer enhanced possibilities for nucleation by fringed micelle structures with stems from different chains. Basal or ``end'' surface energy is estimated for unfolded and folded chain nuclei and employed with classical nucleation theory to distinguish between nucleation rates in the two cases. The effect of chain length on the nucleation barrier offers a way to test model predictions.

  3. 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

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

    PubMed

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

    2016-01-01

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

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

    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.

  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. 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.

  8. RNAiFOLD: a constraint programming algorithm for RNA inverse folding and molecular design.

    PubMed

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

    2013-04-01

    Synthetic biology is a rapidly emerging discipline with long-term ramifications that range from single-molecule detection within cells to the creation of synthetic genomes and novel life forms. Truly phenomenal results have been obtained by pioneering groups--for instance, the combinatorial synthesis of genetic networks, genome synthesis using BioBricks, and hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment, biomolecular self-assembly pathways, etc. Such work strongly suggests that nanotechnology and synthetic biology together seem poised to constitute the most transformative development of the 21st century. In this paper, we present a Constraint Programming (CP) approach to solve the RNA inverse folding problem. Given a target RNA secondary structure, we determine an RNA sequence which folds into the target structure; i.e. whose minimum free energy structure is the target structure. Our approach represents a step forward in RNA design--we produce the first complete RNA inverse folding approach which allows for the specification of a wide range of design constraints. We also introduce a Large Neighborhood Search approach which allows us to tackle larger instances at the cost of losing completeness, while retaining the advantages of meeting design constraints (motif, GC-content, etc.). Results demonstrate that our software, RNAiFold, performs as well or better than all state-of-the-art approaches; nevertheless, our approach is unique in terms of completeness, flexibility, and the support of various design constraints. The algorithms presented in this paper are publicly available via the interactive webserver http://bioinformatics.bc.edu/clotelab/RNAiFold; additionally, the source code can be downloaded from that site. PMID:23600819

  9. 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.

  10. Plastic folding of buckling structures.

    PubMed

    Colin, Jérôme; Coupeau, Christophe; Grilhé, Jean

    2007-07-27

    Atomic force microscopy observations of the free surface of gold thin films deposited on silicon substrates have evidenced the buckling of the films and the formation of blister patterns undergoing plastic folding. The classical elastic buckling and plastic deformation of the films are analyzed in the framework of the Föppl-Von Kármán theory of thin plates introducing the notion of low-angle tilt boundaries and dislocation distributions to describe this folding effect. It is demonstrated that, in agreement with elementary plasticity of bent crystals, the presence of such tilt-boundaries results in the formation of buckling patterns of lower energy than "classical" elastic blisters. PMID:17678376

  11. Folding and assembly of proteorhodopsin.

    PubMed

    Klyszejko, Adriana L; Shastri, Sarika; Mari, Stefania A; Grubmüller, Helmut; Muller, Daniel J; Glaubitz, Clemens

    2008-02-01

    Proteorhodopsins (PRs), the recently discovered light-driven proton pumps, play a major role in supplying energy for microbial organisms of oceans. In contrast to PR, rhodopsins found in Archaea and Eukarya are structurally well characterized. Using single-molecule microscopy and spectroscopy, we observed the oligomeric assembly of native PR molecules and detected their folding in the membrane. PR showed unfolding patterns identical with those of bacteriorhodopsin and halorhodopsin, indicating that PR folds similarly to archaeal rhodopsins. Surprisingly, PR predominantly assembles into hexameric oligomers, with a smaller fraction assembling into pentamers. Within these oligomers, PR arranged into radial assemblies. We suggest that this structural assembly of PR may have functional implications. PMID:18155728

  12. Folded waveguide gyrotron traveling-wave-tube amplifier

    SciTech Connect

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

    1995-03-01

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

  13. 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.

  14. Evolutionary Strategies for Protein Folding

    NASA Astrophysics Data System (ADS)

    Murthy Gopal, Srinivasa; Wenzel, Wolfgang

    2006-03-01

    The free energy approach for predicting the protein tertiary structure describes the native state of a protein as the global minimum of an appropriate free-energy forcefield. The low-energy region of the free-energy landscape of a protein is extremely rugged. Efficient optimization methods must therefore speed up the search for the global optimum by avoiding high energy transition states, adapt large scale moves or accept unphysical intermediates. Here we investigate an evolutionary strategies(ES) for optimizing a protein conformation in our all-atom free-energy force field([1],[2]). A set of random conformations is evolved using an ES to get a diverse population containing low energy structure. The ES is shown to balance energy improvement and yet maintain diversity in structures. The ES is implemented as a master-client model for distributed computing. Starting from random structures and by using this optimization technique, we were able to fold a 20 amino-acid helical protein and 16 amino-acid beta hairpin[3]. We compare ES to basin hopping method. [1]T. Herges and W. Wenzel,Biophys.J. 87,3100(2004) [2] A. Verma and W. Wenzel Stabilization and folding of beta-sheet and alpha-helical proteins in an all-atom free energy model(submitted)(2005) [3] S. M. Gopal and W. Wenzel Evolutionary Strategies for Protein Folding (in preparation)

  15. 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

  16. Structural properties of compact groups

    NASA Technical Reports Server (NTRS)

    De Carvalho, R. R.; Ribeiro, A. L. B.; Zepf, Stephen E.

    1994-01-01

    We report the results of a systematic study of galaxies in the regions of Hickson compact groups. Our sample is composed of the 22 Hickson groups which are located in the southern hemisphere and have cz less than 9000 km/s. Making use of digitized images of IIIa-J plates that cover an area of 0.5 x 0.5 deg around each group, we were able to detect and classify images down to a magnitude limit of 19.5 in the B band. This limit is typically three magnitudes fainter than previous studies. Most groups show a statistically significant excess of fainter galaxies compared to the background. These fainter galaxies typically have a somewhat more extended spatial distribution than the brighter galaxies originally classified by Hickson. Our data suggest that Hickson groups have a wide range in density and radius, ranging from very compact structures with overdensities of the order of 10(exp 2) and crossing times of roughly 0.01 H(sub 0 sup -1), to much more diffuse structures, similar to loose groups, with overdensities of about 3 and crossing times of roughly 0.5 H(sub 0 sup -1).

  17. Distribution of linear mesostructures in oblique folded surfaces: Unravelling superposed Ordovician and Variscan folds in the Pyrenees

    NASA Astrophysics Data System (ADS)

    Casas, Josep Maria; Queralt, Pilar; Mencos, Joana; Gratacós, Oscar

    2012-11-01

    Detailed mapping and structural analysis yielded new data on the geometry of Ordovician folds in the Pyrenees. These folds caused the Variscan mainphase folds to develop over non-horizontal bedding surfaces in the pre-Upper Ordovician rocks. As a result, the Variscan mainphase fold axes and intersection lineations in these rocks present a wide range of orientations. Bedding surfaces exhibit a complex pattern in map view making it necessary to reconstruct the structure in 3D. Computer aided reconstruction tools such as FoldPlot proved useful for visualizing and reconstructing the geometry of such refolded structures in 3D. In the absence of map-scale key horizons, evidence of superposed folds is provided by detailed mapping of mesostructures. This requires a good and continuous outcrop over an extended area since one single fold system can account for a complex distribution of the subsequent intersection lineation. As a result, a cartographic study and a structural analysis are warranted because the direction of the Ordovician folds cannot be established only by the orientation of the L2 mesostructures.

  18. Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein.

    PubMed

    Navon, A; Ittah, V; Landsman, P; Scheraga, H A; Haas, E

    2001-01-01

    The purpose of this investigation is to characterize the reduced state of RNase A (r-RNase A) in terms of (i) intramolecular distances, (ii) the sequence of formation of stable loops in the initial stages of folding, and (iii) the unfolding transitions induced by GdnHCl. This is accomplished by identifying specific subdomain structures and local and long-range interactions that direct the folding process of this protein and lead to the native fold and formation of the disulfide bonds. Eleven pairs of dispersed sites in the RNase A molecule were labeled with fluorescent donor and acceptor probes, and the distributions of intramolecular distances (IDDs) were determined by means of time-resolved dynamic nonradiative excitation energy transfer (TR-FRET) measurements. The mutants were designed to search for (a) a possible nonrandom fold of the backbone in the collapsed state and (b) possible loops stabilized by long-range interactions. It was found that, under folding conditions, (i) the labeled mutants of r-RNase A in refolding buffer (the R(N) state) exhibit features of specific (nonrandom) compact but very dispersed subdomain structures (indicated by short mean distances, broad IDDs, and a weak dependence of the mean distances on segment length), (ii) the backbone fold in the C-terminal beta-like portion of the molecule appears to adopt a native-like overall fold, (iii) the N-terminal alpha-like portion of the chain is separated from the C-terminal core by very large intramolecular distances, larger than those in the crystal structure, and (iv) perturbations by addition of GdnHCl reveal several conformational transitions in different sections of the chain. Addition of GdnHCl to the native disulfide-intact protein provided a reference state for the extent of expansion of intramolecular distances under denaturing conditions. In conclusion, r-RNase A under folding conditions (the R(N) state) is poised for the final folding step(s) with a native-like trace of the chain

  19. 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…

  20. Protein folding in a force clamp

    NASA Astrophysics Data System (ADS)

    Cieplak, Marek; Szymczak, P.

    2006-05-01

    Kinetics of folding of a protein held in a force clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations in the end-to-end distance reflect microscopic events during folding. However, the folding scenarios in and out of the force clamp are distinct.

  1. 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. PMID:24059538

  2. Towards endoscopic ultrafast laser microsurgery of vocal folds.

    PubMed

    Hoy, Christopher L; Everett, W Neil; Yildirim, Murat; Kobler, James; Zeitels, Steven M; Ben-Yakar, Adela

    2012-03-01

    Vocal fold scarring is a predominant cause of voice disorders yet lacks a reliable treatment method. The injection of soft biomaterials to improve mechanical compliance of the vocal folds has emerged as a promising treatment. Here, we study the use of precise femtosecond laser microsurgery to ablate subsurface voids, with a goal of eventually creating a plane in dense subepithelial scar tissue into which biomaterials can be injected for their improved localization. Specifically, we demonstrate the ablation of small subepithelial voids in porcine vocal fold tissue up to 120 [micro sign]m below the surface such that larger voids in the active area of vocal fold mucosa (~3×10 mm(2)) can eventually be ablated in about 3 min. We use sub-μJ, 776-nm pulses from a compact femtosecond fiber laser system operating at a 500-kHz repetition rate. The use of relatively high repetition rates, with a small number of overlapping pulses, is critical to achieving ablation in a very short time while still avoiding significant heat deposition. Additionally, we use the same laser for nonlinear optical imaging to provide visual feedback of tissue structure and to confirm successful ablation. The ablation parameters, including pulse duration, pulse energy, spot size, and scanning speed, are comparable to the specifications in our recently developed miniaturized femtosecond laser surgery probes, illustrating the feasibility of developing an ultrafast laser surgical instrument. PMID:22502583

  3. Folded path LWIR system for SWAP constrained platforms

    NASA Astrophysics Data System (ADS)

    Fleet, Erin F.; Wilson, Michael L.; Linne von Berg, Dale; Giallorenzi, Thomas; Mathieu, Barry

    2014-06-01

    Folded path reflection and catadioptric optics are of growing interest, especially in the long wave infrared (LWIR), due to continuing demands for reductions in imaging system size, weight and power (SWAP). We present the optical design and laboratory data for a 50 mm focal length low f/# folded-path compact LWIR imaging system. The optical design uses 4 concentric aspheric mirrors, each of which is described by annular aspheric functions well suited to the folded path design space. The 4 mirrors are diamond turned onto two thin air-spaced aluminum plates which can be manually focused onto the uncooled LWIR microbolometer array detector. Stray light analysis will be presented to show how specialized internal baffling can be used to reduce stray light propagation through the folded path optical train. The system achieves near diffraction limited performance across the FOV with a 15 mm long optical train and a 5 mm back focal distance. The completed system is small enough to reside within a 3 inch diameter ball gimbal.

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

    SciTech Connect

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

    2009-09-11

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

  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. Molecular Crowding Affects the Conformational Fluctuations, Peroxidase Activity, and Folding Landscape of Yeast Cytochrome c.

    PubMed

    Paul, Simanta Sarani; Sil, Pallabi; Chakraborty, Ritobrita; Haldar, Shubhasis; Chattopadhyay, Krishnananda

    2016-04-26

    To understand how a protein folds and behaves inside living cells, the effects of synthetic crowding media on protein folding, function, stability, and association have been studied in detail. Because the effect of excluded volume is more prominent in an extended state than in the native protein, a majority of these studies have been conducted in the unfolded state of different model proteins. Here, we have used fluorescence correlation spectroscopy (FCS) and other biophysical methods to investigate the effect of crowding agents Ficoll70 and Dextran70 on the nativelike state of cytochrome c from yeast. Yeast cytochrome c (y-cytc) contains a substantial expanded state in its native folded condition, which is present in equilibrium with a compact conformer in aqueous buffer. We have found that the crowding medium affects the native state equilibrium between compact and expanded states, shifting its population toward the compact conformer. As a result, the peroxidase activity of y-cytc decreases. Urea-induced protein stability measurements show that the compaction destabilizes the protein due to charge repulsions between similar charged clusters. Interestingly, the time constant of conformational fluctuations between the compact and expanded conformers has been found to increase in the crowded milieu, suggesting a crucial role of the solution microviscosity. PMID:27050502

  7. Imprint of Ancient Evolution on rRNA Folding.

    PubMed

    Lanier, Kathryn A; Athavale, Shreyas S; Petrov, Anton S; Wartell, Roger; Williams, Loren Dean

    2016-08-23

    In a model describing the origin and evolution of the translation system, ribosomal RNA (rRNA) grew in size by accretion [Petrov, A. S., et al. (2015) History of the Ribosome and the Origin of Translation. Proc. Natl. Acad. Sci. U.S.A. 112, 15396-15401]. Large rRNAs were built up by iterative incorporation and encasement of small folded RNAs, in analogy with addition of new LEGOs onto the surface of a preexisting LEGO assembly. In this model, rRNA robustness in folding arises from inherited autonomy of local folding. We propose that rRNAs can be decomposed at various granularities, retaining folding mechanism and folding competence. To test these predictions, we disassembled Domain III of the large ribosomal subunit (LSU). We determined whether local rRNA structure, stability, and folding pathways are autonomous. Thermal melting, chemical footprinting, and circular dichroism were used to infer rules that govern folding of rRNA. We deconstructed Domain III of the LSU rRNA by mapping out its complex multistep melting pathway. We studied Domain III and two equal-size "sub-Domains" of Domain III. The combined results are consistent with a model in which melting transitions of Domain III are conserved upon cleavage into sub-Domains. Each of the eight melting transitions of Domain III corresponds in Tm and ΔH with a transition observed in one of the two isolated sub-Domains. The results support a model in which structure, stability, and folding mechanisms are dominated by local interactions and are unaffected by separation of the sub-Domains. Domain III rRNA is distinct from RNAs that form long-range cooperative interaction networks at early stages of folding or that do not fold reversibly. PMID:27428664

  8. Quantifying the similarities within fold space.

    PubMed

    Harrison, Andrew; Pearl, Frances; Mott, Richard; Thornton, Janet; Orengo, Christine

    2002-11-01

    We have used GRATH, a graph-based structure comparison algorithm, to map the similarities between the different folds observed in the CATH domain structure database. Statistical analysis of the distributions of the fold similarities has allowed us to assess the significance for any similarity. Therefore we have examined whether it is best to represent folds as discrete entities or whether, in fact, a more accurate model would be a continuum wherein folds overlap via common motifs. To do this we have introduced a new statistical measure of fold similarity, termed gregariousness. For a particular fold, gregariousness measures how many other folds have a significant structural overlap with that fold, typically comprising 40% or more of the larger structure. Gregarious folds often contain commonly occurring super-secondary structural motifs, such as beta-meanders, greek keys, alpha-beta plait motifs or alpha-hairpins, which are matching similar motifs in other folds. Apart from one example, all the most gregarious folds matching 20% or more of the other folds in the database, are alpha-beta proteins. They also occur in highly populated architectural regions of fold space, adopting sandwich-like arrangements containing two or more layers of alpha-helices and beta-strands.Domains that exhibit a low gregariousness, are those that have very distinctive folds, with few common motifs or motifs that are packed in unusual arrangements. Most of the superhelices exhibit low gregariousness despite containing some commonly occurring super-secondary structural motifs. In these folds, these common motifs are combined in an unusual way and represent a small proportion of the fold (<10%). Our results suggest that fold space may be considered as continuous for some architectural arrangements (e.g. alpha-beta sandwiches), in that super-secondary motifs can be used to link neighbouring fold groups. However, in other regions of fold space much more discrete topologies are observed with

  9. Compact Electric- And Magnetic-Field Sensor

    NASA Technical Reports Server (NTRS)

    Winterhalter, Daniel; Smith, Edward

    1994-01-01

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

  10. Analysis of Technology for Compact Coherent Lidar

    NASA Technical Reports Server (NTRS)

    Amzajerdian, Farzin

    1997-01-01

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

  11. Limestone compaction: an enigma

    USGS Publications Warehouse

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

    1977-01-01

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

  12. 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.

  13. 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…

  14. Development of MWID continuous zoom with large zoom range

    NASA Astrophysics Data System (ADS)

    Sanson, Mark C.; Cornell, James; Roy, Brian; Herbert, Stephen; Woodard, Ken; Sawyer, Kent

    2011-06-01

    A thermal imaging zoom system has been developed for the mid wave infrared band with greater than 30X zoom range. The zoom system provides continuous changes in the field of view from the narrow field of view to the wide field of view. Athermalization was also a key feature included in the design. An active thermal compensation approach is being used to cover a broad thermal range. A preloaded rail approach is used to maintain boresight and vibration requirements. The final optical layout and mechanical design resulted in a system suitable for tactical and other harsh environments. The current design is very compact for the extremely large zoom range but, the lens layout also provides adequate space for folding. In this way the zoom system can be easily configured for applications with compact space claims such as small turrets or gimbals. The fundamental optical design has also been found to be capable of accommodating different camera formats (focal plane array size and F number).

  15. Folded MEMS approach to NMRG

    NASA Astrophysics Data System (ADS)

    Gundeti, Venu Madhav

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

  16. Effects of compaction pressure and particle shape on the porosity and compression mechanical properties of sintered Ti6Al4V powder compacts for hard tissue implantation.

    PubMed

    Güden, Mustafa; Celik, Emrah; Hizal, Alpay; Altindiş, Mustafa; Cetiner, Sinan

    2008-05-01

    Sintered Ti6Al4V powder compacts potentially to be used in implant applications were prepared using commercially available spherical and angular powders (100-200 mum) within the porosity range of 34-54%. Cylindrical green powder compacts were cold compacted at various pressures and then sintered at 1200 degrees C for 2 h. The final percent porosity and mean pore sizes were determined as functions of the applied compaction pressure and powder type. The mechanical properties were investigated through compression testing. Results have shown that yield strength of the powder compacts of 40-42% porosity was comparable with that of human cortical bone. As compared with previously investigated Ti powder compacts, Ti6Al4V powder compacts showed higher strength at similar porosity range. Microscopic observations on the failed compact samples revealed that failure occurred primarily by the separation of interparticle bond regions in the planes 45 degrees to the loading axis. PMID:18076095

  17. Paradoxic vocal fold movement disorder.

    PubMed

    Matrka, Laura

    2014-02-01

    Paradoxical Vocal Fold Movement Disorder (PVFMD) is a cause of dyspnea that can mimic or occur alongside asthma or other pulmonary disease. Treatment with Laryngeal Control Therapy is very effective once the entity is properly diagnosed and contributing comorbidities are managed appropriately. In understanding the etiology of PVFMD, focus has broadened beyond psychiatric factors alone to include the spectrum of laryngeal irritants (laryngopharyngeal reflux, allergic and sinus disease, sicca, and possibly obstructive sleep apnea). The following is a discussion of the history, terminology, epidemiology, diagnosis, comorbid conditions, and treatment of this entity. PMID:24286687

  18. Hydrodynamic interactions in protein folding

    NASA Astrophysics Data System (ADS)

    Cieplak, Marek; Niewieczerzał, Szymon

    2009-03-01

    We incorporate hydrodynamic interactions (HIs) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HIs facilitate folding. We also study HIV-1 protease and show that HIs make the flap closing dynamics faster. The HIs are found to affect time correlation functions in the vicinity of the native state even though they have no impact on same time characteristics of the structure fluctuations around the native state.

  19. Hydrodynamic interactions in protein folding.

    PubMed

    Cieplak, Marek; Niewieczerzał, Szymon

    2009-03-28

    We incorporate hydrodynamic interactions (HIs) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HIs facilitate folding. We also study HIV-1 protease and show that HIs make the flap closing dynamics faster. The HIs are found to affect time correlation functions in the vicinity of the native state even though they have no impact on same time characteristics of the structure fluctuations around the native state. PMID:19334888

  20. 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

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

    PubMed

    Eidini, Maryam; Paulino, Glaucio H

    2015-09-01

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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. Kinematics and thermodynamics of a folding heteropolymer.

    PubMed Central

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

    1993-01-01

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

  10. 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

  11. 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.

  12. Compact waveguide splitter networks.

    PubMed

    Qian, Yusheng; Song, Jiguo; Kim, Seunghyun; Hu, Weisheng; Nordin, Gregory P

    2008-03-31

    We demonstrate compact waveguide splitter networks in siliconon- insulator (SOI) rib waveguides using trench-based splitters (TBSs) and bends (TBBs). Rather than a 90 degrees geometry, we use 105 degrees TBSs to facilitate reliable fabrication of high aspect ratio trenches suitable for 50/50 splitting when filled with SU8. Three dimensional (3D) finite difference time domain (FDTD) simulation is used for splitter and bend design. Measured TBB and TBS optical efficiencies are 84% and 68%, respectively. Compact 105 degrees 1 x 4, 1 x 8, and 1 x 32 trench-based splitter networks (TBSNs) are demonstrated. The measured total optical loss of the 1 x 32 TBSN is 9.15 dB. Its size is only 700 microm x 1600 microm for an output waveguide spacing of 50 microm. PMID:18542598

  13. 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.

  14. 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.

  15. Compact heat exchangers

    SciTech Connect

    Kays, W.M.; London, A.L.

    1984-01-01

    This third edition is an update of the second edition published in 1964. New data and more modern theoretical solutions for flow in the simple geometries are included, although this edition does not differ radically from the second edition. It contains basic test data for eleven new surface configurations, including some of the very compact ceramic matrices. Al dimensions are given in both the English and the Systeme International (SI) system of units.

  16. Compact infrared detector

    NASA Technical Reports Server (NTRS)

    Gupta, A.; Hong, S.; Moacanin, J.

    1981-01-01

    Broadband IR detector integrated into compact package for pollution monitoring and weather prediction is small, highly responsive, and immune to high noise. Sensing material is transparent sheet metalized with reflecting coating and overcoated with black material on same side. Pulse produced by chopping of infrared source beam creates transient "thermal lens" that temporarily defocuses laser beam probe. Detector monitoring beam measures defocusing which parallels infrared intensity.

  17. Granule consolidation during compaction.

    PubMed

    Rubinstein, M H

    1976-03-01

    The deformation of small cylindrical aggregates of dibasic calcium phosphate was measured during compaction. An analogy between these aggregates and cylindrical granules was proposed. No change in the original shape of the aggregates occurred; the cylindrical shape was maintained even at high compaction pressures. Relaxation of the aggregates occurred at pressures higher than 420 MNm-2 (60.9 x 10(3) lb in.-2) when removed from the compacts, but no relaxation took place at pressures below this value. In addition, the aggregates relaxed by an increase in thickness only; there was no corresponding change in diameter. Up to a pressure of 200 MNm-2 (29.0 x 10(3) lb in.-2), an increase in aggregate diameter occurred, which was accompanied by a reduction in thickness. This change produced only a small reduction in volume, which was attributable to interparticulate slippage resulting in a closer packed arrangement. At a pressure of 200 MNm-2, the aggregate diameter no longer increased because solid bridges were formed between the particles and the die wall, preventing further spreading. From 200 to 420 MNm-2, failure of the material occurred by plastic deformation, which produced only a decrease in aggregate thickness. From 420 to 800 MNm-2 (116.0 x 10(3) lb in.-2), a structure was formed that could support the applied load without further reduction of thickness, and this structure was shown to behave elastically. PMID:1263085

  18. Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

    PubMed Central

    Rangan, Prashanth; Masquida, Benoît; Westhof, Eric; Woodson, Sarah A.

    2003-01-01

    Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNAile. Base pairing of the ribozyme core requires 10-fold less Mg2+ than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37°C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4–P6 and P3–P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding. PMID:12574513

  19. 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.

  20. Universality Classes in Folding Times of Proteins

    PubMed Central

    Cieplak, Marek; Hoang, Trinh Xuan

    2003-01-01

    Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider three variants of the Go models with different contact potentials and demonstrate scaling described by power laws and no correlation with the relative contact order parameter. We demonstrate existence of at least three kinetic universality classes that are correlated with the types of structure: the α-, α-β-, and β- proteins have the scaling exponents of ∼1.7, 2.5, and 3.2, respectively. The three classes merge into one when the contact range is truncated at a reasonable value. We elucidate the role of the potential associated with the chirality of a protein. PMID:12524300

  1. Protein folding in a force-clamp

    NASA Astrophysics Data System (ADS)

    Cieplak, Marek; Szymczak, Piotr

    2006-03-01

    Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed rapid changes in the end-to-end distance mirror microscopic events during folding. However, the folding scenarios in and out of the force-clamp are distinct.

  2. 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

  3. 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)

  4. Folded Symplectic Toric Four-Manifolds

    ERIC Educational Resources Information Center

    Lee, Christopher R.

    2009-01-01

    A folded symplectic form on an even-dimensional manifold is a closed two-form that degenerates in a suitably controlled way along a smooth hypersurface. When a torus having half the dimension of the manifold acts in a way preserving the folded symplectic form and admitting a moment map, the manifold is called a folded symplectic toric manifold.…

  5. 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…

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

    PubMed Central

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

    2015-01-01

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

  7. Negative activation enthalpies in the kinetics of protein folding.

    PubMed

    Oliveberg, M; Tan, Y J; Fersht, A R

    1995-09-12

    Although the rates of chemical reactions become faster with increasing temperature, the converse may be observed with protein-folding reactions. The rate constant for folding initially increases with temperature, goes through a maximum, and then decreases. The activation enthalpy is thus highly temperature dependent because of a large change in specific heat (delta Cp). Such a delta Cp term is usually presumed to be a consequence of a large decrease in exposure of hydrophobic surfaces to water as the reaction proceeds from the denatured state to the transition state for folding: the hydrophobic side chains are surrounded by "icebergs" of water that melt with increasing temperature, thus making a large contribution to the Cp of the denatured state and a smaller one to the more compact transition state. The rate could also be affected by temperature-induced changes in the conformational population of the ground state: the heat required for the progressive melting of residual structure in the denatured state will contribute to delta Cp. By examining two proteins with different refolding mechanisms, we are able to find both of these two processes; barley chymotrypsin inhibitor 2, which refolds from a highly unfolded state, fits well to a hydrophobic interaction model with a constant delta Cp of activation, whereas barnase, which refolds from a more structured denatured state, deviates from this ideal behavior. PMID:7568045

  8. 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

  9. Time-resolved NMR studies of RNA folding.

    PubMed

    Fürtig, Boris; Buck, Janina; Manoharan, Vijayalaxmi; Bermel, Wolfgang; Jäschke, Andres; Wenter, Philipp; Pitsch, Stefan; Schwalbe, Harald

    The application of real-time NMR experiments to the study of RNA folding, as reviewed in this article, is relatively new. For many RNA folding events, current investigations suggest that the time scales are in the second to minute regime. In addition, the initial investigations suggest that different folding rates are observed for one structural transition may be due to the hierarchical folding units of RNA. Many of the experiments developed in the field of NMR of protein folding cannot directly be transferred to RNA: hydrogen exchange experiments outside the spectrometer cannot be applied since the intrinsic exchange rates are too fast in RNA, relaxation dispersion experiments on the other require faster structural transitions than those observed in RNA. On the other hand, information derived from time-resolved NMR experiments, namely the acquisition of native chemical shifts, can be readily interpreted in light of formation of a single long-range hydrogen bonding interaction. Together with mutational data that can readily be obtained for RNA and new ligation technologies that enhance site resolution even further, time-resolved NMR may become a powerful tool to decipher RNA folding. Such understanding will be of importance to understand the functions of coding and non-coding RNAs in cells. PMID:17595685

  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. 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.

  12. 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.

  13. Compact Radio Sources in NGC 660

    NASA Astrophysics Data System (ADS)

    Wiercigroch, A. B.

    1995-12-01

    The nuclei of starburst galaxies are often obscured by dust and hence are probed best in non-visual wavelength regimes such as the infrared and radio. For example, radio studies of classical starburst galaxies such as NGC 253 and M82 have identified ~ 50 compact sources in each galaxy. One of the purposes of this type of observing program has been to classify the compact radio sources as H II regions or radio supernovae, and to estimate the supernova rates. If obtainable, spectral indices are used to identify the compact structures; otherwise supporting evidence or assumptions are needed. NGC 660, located at a distance of 7.5 Mpc, is a strong candidate for a search for compact radio sources. It is a relatively strong infrared emitter, has far infrared colors similar to NGC 253 and M82, and shows several peaks in published Very Large Array (VLA) maps at 6 cm and 20 cm. We therefore observed NGC 660 at 3.6 cm in the A-configuration of the VLA on 1995 July 13--14. Total integration time on-source was 4.8 hrs. The image shows a large family ( ~ 20) of compact radio structures with a flux density range of 0.1--3.4 mJy, three of which have fluxes > 2.0 mJy. The source luminosities are comparable to those of the stronger sources in M82 and NGC 253, typically a few times more powerful than Cas A. A number of the compact sources appear to lie along a ring projected against the more diffuse radio emission in the galaxy's nuclear region. The work described in this paper was carried out by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration.

  14. 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

  15. Hydrophobic folding units derived from dissimilar monomer structures and their interactions.

    PubMed Central

    Tsai, C. J.; Nussinov, R.

    1997-01-01

    We have designed an automated procedure to cut a protein into compact hydrophobic folding units. The hydrophobic units are large enough to contain tertiary non-local interactions, reflecting potential nucleation sites during protein folding. The quality of a hydrophobic folding unit is evaluated by four criteria. The first two correspond to visual characterization of a structural domain, namely, compactness and extent of isolation. We use the definition of Zehfus and Rose (Zehfus MH, Rose GD, 1986, Biochemistry 25:35-340) to calculate the compactness of a cut protein unit. The isolation of a unit is based on the solvent accessible surface area (ASA) originally buried in the interior and exposed to the solvent after cutting. The third quantity is the hydrophobicity, equivalent to the fraction of the buried non-polar ASA with respect to the total non-polar ASA. The last criterion in the evaluation of a folding unit is the number of segments it includes. To conform with the rationale of obtaining hydrophobic units, which may relate to early folding events, the hydrophobic interactions are implicitly and explicitly applied in their generation and assessment. We follow Holm and Sander (Holm L, Sander C, 1994, Proteins 19:256-268) to reduce the multiple cutting-point problem to a one-dimensional search for all reasonable trial cuts. However, as here we focus on the hydrophobic cores, the contact matrix used to obtain the first non-trivial eigenvector contains only hydrophobic contracts, rather than all, hydrophobic and hydrophilic, interactions. This dataset of hydrophobic folding units, derived from structurally dissimilar single chain monomers, is particularly useful for investigations of the mechanism of protein folding. For cases where there are kinetic data, the one or more hydrophobic folding units generated for a protein correlate with the two or with the three-state folding process observed. We carry out extensive amino acid sequence order independent structural

  16. Photometry of compact galaxies.

    NASA Technical Reports Server (NTRS)

    Shen, B. S. P.; Usher, P. D.; Barrett, J. W.

    1972-01-01

    Photometric histories of the N galaxies 3C 390.3 and PKS 0521-36. Four other compact galaxies, Markarian 9, I Zw 92, 2 Zw 136, and III Zw 77 showed no evidence of variability. The photometric histories were obtained from an exhaustive study of those plates of the Harvard collection taken with large aperture cameras. The images of all galaxies reported were indistinguishable from stars due to the camera f-ratios and low surface brightness of the outlying nebulosities of the galaxies. Standard techniques for the study of variable stars are therefore applicable.

  17. 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.

  18. 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.

  19. Compact multiframe blind deconvolution.

    PubMed

    Hope, Douglas A; Jefferies, Stuart M

    2011-03-15

    We describe a multiframe blind deconvolution (MFBD) algorithm that uses spectral ratios (the ratio of the Fourier spectra of two data frames) to model the inherent temporal signatures encoded by the observed images. In addition, by focusing on the separation of the object spectrum and system transfer functions only at spatial frequencies where the measured signal is above the noise level, we significantly reduce the number of unknowns to be determined. This "compact" MFBD yields high-quality restorations in a much shorter time than is achieved with MFBD algorithms that do not model the temporal signatures; it may also provide higher-fidelity solutions. PMID:21403711

  20. 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.

  1. 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)

  2. 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.

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Compact electrostatic comb actuator

    DOEpatents

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

    2000-01-01

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

  13. 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.

  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. The energy landscape for folding and function

    NASA Astrophysics Data System (ADS)

    Onuchic, Jose

    2006-03-01

    Globally the energy landscape of a folding protein resembles a partially rough funnel. The local roughness of the funnel reflects transient trapping of the protein configurations in local free energy minima. The kinetics of folding is best considered as a progressive organization of an ensemble of partially folded structures through which the protein passes through on its way to the folded structure. The folding mechanisms for several fast-folding proteins can be described using an energy landscape theory to set up the correspondence with simulations of protein minimalist models. Using these simulations together with analytical theory, we can learn about good (minimally frustrated) folding sequences and non-folding (frustrated) sequences. An important idea that emerges from this theory is that subtle features of the protein landscape can profoundly affect the apparent mechanism of folding. Experiments on the dependence of the folding/unfolding times, and the stability of these proteins to denaturant concentration and site-directed mutagenesis, and on the early events of folding allow to infer the global characteristics of the landscape. In addition to need to minimize energetic frustration, the topology of the native fold also plays a major role in the folding mechanism. Some folding motifs are easier to design than others suggesting the possibility that evolution not only selected sequences with sufficiently small energetic frustration but also selected more easily designable native structures. Several proteins (such as CI2 and SH3) have sufficiently reduced energetic frustration) that much of the heterogeneity observed in their transition state ensemble (TSE) is determined by topology. Topological effects go beyond the structure of the TSE. The overall structure of the on-route and off-route (traps) intermediates for the folding of more complex proteins is also influenced by topology. Utilizing this theoretical framework, simulations of minimalist models and

  16. 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

  17. 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.

  18. 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.

  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. PMID:25641420

  20. Viscoelastic properties of the false vocal fold

    NASA Astrophysics Data System (ADS)

    Chan, Roger W.

    2001-05-01

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

  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. 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

  3. A compact high voltage pulse generator

    SciTech Connect

    Rohwein, G.J.; Babcock, S.R.

    1994-07-01

    A compact, easily transportable, pulse generator has been developed for a variety of applications that require a pulse duration in the range of 1 {mu} sec., voltages from 150 to 300 KV and current levels from 2,000 to 3,000 amps. The generator has a simple cylindrical configuration and modular construction to facilitate assembly and service. The generator may be operated single-pulse or repetitively at pulse repetition rates to 50 Hz in a burst mode.

  4. Protein Folding in the Cytoplasm and the Heat Shock Response

    PubMed Central

    Vabulas, R. Martin; Raychaudhuri, Swasti; Hayer-Hartl, Manajit; Hartl, F. Ulrich

    2010-01-01

    Proteins generally must fold into precise three-dimensional conformations to fulfill their biological functions. In the cell, this fundamental process is aided by molecular chaperones, which act in preventing protein misfolding and aggregation. How this machinery assists newly synthesized polypeptide chains in navigating the complex folding energy landscape is now being understood in considerable detail. The mechanisms that ensure the maintenance of a functional proteome under normal and stress conditions are also of great medical relevance, as the aggregation of proteins that escape the cellular quality control underlies a range of debilitating diseases, including many age-of-onset neurodegenerative disorders. PMID:21123396

  5. 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.

  6. 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.)

  7. Folding with thermal-mechanical feedback: Discussion

    NASA Astrophysics Data System (ADS)

    Treagus, Susan H.; Hudleston, Peter J.

    2009-07-01

    A recent paper in this Journal by Bruce Hobbs, Klaus Regenauer-Lieb and Alison Ord [Hobbs, B., Regenauer-Lieb, K., Ord, A., 2008. Folding with thermal-mechanical feedback. Journal of Structural Geology 30, 1572-1592] presents an alternative theory to the traditional Biot-Ramberg theory for folding of viscous rocks that involves non-equilibrium thermodynamics and thermal-mechanical feedback. The authors convey a strong message throughout their paper that the folds produced by this theoretical and numerical modelling are geologically realistic and provide a better explanation for many natural folds than the traditional theory. They promise the same approach for boudinage, and present this folding paper as part of a "unified framework for rock deformation processes". Readers of the Journal of Structural Geology might be led to conclude that this paper provides a good alternative model for folding of rocks. Our discussion will disagree, on four counts.

  8. 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

  9. The evolution of glaciotectonic fault-propagation folds

    NASA Astrophysics Data System (ADS)

    Brandes, C.; Le Heron, D. P.

    2009-04-01

    Glacial deposits may serve as important oil and gas reservoirs and they are often disrupted and deformed. This deformation contributes to glaciogenic reservoir heterogeneity. Therefore, we examined a range of Pleistocene outcrops as analogues to specify the styles of deformation that may be encountered within glaciogenic reservoirs. An interesting feature are fault-propagation folds. They are an important but only seldom recognised structural style within sediments affected by glacier induced deformation. Fault-propagation folds develop in the hanging wall of low angle thrust faults and compensate part of the slip along the fault. Field examples are recognised in northern Europe, formed by different ice advances in the Quaternary. The recognition of the fault-propagation fold mechanism in glaciotectonic deformation is extremely important because resultant structures are related to exactly the same phase of deformation (i.e. the same phase of ice advance), and thus may play a critical role in analyses of the temporal and spatial evolution of glacier induced deformation. Some of these examples are in good agreement with the predictions of the trishear kinematic theory. They show curved forelimbs and monoclinal geometries. The technique of tectonic forward modelling was used to quantify the controlling factors for the evolution of glacier induced fault-propagation folding. The geometry of folds and faults was examined and measured in the field. Special emphasis was placed on the assessment of the interplay of faulting and folding. For the tectonic forward modelling we used the program FaultFold 4.5.4©, which assumes trishear kinematics to simulate the evolution of fault-propagation folds (Allmendinger, 1998). Modelling focused on the geometry and position of thrusts, the displacement and the propagation-to-slip ratio. The simulations were carried out based on field data, to reconstruct the structural evolution of 2D sections from an undeformed to deformed state. The

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Compact SPS - Power delivery

    NASA Astrophysics Data System (ADS)

    Pospisil, M.; Pospisilova, L.

    1982-09-01

    The power deliverable by a compact solar Space Power Station (SPS) is a function of its outer surface shape. Methods of fitting the power delivery curve of such a system to different patterns of daily power demand are considered that involve the appropriate choice of the number of satellites, their maximal power, height to width ratio and the shift of longitude with respect to the receiving station. Changes in the daily delivery curve can be made by altering the longitudes and orientations of the satellites. Certain limitations to the choice of parameters exist, such as: the height to width ratio should be near 1.2, and the sum of longitude and orientation changes will probably not be greater than 50 deg. The optimization of the peak to average power ratio is also discussed.

  16. 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.

  17. Compact acoustic refrigerator

    SciTech Connect

    Bennett, G.A.

    1991-12-31

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

  18. 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.

  19. 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.

  20. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions

    PubMed Central

    Yazdi, Nastaran Hadizadeh; Guet, Calin C.; Johnson, Reid C.; Marko, John F.

    2012-01-01

    Summary We examine whether the E. coli chromosome is folded into a self-adherent nucleoprotein complex, or alternately is a confined but otherwise unconstrained self-avoiding polymer. We address this through in vivo visualization, using an inducible GFP fusion to the nucleoid-associated protein Fis to non-specifically decorate the entire chromosome. For a range of different growth conditions, the chromosome is a compact structure that does not fill the volume of the cell, and which moves from the new pole to the cell center. During rapid growth, chromosome segregation occurs well before cell division, with daughter chromosomes coupled by a thin inter-daughter filament before complete segregation, whereas during slow growth chromosomes stay adjacent until cell division occurs. Image correlation analysis indicates that sub-nucleoid structure is stable on a one-minute timescale, comparable to the time scale for redistribution time measured for GFP-Fis after photobleaching. Optical deconvolution and writhe calculation analysis indicate that the nucleoid has a large-scale coiled organization rather than being an amorphous mass. Our observations are consistent with the chromosome having a self-adherent filament organization. PMID:23078205

  1. Hydration and protein folding in water and in reverse micelles: compressibility and volume changes.

    PubMed

    Valdez, D; Le Huérou, J Y; Gindre, M; Urbach, W; Waks, M

    2001-06-01

    The partial specific volume and adiabatic compressibility of proteins reflect the hydration properties of the solvent-exposed protein surface, as well as changes in conformational states. Reverse micelles, or water-in-oil microemulsions, are protein-sized, optically-clear microassemblies in which hydration can be experimentally controlled. We explore, by densimetry and ultrasound velocimetry, three basic proteins: cytochrome c, lysozyme, and myelin basic protein in reverse micelles made of sodium bis (2-ethylhexyl) sulfosuccinate, water, and isooctane and in aqueous solvents. For comparison, we use beta-lactoglobulin (pI = 5.1) as a reference protein. We examine the partial specific volume and adiabatic compressibility of the proteins at increasing levels of micellar hydration. For the lowest water content compatible with complete solubilization, all proteins display their highest compressibility values, independent of their amino acid sequence and charge. These values lie within the range of empirical intrinsic protein compressibility estimates. In addition, we obtain volumetric data for the transition of myelin basic protein from its initially unfolded state in water free of denaturants, to a folded, compact conformation within the water-controlled microenvironment of reverse micelles. These results disclose yet another aspect of the protein structural properties observed in membrane-mimetic molecular assemblies. PMID:11371450

  2. Hydration and protein folding in water and in reverse micelles: compressibility and volume changes.

    PubMed Central

    Valdez, D; Le Huérou, J Y; Gindre, M; Urbach, W; Waks, M

    2001-01-01

    The partial specific volume and adiabatic compressibility of proteins reflect the hydration properties of the solvent-exposed protein surface, as well as changes in conformational states. Reverse micelles, or water-in-oil microemulsions, are protein-sized, optically-clear microassemblies in which hydration can be experimentally controlled. We explore, by densimetry and ultrasound velocimetry, three basic proteins: cytochrome c, lysozyme, and myelin basic protein in reverse micelles made of sodium bis (2-ethylhexyl) sulfosuccinate, water, and isooctane and in aqueous solvents. For comparison, we use beta-lactoglobulin (pI = 5.1) as a reference protein. We examine the partial specific volume and adiabatic compressibility of the proteins at increasing levels of micellar hydration. For the lowest water content compatible with complete solubilization, all proteins display their highest compressibility values, independent of their amino acid sequence and charge. These values lie within the range of empirical intrinsic protein compressibility estimates. In addition, we obtain volumetric data for the transition of myelin basic protein from its initially unfolded state in water free of denaturants, to a folded, compact conformation within the water-controlled microenvironment of reverse micelles. These results disclose yet another aspect of the protein structural properties observed in membrane-mimetic molecular assemblies. PMID:11371450

  3. Dependence of Internal Friction on Folding Mechanism

    PubMed Central

    2016-01-01

    An outstanding challenge in protein folding is understanding the origin of “internal friction” in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein. PMID:25721133

  4. 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.

  5. Protein Folding and Self-Organized Criticality

    NASA Astrophysics Data System (ADS)

    Bajracharya, Arun; Murray, Joelle

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

  6. 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

  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. 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.

  9. 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.

  10. 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

  11. 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 ...

  12. 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…

  13. 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.

  14. Energy Landscapes and Solved Protein Folding Problems

    NASA Astrophysics Data System (ADS)

    Wolynes, Peter

    2004-03-01

    Peter G. Wolynes Center for Theoretical Biological Physics Department of Chemistry and Biochemistry and Physics University of California, San Diego La Jolla, CA 92093-0371 Fifteen years ago, how proteins folded into organized structures on the basis of their sequence was a great mystery. By characterizing the energy landscapes of proteins with tools from the statistical mechanics of disordered systems like spin glasses, a "new view' of the folding process became possible. Energy landscape theory provided an incentive to pursue heroic new experiments and to carry out difficult computer simulations addressing protein folding mechanisms. Many aspects of folding kinetics revealed by these studies can be quantitatively understood using the simple idea that the topography of the energy landscape is that of a "rugged funnel". Energy landscape theory provided a quantitative means of characterizing which amino acid sequences can rapidly fold. Algorithms based on energy landscape theory have been used to successfully design novel sequences that fold to a given structure in the laboratory. Energy landscape ideas have begun to transform the prediction of protein structure from sequence data from being an art to being a science. The success of energy landscape- based algorithms in predicting protein structure from sequence will be highlighted. While there is still much to learn about folding mechanisms and much work to do achieving universally reliable structure prediction, many parts of what used to be called "the protein folding problem" can now be considered solved.

  15. Stochastic Resonance in Protein Folding Dynamics.

    PubMed

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

    2016-05-01

    Although protein folding reactions are usually studied under static external conditions, it is likely that proteins fold in a locally fluctuating cellular environment in vivo. To mimic such behavior in in vitro experiments, the local temperature of the solvent can be modulated either harmonically or using correlated noise. In this study, coarse-grained molecular simulations are used to investigate these possibilities, and it is found that both periodic and correlated random fluctuations of the environment can indeed accelerate folding kinetics if the characteristic frequencies of the applied fluctuations are commensurate with the internal timescale of the folding reaction; this is consistent with the phenomenon of stochastic resonance observed in many other condensed-matter processes. To test this theoretical prediction, the folding dynamics of phosphoglycerate kinase under harmonic temperature fluctuations are experimentally probed using Förster resonance energy transfer fluorescence measurements. To analyze these experiments, a combination of theoretical approaches is developed, including stochastic simulations of folding kinetics and an analytical mean-field kinetic theory. The experimental observations are consistent with the theoretical predictions of stochastic resonance in phosphoglycerate kinase folding. When combined with an alternative experiment on the protein VlsE using a power spectrum analysis, elaborated in Dave et al., ChemPhysChem 2016, 10.1002/cphc.201501041, the overall data overwhelmingly point to the experimental confirmation of stochastic resonance in protein folding dynamics. PMID:26992148

  16. 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.

  17. 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…

  18. 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

  19. 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

  20. Cooperative Tertiary Interaction Network Guides RNA Folding

    SciTech Connect

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

    2013-04-08

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

  1. Molecular gymnastics: serpin structure, folding and misfolding.

    PubMed

    Whisstock, James C; Bottomley, Stephen P

    2006-12-01

    The native state of serpins represents a long-lived intermediate or metastable structure on the serpin folding pathway. Upon interaction with a protease, the serpin trap is sprung and the molecule continues to fold into a more stable conformation. However, thermodynamic stability can also be achieved through alternative, unproductive folding pathways that result in the formation of inactive conformations. Our increasing understanding of the mechanism of protease inhibition and the dynamics of native serpin structures has begun to reveal how evolution has harnessed the actual process of protein folding (rather than the final folded outcome) to elegantly achieve function. The cost of using metastability for function, however, is an increased propensity for misfolding. PMID:17079131

  2. Protein folding at single-molecule resolution

    PubMed Central

    Ferreon, Allan Chris M.; Deniz, Ashok A.

    2011-01-01

    The protein folding reaction carries great significance for cellular function and hence continues to be the research focus of a large interdisciplinary protein science community. Single-molecule methods are providing new and powerful tools for dissecting the mechanisms of this complex process by virtue of their ability to provide views of protein structure and dynamics without associated ensemble averaging. This review briefly introduces common FRET and force methods, and then explores several areas of protein folding where single-molecule experiments have yielded insights. These include exciting new information about folding landscapes, dynamics, intermediates, unfolded ensembles, intrinsically disordered proteins, assisted folding and biomechanical unfolding. Emerging and future work is expected to include advances in single-molecule techniques aimed at such investigations, and increasing work on more complex systems from both the physics and biology standpoints, including folding and dynamics of systems of interacting proteins and of proteins in cells and organisms. PMID:21303706

  3. Fan-fold shielded electrical leads

    DOEpatents

    Rohatgi, Rajeev R.; Cowan, Thomas E.

    1996-01-01

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

  4. 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

  5. Single-molecule Studies of Riboswitch Folding

    PubMed Central

    Savinov, Andrew; Perez, Christian F.; Block, Steven M.

    2014-01-01

    The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. PMID:24727093

  6. Method for agglomerating powdered coal by compaction

    SciTech Connect

    Byrne, L.D.; Byrne, B.J.

    1987-07-21

    A method is described for preparing a powdered carboniferous composition and forming this composition into solid product shapes suitable for handling, transporting and burning, comprising the steps of: (a) mixing (1) powdered carboniferous material with (2) an amount of surfactant effective for wetting the powdered carboniferous material with water but for which no appreciable binding occurs between the surfactant and carboniferous material upon compaction and (3) an amount of water effective to bring the moisture content of the resultant mixture within the range of about 32 to 35% by weight; (b) working the mixture to obtain a homogeneous composition comprising a uniform dispersion of the water, surfactant, and powdered carboniferous material; and (c) compacting the resultant homogeneous composition into the desired solid product shape by extruding the homogeneous composition through a ring pelletizing extruder.

  7. 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.

  8. Compact dusty clouds in cosmic environment

    NASA Astrophysics Data System (ADS)

    Ivlev, Alexei; Tsytovich, Vadim; Burkert, Andreas

    We propose and discus a novel mechanism of the formation of compact dusty clouds in astrophysical environments. We show that the balance of forces operating in space dusty plasmas can cause the effect of dust self-confinement. As the result, cosmic dust can form stable spherical clouds (with typical sizes of the order of 10-100 AU or less and with total masses of the order of 10(-3) Earth mass or below), where the dust density can exceed the ambient level by many orders of magnitude. We predict that the formation of such clouds can occur in a broad range of plasma parameters, which indicates that this might be a fairly universal phenomenon operating in different astrophysical media. We argue that compact dusty clouds can be centers of rapid coagulations, and also operate as condensation seeds for a population of small-scale, cold, gaseous clumps in the diffuse interstellar medium.

  9. A Compact Ring Design with Tunable Momentum Compaction

    SciTech Connect

    Sun, Y.; /SLAC

    2012-05-17

    A storage ring with tunable momentum compaction has the advantage in achieving different RMS bunch length with similar RF capacity, which is potentially useful for many applications, such as linear collider damping ring and predamping ring where injected beam has a large energy spread and a large transverse emittance. A tunable bunch length also makes the commissioning and fine tuning easier in manipulating the single bunch instabilities. In this paper, a compact ring design based on a supercell is presented, which achieves a tunable momentum compaction while maintaining a large dynamic aperture.

  10. 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

  11. 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

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

    PubMed

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

    2008-09-16

    The earliest steps in the folding of proteins are complete on an extremely rapid time scale that is difficult to access experimentally. We have used rapid-mixing quench-flow methods to extend the time resolution of folding studies on apomyoglobin and elucidate the structural and dynamic features of members of the ensemble of intermediate states that are populated on a submillisecond time scale during this process. The picture that emerges is of a continuum of rapidly interconverting states. Even after only 0.4 ms of refolding time a compact state is formed that contains major parts of the A, G, and H helices, which are sufficiently well folded to protect amides from exchange. The B, C, and E helix regions fold more slowly and fluctuate rapidly between open and closed states as they search docking sites on this core; the secondary structure in these regions becomes stabilized as the refolding time is increased from 0.4 to 6 ms. No further stabilization occurs in the A, G, H core at 6 ms of folding time. These studies begin to time-resolve a progression of compact states between the fully unfolded and native folded states and confirm the presence an ensemble of intermediates that interconvert in a hierarchical sequence as the protein searches conformational space on its folding trajectory. PMID:18779573

  13. Compact plasma accelerator

    NASA Technical Reports Server (NTRS)

    Foster, John E. (Inventor)

    2004-01-01

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

  14. Compact 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. On the usefulness of sheath folds as kinematic indicators

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  20. Folding kinematics expressed in fracture patterns: An example from the Anti-Atlas fold belt, Morocco

    NASA Astrophysics Data System (ADS)

    Ismat, Zeshan

    2008-11-01

    The Anti-Atlas fold belt, Morocco, formed during the same Variscan collisional event that produced the Valley-and-Ridge fold-thrust belt of the Appalachian mountains. Both are external belts of the Appalachian-Ouachita-Mauritanides chain and at the map scale have very similar topographic expressions. The Anti-Atlas, however, consists of map-scale folds that are buckle-related, detachment folds, whereas the Valley-and-Ridge folds developed in response to imbricate thrusting. For this reason, the Anti-Atlas is referred to as a fold belt rather than a fold-thrust belt. This paper examines Variscan folding processes in the Anti-Atlas Mountains. Folding in some layers occurred by sliding along a penetrative network of mesoscale fractures, i.e. cataclastic flow, during buckling. Layer-parallel shortening fractures were reactivated in the later stages of folding to accommodate limb rotation. Although 'boutonnieres', i.e. basement uplifts, punctuate the fold belt, the fracture patterns indicate that the uplifts failed to provide any 'bending' component. Folding is also interpreted to occur under low to moderate confining pressures because the fracture network includes conjugate shear fractures with very small (˜20°) dihedral angles.

  1. 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.

  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. The nature of protein folding pathways.

    PubMed

    Englander, S Walter; Mayne, Leland

    2014-11-11

    How do proteins fold, and why do they fold in that way? This Perspective integrates earlier and more recent advances over the 50-y history of the protein folding problem, emphasizing unambiguously clear structural information. Experimental results show that, contrary to prior belief, proteins are multistate rather than two-state objects. They are composed of separately cooperative foldon building blocks that can be seen to repeatedly unfold and refold as units even under native conditions. Similarly, foldons are lost as units when proteins are destabilized to produce partially unfolded equilibrium molten globules. In kinetic folding, the inherently cooperative nature of foldons predisposes the thermally driven amino acid-level search to form an initial foldon and subsequent foldons in later assisted searches. The small size of foldon units, ∼ 20 residues, resolves the Levinthal time-scale search problem. These microscopic-level search processes can be identified with the disordered multitrack search envisioned in the "new view" model for protein folding. Emergent macroscopic foldon-foldon interactions then collectively provide the structural guidance and free energy bias for the ordered addition of foldons in a stepwise pathway that sequentially builds the native protein. These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process. Additionally, these observations answer the "how" and the "why" questions. The protein folding pathway depends on the same foldon units and foldon-foldon interactions that construct the native structure. PMID:25326421

  4. Compaction managed mirror bend achromat

    DOEpatents

    Douglas, David

    2005-10-18

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

  5. 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

  6. The subcutaneous fat compartments in relation to aesthetically important facial folds and rhytides.

    PubMed

    Gierloff, M; Stöhring, C; Buder, T; Wiltfang, J

    2012-10-01

    The ideal treatment of the nasolabial fold, the tear trough, the labiomandibular fold and the mentolabial sulcus is still discussed controversially. The detailed topographical anatomy of the fat compartments may clarify the anatomy of facial folds and may offer valuable information for choosing the adequate treatment modality. Nine non-fixed cadaver heads in the age range between 72 and 89 years (five female and four male) were investigated. Computed tomographic scans were performed after injection of a radiographic contrast medium directly into the fat compartments surrounding prominent facial folds. The data were analysed after multiplanar image reconstruction. The fat compartments surrounding the facial folds could be defined in each subject. Different arrangement patterns of the fat compartments around the facial rhytides were found. The nasolabial fold, the tear trough and the labiomandibular fold represent an anatomical border between adjacent fat compartments. By contrast, the glabellar fold and the labiomental sulcus have no direct relation to the boundaries of facial fat. Deep fat, underlying a facial rhytide, was identified underneath the nasolabial crease and the labiomental sulcus. In conclusion, an improvement by a compartment-specific volume augmentation of the nasolabial fold, the tear trough and the labiomandibular fold is limited by existing boundaries that extend into the skin. In the area of the nasolabial fold and the mentolabial sulcus, deep fat exists which can be used for augmentation and subsequent elevation of the folds. The treatment of the tear trough deformity appears anatomically the most challenging area since the superficial and deep fat compartments are separated by an osseo-cutaneous barrier, the orbicularis retaining ligament. In severe cases, a surgical treatment should be considered. By contrast, the glabellar fold shows the most simple anatomical architecture. The fold lies above one subcutaneous fat compartment that can be used

  7. 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

  8. 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).

  9. 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

  10. Protein Folding and Unfolding Under Force

    PubMed Central

    Jagannathan, Bharat; Marqusee, Susan

    2014-01-01

    The recent revolution in optics and instrumentation has enabled the study of protein folding using extremely low mechanical forces as the denaturant. This exciting development has led to the observation of the protein folding process at single molecule resolution and its response to mechanical force. Here, we describe the principles and experimental details of force spectroscopy on proteins, with a focus on the optical tweezers instrument. Several recent results will be discussed to highlight the importance of this technique in addressing a variety of questions in the protein folding field. PMID:23784721

  11. 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

  12. Compact dc link

    SciTech Connect

    Flairty, C. )

    1991-10-01

    The EPRI Compact Substation Project (a HVDC Converter Station) was developed, designed, and constructed per EPRI Agreement RP213. In December 1983, the converter station operated at its rating (100 MW power transmission and 300 kV dc bias plus 100 kV operating voltage). From January to May 1984, the converter station operated at various power transmission levels. Operation was intermittent due to a randomly occurring voltage breakdown. The voltage breakdown was isolated to the steel tanks containing the thyristor valves in an SF{sub 6} environment. The type of insulators stressed within the valve tanks were: (1) the epoxy cone shape insulators providing an interface to the bus entering the valve tank; (2) epoxy fiberglass hydraulic columns for the flow of the R113 refrigerant to and from the thyristor valves; and (3) the epoxy fiberglass support columns supporting the thyristor valves from the floor of the valve tank. The cause of the randomly occurring breakdown was investigated and determined to be the epoxy fiberglass support columns. The random dielectric breakdowns were due to excessive voltage gradients existing at the epoxy fiberglass support columns. This probably was caused by the misplacement of an internal insert within the column with respect to an external shield on the column. The cost and time to retrofit the support columns outweighed the benefits expected from resuming the project. Consequently, work was terminated and the equipment disassembled. Examination of the epoxy fiberglass support columns revealed several arcing tracks along the inside surface confirming the earlier hypothesis. 53 figs., 32 tabs.

  13. 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.

  14. Compact Holographic Data Storage

    NASA Technical Reports Server (NTRS)

    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.

  15. 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.

  16. 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.

  17. 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

  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 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

  20. 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

  1. Range Ecosystems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    After more than two hundred years, grazing remains California’s most extensive land use. The ‘Range Ecosystems’ chapter in the ‘Ecosystems of California’ sourcebook provides an integrated picture of the biophysical, social, and economic aspects of lands grazed by livestock in the state. Grazing mana...

  2. 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

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

    SciTech Connect

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

    2014-09-20

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

  4. 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.

  5. 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.

  6. A compact rotary vane attenuator

    NASA Technical Reports Server (NTRS)

    Nixon, D. L.; Otosh, T. Y.; Stelzried, C. T.

    1969-01-01

    Rotary vane attenuator, when used as a front end attenuator, introduces an insertion loss that is proportional to the angle of rotation. New technique allows the construction of a shortened compact unit suitable for most installations.

  7. 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)

  8. A Compact Beam Measurement Setup

    NASA Astrophysics Data System (ADS)

    Graf, Urs U.

    2016-03-01

    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.

  9. 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.

  10. 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.

  11. 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.

  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. 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

  14. Frustration in Condensed Matter and Protein Folding

    NASA Astrophysics Data System (ADS)

    Li, Z.; Tanner, S.; Conroy, B.; Owens, F.; Tran, M. M.; Boekema, C.

    2014-03-01

    By means of computer modeling, we are studying frustration in condensed matter and protein folding, including the influence of temperature and Thomson-figure formation. Frustration is due to competing interactions in a disordered state. The key issue is how the particles interact to reach the lowest frustration. The relaxation for frustration is mostly a power function (randomly assigned pattern) or an exponential function (regular patterns like Thomson figures). For the atomic Thomson model, frustration is predicted to decrease with the formation of Thomson figures at zero kelvin. We attempt to apply our frustration modeling to protein folding and dynamics. We investigate the homogeneous protein frustration that would cause the speed of the protein folding to increase. Increase of protein frustration (where frustration and hydrophobicity interplay with protein folding) may lead to a protein mutation. Research is supported by WiSE@SJSU and AFC San Jose.

  15. 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 ( ...

  16. 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.

  17. Cotranslational folding of deeply knotted proteins

    NASA Astrophysics Data System (ADS)

    Chwastyk, Mateusz; Cieplak, Marek

    2015-09-01

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

  18. Cotranslational folding of deeply knotted proteins.

    PubMed

    Chwastyk, Mateusz; Cieplak, Marek

    2015-09-01

    Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot. PMID:26292194

  19. 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. PMID:26080256

  20. Folded Resonant Horns for Power Ultrasonic Applications

    NASA Technical Reports Server (NTRS)

    Sherrit, Stewart; Askins, Stephen; Gradziel, Michael; Bao, Xiaoqi; Chang, Zensheu; Dolgin, Benjamin; Bar-Cohen, Yoseph; Peterson, Tom

    2003-01-01

    Folded horns have been conceived as alternatives to straight horns used as resonators and strain amplifiers in power ultrasonic systems. Such systems are used for cleaning, welding, soldering, cutting, and drilling in a variety of industries. In addition, several previous NASA Tech Briefs articles have described instrumented drilling, coring, and burrowing machines that utilize combinations of sonic and ultrasonic vibrational actuation. The main advantage of a folded horn, relative to a straight horn of the same resonance frequency, is that the folded horn can be made shorter (that is, its greatest linear dimension measured from the outside can be made smaller). Alternatively, for a given length, the resonance frequency can be reduced. Hence, the folded-horn concept affords an additional degree of design freedom for reducing the length of an ultrasonic power system that includes a horn.

  1. 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.

  2. 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.

  3. Flow and compaction behaviour of ultrafine coated ibuprofen.

    PubMed

    More, Parth K; Khomane, Kailas S; Bansal, Arvind K

    2013-01-30

    Good flow and compaction properties are prerequisites for successful compaction process. Apart from initial profile, mechanical properties of pharmaceutical powders can get modified during unit processes like milling. Milled powders can exhibit a wide range of particle size distribution. Further downstream processing steps like compaction can be affected by this differential particle size distribution. This has greatest implications for formulations like high dose drugs wherein the active pharmaceutical ingredient (API) contributes the maximum bulk in the final formulation. The present study assesses the impact of dry coating with ultrafine particles of same material, on the flow and compaction properties of the core material. Ibuprofen was selected as model drug as it has been reported to have poor mechanical properties. Ultrafine ibuprofen (average size 1.75 μm) was generated by Dyno(®) milling and was dry coated onto the core ibuprofen particles (average size 180 μm). Compaction studies were performed using a fully instrumented rotary tablet press. Compaction data was analyzed for compressibility, tabletability, compactibility profiles and Heckel plot. Dry coating of the ibuprofen exhibited greater compressibility and tabletability, at lower compaction pressure. However, at compaction pressure above 220 MPa, compressibility and tabletability of coated as well as uncoated materials were found to be similar. Heckel analysis also supported the above findings, as P(y) value of uncoated ibuprofen was found to be 229.49 MPa and for 2.0% ultrafine coated ibuprofen was found to be 158.53 MPa. Lower P(y) value of ultrafine coated ibuprofen indicated ease of plastic deformation. Superior compressibility and deformation behaviour of ultrafine coated ibuprofen attributed to increased interparticulate bonding area. This strategy can also be explored for improving tabletability of high dose poorly compressible drugs. PMID:23142495

  4. Compact Ho:YLF Laser

    NASA Technical Reports Server (NTRS)

    Hemmati, H.

    1988-01-01

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

  5. Self-folding with shape memory composites at the millimeter scale

    NASA Astrophysics Data System (ADS)

    Felton, S. M.; Becker, K. P.; Aukes, D. M.; Wood, R. J.

    2015-08-01

    Self-folding is an effective method for creating 3D shapes from flat sheets. In particular, shape memory composites—laminates containing shape memory polymers—have been used to self-fold complex structures and machines. To date, however, these composites have been limited to feature sizes larger than one centimeter. We present a new shape memory composite capable of folding millimeter-scale features. This technique can be activated by a global heat source for simultaneous folding, or by resistive heaters for sequential folding. It is capable of feature sizes ranging from 0.5 to 40 mm, and is compatible with multiple laminate compositions. We demonstrate the ability to produce complex structures and mechanisms by building two self-folding pieces: a model ship and a model bumblebee.

  6. 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

  7. Paramagnetism in colour superconductivity and compact stars

    NASA Astrophysics Data System (ADS)

    Ferrer, Efrain J.; de la Incera, Vivian

    2007-06-01

    It is quite plausible that colour superconductivity occurs in the inner regions of neutron stars. At the same time, it is known that strong magnetic fields exist in the interior of these compact objects. In this paper we discuss some important effects that can occur in the colour superconducting core of compact stars due to the presence of the stars' magnetic field. In particular, we consider the modification of the gluon dynamics for a colour superconductor with three massless quark flavours in the presence of an external magnetic field. We show that the long-range component of the external magnetic field that penetrates the colour-flavour locked phase produces an instability for field values larger than the charged gluons' Meissner mass. As a consequence, the ground state is restructured forming a vortex state characterized by the condensation of charged gluons and the creation of magnetic flux tubes. In the vortex state the magnetic field outside the flux tubes is equal to the applied one, while inside the tubes its strength increases by an amount that depends on the amplitude of the gluon condensate. This paramagnetic behaviour of the colour superconductor can be relevant for the physics of compact stars.

  8. 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

  9. Superposed fold-thrust events at the Nevada Test Site

    USGS Publications Warehouse

    Cashman, Patricia H.; Cole, James C.; Trexler, James H., Jr.

    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.

  10. 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.

  11. [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

  12. Protein folding and misfolding: mechanism and principles.

    PubMed

    Englander, S Walter; Mayne, Leland; Krishna, Mallela M G

    2007-11-01

    Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors

  13. Protein folding, protein homeostasis, and cancer

    PubMed Central

    Van Drie, John H.

    2011-01-01

    Proteins fold into their functional 3-dimensional structures from a linear amino acid sequence. In vitro this process is spontaneous; while in vivo it is orchestrated by a specialized set of proteins, called chaperones. Protein folding is an ongoing cellular process, as cellular proteins constantly undergo synthesis and degradation. Here emerging links between this process and cancer are reviewed. This perspective both yields insights into the current struggle to develop novel cancer chemotherapeutics and has implications for future chemotherapy discovery. PMID:21272445

  14. 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

  15. Folding thermodynamics of pseudoknotted chain conformations

    NASA Astrophysics Data System (ADS)

    Kopeikin, Zoia; Chen, Shi-Jie

    2006-04-01

    We develop a statistical mechanical framework for the folding thermodynamics of pseudoknotted structures. As applications of the theory, we investigate the folding stability and the free energy landscapes for both the thermal and the mechanical unfolding of pseudoknotted chains. For the mechanical unfolding process, we predict the force-extension curves, from which we can obtain the information about structural transitions in the unfolding process. In general, a pseudoknotted structure unfolds through multiple structural transitions. The interplay between the helix stems and the loops plays an important role in the folding stability of pseudoknots. For instance, variations in loop sizes can lead to the destabilization of some intermediate states and change the (equilibrium) folding pathways (e.g., two helix stems unfold either cooperatively or sequentially). In both thermal and mechanical unfolding, depending on the nucleotide sequence, misfolded intermediate states can emerge in the folding process. In addition, thermal and mechanical unfoldings often have different (equilibrium) pathways. For example, for certain sequences, the misfolded intermediates, which generally have longer tails, can fold, unfold, and refold again in the pulling process, which means that these intermediates can switch between two different average end-end extensions.

  16. "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.

  17. 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

  18. 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

  19. 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.

  20. 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

  1. Characteristics of tropopause folds over Arctic latitudes

    NASA Astrophysics Data System (ADS)

    Rao, T. Narayana; Kirkwood, S.

    2005-09-01

    Characteristics of tropopause folds over Arctic latitudes have been studied using VHF radar measurements supplemented by balloon measurements. The variation of the radar parameters during the passage of tropopause folds is discussed in detail. To our knowledge, these observations constitute the first spaced antenna (SA) radar measurements during the passage of tropopause folds. This allows us to compare the parameters detectable using this mode with those observed using other configurations, such as the Doppler beam swinging (DBS) technique. In general, the structural characteristics, such as the slope of folds, seem to be similar at Arctic latitudes to that at midlatitudes; however, the height of the tropopause and the axis of the jet stream (and hence the folding) are found to be lower by 1-2 km than their counterparts in midlatitudes. In the case studies the radar-derived parameters, such as the signal-to-noise ratio (SNR) and vertical shear of horizontal wind, clearly show the upper-air frontal zone. The frontal circulation, conceived from vertical velocity, including the warm conveyer belt flow and the dry intrusion, is clearly visible in the first case, whereas it is masked by high-amplitude mountain lee waves in the second case. Further, the frontal zone seems to be acting as a critical layer to mountain lee wave activity by absorbing/filtering the wave activity. The aspect angles derived from the present analysis agree well with those estimated by vertical beam spectral width but are small in comparison with those estimated by the power ratio method. The mean full correlation analysis (FCA) turbulent velocity is estimated using the ESRAD data obtained during the passage of 15 tropopause folds. The mean eddy diffusion coefficients, Kz, near the tropopause and in the upper portion of the fold, where strong turbulence is seen in case studies, are found to be 3.54 and 6.4 m2 s-1, respectively. Utilizing the mean Kz and the mean ozone gradient (obtained from

  2. 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.

  3. 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.

  4. 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.

  5. Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin.

    PubMed

    Bandaria, Jigar N; Qin, Peiwu; Berk, Veysel; Chu, Steven; Yildiz, Ahmet

    2016-02-11

    Telomeres, repetitive DNA sequences at chromosome ends, are shielded against the DNA damage response (DDR) by the shelterin complex. To understand how shelterin protects telomere ends, we investigated the structural organization of telomeric chromatin in human cells using super-resolution microscopy. We found that telomeres form compact globular structures through a complex network of interactions between shelterin subunits and telomeric DNA, but not by DNA methylation, histone deacetylation, or histone trimethylation at telomeres and subtelomeric regions. Mutations that abrogate shelterin assembly or removal of individual subunits from telomeres cause up to a 10-fold increase in telomere volume. Decompacted telomeres accumulate DDR signals and become more accessible to telomere-associated proteins. Recompaction of telomeric chromatin using an orthogonal method displaces DDR signals from telomeres. These results reveal the chromatin remodeling activity of shelterin and demonstrate that shelterin-mediated compaction of telomeric chromatin provides robust protection of chromosome ends against the DDR machinery. PMID:26871633

  6. 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

  7. The nature of protein folding pathways

    PubMed Central

    Englander, S. Walter; Mayne, Leland

    2014-01-01

    How do proteins fold, and why do they fold in that way? This Perspective integrates earlier and more recent advances over the 50-y history of the protein folding problem, emphasizing unambiguously clear structural information. Experimental results show that, contrary to prior belief, proteins are multistate rather than two-state objects. They are composed of separately cooperative foldon building blocks that can be seen to repeatedly unfold and refold as units even under native conditions. Similarly, foldons are lost as units when proteins are destabilized to produce partially unfolded equilibrium molten globules. In kinetic folding, the inherently cooperative nature of foldons predisposes the thermally driven amino acid-level search to form an initial foldon and subsequent foldons in later assisted searches. The small size of foldon units, ∼20 residues, resolves the Levinthal time-scale search problem. These microscopic-level search processes can be identified with the disordered multitrack search envisioned in the “new view” model for protein folding. Emergent macroscopic foldon–foldon interactions then collectively provide the structural guidance and free energy bias for the ordered addition of foldons in a stepwise pathway that sequentially builds the native protein. These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process. Additionally, these observations answer the “how” and the “why” questions. The protein folding pathway depends on the same foldon units and foldon–foldon interactions that construct the native structure. PMID:25326421

  8. 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

  9. 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.

  10. 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

  11. Compact boson stars in K field theories

    NASA Astrophysics Data System (ADS)

    Adam, C.; Grandi, N.; Klimas, P.; Sánchez-Guillén, J.; Wereszczyński, A.

    2010-11-01

    We study a scalar field theory with a non-standard kinetic term minimally coupled to gravity. We establish the existence of compact boson stars, that is, static solutions with compact support of the full system with self-gravitation taken into account. Concretely, there exist two types of solutions, namely compact balls on the one hand, and compact shells on the other hand. The compact balls have a naked singularity at the center. The inner boundary of the compact shells is singular, as well, but it is, at the same time, a Killing horizon. These singular, compact shells therefore resemble black holes.

  12. 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

  13. Viral infections of the folds (intertriginous areas).

    PubMed

    Adışen, Esra; Önder, Meltem

    2015-01-01

    Viruses are considered intracellular obligates with a nucleic acid, either RNA or DNA. They have the ability to encode proteins involved in viral replication and production of the protective coat within the host cells but require host cell ribosomes and mitochondria for translation. The members of the families Herpesviridae, Poxviridae, Papovaviridae, and Picornaviridae are the most commonly known agents for the cutaneous viral diseases, but other virus families, such as Adenoviridae, Togaviridae, Parvoviridae, Paramyxoviridae, Flaviviridae, and Hepadnaviridae, can also infect the skin. Though the cutaneous manifestations of viral infections are closely related to the type and the transmission route of the virus, viral skin diseases may occur in almost any part of the body. In addition to friction caused by skin-to-skin touch, skin folds are warm and moist areas of the skin that have limited air circulation. These features provide a fertile breeding ground for many kinds of microorganisms, including bacteria and fungi. In contrast to specific bacterial and fungal agents that have an affinity for the skin folds, except for viral diseases of the anogenital area, which have well-known presentations, viral skin infections that have a special affinity to the skin folds are not known. Many viral exanthems may affect the skin folds during the course of the infection, but here we focus only on the ones that usually affect the fold areas and also on the less well-known conditions or recently described associations. PMID:26051057

  14. 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

  15. 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).

  16. Protein Folding and Mechanisms of Proteostasis.

    PubMed

    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

  17. 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.

  18. 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…

  19. Modelling of compaction in planetesimals

    NASA Astrophysics Data System (ADS)

    Neumann, Wladimir; Breuer, Doris; Spohn, Tilman

    2014-07-01

    Aims: Compaction of initially porous material prior to melting is an important process that has influenced the interior structure and the thermal evolution of planetesimals in their early history. On the one hand, compaction decreases the porosity resulting in a reduction of the radius and on the other hand, the loss of porosity results in an increase of the thermal conductivity of the material and thus in a more efficient cooling. Porosity loss by hot pressing is the most efficient process of compaction in planetesimals and can be described by creep flow, which depends on temperature and stress. Hot pressing has been repeatedly modelled using a simplified approach, for which the porosity is gradually reduced in some fixed temperature interval between ≈650 K and 700 K. This approach neglects the dependence of compaction on stress and other factors such as matrix grain size and creep activation energy. In the present study, we compare this parametrised method with a self-consistent calculation of porosity loss via a creep related approach. Methods: We use our thermal evolution model from previous studies to model compaction of an initially porous body and consider four basic packings of spherical dust grains (simple cubic, orthorhombic, rhombohedral, and body-centred cubic). Depending on the grain packing, we calculate the effective stress and the associated porosity change via the thermally activated creep flow. For comparison, compaction is also modelled by simply reducing the initial porosity linearly to zero between 650 K and 700 K. As we are interested in thermal metamorphism and not melting, we only consider bodies that experience a maximum temperature below the solidus temperature of the metal phase. Results: For the creep related approach, the temperature interval in which compaction takes place depends strongly on the size of the planetesimal and is not fixed as assumed in the parametrised approach. Depending on the radius, the initial grain size, the

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. Compact architecture for power scaling bounce geometry lasers.

    PubMed

    Chard, S P; Damzen, M J

    2009-02-16

    We demonstrate the compact high-power scaling of bounce geometry lasers with a new dual-pumped folded amplifier design. A Q-switched laser oscillator built with this amplifier is shown to produce over 30 W of average power from 80 W of pump power at up to 600 kHz repetition rate. In a master-oscillator power-amplifier (MOPA) configuration using the dual-pumped amplifier, we demonstrate over 100 W of output power from 250 W of pump power. We also demonstrate very high repetition rate Q-switching (1.7 MHz) of the master oscillator. PMID:19219125

  6. 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.

  7. 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

  8. 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

  9. Proteins with Highly Similar Native Folds Can Show Vastly Dissimilar Folding Behavior When Desolvated**

    PubMed Central

    Schennach, Moritz; Breuker, Kathrin

    2014-01-01

    Proteins can be exposed to vastly different environments such as the cytosol or membranes, but the delicate balance between external factors and intrinsic determinants of protein structure, stability, and folding is only poorly understood. Here we used electron capture dissociation to study horse and tuna heart Cytochromes c in the complete absence of solvent. The significantly different stability of their highly similar native folds after transfer into the gas phase, and their strikingly different folding behavior in the gas phase, can be rationalized on the basis of electrostatic interactions such as salt bridges. In the absence of hydrophobic bonding, protein folding is far slower and more complex than in solution. PMID:24259450

  10. Quasi-static compaction studies of a porous pyrotechnic powder

    NASA Astrophysics Data System (ADS)

    Atwood, A. I.; Curran, P. O.; Price, C. F.; Wiknich, J.

    1996-05-01

    The compaction and relaxation properties of a live and an inert pyrotechnic powder simulant mixture have been evaluated under quasi-static loading conditions. The pyrotechnic powder consisted of a mixture of potassium perchlorate, magnesium-aluminum alloy, and inert binder. Potassium chloride replaced the potassium perchlorate in the inert mixture. Porous beds of powder were compacted using a double acting piston arrangement, operating at a constant loading rate of 0.11 in/min. Applied and transmitted forces were measured using either 7,500 or 20,000 lbf capacity strain gage load cells. The intragranular stress as a function of percent TMD was determined from the compaction data. The experimental intragranular stress data were further analyzed using a modified Carroll-Holt model to describe the compaction process and to allow extrapolation to a density range not achievable by experiment. The porous bed of pyrotechnic powder was much more rigid than homogeneous crystalline powders such as ammonium perchlorate (AP). Microscopic examination of the compacted material showed only light damage to the crystalline particles with little fracture. Bed relaxation resulted in a 2.8 to 4.5 percent change in bed height after compaction. These data demonstrate the presence of elastic deformation properties in a porous bed of non-viscoelastic material.

  11. 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. PMID:26931593

  12. Stretching and folding in finite time

    NASA Astrophysics Data System (ADS)

    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.

  13. Thermal stability of idealized folded carbyne loops.

    PubMed

    Cranford, Steven W

    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

  14. Analysis of High-Fold Gamma Data

    SciTech Connect

    Beyer, C.J.; Cromaz, M.; Radford, D.C.

    1998-08-10

    Historically, {gamma}-{gamma} and {gamma}-{gamma}-{gamma} coincidence spectra were utilized to build nuclear level schemes. With the development of large detector arrays, it has became possible to analyze higher fold coincidence data sets. This paper briefly reports on software to analyze 4-fold coincidence data sets that allows creation of 4-fold histograms (hypercubes) of at least 1024 channels per side (corresponding to a 43 gigachannel data space) that will fit onto a few gigabytes of disk space, and extraction of triple-gated spectra in a few seconds. Future detector arrays may have even higher efficiencies, and detect an many as 15 or 20 {gamma} rays simultaneously; such data will require very different algorithms for storage and analysis. Difficulties inherent in the analysis of such data are discussed, and two possible new solutions are presented, namely adaptive list-mode systems and list-list-mode storage.

  15. Exact folded-band chaotic oscillator.

    PubMed

    Corron, Ned J; Blakely, Jonathan N

    2012-06-01

    An exactly solvable chaotic oscillator with folded-band dynamics is shown. The oscillator is a hybrid dynamical system containing a linear ordinary differential equation and a nonlinear switching condition. Bounded oscillations are provably chaotic, and successive waveform maxima yield a one-dimensional piecewise-linear return map with segments of both positive and negative slopes. Continuous-time dynamics exhibit a folded-band topology similar to Rössler's oscillator. An exact solution is written as a linear convolution of a fixed basis pulse and a discrete binary sequence, from which an equivalent symbolic dynamics is obtained. The folded-band topology is shown to be dependent on the symbol grammar. PMID:22757520

  16. Computing folding pathways between RNA secondary structures.

    PubMed

    Dotu, Ivan; Lorenz, William A; Van Hentenryck, Pascal; Clote, Peter

    2010-03-01

    Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are computed by RNAtabupath in a fraction of the time required by the barriers program of Vienna RNA Package. We benchmark RNAtabupath with other algorithms to compute low energy folding pathways between experimentally known structures of several conformational switches. The RNApathfinder web server, source code for algorithms to compute and analyze pathways and supplementary data are available at http://bioinformatics.bc.edu/clotelab/RNApathfinder. PMID:20044352

  17. 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

  18. 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

  19. 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. PMID:27009180

  20. 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