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Sample records for low-resolution structural studies

  1. Crystallographic study of a MATE transporter presents a difficult case in structure determination with low-resolution, anisotropic data and crystal twinning.

    PubMed

    Symersky, Jindrich; Guo, Yi; Wang, Jimin; Lu, Min

    2015-11-01

    NorM from Neisseria gonorrhoeae (NorM-NG) belongs to the multidrug and toxic compound extrusion (MATE) family of membrane-transport proteins, which can extrude cytotoxic chemicals across cell membranes and confer multidrug resistance. Here, the structure determination of NorM-NG is described, which had been hampered by low resolution (∼ 4 Å), data anisotropy and pseudo-merohedral twinning. The crystal structure was solved using molecular replacement and was corroborated by conducting a difference Fourier analysis. The NorM-NG structure displays an extracellular-facing conformation, similar to that of NorM-NG bound to a crystallization chaperone. The approaches taken to determine the NorM-NG structure and the lessons learned from this study are discussed, which may be useful for analyzing X-ray diffraction data with similar shortcomings.

  2. Deformable complex network for refining low-resolution X-ray structures

    SciTech Connect

    Zhang, Chong; Wang, Qinghua; Ma, Jianpeng

    2015-10-27

    A new refinement algorithm called the deformable complex network that combines a novel angular network-based restraint with a deformable elastic network model in the target function has been developed to aid in structural refinement in macromolecular X-ray crystallography. In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint with the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.

  3. Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

    PubMed

    Croll, Tristan Ian; Andersen, Gregers Rom

    2016-09-01

    While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of <1.7, and strategies for working with such challenging data sets are suggested. Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement.

  4. Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

    PubMed

    Croll, Tristan Ian; Andersen, Gregers Rom

    2016-09-01

    While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of <1.7, and strategies for working with such challenging data sets are suggested. Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement. PMID

  5. Knowledge-based real-space explorations for low-resolution structure determination.

    PubMed

    Furnham, Nicholas; Doré, Andrew S; Chirgadze, Dimitri Y; de Bakker, Paul I W; Depristo, Mark A; Blundell, Tom L

    2006-08-01

    The accurate and effective interpretation of low-resolution data in X-ray crystallography is becoming increasingly important as structural initiatives turn toward large multiprotein complexes. Substantial challenges remain due to the poor information content and ambiguity in the interpretation of electron density maps at low resolution. Here, we describe a semiautomated procedure that employs a restraint-based conformational search algorithm, RAPPER, to produce a starting model for the structure determination of ligase interacting factor 1 in complex with a fragment of DNA ligase IV at low resolution. The combined use of experimental data and a priori knowledge of protein structure enabled us not only to generate an all-atom model but also to reaffirm the inferred sequence registry. This approach provides a means to extract quickly from experimental data useful information that would otherwise be discarded and to take into account the uncertainty in the interpretation--an overriding issue for low-resolution data.

  6. xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

    SciTech Connect

    McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

    2014-09-01

    A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

  7. Automated refinement of macromolecular structures at low resolution using prior information

    PubMed Central

    Kovalevskiy, Oleg; Nicholls, Robert A.; Murshudov, Garib N.

    2016-01-01

    Since the ratio of the number of observations to adjustable parameters is small at low resolution, it is necessary to use complementary information for the analysis of such data. ProSMART is a program that can generate restraints for macromolecules using homologous structures, as well as generic restraints for the stabilization of secondary structures. These restraints are used by REFMAC5 to stabilize the refinement of an atomic model. However, the optimal refinement protocol varies from case to case, and it is not always obvious how to select appropriate homologous structure(s), or other sources of prior information, for restraint generation. After running extensive tests on a large data set of low-resolution models, the best-performing refinement protocols and strategies for the selection of homologous structures have been identified. These strategies and protocols have been implemented in the Low-Resolution Structure Refinement (LORESTR) pipeline. The pipeline performs auto-detection of twinning and selects the optimal scaling method and solvent parameters. LORESTR can either use user-supplied homologous structures, or run an automated BLAST search and download homologues from the PDB. The pipeline executes multiple model-refinement instances using different parameters in order to find the best protocol. Tests show that the automated pipeline improves R factors, geometry and Ramachandran statistics for 94% of the low-resolution cases from the PDB included in the test set. PMID:27710936

  8. FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics.

    PubMed

    Frankenstein, Ziv; Sperling, Joseph; Sperling, Ruth; Eisenstein, Miriam

    2008-01-01

    Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching) and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top. PMID:18974836

  9. FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics.

    PubMed

    Frankenstein, Ziv; Sperling, Joseph; Sperling, Ruth; Eisenstein, Miriam

    2008-01-01

    Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching) and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top.

  10. Stealth carriers for low-resolution structure determination of membrane proteins in solution.

    PubMed

    Maric, Selma; Skar-Gislinge, Nicholas; Midtgaard, Søren; Thygesen, Mikkel B; Schiller, Jürgen; Frielinghaus, Henrich; Moulin, Martine; Haertlein, Michael; Forsyth, V Trevor; Pomorski, Thomas Günther; Arleth, Lise

    2014-02-01

    Structural studies of membrane proteins remain a great experimental challenge. Functional reconstitution into artificial nanoscale bilayer disc carriers that mimic the native bilayer environment allows the handling of membrane proteins in solution. This enables the use of small-angle scattering techniques for fast and reliable structural analysis. The difficulty with this approach is that the carrier discs contribute to the measured scattering intensity in a highly nontrivial fashion, making subsequent data analysis challenging. Here, an elegant solution to circumvent the intrinsic complexity brought about by the presence of the carrier disc is presented. In combination with small-angle neutron scattering (SANS) and the D2O/H2O-based solvent contrast-variation method, it is demonstrated that it is possible to prepare specifically deuterated carriers that become invisible to neutrons in 100% D2O at the length scales relevant to SANS. These `stealth' carrier discs may be used as a general platform for low-resolution structural studies of membrane proteins using well established data-analysis tools originally developed for soluble proteins. PMID:24531466

  11. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

    PubMed Central

    Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; Read, Randy J.; Wiedenheft, Blake

    2015-01-01

    Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging. Here we present a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and X-ray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective. PMID:26226459

  12. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement.

    PubMed

    Jackson, Ryan N; McCoy, Airlie J; Terwilliger, Thomas C; Read, Randy J; Wiedenheft, Blake

    2015-09-01

    Structures of multisubunit macromolecular machines are primarily determined either by electron microscopy (EM) or by X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at a higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for the generation of atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the 'phase' information that is missing from an X-ray crystallography experiment; however, integration of EM and X-ray diffraction data has been technically challenging. Here we present a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over noncrystallographic symmetry. As the resolution gap between EM and X-ray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.

  13. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

    DOE PAGESBeta

    Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; Read, Randy J.; Wiedenheft, Blake

    2015-07-30

    Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

  14. X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

    SciTech Connect

    Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; Read, Randy J.; Wiedenheft, Blake

    2015-07-30

    Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging. Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.

  15. Low-resolution characterization of the 3D structure of the Euglena gracilis photoreceptor

    SciTech Connect

    Barsanti, Laura; Coltelli, Primo; Evangelista, Valtere; Passarelli, Vincenzo; Frassanito, Anna Maria; Vesentini, Nicoletta; Gualtieri, Paolo

    2008-10-24

    This paper deals with the first characterization of the structure of the photoreceptive organelle of the unicellular alga Euglena gracilis (Euglenophyta). This organelle has a three-dimensional organization consisting of up to 50 closely stacked membrane lamellae. Ionically induced unstacking of the photoreceptor lamellae revealed ordered arrays well suited to structural analysis by electron microscopy and image analysis, which ultimately yielded a low-resolution picture of the structure. Each lamella is formed by the photoreceptive membrane protein of the cell assembled within the membrane layer in a hexagonal lattice. The first order diffraction spots in the calculated Fourier transform reveals the presence of 6-fold symmetrized topography (better resolution about 90 A). The 2D and 3D structural data are very similar with those recently published on proteorodopsin, a membrane protein used by marine bacterio-plankton as light-driven proton pump. In our opinion these similarity indicate that a photoreceptive protein belonging to the same superfamily of proteorodopsin could form the Euglena photoreceptor.

  16. Low Resolution Structural Studies Indicate that the Activator of Hsp90 ATPase 1 (Aha1) of Leishmania braziliensis Has an Elongated Shape Which Allows Its Interaction with Both N- and M-Domains of Hsp90

    PubMed Central

    Seraphim, Thiago V.; Alves, Marina M.; Silva, Indjara M.; Gomes, Francisco E. R.; Silva, Kelly P.; Murta, Silvane M. F.; Barbosa, Leandro R. S.; Borges, Júlio C.

    2013-01-01

    The Hsp90 molecular chaperone is essential for protein homeostasis and in the maturation of proteins involved with cell-cycle control. The low ATPase activity of Hsp90 is critical to drive its functional cycle, which is dependent on the Hsp90 cochaperones. The Activator of Hsp90 ATPase-1 (Aha1) is a protein formed by two domains, N- and C-terminal, that stimulates the Hsp90 ATPase activity by several folds. Although the relevance of Aha1 for Hsp90 functions has been proved, as well as its involvement in the desensitization to inhibitors of the Hsp90, the knowledge on its overall structure and behavior in solution is limited. In this work we present the functional and structural characterization of Leishmania braziliensis Aha1 (LbAha1). This protozoan is the causative agent of cutaneous and mucocutaneous leishmaniasis, a neglected disease. The recombinant LbAha1 behaves as an elongated monomer and is organized into two folded domains interconnected by a flexible linker. Functional experiments showed that LbAha1 interacts with L. braziliensis Hsp90 (LbHsp90) with micromolar dissociation constant in a stoichiometry of 2 LbAha1 to 1 LbHsp90 dimer and stimulates 10-fold the LbHsp90 ATPase activity showing positive cooperativity. Furthermore, the LbHsp90::LbAha1 complex is directed by enthalphy and opposed by entropy, probably due to the spatial freedom restrictions imposed by the proteins’ interactions. Small-angle X-ray scattering data allowed the reconstruction of low resolution models and rigid body simulations of LbAha1, indicating its mode of action on LbHsp90. Western blot experiments allowed Aha1 identification (as well as Hsp90) in three Leishmania species at two temperatures, suggesting that Aha1 is a cognate protein. All these data shed light on the LbAha1 mechanism of action, showing that it has structural dimensions and flexibility that allow interacting with both N-terminal and middle domains of the LbHsp90. PMID:23826147

  17. Low resolution structural studies indicate that the activator of Hsp90 ATPase 1 (Aha1) of Leishmania braziliensis has an elongated shape which allows its interaction with both N- and M-domains of Hsp90.

    PubMed

    Seraphim, Thiago V; Alves, Marina M; Silva, Indjara M; Gomes, Francisco E R; Silva, Kelly P; Murta, Silvane M F; Barbosa, Leandro R S; Borges, Júlio C

    2013-01-01

    The Hsp90 molecular chaperone is essential for protein homeostasis and in the maturation of proteins involved with cell-cycle control. The low ATPase activity of Hsp90 is critical to drive its functional cycle, which is dependent on the Hsp90 cochaperones. The Activator of Hsp90 ATPase-1 (Aha1) is a protein formed by two domains, N- and C-terminal, that stimulates the Hsp90 ATPase activity by several folds. Although the relevance of Aha1 for Hsp90 functions has been proved, as well as its involvement in the desensitization to inhibitors of the Hsp90, the knowledge on its overall structure and behavior in solution is limited. In this work we present the functional and structural characterization of Leishmania braziliensis Aha1 (LbAha1). This protozoan is the causative agent of cutaneous and mucocutaneous leishmaniasis, a neglected disease. The recombinant LbAha1 behaves as an elongated monomer and is organized into two folded domains interconnected by a flexible linker. Functional experiments showed that LbAha1 interacts with L. braziliensis Hsp90 (LbHsp90) with micromolar dissociation constant in a stoichiometry of 2 LbAha1 to 1 LbHsp90 dimer and stimulates 10-fold the LbHsp90 ATPase activity showing positive cooperativity. Furthermore, the LbHsp90::LbAha1 complex is directed by enthalphy and opposed by entropy, probably due to the spatial freedom restrictions imposed by the proteins' interactions. Small-angle X-ray scattering data allowed the reconstruction of low resolution models and rigid body simulations of LbAha1, indicating its mode of action on LbHsp90. Western blot experiments allowed Aha1 identification (as well as Hsp90) in three Leishmania species at two temperatures, suggesting that Aha1 is a cognate protein. All these data shed light on the LbAha1 mechanism of action, showing that it has structural dimensions and flexibility that allow interacting with both N-terminal and middle domains of the LbHsp90. PMID:23826147

  18. Low resolution structural characterization of the Hsp70-interacting protein - Hip - from Leishmania braziliensis emphasizes its high asymmetry.

    PubMed

    Dores-Silva, P R; Silva, E R; Gomes, F E R; Silva, K P; Barbosa, L R S; Borges, J C

    2012-04-15

    The Hsp70 is an essential molecular chaperone in protein metabolism since it acts as a pivot with other molecular chaperone families. Several co-chaperones act as regulators of the Hsp70 action cycle, as for instance Hip (Hsp70-interacting protein). Hip is a tetratricopeptide repeat protein (TPR) that interacts with the ATPase domain in the Hsp70-ADP state, stabilizing it and preventing substrate dissociation. Molecular chaperones from protozoans, which can cause some neglected diseases, are poorly studied in terms of structure and function. Here, we investigated the structural features of Hip from the protozoa Leishmania braziliensis (LbHip), one of the causative agents of the leishmaniasis disease. LbHip was heterologously expressed and purified in the folded state, as attested by circular dichroism and intrinsic fluorescence emission techniques. LbHip forms an elongated dimer, as observed by analytical gel filtration chromatography, analytical ultracentrifugation and small angle X-ray scattering (SAXS). With the SAXS data a low resolution model was reconstructed, which shed light on the structure of this protein, emphasizing its elongated shape and suggesting its domain organization. We also investigated the chemical-induced unfolding behavior of LbHip and two transitions were observed. The first transition was related to the unfolding of the TPR domain of each protomer and the second transition of the dimer dissociation. Altogether, LbHip presents a similar structure to mammalian Hip, despite their low level of conservation, suggesting that this class of eukaryotic protein may use a similar mechanism of action. PMID:22387434

  19. Low-resolution molecular structures of isolated functional units from arthropodan and molluscan hemocyanin.

    PubMed Central

    Grossmann, J G; Ali, S A; Abbasi, A; Zaidi, Z H; Stoeva, S; Voelter, W; Hasnain, S S

    2000-01-01

    Synchrotron x-ray scattering measurements were performed on dilute solutions of the purified hemocyanin subunit (Bsin1) from scorpion (Buthus sindicus) and the N-terminal functional unit (Rta) from a marine snail (Rapana thomasiana). The model-independent approach based on spherical harmonics was applied to calculate the molecular envelopes directly from the scattering profiles. Their molecular shapes in solution could be restored at 2-nm resolution. We show that these units represent stable, globular building blocks of the two hemocyanin families and emphasize their conformational differences on a subunit level. Because no crystallographic or electron microscopy data are available for isolated functional units, this study provides for the first time structural information for isolated, monomeric functional subunits from both hemocyanin families. This has been made possible through the use of low protein concentrations (< or = 1 mg/ml). The observed structural differences may offer advantages in building very different overall molecular architectures of hemocyanin by the two phyla. PMID:10653810

  20. Low resolution structures of cold, warm, and chemically denatured cytochrome-c via SAXS

    NASA Astrophysics Data System (ADS)

    Asta, Christopher; Banks, Anthony; Elmer, Margaret; Grandpre, Trevor; Landahl, Eric

    2013-03-01

    The results of a small-angle x-ray scattering (SAXS) study of equine cytochrome-c protein under different unfolding conditions are discussed. Although the measured radius of gyration of this protein over a wide range of temperatures and GuHCl concentrations conform to a two-state model, we find different levels of residual structure present depending on whether the protein is cold- or warm- denatured. We present DAMMIF reconstructions of these different unfolded states using 1532 dummy atoms with a 1.5 Angstrom radius, and suggest ways that these different states may be described by the same folding free energy. To whom correspondence should be addressed.

  1. Low resolution solution structure of HAMLET and the importance of its alpha-domains in tumoricidal activity.

    PubMed

    Ho, C S James; Rydstrom, Anna; Manimekalai, Malathy Sony Subramanian; Svanborg, Catharina; Grüber, Gerhard

    2012-01-01

    HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) is the first member in a new family of protein-lipid complexes with broad tumoricidal activity. Elucidating the molecular structure and the domains crucial for HAMLET formation is fundamental for understanding its tumoricidal function. Here we present the low-resolution solution structure of the complex of oleic acid bound HAMLET, derived from small angle X-ray scattering data. HAMLET shows a two-domain conformation with a large globular domain and an extended part of about 2.22 nm in length and 1.29 nm width. The structure has been superimposed into the related crystallographic structure of human α-lactalbumin, revealing that the major part of α-lactalbumin accommodates well in the shape of HAMLET. However, the C-terminal residues from L105 to L123 of the crystal structure of the human α-lactalbumin do not fit well into the HAMLET structure, resulting in an extended conformation in HAMLET, proposed to be required to form the tumoricidal active HAMLET complex with oleic acid. Consistent with this low resolution structure, we identified biologically active peptide epitopes in the globular as well as the extended domains of HAMLET. Peptides covering the alpha1 and alpha2 domains of the protein triggered rapid ion fluxes in the presence of sodium oleate and were internalized by tumor cells, causing rapid and sustained changes in cell morphology. The alpha peptide-oleate bound forms also triggered tumor cell death with comparable efficiency as HAMLET. In addition, shorter peptides corresponding to those domains are biologically active. These findings provide novel insights into the structural prerequisites for the dramatic effects of HAMLET on tumor cells.

  2. Low Resolution Structure and Dynamics of a Colicin-Receptor Complex Determined by Neutron Scattering

    SciTech Connect

    Clifton, Luke A; Johnson, Christopher L; Solovyova, Alexandra; Callow, Phil; Weiss, Kevin L; Ridley, Helen; Le Brun, Anton P; Kinane, Christian; Webster, John; Holt, Stephen A; Lakey, Jeremy H

    2012-01-01

    Proteins that translocate across cell membranes need to overcome a significant hydrophobic barrier. This is usually accomplished via specialized protein complexes, which provide a polar transmembrane pore. Exceptions to this include bacterial toxins, which insert into and cross the lipid bilayer itself. We are studying the mechanism by which large antibacterial proteins enter Escherichia coli via specific outer membrane proteins. Here we describe the use of neutron scattering to investigate the interaction of colicin N with its outer membrane receptor protein OmpF. The positions of lipids, colicin N, and OmpF were separately resolved within complex structures by the use of selective deuteration. Neutron reflectivity showed, in real time, that OmpF mediates the insertion of colicin N into lipid monolayers. This data were complemented by Brewster Angle Microscopy images, which showed a lateral association of OmpF in the presence of colicin N. Small angle neutron scattering experiments then defined the three-dimensional structure of the colicin N-OmpF complex. This revealed that colicin N unfolds and binds to the OmpF-lipid interface. The implications of this unfolding step for colicin translocation across membranes are discussed.

  3. Membrane positioning for high- and low-resolution protein structures through a binary classification approach.

    PubMed

    Postic, Guillaume; Ghouzam, Yassine; Guiraud, Vincent; Gelly, Jean-Christophe

    2016-03-01

    The critical importance of algorithms for orienting proteins in the lipid bilayer stems from the extreme difficulty in obtaining experimental data about the membrane boundaries. Here, we present a computational method for positioning protein structures in the membrane, based on the sole alpha carbon coordinates and, therefore, compatible with both high and low structural resolutions. Our algorithm follows a new and simple approach, by treating the membrane assignment problem as a binary classification. Compared with the state-of-the-art algorithms, our method achieves similar accuracy, while being faster. Finally, our open-source software is also capable of processing coarse-grained models of protein structures. PMID:26685702

  4. A novel analytical ultracentrifugation based approach to the low resolution structure of gum arabic.

    PubMed

    Gillis, Richard B; Adams, Gary G; Alzahrani, Qushmua; Harding, Stephen E

    2016-09-01

    Under investigation are the structural properties of gum arabic, an industrially important biopolymer for use as a stabilizer or in drug delivery, using Analytical Ultracentrifugation-a well-established, matrix-free probe for macromolecular size and shape. These results are combined with chromatographically-coupled methods (multi-angle light scattering, differential press imbalance viscometry) to provide a global analysis of its structure in varying ionic strength conditions. This analysis indicates that gum Arabic may have a compact, elliptical structure in solution, the significance of which for biotechnological use is indicated. This modelling method can be applied to other biopolymers and synthetic polymers. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 618-625, 2016. PMID:26899968

  5. The low-resolution structure of nHDL reconstituted with DMPC with and without cholesterol reveals a mechanism for particle expansion[S

    PubMed Central

    Gogonea, Valentin; Gerstenecker, Gary S.; Wu, Zhiping; Lee, Xavier; Topbas, Celalettin; Wagner, Matthew A.; Tallant, Thomas C.; Smith, Jonathan D.; Callow, Philip; Pipich, Vitaliy; Malet, Hélène; Schoehn, Guy; DiDonato, Joseph A.; Hazen, Stanley L.

    2013-01-01

    Small-angle neutron scattering (SANS) with contrast variation was used to obtain the low-resolution structure of nascent HDL (nHDL) reconstituted with dimyristoyl phosphatidylcholine (DMPC) in the absence and presence of cholesterol, [apoA1:DMPC (1:80, mol:mol) and apoA1:DMPC:cholesterol (1:86:9, mol:mol:mol)]. The overall shape of both particles is discoidal with the low-resolution structure of apoA1 visualized as an open, contorted, and out of plane conformation with three arms in nascent HDL/dimyristoyl phosphatidylcholine without cholesterol (nHDLDMPC) and two arms in nascent HDL/dimyristoyl phosphatidylcholine with cholesterol (nHDLDMPC+Chol). The low-resolution shape of the lipid phase in both nHDLDMPC and nHDLDMPC+Chol were oblate ellipsoids, and fit well within their respective protein shapes. Modeling studies indicate that apoA1 is folded onto itself in nHDLDMPC, making a large hairpin, which was also confirmed independently by both cross-linking mass spectrometry and hydrogen-deuterium exchange (HDX) mass spectrometry analyses. In nHDLDMPC+Chol, the lipid was expanded and no hairpin was visible. Importantly, despite the overall discoidal shape of the whole particle in both nHDLDMPC and nHDLDMPC+Chol, an open conformation (i.e., not a closed belt) of apoA1 is observed. Collectively, these data show that full length apoA1 retains an open architecture that is dictated by its lipid cargo. The lipid is likely predominantly organized as a bilayer with a micelle domain between the open apoA1 arms. The apoA1 configuration observed suggests a mechanism for accommodating changing lipid cargo by quantized expansion of hairpin structures. PMID:23349207

  6. Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations.

    PubMed

    Peng, Junhui; Zhang, Zhiyong

    2016-07-05

    Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1-3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.

  7. Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations

    NASA Astrophysics Data System (ADS)

    Peng, Junhui; Zhang, Zhiyong

    2016-07-01

    Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1-3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.

  8. Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations

    NASA Astrophysics Data System (ADS)

    Peng, Junhui; Zhang, Zhiyong

    2016-07-01

    Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1–3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.

  9. Low resolution brain electromagnetic tomography in a realistic geometry head model: a simulation study.

    PubMed

    Ding, Lei; Lai, Yuan; He, Bin

    2005-01-01

    It is of importance to localize neural sources from scalp recorded EEG. Low resolution brain electromagnetic tomography (LORETA) has received considerable attention for localizing brain electrical sources. However, most such efforts have used spherical head models in representing the head volume conductor. Investigation of the performance of LORETA in a realistic geometry head model, as compared with the spherical model, will provide useful information guiding interpretation of data obtained by using the spherical head model. The performance of LORETA was evaluated by means of computer simulations. The boundary element method was used to solve the forward problem. A three-shell realistic geometry (RG) head model was constructed from MRI scans of a human subject. Dipole source configurations of a single dipole located at different regions of the brain with varying depth were used to assess the performance of LORETA in different regions of the brain. A three-sphere head model was also used to approximate the RG head model, and similar simulations performed, and results compared with the RG-LORETA with reference to the locations of the simulated sources. Multisource localizations were discussed and examples given in the RG head model. Localization errors employing the spherical LORETA, with reference to the source locations within the realistic geometry head, were about 20-30 mm, for four brain regions evaluated: frontal, parietal, temporal and occipital regions. Localization errors employing the RG head model were about 10 mm over the same four brain regions. The present simulation results suggest that the use of the RG head model reduces the localization error of LORETA, and that the RG head model based LORETA is desirable if high localization accuracy is needed.

  10. Quantifying trabecular bone material anisotropy and orientation using low resolution clinical CT images: A feasibility study.

    PubMed

    Nazemi, S Majid; Cooper, David M L; Johnston, James D

    2016-09-01

    Accounting for spatial variation of trabecular material anisotropy and orientation can improve the accuracy of quantitative computed tomography-based finite element (FE) modeling of bone. The objective of this study was to investigate the feasibility of quantifying trabecular material anisotropy and orientation using clinical computed tomography (CT). Forty four cubic volumes of interest were obtained from micro-CT images of the human radius. Micro-FE modeling was performed on the samples to obtain orthotropic stiffness entries as well as trabecular orientation. Simulated computed tomography images (0.32, 0.37, and 0.5mm isotropic voxel sizes) were created by resampling micro-CT images with added image noise. The gray-level structure tensor was used to derive fabric eigenvalues and eigenvectors in simulated CT images. For 'best case' comparison purposes, Mean Intercept Length was used to define fabric from micro-CT images. Regression was used in combination with eigenvalues, imaged density and FE to inversely derive the constants used in Cowin and Zysset-Curnier fabric-elasticity equations, and for comparing image derived fabric-elasticity stiffness entries to those obtained using micro-FE. Image derived eigenvectors (which indicated trabecular orientation) were then compared to orientation derived using micro-FE. When using clinically available voxel sizes, gray-level structure tensor derived fabric combined with Cowin's equations was able to explain 94-97% of the variance in orthotropic stiffness entries while Zysset-Curnier equations explained 82-88% of the variance in stiffness. Image derived orientation deviated by 4.4-10.8° from micro-FE derived orientation. Our results indicate potential to account for spatial variation of trabecular material anisotropy and orientation in subject-specific finite element modeling of bone using clinically available CT. PMID:27372175

  11. Quantifying trabecular bone material anisotropy and orientation using low resolution clinical CT images: A feasibility study.

    PubMed

    Nazemi, S Majid; Cooper, David M L; Johnston, James D

    2016-09-01

    Accounting for spatial variation of trabecular material anisotropy and orientation can improve the accuracy of quantitative computed tomography-based finite element (FE) modeling of bone. The objective of this study was to investigate the feasibility of quantifying trabecular material anisotropy and orientation using clinical computed tomography (CT). Forty four cubic volumes of interest were obtained from micro-CT images of the human radius. Micro-FE modeling was performed on the samples to obtain orthotropic stiffness entries as well as trabecular orientation. Simulated computed tomography images (0.32, 0.37, and 0.5mm isotropic voxel sizes) were created by resampling micro-CT images with added image noise. The gray-level structure tensor was used to derive fabric eigenvalues and eigenvectors in simulated CT images. For 'best case' comparison purposes, Mean Intercept Length was used to define fabric from micro-CT images. Regression was used in combination with eigenvalues, imaged density and FE to inversely derive the constants used in Cowin and Zysset-Curnier fabric-elasticity equations, and for comparing image derived fabric-elasticity stiffness entries to those obtained using micro-FE. Image derived eigenvectors (which indicated trabecular orientation) were then compared to orientation derived using micro-FE. When using clinically available voxel sizes, gray-level structure tensor derived fabric combined with Cowin's equations was able to explain 94-97% of the variance in orthotropic stiffness entries while Zysset-Curnier equations explained 82-88% of the variance in stiffness. Image derived orientation deviated by 4.4-10.8° from micro-FE derived orientation. Our results indicate potential to account for spatial variation of trabecular material anisotropy and orientation in subject-specific finite element modeling of bone using clinically available CT.

  12. Study of the F ring core at high and low resolutions with Cassini ISS

    NASA Astrophysics Data System (ADS)

    Deau, Estelle

    2014-11-01

    Saturn’s F ring evolution is still a mystery since its discovery by Pioneer 11. This ring is unique by its changing appearance, its spiral shape, its shepherd satellites Prometheus and Pandora, its ephemeral satellites, and its chaotic behavior. We focus here on the brightest and central region of the F ring called the core. Using Voyager data, the core was primarily believed to be one of the four strands of the F ring (Murray et al., 1997, Icarus, vol.129, p.304-316). However, the core is very different from the other stands, because we have demonstrated previously that the core reconnects on itself over 360 degrees, while the strands don't (Charnoz et al. 2005, Science, vol.310, p.1300-1304). Indeed, the strands originate from the core and are connected between themselves in a single feature that is a spiral, as explained in our previous works (Charnoz et al. 2005, Science, vol.310, p.1300-1304, Deau, 2007, PhD thesis University Paris 7 Denis Diderot). Our present study focus on the F ring core. We have established a protocol in (Deau, 2007, PhD thesis University Paris 7 Denis Diderot) to calculate the radial width and the radial local variations of the core using a Gaussian model. We use this method on Cassini ISS data to derive azimuthal profiles of core's radial width and local kicks. Our study shows that the F ring core is very stable on scale of several months, as suggested by the recent chaos theory of Cuzzi et al. (2014, Icarus, vol.232, p.157-175), while the spiral has a much smaller timescale, i.e. the order of a few weeks.

  13. Low-resolution structure of the full-length barley (Hordeum vulgare) SGT1 protein in solution, obtained using small-angle X-ray scattering.

    PubMed

    Taube, Michał; Pieńkowska, Joanna R; Jarmołowski, Artur; Kozak, Maciej

    2014-01-01

    SGT1 is an evolutionarily conserved eukaryotic protein involved in many important cellular processes. In plants, SGT1 is involved in resistance to disease. In a low ionic strength environment, the SGT1 protein tends to form dimers. The protein consists of three structurally independent domains (the tetratricopeptide repeats domain (TPR), the CHORD- and SGT1-containing domain (CS), and the SGT1-specific domain (SGS)), and two less conserved variable regions (VR1 and VR2). In the present study, we provide the low-resolution structure of the barley (Hordeum vulgare) SGT1 protein in solution and its dimer/monomer equilibrium using small-angle scattering of synchrotron radiation, ab-initio modeling and circular dichroism spectroscopy. The multivariate curve resolution least-square method (MCR-ALS) was applied to separate the scattering data of the monomeric and dimeric species from a complex mixture. The models of the barley SGT1 dimer and monomer were formulated using rigid body modeling with ab-initio structure prediction. Both oligomeric forms of barley SGT1 have elongated shapes with unfolded inter-domain regions. Circular dichroism spectroscopy confirmed that the barley SGT1 protein had a modular architecture, with an α-helical TPR domain, a β-sheet sandwich CS domain, and a disordered SGS domain separated by VR1 and VR2 regions. Using molecular docking and ab-initio protein structure prediction, a model of dimerization of the TPR domains was proposed.

  14. Comparison of Low Resolution Electromagnetic Tomography Imaging Between Subjects With Mild and Severe Obstructive Sleep Apnea Syndrome: A Preliminary Study

    PubMed Central

    Lee, Hyun-Kwon; Shin, Hyun-Sil; Hong, Seok-Chan

    2008-01-01

    Objective The purpose of this study was to identify the regions of the brain associated with recurrent nocturnal chronic hypoxic episodes in patients with untreated obstructive sleep apnea syndrome (OSAS) using low-resolution electromagnetic tomography (LORETA) and quantitative electroencephalography (QEEG). Methods Nocturnal polysomnograph (NPSG) and subsequent morning electroencephalograph (EEG) were measured in 20 subjects with OSAS. Mild (n=10 ages 39.5±12.1 years) and severe (n=10 ages 41.7±13.6 years) right-handed male OSAS subjects were selected by interview and questionnaires including the NPSG, Beck Depression Inventory, Beck Anxiety Inventory, Epworth Sleepiness Scale, and Pittsburgh Sleep Quality Index. The LORETA and QEEG were compared between the severe and mild OSAS groups by frequency bands (delta 1-3 Hz, theta 4-7 Hz, alpha 8-12 Hz, beta1 13-18 Hz, beta2 19-21 Hz, beta3 22-30 Hz, and total 1-30 Hz) made by spectral analysis during resting with the eyes closed. Results The LORETA analysis showed decreased alpha activity at the right posterior cingulate gyrus (Brodmann area 23) in cases with severe OSAS compared to mild OSAS (p<0.05). For the QEEG, the absolute power of the alpha activity (8-12 Hz) was decreased in P3 (p=0.047), PZ (p=0.039) and O2 (p=0.04) in cases with severe OSAS compared to mild OSAS cases. The LORETA and QEEG analyses had similar results with regard to band, activation and location. Conclusion The decreased activity of the alpha frequency in the right posterior cingulate gyrus, in patients with severe OSAS compared to those with mild OSAS, suggests that chronic repeated short-term hypoxia during sleep, in OSAS, could provoke cortical brain dysfunction associated with cognitive dysfunction such as memory and attention. PMID:20046408

  15. Using selenomethionyl derivatives to assign sequence in low-resolution structures of the AP2 clathrin adaptor

    PubMed Central

    Kelly, Bernard T.; Graham, Stephen C.; Owen, David J.

    2016-01-01

    Selenomethionine incorporation is a powerful technique for assigning sequence to regions of electron density at low resolution. Genetic introduction of methionine point mutations and the subsequent preparation and crystallization of selenomethionyl derivatives permits unambiguous sequence assignment by enabling the placement of the anomalous scatterers (Se atoms) thus introduced. Here, the use of this approach in the assignment of sequence in a part of the AP2 clathrin adaptor complex that is responsible for clathrin binding is described. AP2 plays a pivotal role in clathrin-mediated endocytosis, a tightly regulated process in which cell-surface transmembrane proteins are internalized from the plasma membrane by incorporation into lipid-enclosed transport vesicles. AP2 binds cargo destined for internalization and recruits clathrin, a large trimeric protein that helps to deform the membrane to produce the transport vesicle. By selenomethionine labelling of point mutants, it was shown that the clathrin-binding site is buried within a deep cleft of the AP2 complex. A membrane-stimulated conformational change in AP2 releases the clathrin-binding site from autoinhibition, thereby linking clathrin recruitment to membrane localization. PMID:26960121

  16. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    SciTech Connect

    Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

    2015-03-01

    A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

  17. Determination of three-dimensional low-resolution viral structure from solution x-ray scattering data.

    PubMed Central

    Zheng, Y; Doerschuk, P C; Johnson, J E

    1995-01-01

    The capsid is modeled as a region of constant electron density located between inner and outer envelopes that exhibit icosahedral symmetry. For computational purposes the envelopes are represented as truncated sums of weighted icosahedral harmonics. Methods are described for estimating the weights from x-ray solution scattering patterns based on nonlinear least squares, and two examples of the procedure, for viruses with known atomic-resolution structures, are given. Images FIGURE 8 FIGURE 9 FIGURE 14 FIGURE 17 FIGURE 20 FIGURE 23 PMID:8527677

  18. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    PubMed Central

    Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

    2015-01-01

    Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx. PMID:25760616

  19. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps.

    PubMed

    Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M

    2015-03-01

    Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

  20. Deformable elastic network refinement for low-resolution macromolecular crystallography.

    PubMed

    Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

    2014-09-01

    Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  1. Deformable elastic network refinement for low-resolution macromolecular crystallography

    SciTech Connect

    Schröder, Gunnar F.; Levitt, Michael; Brunger, Axel T.

    2014-09-01

    An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations for its optimal usage. Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  2. Development of a low resolution (1)H NMR spectroscopic technique for the study of matrix mobility in fresh and freeze-thawed hen egg yolk.

    PubMed

    Au, Carmen; Wang, Tong; Acevedo, Nuria C

    2016-08-01

    Three experiments were conducted in developing a low resolution proton nuclear magnetic resonance ((1)H NMR) spectroscopic technique to study matrix mobility in fresh and freeze-thawed gelled yolk. The Carr-Purcell-Meiboom-Gill (CPMG) sequence was used to measure spin-spin relaxation times of proton pools representing major yolk constituents. A component identification test distinguished 3-4 pools. The least mobile pool was assigned to proteins, protein-lipid and protein-water interactions, and the most mobile to unbound water. The remaining pools were assigned to lipids, lipid-protein and lipid-water interactions. A stability test indicated that yolk had varied matrix mobility within the same sample across five days of refrigeration storage. A reproducibility test demonstrated high repeatability of fresh yolk measurements, but significant differences (p<0.05) were found within gelled yolk samples. This research determined that (1)H NMR spectroscopy, a non-destructive technique, can identify yolk components and detect changes in the matrix.

  3. Effect of the 5-HT(1A) partial agonist buspirone on regional brain electrical activity in man: a functional neuroimaging study using low-resolution electromagnetic tomography (LORETA).

    PubMed

    Anderer, P; Saletu, B; Pascual-Marqui, R D

    2000-12-01

    In a double-blind, placebo-controlled study, the effects of 20 mg buspirone - a 5-HT(1A) partial agonist - on regional electrical generators within the human brain were investigated utilizing three-dimensional EEG tomography. Nineteen-channel vigilance-controlled EEG recordings were carried out in 20 healthy subjects before and 1, 2, 4, 6 and 8 h after drug intake. Low-resolution electromagnetic tomography (LORETA; Key Institute for Brain-Mind Research, software: http://www.keyinst.unizh.ch) was computed from spectrally analyzed EEG data, and differences between drug- and placebo-induced changes were displayed as statistical parametric maps. Data were registered to the Talairach-Tournoux human brain atlas available as a digitized MRI (McConnell Brain Imaging Centre: http://www.bic.mni.mcgill.ca). At the pharmacodynamic peak (1st hour), buspirone increased theta and decreased fast alpha and beta sources. Areas of theta increase were mainly the left temporo-occipito-parietal and left prefrontal cortices, which is consistent with PET studies on buspirone-induced decreases in regional cerebral blood flow and fenfluramine-induced serotonin activation demonstrated by changes in regional cerebral glucose metabolism. In later hours (8th hour) with lower buspirone plasma levels, delta, theta, slow alpha and fast beta decreased, predominantly in the prefrontal and anterior limbic lobe. Whereas the results of the 1st hour speak for a slight CNS sedation (more in the sense of relaxation), those obtained in the 8th hour indicate activation. Thus, LORETA may provide useful and direct information on drug-induced changes in central nervous system function in man.

  4. Low-resolution gait recognition.

    PubMed

    Zhang, Junping; Pu, Jian; Chen, Changyou; Fleischer, Rudolf

    2010-08-01

    Unlike other biometric authentication methods, gait recognition is noninvasive and effective from a distance. However, the performance of gait recognition will suffer in the low-resolution (LR) case. Furthermore, when gait sequences are projected onto a nonoptimal low-dimensional subspace to reduce the data complexity, the performance of gait recognition will also decline. To deal with these two issues, we propose a new algorithm called superresolution with manifold sampling and backprojection (SRMS), which learns the high-resolution (HR) counterparts of LR test images from a collection of HR/LR training gait image patch pairs. Then, we incorporate SRMS into a new algorithm called multilinear tensor-based learning without tuning parameters (MTP) for LR gait recognition. Our contributions include the following: 1) With manifold sampling, the redundancy of gait image patches is remarkably decreased; thus, the superresolution procedure is more efficient and reasonable. 2) Backprojection guarantees that the learned HR gait images and the corresponding LR gait images can be more consistent. 3) The optimal subspace dimension for dimension reduction is automatically determined without introducing extra parameters. 4) Theoretical analysis of the algorithm shows that MTP converges. Experiments on the USF human gait database and the CASIA gait database show the increased efficiency of the proposed algorithm, compared with previous algorithms. PMID:20199936

  5. Prediction of Treatment Outcome in Patients with Obsessive-Compulsive Disorder with Low-Resolution Brain Electromagnetic Tomography: A Prospective EEG Study.

    PubMed

    Krause, Daniela; Folkerts, Malte; Karch, Susanne; Keeser, Daniel; Chrobok, Agnieszka I; Zaudig, Michael; Hegerl, Ulrich; Juckel, Georg; Pogarell, Oliver

    2015-01-01

    The issue of predicting treatment response and identifying, in advance, which patient will profit from treating obsessive-compulsive disorder (OCD) seems to be an elusive goal. This prospective study investigated brain electric activity [using Low-Resolution Brain Electromagnetic Tomography (LORETA)] for the purpose of predicting response to treatment. Forty-one unmedicated patients with a DSM-IV diagnosis of OCD were included. A resting 32-channel EEG was obtained from each participant before and after 10 weeks of standardized treatment with sertraline and behavioral therapy. LORETA was used to localize the sources of brain electrical activity. At week 10, patients were divided into responders and non-responders (according to a reduction of symptom severity >50% on the Y-BOCS). LORETA analysis revealed that at baseline responders showed compared to non-responders a significantly lower brain electric activity within the beta 1 (t = 2.86, p < 0.05), 2 (t = 2.81, p < 0.05), and 3 (t = 2.76, p < 0.05) frequency bands and ROI analysis confirmed a reduced activity in alpha 2 (t = 2.06, p < 0.05) in the anterior cingulate cortex (ACC). When baseline LORETA data were compared to follow-up data, the analysis showed in the responder group a significantly lower brain electrical resting activity in the beta 1 (t = 3.17. p < 0.05) and beta 3 (t = 3.11. p < 0.05) frequency bands and equally for the ROI analysis of the orbitofrontal cortex (OFC) in the alpha 2 (t = 2.15. p < 0.05) frequency band. In the group of non-responders the opposite results were found. In addition, a positive correlation between frequency alpha 2 (rho = 0.40, p = 0.010), beta 3 (rho = 0.42, p = 0.006), delta (rho = 0.33, p = 0.038), theta (rho = 0.34, p = 0.031), alpha 1 (rho = 0.38, p = 0.015), and beta1 (rho = 0.34, p = 0.028) of the OFC and the bands delta (rho = 0.33, p = 0.035), alpha 1 (rho = 0.36, p = 0.019), alpha 2 (rho = 0.34, p = 0.031), and beta 3 (rho = 0.38, p = 0.015) of the ACC with a

  6. Three-dimensional localization of abnormal EEG activity in migraine: a low resolution electromagnetic tomography (LORETA) study of migraine patients in the pain-free interval.

    PubMed

    Clemens, Béla; Bánk, József; Piros, Pálma; Bessenyei, Mónika; Veto, Sára; Tóth, Márton; Kondákor, István

    2008-09-01

    Investigating the brain of migraine patients in the pain-free interval may shed light on the basic cerebral abnormality of migraine, in other words, the liability of the brain to generate migraine attacks from time to time. Twenty unmedicated "migraine without aura" patients and a matched group of healthy controls were investigated in this explorative study. 19-channel EEG was recorded against the linked ears reference and was on-line digitized. 60 x 2-s epochs of eyes-closed, waking-relaxed activity were subjected to spectral analysis and a source localization method, low resolution electromagnetic tomography (LORETA). Absolute power was computed for 19 electrodes and four frequency bands (delta: 1.5-3.5 Hz, theta: 4.0-7.5 Hz, alpha: 8.0-12.5 Hz, beta: 13.0-25.0 Hz). LORETA "activity" (=current source density, ampers/meters squared) was computed for 2394 voxels and the above specified frequency bands. Group comparison was carried out for the specified quantitative EEG variables. Activity in the two groups was compared on a voxel-by-voxel basis for each frequency band. Statistically significant (uncorrected P < 0.01) group differences were projected to cortical anatomy. Spectral findings: there was a tendency for more alpha power in the migraine that in the control group in all but two (F4, C3) derivations. However, statistically significant (P < 0.01, Bonferroni-corrected) spectral difference was only found in the right occipital region. The main LORETA-finding was that voxels with P < 0.01 differences were crowded in anatomically contiguous cortical areas. Increased alpha activity was found in a cortical area including part of the precuneus, and the posterior part of the middle temporal gyrus in the right hemisphere. Decreased alpha activity was found bilaterally in medial parts of the frontal cortex including the anterior cingulate and the superior and medial frontal gyri. Neither spectral analysis, nor LORETA revealed statistically significant differences in

  7. Prediction of Treatment Outcome in Patients with Obsessive-Compulsive Disorder with Low-Resolution Brain Electromagnetic Tomography: A Prospective EEG Study

    PubMed Central

    Krause, Daniela; Folkerts, Malte; Karch, Susanne; Keeser, Daniel; Chrobok, Agnieszka I.; Zaudig, Michael; Hegerl, Ulrich; Juckel, Georg; Pogarell, Oliver

    2016-01-01

    The issue of predicting treatment response and identifying, in advance, which patient will profit from treating obsessive-compulsive disorder (OCD) seems to be an elusive goal. This prospective study investigated brain electric activity [using Low-Resolution Brain Electromagnetic Tomography (LORETA)] for the purpose of predicting response to treatment. Forty-one unmedicated patients with a DSM-IV diagnosis of OCD were included. A resting 32-channel EEG was obtained from each participant before and after 10 weeks of standardized treatment with sertraline and behavioral therapy. LORETA was used to localize the sources of brain electrical activity. At week 10, patients were divided into responders and non-responders (according to a reduction of symptom severity >50% on the Y-BOCS). LORETA analysis revealed that at baseline responders showed compared to non-responders a significantly lower brain electric activity within the beta 1 (t = 2.86, p < 0.05), 2 (t = 2.81, p < 0.05), and 3 (t = 2.76, p < 0.05) frequency bands and ROI analysis confirmed a reduced activity in alpha 2 (t = 2.06, p < 0.05) in the anterior cingulate cortex (ACC). When baseline LORETA data were compared to follow-up data, the analysis showed in the responder group a significantly lower brain electrical resting activity in the beta 1 (t = 3.17. p < 0.05) and beta 3 (t = 3.11. p < 0.05) frequency bands and equally for the ROI analysis of the orbitofrontal cortex (OFC) in the alpha 2 (t = 2.15. p < 0.05) frequency band. In the group of non-responders the opposite results were found. In addition, a positive correlation between frequency alpha 2 (rho = 0.40, p = 0.010), beta 3 (rho = 0.42, p = 0.006), delta (rho = 0.33, p = 0.038), theta (rho = 0.34, p = 0.031), alpha 1 (rho = 0.38, p = 0.015), and beta1 (rho = 0.34, p = 0.028) of the OFC and the bands delta (rho = 0.33, p = 0.035), alpha 1 (rho = 0.36, p = 0.019), alpha 2 (rho = 0.34, p = 0.031), and beta 3 (rho = 0.38, p = 0.015) of the ACC with a

  8. IRAS Low Resolution Spectra of Asteroids

    NASA Technical Reports Server (NTRS)

    Cohen, Martin; Walker, Russell G.

    2002-01-01

    Optical/near-infrared studies of asteroids are based on reflected sunlight and surface albedo variations create broad spectral features, suggestive of families of materials. There is a significant literature on these features, but there is very little work in the thermal infrared that directly probes the materials emitting on the surfaces of asteroids. We have searched for and extracted 534 thermal spectra of 245 asteroids from the original Dutch (Groningen) archive of spectra observed by the IRAS Low Resolution Spectrometer (LRS). We find that, in general, the observed shapes of the spectral continua are inconsistent with that predicted by the standard thermal model used by IRAS. Thermal models such as proposed by Harris (1998) and Harris et al.(1998) for the near-earth asteroids with the "beaming parameter" in the range of 1.0 to 1.2 best represent the observed spectral shapes. This implies that the IRAS Minor Planet Survey (IMPS, Tedesco, 1992) and the Supplementary IMPS (SIMPS, Tedesco, et al., 2002) derived asteroid diameters are systematically underestimated, and the albedos are overestimated. We have tentatively identified several spectral features that appear to be diagnostic of at least families of materials. The variation of spectral features with taxonomic class hints that thermal infrared spectra can be a valuable tool for taxonomic classification of asteroids.

  9. Low Resolution Picture Transmission (LRPT) Demonstration System

    NASA Technical Reports Server (NTRS)

    Fong, Wai; Yeh, Pen-Shu; Sank, Victor; Nyugen, Xuan; Xia, Wei; Duran, Steve; Day, John H. (Technical Monitor)

    2002-01-01

    Low-Resolution Picture Transmission (LRPT) is a proposed standard for direct broadcast transmission of satellite weather images. This standard is a joint effort by the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and the National Oceanic Atmospheric Administration (NOAA). As a digital transmission scheme, its purpose is to replace the current analog Automatic Picture Transmission (APT) system for use in the Meteorological Operational (METOP) satellites. Goddard Space Flight Center has been tasked to build an LRPT Demonstration System (LDS). It's main objective is to develop or demonstrate the feasibility of a low-cost receiver utilizing a Personal Computer (PC) as the primary processing component and determine the performance of the protocol in the simulated Radio Frequency (RF) environment. The approach would consist of two phases. In the phase 1, a Commercial-off-the-Shelf (COTS) Modulator-Demodulator (MODEM) board that would perform RF demodulation would be purchased allowing the Central Processing Unit (CPU) to perform the Consultative Committee for Space Data Systems (CCSDS) protocol processing. Also since the weather images are compressed the PC would perform the decompression. Phase 1 was successfully demonstrated on December 1997. Phase 2 consists of developing a high-fidelity receiver, transmitter and environment simulator. Its goal is to find out how the METOP Specification performs in a simulated noise environment in a cost-effective receiver. The approach would be to produce a receiver using as much software as possible to perform front-end processing to take advantage of the latest high-speed PCs. Thus the COTS MODEM used in Phase 1 is performing RF demodulation along with data acquisition providing data to the receiving software. Also, environment simulator is produced using the noise patterns generated by Institute for Telecommunications Sciences (ITS) from their noise environment study.

  10. Low resolution and high resolution MS for studies on the metabolism and toxicological detection of the new psychoactive substance methoxypiperamide (MeOP).

    PubMed

    Meyer, Markus R; Holderbaum, Anna; Kavanagh, Pierce; Maurer, Hans H

    2015-10-01

    In 2013, the new psychoactive substance methoxypiperamide (MeOP) was first reported to the European Monitoring Centre for Drug and Drug Addiction. Its structural similarity to already controlled piperazine designer drugs might have contributed to the decision to offer MeOP for online purchase. The aims of this work were to identify the phase I/II metabolites of MeOP in rat urine and the human cytochrome P450 (CYP) isoenzymes responsible for the initial metabolic steps. Finally, the detectability of MeOP in rat urine by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography coupled with multistage mass spectrometry (LC-MS(n)) standard urine screening approaches (SUSAs) was evaluated. After sample preparation by cleavage of conjugates followed by extraction for elucidating phase I metabolites, the analytes were separated and identified by GC-MS as well as liquid chromatography-high resolution-tandem mass spectrometry (LC-HR-MS/MS). For detection of phase II metabolites, the analytes were separated and identified after urine precipitation followed by LC-HR-MS/MS. The following metabolic steps could be postulated: hydrolysis of the amide, N-oxide formation, N- and/or O-demethylation, oxidation of the piperazine ring to the corresponding keto-piperazine, piperazine ring opening followed by oxidation of a methylene group to the corresponding imide, and hydroxylation of the phenyl group. Furthermore, N-acetylation, glucuronidation and sulfation were observed. Using human CYPs, CYP1A2, CYP2C19, CYP2D6, and/or CYP3A4 were found to catalyze N-oxide formation and N-, O-demethylation and/or oxidation. Mostly MeOP and N-oxide-MeOP but to a minor degree also other metabolites could be detected in the GC-MS and LC-MS(n) SUSAs. PMID:26456786

  11. THz Low Resolution Spectroscopy for Astronomy

    NASA Astrophysics Data System (ADS)

    Stacey, Gordon J.

    2011-09-01

    The THz spectral regime provides a wide range of spectral lines that are invaluable probes of star formation and AGN activity in galaxies both in the local Universe and at the earliest times. We review the utility of these lines, give examples of the science they deliver, and detail the properties of successful low resolution direct detection spectrometers for work in the THz regime. We finish with a discussion of the exciting new science we expect with the next direct detection generation spectrometers on new facilities such as SOFIA, CCAT, SPICA, and ALMA.

  12. Low-resolution refinement tools in REFMAC5

    PubMed Central

    Nicholls, Robert A.; Long, Fei; Murshudov, Garib N.

    2012-01-01

    Two aspects of low-resolution macromolecular crystal structure analysis are considered: (i) the use of reference structures and structural units for provision of structural prior information and (ii) map sharpening in the presence of noise and the effects of Fourier series termination. The generation of interatomic distance restraints by ProSMART and their subsequent application in REFMAC5 is described. It is shown that the use of such external structural information can enhance the reliability of derived atomic models and stabilize refinement. The problem of map sharpening is considered as an inverse deblurring problem and is solved using Tikhonov regularizers. It is demonstrated that this type of map sharpening can automatically produce a map with more structural features whilst maintaining connectivity. Tests show that both of these directions are promising, although more work needs to be performed in order to further exploit structural information and to address the problem of reliable electron-density calculation. PMID:22505260

  13. Very low resolution face recognition problem.

    PubMed

    Zou, Wilman W W; Yuen, Pong C

    2012-01-01

    This paper addresses the very low resolution (VLR) problem in face recognition in which the resolution of the face image to be recognized is lower than 16 × 16. With the increasing demand of surveillance camera-based applications, the VLR problem happens in many face application systems. Existing face recognition algorithms are not able to give satisfactory performance on the VLR face image. While face super-resolution (SR) methods can be employed to enhance the resolution of the images, the existing learning-based face SR methods do not perform well on such a VLR face image. To overcome this problem, this paper proposes a novel approach to learn the relationship between the high-resolution image space and the VLR image space for face SR. Based on this new approach, two constraints, namely, new data and discriminative constraints, are designed for good visuality and face recognition applications under the VLR problem, respectively. Experimental results show that the proposed SR algorithm based on relationship learning outperforms the existing algorithms in public face databases. PMID:21775262

  14. A super resolution framework for low resolution document image OCR

    NASA Astrophysics Data System (ADS)

    Ma, Di; Agam, Gady

    2013-01-01

    Optical character recognition is widely used for converting document images into digital media. Existing OCR algorithms and tools produce good results from high resolution, good quality, document images. In this paper, we propose a machine learning based super resolution framework for low resolution document image OCR. Two main techniques are used in our proposed approach: a document page segmentation algorithm and a modified K-means clustering algorithm. Using this approach, by exploiting coherence in the document, we reconstruct from a low resolution document image a better resolution image and improve OCR results. Experimental results show substantial gain in low resolution documents such as the ones captured from video.

  15. MEASURING ORGANIC MOLECULAR EMISSION IN DISKS WITH LOW-RESOLUTION SPITZER SPECTROSCOPY

    SciTech Connect

    Teske, Johanna K.; Najita, Joan R.; Carr, John S.; Pascucci, Ilaria; Apai, Daniel; Henning, Thomas E-mail: najita@noao.edu E-mail: pascucci@stsci.edu E-mail: henning@mpia.de

    2011-06-10

    We explore the extent to which Spitzer Infrared Spectrograph (IRS) spectra taken at low spectral resolution can be used in quantitative studies of organic molecular emission from disks surrounding low-mass young stars. We use Spitzer IRS spectra taken in both the high- and low-resolution modules for the same sources to investigate whether it is possible to define line indices that can measure trends in the strength of the molecular features in low-resolution data. We find that trends in the HCN emission strength seen in the high-resolution data can be recovered in low-resolution data. In examining the factors that influence the HCN emission strength, we find that the low-resolution HCN flux is modestly correlated with stellar accretion rate and X-ray luminosity. Correlations of this kind are perhaps expected based on recent observational and theoretical studies of inner disk atmospheres. Our results demonstrate the potential of using the large number of low-resolution disk spectra that reside in the Spitzer archive to study the factors that influence the strength of molecular emission from disks. Such studies would complement results for the much smaller number of circumstellar disks that have been observed at high resolution with IRS.

  16. THE COSMIC INFRARED BACKGROUND EXPERIMENT (CIBER): THE LOW RESOLUTION SPECTROMETER

    SciTech Connect

    Tsumura, K.; Arai, T.; Matsumoto, T.; Matsuura, S.; Murata, K.; Battle, J.; Bock, J.; Brown, S.; Lykke, K.; Smith, A.; Cooray, A.; Hristov, V.; Levenson, L. R.; Mason, P.; Keating, B.; Renbarger, T.; Kim, M. G.; Lee, D. H.; Nam, U. W.; Sullivan, I.; and others

    2013-08-15

    Absolute spectrophotometric measurements of diffuse radiation at 1 {mu}m to 2 {mu}m are crucial to our understanding of the radiative content of the universe from nucleosynthesis since the epoch of reionization, the composition and structure of the zodiacal dust cloud in our solar system, and the diffuse galactic light arising from starlight scattered by interstellar dust. The Low Resolution Spectrometer (LRS) on the rocket-borne Cosmic Infrared Background Experiment is a {lambda}/{Delta}{lambda} {approx} 15-30 absolute spectrophotometer designed to make precision measurements of the absolute near-infrared sky brightness between 0.75 {mu}m <{lambda} < 2.1 {mu}m. This paper presents the optical, mechanical, and electronic design of the LRS, as well as the ground testing, characterization, and calibration measurements undertaken before flight to verify its performance. The LRS is shown to work to specifications, achieving the necessary optical and sensitivity performance. We describe our understanding and control of sources of systematic error for absolute photometry of the near-infrared extragalactic background light.

  17. An Alternative Procedure for Extracting IUE Low Resolution Spectra

    NASA Astrophysics Data System (ADS)

    Crivellari, L.; Morossi, C.

    1982-02-01

    This paper presents an alternative procedure which extracts spectra from IUE low resolution images. The -by-line image is scanned perpendicularly to the direction of dispersion . The resulting cross-cuts are then fitted with a known-form analytical function, which consists of a linear base-line describing the background plus as many bands as there are spectra in the image under study. At each wavelength point the value of the spectrum is assumed to be the area of the corresponding band. A proper choice of the band profile allows us to recover the light scattered perpendicularly to the direction of dispersion, due to the "halation" effect in the on-board UV-to-visible image converter. In such a way a more correct extracting procedure is achieved. It furnishes noticeably better results than the standard VILSPA extracting routine in the case of highly exposed images. As a by-product, some properties of the Point Spread Function perpendicular to the direction of dispersion are determined.

  18. How to Deal with Low-Resolution Target Structures: Using SAR, Ensemble Docking, Hydropathic Analysis, and 3D-QSAR to Definitively Map the αβ-Tubulin Colchicine Site

    PubMed Central

    Da, Chenxiao; Mooberry, Susan L.; Gupton, John T.; Kellogg, Glen E.

    2013-01-01

    αβ-tubulin colchicine site inhibitors (CSIs) from four scaffolds that we previously tested for antiproliferative activity were modeled to better understand their effect on microtubules. Docking models, constructed by exploiting the SAR of a pyrrole subset and HINT scoring, guided ensemble docking of all 59 compounds. This conformation set and two variants having progressively less structure knowledge were subjected to CoMFA, CoMFA+HINT, and CoMSIA 3D-QSAR analyses. The CoMFA+HINT model (docked alignment) showed the best statistics: leave-one-out q2 of 0.616, r2 of 0.949 and r2pred (internal test set) of 0.755. An external (tested in other laboratories) collection of 24 CSIs from eight scaffolds were evaluated with the 3D-QSAR models, which correctly ranked their activity trends in 7/8 scaffolds for CoMFA+HINT (8/8 for CoMFA). The combination of SAR, ensemble docking, hydropathic analysis and 3D-QSAR provides an atomic-scale colchicine site model more consistent with a target structure resolution much higher than the ~3.6 Å available for αβ-tubulin. PMID:23961916

  19. Human Mobility Monitoring in Very Low Resolution Visual Sensor Network

    PubMed Central

    Bo Bo, Nyan; Deboeverie, Francis; Eldib, Mohamed; Guan, Junzhi; Xie, Xingzhe; Niño, Jorge; Van Haerenborgh, Dirk; Slembrouck, Maarten; Van de Velde, Samuel; Steendam, Heidi; Veelaert, Peter; Kleihorst, Richard; Aghajan, Hamid; Philips, Wilfried

    2014-01-01

    This paper proposes an automated system for monitoring mobility patterns using a network of very low resolution visual sensors (30 × 30 pixels). The use of very low resolution sensors reduces privacy concern, cost, computation requirement and power consumption. The core of our proposed system is a robust people tracker that uses low resolution videos provided by the visual sensor network. The distributed processing architecture of our tracking system allows all image processing tasks to be done on the digital signal controller in each visual sensor. In this paper, we experimentally show that reliable tracking of people is possible using very low resolution imagery. We also compare the performance of our tracker against a state-of-the-art tracking method and show that our method outperforms. Moreover, the mobility statistics of tracks such as total distance traveled and average speed derived from trajectories are compared with those derived from ground truth given by Ultra-Wide Band sensors. The results of this comparison show that the trajectories from our system are accurate enough to obtain useful mobility statistics. PMID:25375754

  20. New low-resolution spectrometer spectra for IRAS sources

    NASA Technical Reports Server (NTRS)

    Volk, Kevin; Kwok, Sun; Stencel, R. E.; Brugel, E.

    1991-01-01

    Low-resolution spectra of 486 IRAS point sources with F sub nu(12 microns) in the range 20-40 Jy are presented. This is part of an effort to extract and classify spectra that were not included in the Atlas of Low-Resolution Spectra and represents an extension of the earlier work by Volk and Cohen which covers sources with F sub nu(12 microns) greater than 40 Jy. The spectra have been examined by eye and classified into nine groups based on the spectral morphology. This new classification scheme is compared with the mechanical classification of the Atlas, and the differences are noted. Oxygen-rich stars of the asymptotic giant branch make up 33 percent of the sample. Solid state features dominate the spectra of most sources. It is found that the nature of the sources as implied by the present spectral classification is consistent with the classifications based on broad-band colors of the sources.

  1. LORES: Low resolution shape program for the calculation of small angle scattering profiles for biological macromolecules in solution

    NASA Astrophysics Data System (ADS)

    Zhou, J.; Deyhim, A.; Krueger, S.; Gregurick, S. K.

    2005-08-01

    A program for determining the low resolution shape of biological macromolecules, based on the optimization of a small angle neutron scattering profile to experimental data, is presented. This program, termed LORES, relies on a Monte Carlo optimization procedure and will allow for multiple scattering length densities of complex structures. It is therefore more versatile than utilizing a form factor approach to produce low resolution structural models. LORES is easy to compile and use, and allows for structural modeling of biological samples in real time. To illustrate the effectiveness and versatility of the program, we present four specific biological examples, Apoferritin (shell model), Ribonuclease S (ellipsoidal model), a 10-mer dsDNA (duplex helix) and a construct of a 10-mer DNA/PNA duplex helix (heterogeneous structure). These examples are taken from protein and nucleic acid SANS studies, of both large and small scale structures. We find, in general, that our program will accurately reproduce the geometric shape of a given macromolecule, when compared with the known crystallographic structures. We also present results to illustrate the lower limit of the experimental resolution which the LORES program is capable of modeling. Program summaryTitle of program:LORES Catalogue identifier: ADVC Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVC Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer:SGI Origin200, SGI Octane, SGI Linux, Intel Pentium PC Operating systems:UNIX64 6.5 and LINUX 2.4.7 Programming language used:C Memory required to execute with typical data:8 MB No. of lines in distributed program, including test data, etc.:2270 No. of bytes in distributed program, including test data, etc.:13 302 Distribution format:tar.gz External subprograms used:The entire code must be linked with the MATH library

  2. Neural network application for thermal image recognition of low-resolution objects

    NASA Astrophysics Data System (ADS)

    Fang, Yi-Chin; Wu, Bo-Wen

    2007-02-01

    In the ever-changing situation on a battle field, accurate recognition of a distant object is critical to a commander's decision-making and the general public's safety. Efficiently distinguishing between an enemy's armoured vehicles and ordinary civilian houses under all weather conditions has become an important research topic. This study presents a system for recognizing an armoured vehicle by distinguishing marks and contours. The characteristics of 12 different shapes and 12 characters are used to explore thermal image recognition under the circumstance of long distance and low resolution. Although the recognition capability of human eyes is superior to that of artificial intelligence under normal conditions, it tends to deteriorate substantially under long-distance and low-resolution scenarios. This study presents an effective method for choosing features and processing images. The artificial neural network technique is applied to further improve the probability of accurate recognition well beyond the limit of the recognition capability of human eyes.

  3. Q-DockLHM: Low-resolution refinement for ligand comparative modeling

    PubMed Central

    Brylinski, Michal; Skolnick, Jeffrey

    2009-01-01

    The success of ligand docking calculations typically depends on the quality of the receptor structure. Given improvements in protein structure prediction approaches, approximate protein models now can be routinely obtained for the majority of gene products in a given proteome. Structure-based virtual screening of large combinatorial libraries of lead candidates against theoretically modeled receptor structures requires fast and reliable docking techniques capable of dealing with structural inaccuracies in protein models. Here, we present Q-DockLHM, a method for low-resolution refinement of binding poses provided by FINDSITELHM, a ligand homology modeling approach. We compare its performance to that of classical ligand docking approaches in ligand docking against a representative set of experimental (both holo and apo) as well as theoretically modeled receptor structures. Docking benchmarks reveal that unlike all-atom docking, Q-DockLHM exhibits the desired tolerance to the receptor’s structure deformation. Our results suggest that the use of an evolution-based approach to ligand homology modeling followed by fast low-resolution refinement is capable of achieving satisfactory performance in ligand-binding pose prediction with promising applicability to proteome-scale applications. PMID:19827144

  4. Detecting aircraft with a low-resolution infrared sensor.

    PubMed

    Jakubowicz, Jérémie; Lefebvre, Sidonie; Maire, Florian; Moulines, Eric

    2012-06-01

    Existing computer simulations of aircraft infrared signature (IRS) do not account for dispersion induced by uncertainty on input data, such as aircraft aspect angles and meteorological conditions. As a result, they are of little use to estimate the detection performance of IR optronic systems; in this case, the scenario encompasses a lot of possible situations that must be indeed addressed, but cannot be singly simulated. In this paper, we focus on low-resolution infrared sensors and we propose a methodological approach for predicting simulated IRS dispersion of poorly known aircraft and performing aircraft detection on the resulting set of low-resolution infrared images. It is based on a sensitivity analysis, which identifies inputs that have negligible influence on the computed IRS and can be set at a constant value, on a quasi-Monte Carlo survey of the code output dispersion, and on a new detection test taking advantage of level sets estimation. This method is illustrated in a typical scenario, i.e., a daylight air-to-ground full-frontal attack by a generic combat aircraft flying at low altitude, over a database of 90,000 simulated aircraft images. Assuming a white noise or a fractional Brownian background model, detection performances are very promising.

  5. Amyloids in solid-state nuclear magnetic resonance: potential causes of the usually low resolution.

    PubMed

    Espargaró, Alba; Busquets, Maria Antònia; Estelrich, Joan; Sabate, Raimon

    2015-01-01

    Amyloids are non-crystalline and insoluble, which imply that the classical structural biology tools, ie, X-ray crystallography and solution nuclear magnetic resonance (NMR), are not suitable for their analysis. In the last years, solid-state NMR (ssNMR) has emerged as an alternative tool to decrypt the structural signatures of amyloid fibrils, providing major contributions to our understanding of molecular structures of amyloids such as β-amyloid peptide associated with Alzheimer's disease or fungal prions, among others. Despite this, the wide majority of amyloid fibrils display low resolution by ssNMR. Usually, this low resolution has been attributed to a high disorder or polymorphism of the fibrils, suggesting the existence of diverse elementary β-sheet structures. Here, we propose that a single β-sheet structure could be responsible for the broadening of the line widths in the ssNMR spectra. Although the fibrils and fibers consist of a single elementary structure, the angle of twist of each individual fibril in the mature fiber depends on the number of individual fibrils as well as the fibril arrangement in the final mature fiber. Thus, a wide range of angles of twist could be observed in the same amyloid sample. These twist variations involve changes in amino acid alignments that could be enough to limit the ssNMR resolution. PMID:26635473

  6. Amyloids in solid-state nuclear magnetic resonance: potential causes of the usually low resolution

    PubMed Central

    Espargaró, Alba; Busquets, Maria Antònia; Estelrich, Joan; Sabate, Raimon

    2015-01-01

    Amyloids are non-crystalline and insoluble, which imply that the classical structural biology tools, ie, X-ray crystallography and solution nuclear magnetic resonance (NMR), are not suitable for their analysis. In the last years, solid-state NMR (ssNMR) has emerged as an alternative tool to decrypt the structural signatures of amyloid fibrils, providing major contributions to our understanding of molecular structures of amyloids such as β-amyloid peptide associated with Alzheimer’s disease or fungal prions, among others. Despite this, the wide majority of amyloid fibrils display low resolution by ssNMR. Usually, this low resolution has been attributed to a high disorder or polymorphism of the fibrils, suggesting the existence of diverse elementary β-sheet structures. Here, we propose that a single β-sheet structure could be responsible for the broadening of the line widths in the ssNMR spectra. Although the fibrils and fibers consist of a single elementary structure, the angle of twist of each individual fibril in the mature fiber depends on the number of individual fibrils as well as the fibril arrangement in the final mature fiber. Thus, a wide range of angles of twist could be observed in the same amyloid sample. These twist variations involve changes in amino acid alignments that could be enough to limit the ssNMR resolution. PMID:26635473

  7. An Analysis of the Automated Meteorological Profiling System Low Resolution Flight Element

    NASA Technical Reports Server (NTRS)

    Leahy, Frank B.; Overbey, B. Glenn

    2003-01-01

    A study was conducted to determine the quality of thermodynamic and wind data measured by or derived from the Low Resolution Flight Element (LRFE) of the Automated Meteorological Profiling System (AMPS). The AMPS LRFE replaced the Meteorological Sounding System (MSS), which was used to provide vertical profiles of thermodynamic and low-resolution wind data in support of spacecraft launch operations at the Cape Canaveral Air Force Station (CCAFS) and NASA Kennedy Space Center (KSC), Florida. Air temperature, relative humidity, and height, which are directly measured by the LRFE, are used to derive air pressure and density. Test flights were conducted where an LRFE sonde and an MSS sonde were attached to the same balloon and the two profiles were compared. MSS data was used as the standard reference data. The objective of the thermodynamic testing was to determine a) if the LRFE met Space Shuttle Program (SSP) accuracy requirements outlined in the Space Shuttle Launch and Landing Program Requirements Document (PRD) and/or, b) if the LRFE met or exceeded MSS data quality. AMPS uses the Global Positioning System (GPS) to determine wind speed and direction. In order to provide a basis for comparison, either an AMPS High Resolution Flight Element (HRFE) or a radar tracked Jimsphere was released simultaneously with each AMPS LRFE at CCAFS. The goal of these tests was to determine if the LRFE wind data met the requirement for low-resolution wind data defined in the Shuttle PRD. Based on the available data, the LRFE is shown to produce more consistent thermodynamic measurements than the MSS. The LRFE is also shown to meet the Shuttle PRD requirements for low resolution wind data.

  8. Facial identification in very low-resolution images simulating prosthetic vision.

    PubMed

    Chang, M H; Kim, H S; Shin, J H; Park, K S

    2012-08-01

    Familiar facial identification is important to blind or visually impaired patients and can be achieved using a retinal prosthesis. Nevertheless, there are limitations in delivering the facial images with a resolution sufficient to distinguish facial features, such as eyes and nose, through multichannel electrode arrays used in current visual prostheses. This study verifies the feasibility of familiar facial identification under low-resolution prosthetic vision and proposes an edge-enhancement method to deliver more visual information that is of higher quality. We first generated a contrast-enhanced image and an edge image by applying the Sobel edge detector and blocked each of them by averaging. Then, we subtracted the blocked edge image from the blocked contrast-enhanced image and produced a pixelized image imitating an array of phosphenes. Before subtraction, every gray value of the edge images was weighted as 50% (mode 2), 75% (mode 3) and 100% (mode 4). In mode 1, the facial image was blocked and pixelized with no further processing. The most successful identification was achieved with mode 3 at every resolution in terms of identification index, which covers both accuracy and correct response time. We also found that the subjects recognized a distinctive face especially more accurately and faster than the other given facial images even under low-resolution prosthetic vision. Every subject could identify familiar faces even in very low-resolution images. And the proposed edge-enhancement method seemed to contribute to intermediate-stage visual prostheses.

  9. Enhanced Landmine Detection from Low Resolution IR Image Sequences

    NASA Astrophysics Data System (ADS)

    Wang, Tiesheng; Gu, Irene Yu-Hua; Tjahjadi, Tardi

    We deal with the problem of landmine field detection using low-resolution infrared (IR) image sequences measured from airborne or vehicle-borne passive IR cameras. The proposed scheme contains two parts: a) employ a multi-scale detector, i.e., a special type of isotropic bandpass filters, to detect landmine candidates in each frame; b) enhance landmine detection through seeking maximum consensus of corresponding landmine candidates over image frames. Experiments were conducted on several IR image sequences measured from airborne and vehicle-borne cameras, where some results are included. As shown in our experiments, the landmine signatures have been significantly enhanced using the proposed scheme, and automatic detection results are reasonably good. These methods can therefore be applied to assisting humanitarian demining work for landmine field detection.

  10. Performance and sensitivity of low-resolution spectrographs for LAMOST

    NASA Astrophysics Data System (ADS)

    Hou, Yonghui; Zhu, Yongtian; Hu, Zhongwen; Wang, Lei; Wang, Jianing

    2010-07-01

    The 16 low resolution spectrographs (LRS) have been successfully commissioned for the LAMOST. The LRS design employs a dual-beamed and bench-mounted, with large-beamed, fast Schmidt cameras and Volume Phase Holographic (VPH) transmission gratings. The design wavelength range is 370-900nm, at resolutions of R=1000and R=10000. Each spectrograph is fed by 250 fibers with 320 micron in diameter (corresponding 3.3 arcsec), composed of one F/4 Schmidt collimator, a dichroic beam-splitter, four VPH gratings, articulating Schmidt cameras that are optimized at blue band (370-590 nm) and red band (570-900 nm), and field lens near the focal plane service as the vacuum window of CCD detector cryogenic head. In this paper, we present the testing result of the LRS on the image quality, spectra resolution, efficiency and observing spectra.

  11. Model-building strategies for low-resolution X-ray crystallographic data

    SciTech Connect

    Karmali, Anjum M.; Blundell, Tom L.; Furnham, Nicholas

    2009-02-01

    Interpretation of low-resolution X-ray crystallographic data can prove to be a difficult task. The challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 Å is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered.

  12. Hobby-Eberly Telescope low-resolution spectrograph: optical design

    NASA Astrophysics Data System (ADS)

    Cobos Duenas, Francisco J.; Tejada, Carlos; Hill, Gary J.; Perez G., F.

    1998-07-01

    The Hobby Eberly Telescope (HET) is a revolutionary large telescope of 9.2 meter aperture, which is currently undergoing commissioning at McDonald Observatory. First light was obtained on December 11, 1996. Scientific operations are expected in 1998. The Low Resolution Spectrograph (LRS, a collaboration between the University of Texas at Austin, the Instituto de Astronomia de la Universidad Nacional Autonoma de Mexico, Stanford University, Ludwig-Maximillians-Universitat, Munich and Georg-August-Universitat, Gottingen) is a high throughput, imaging spectrograph which rides on the HET tracker at prime focus. The LRS will be the first HET facility instrument. The unique nature of the HET has led to interesting optical design solutions for the LRS, aimed at high performance and simplicity. The LRS is a grism spectrograph with a refractive collimator and a catadioptric f/1.4 camera. The beam size is 140 mm, resulting in resolving powers between (lambda) /(Delta) (lambda) approximately 600 and 3000 with a 1 arcsec wide slit. The LRS optics were designed and partially fabricated at the IAUNAM. We present a description of the LRS specifications and optical design, and describe the manufacturing process.

  13. Hobby-Eberly Telescope low-resolution spectrograph: mechanical design

    NASA Astrophysics Data System (ADS)

    Hill, Gary J.; Nicklas, Harald E.; MacQueen, Phillip J.; Mitsch, Wolfgang; Wellem, Walter; Altmann, Werner; Wesley, Gordon L.; Ray, Frank B.

    1998-07-01

    The Hobby-Eberly Telescope (HET) is a revolutionary large telescope of 9.2 meter aperture, located in West Texas at McDonald Observatory. The Low Resolution Spectrograph [LRS, an international collaboration between the University of Texas at Austin (UT), the Instituto de Astronomia de la Universidad Nacional Autonoma de Mexico (IAUNAM), Stanford University, Ludwig-Maximillians-Universitat, Munich (USM), and Georg- August-Universitat, Gottingen (USG)] is a high throughput, imaging grism spectrograph which rides on the HET tracker at prime focus. The remote location and tight space and weight constraints make the LRS a challenging instrument, built on a limited budget. The mechanical design and fabrication were done in Germany, and the camera and CCD system in Texas. The LRS is a grism spectrograph with three modes of operation: imaging, longslit, and multi-object. Here we present a detailed description of the mechanical design of the LRS. Fabrication, assembly and testing of the LRS will be completed by mid 1998. First light for the LRS on the HET is expected in the summer of 1998.

  14. Cartography of asteroids and comet nuclei from low resolution data

    NASA Technical Reports Server (NTRS)

    Stooke, Philip J.

    1992-01-01

    High resolution images of non-spherical objects, such as Viking images of Phobos and the anticipated Galileo images of Gaspra, lend themselves to conventional planetary cartographic procedures: control network analysis, stereophotogrammetry, image mosaicking in 2D or 3D, and airbrush mapping. There remains the problem of a suitable map projection for bodies which are extremely elongated or irregular in shape. Many bodies will soon be seen at lower resolution (5-30 pixels across the disk) in images from speckle interferometry, the Hubble Space Telescope, ground-based radar, distinct spacecraft encounters, and closer images degraded by smear. Different data with similar effective resolutions are available from stellar occultations, radar or lightcurve convex hulls, lightcurve modeling of albedo variations, and cometary jet modeling. With such low resolution, conventional methods of shape determination will be less useful or will fail altogether, leaving limb and terminator topography as the principal sources of topographic information. A method for shape determination based on limb and terminator topography was developed. It has been applied to the nucleus of Comet Halley and the jovian satellite Amalthea. The Amalthea results are described to give an example of the cartographic possibilities and problems of anticipated data sets.

  15. TGS[underscore]FIT: Image reconstruction software for quantitative, low-resolution tomographic assays

    SciTech Connect

    Estep, R J

    1993-01-01

    We developed the computer program TGS[underscore]FIT to aid in researching the tomographic gamma scanner method of nondestructive assay. This software, written in C-programming, language, implements a full Beer's Law attenuation correction in reconstructing low-resolution emission tomograms. The attenuation coefficients for the corrections are obtained by reconstructing a transmission tomogram of the same resolution. The command-driven interface, combined with (crude) simulation capabilities and command file control, allows design studies to be performed in a semi-automated manner.

  16. Autonomous Motion Segmentation of Multiple Objects in Low Resolution Video Using Variational Level Sets

    SciTech Connect

    Moelich, M

    2003-11-18

    This report documents research that was done during a ten week internship in the Sapphire research group at the Lawrence Livermore National Laboratory during the Summer of 2003. The goal of the study was to develop an algorithm that is capable of isolating (segmenting) moving objects in low resolution video sequences. This capability is currently being developed by the Sapphire research group as the first stage in a longer term video data mining project. This report gives a chronological account of what ideas were tried in developing the algorithm and what was learned from each attempt. The final version of the algorithm, which is described in detail, gives good results and is fast.

  17. Model-building strategies for low-resolution X-ray crystallographic data

    PubMed Central

    Karmali, Anjum M.; Blundell, Tom L.; Furnham, Nicholas

    2009-01-01

    The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 Å is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered. PMID:19171966

  18. The Hobby-Eberly Telescope Low Resolution Spectrograph

    NASA Astrophysics Data System (ADS)

    Hill, G. J.; MacQueen, P. J.; Nicklas, H.; Cobos D., F. J.; Tejada, C.; Mitsch, W.; Wolf, M. J.

    1998-12-01

    The Hobby-Eberly Telescope (HET) is a revolutionary large telescope of 9.2 meter aperture, located in West Texas at McDonald Observatory. First light was obtained on December 11, 1996. Scientific operations are expected in the spring of 1999. The Low Resolution Spectrograph (LRS, an international collaboration between Texas, UNAM, Stanford, Munich and Goettingen) is a high throughput, imaging spectrograph which rides on the HET tracker at prime focus. The LRS will be the first HET facility instrument. The remote location and tight space and weight constraints make the LRS a challenging instrument, built on a limited budget. The optics were partially constructed in Mexico at IAUNAM, the mechanics in Germany, and the camera and CCD system in Texas. The LRS is a grism spectrograph with a number of modes of operation: imaging, longslit, and multi-object. The field of view from the HET is 4-arcminutes in diameter, and the LRS will have a 13-slitlet Multi Object Spectroscopy (MOS) unit covering this field. The MOS unit is described in a separate paper. Resolutions between lambda / {delta lambda } = 500 and 3000 with a 1-arcsec. wide slit will be achieved with a variety of grisms, of which two can be carried by the instrument at any one time. The CCD is a Ford Aerospace 1024x3096 device with 15 micron pixels, and the image scale is approximately 0.25 arcsec. per pixel. We will present a detailed description of the LRS, and provide an overview of the optical and mechanical aspects of its design. Fabrication and assembly of the LRS will be completed by the end of 1998. First light on the HET is expected shortly thereafter.

  19. Investigating short wavelength correlated errors on low resolution mode altimetry

    NASA Astrophysics Data System (ADS)

    Poisson, Jean-Christophe; Thibaut, Pierre; Dibarboure, Gérald; Labroue, Sylvie; Lasne, Yannick; Boy, François; Picot, Nicolas

    2013-04-01

    Although conventional radar altimetry products (Jason1, Jason2, LRM CRYOSAT2, etc) have a spatial resolution as high as 300 m, the observation of ocean scales smaller than 100 km is limited by the existence of a "spectral hump", i.e. a geographically coherent error. In the frame of the future altimetry missions (SAR for Cryosat -2 and Sentinel-3 missions and interferometry for the SWOT mission) it becomes crucial to investigate again and to better understand the signals obtained at small scales by conventional altimeter missions. Through an analysis of simulations, we show that heterogeneous backscattering scenes can result in the corruption of the altimeter waveforms and retracked parameters. The retrackers used in current ground processors cannot well fit the Brown model during backscattering events because this model has been designed for a homogeneous scene. The error is also propagated along-track because of the size and shape of the low resolution mode (LRM) disc-shaped footprint. The hump phenomenon is shown to be almost ubiquitous in the ocean, yet more intense at low latitudes and in the Indian Ocean and Western Pacific Ocean, where backscattering events are more frequent. Its overall signature could be a Gaussian-like random signal smooth for wavelengths smaller than 15 km, i.e. white noise on 1 Hz products. The analysis of current data from 5 altimetry missions highlights the influence of the instrument design and altitude, and the influence of the retracker used. The spectral hump is a systematic response to random events and it is possible to mitigate it with new processing. Simulations and geographically limited datasets from the synthetic aperture radar mode (SARM) of Cryosat-2 show that the thin stripe-shaped synthetic footprint of SARM might be less sensitive to the artifact.

  20. Hobby-Eberly Telescope low-resolution spectrograph

    NASA Astrophysics Data System (ADS)

    Hill, Gary J.; Nicklas, Harald E.; MacQueen, Phillip J.; Tejada, Carlos; Cobos Duenas, Francisco J.; Mitsch, Wolfgang

    1998-07-01

    The Hobby-Eberly Telescope (HET) is a revolutionary large telescope of 9.2 meter aperture, located in West Texas at McDonald Observatory. First light was obtained on December 11, 1996. The start of scientific operations is expected in the late summer of 1998. The Low Resolution Spectrograph [LRS, an international collaboration between the University of Texas at Austin (UT), the Instituto de Astronomia de la Universidad Nacional Autonoma de Mexico (IAUNAM), Stanford University, Ludwig-Maximillians-Universitat, Munich (USM), and Georg- August-Universitat, Gottingen (USG)] is a high throughput, imaging spectrograph which rides on the HET tracker at prime focus. The LRS will be the first HET facility instrument. The remote location and the tight space and weight constraints make the LRS a challenging instrument, built on a limited budget. The optics were partially constructed in Mexico at IAUNAM, the mechanics in Germany, and the camera and CCD system in Texas. The LRS is a grism spectrograph with three modes of operation: imaging, longslit, and multi-object. The field of view of the HET is 4 arcmin in diameter, and the LRS will have a 13-slitlet Multi Object Spectroscopy (MOS) unit covering this field. The MOS unit is based on miniature components and is remotely configurable under computer control. Resolving powers between R equals (lambda) /(Delta) (lambda) approximately 600 and 3000 with a 1 arcsecond wide slit will be achieved with a variety of grisms, of which two can be carried by the instrument at any one time. The CCD is a Ford Aerospace 3072 X 1024 device with 15 micrometer pixels, and the image scale is approximately 0.25 arcsec per pixel. Here we present a detailed description of the LRS, and provide an overview of the optical and mechanical aspects of its design (which are discussed in detail elsewhere in these proceedings). Fabrication, assembly, and testing of the LRS will be completed by mid 1998. First light for the LRS on the HET is expected in the

  1. Progress in low-resolution ab initio phasing with CrowdPhase

    PubMed Central

    Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.

    2016-01-01

    Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data. PMID:26960132

  2. Progress in low-resolution ab initio phasing with CrowdPhase.

    PubMed

    Jorda, Julien; Sawaya, Michael R; Yeates, Todd O

    2016-03-01

    Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data. PMID:26960132

  3. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

    PubMed Central

    Headd, Jeffrey J.; Echols, Nathaniel; Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Chen, Vincent B.; Moriarty, Nigel W.; Richardson, David C.; Richardson, Jane S.; Adams, Paul D.

    2012-01-01

    Traditional methods for macromolecular refinement often have limited success at low resolution (3.0–3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine. Firstly, a ‘reference-model’ method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a ϕ,ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from non­redundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R free and a decreased gap between R work and R free. PMID:22505258

  4. Single-Shot Rotational Raman Thermometry for Turbulent Flames Using a Low-Resolution Bandwidth Technique

    NASA Technical Reports Server (NTRS)

    Kojima, Jun; Nguyen, Quang-Viet

    2007-01-01

    An alternative optical thermometry technique that utilizes the low-resolution (order 10(exp 1)/cm) pure-rotational spontaneous Raman scattering of air is developed to aid single-shot multiscalar measurements in turbulent combustion studies. Temperature measurements are realized by correlating the measured envelope bandwidth of the pure-rotational manifold of the N2/O2 spectrum with a theoretical prediction of a species-weighted bandwidth. By coupling this thermometry technique with conventional vibrational Raman scattering for species determination, we demonstrate quantitative spatially resolved, single-shot measurements of the temperature and fuel/oxidizer concentrations in a high-pressure turbulent Cf4-air flame. Our technique provides not only an effective means of validating other temperature measurement methods, but also serves as a secondary thermometry technique in cases where the anti-Stokes vibrational N2 Raman signals are too low for a conventional vibrational temperature analysis.

  5. Low-resolution electromagnetic tomography (LORETA) of cerebral activity in chronic depressive disorder.

    PubMed

    Lubar, Joel F; Congedo, Marco; Askew, John H

    2003-09-01

    In this study we compared the current density power and power asymmetry in 15 right-handed, medication-free chronically depressed females (of the unipolar type) and age-matched non-clinical female controls. We used frequency domain LORETA (Low-Resolution Electromagnetic Tomography). In the interhemispheric asymmetry analysis, compared with the control group, the depression group exhibited a left-to-right Alpha2 (10-12 Hz) current density dominance in the left postcentral gyrus. The pattern of left-to-right dominance included frontal (especially medial and middle frontal gyri) and temporal locations. The between groups comparison of spectral power revealed decreased activity in the right middle temporal gyrus in the depressed group. The decrease emerged in the whole frequency spectrum analyzed (2-32 Hz), although it reached significance in the Delta (2-3.5 Hz) band only. These findings are discussed in terms of the existing literature on affect using EEG, PET and SPECT.

  6. On the utility of low resolution IUE spectroscopy of the 2800 A Mg II lines as a stellar chromosphere indicator

    NASA Technical Reports Server (NTRS)

    Smith, Graeme H.; Burstein, David; Fanelli, Michael N.; O'Connell, Robert W.; Wu, C.-C.

    1991-01-01

    Low resolution IUE spectroscopy of the 2800-A Mg II h and k lines is shown to provide a useful means for documenting chromospheric activity among relatively young dwarf stars. An index I(Mg II) has been defined which measures the integrated flux in the region 2784-2814 A relative to the flux interpolated from nearby comparison regions. Values of this index have been derived from low resolution IUE spectra for a sample of field dwarfs for which Ca II H and K line indices have been published as part of the Mount Wilson HK program. The large range in chromospheric activity among field dwarfs that is exhibited by the Mount Wilson Ca II S index is found to also be reflected by the lower resolution I(Mg II) index. Using an age calibration of Ca II emission line strengths derived by Barry, it is found that the value of I(Mg II) can be used to distinguish between dwarfs younger and older than 3 Gyr. The low resolution nature of the I(Mg II) index means that it holds potential for use as an age diagnostic for stellar population studies. Among dwarfs of age greater than 3 Gyr there is some evidence that this Mg II index is affected by line blanketing.

  7. High Resolution Image Reconstruction from Projection of Low Resolution Images DIffering in Subpixel Shifts

    NASA Technical Reports Server (NTRS)

    Mareboyana, Manohar; Le Moigne-Stewart, Jacqueline; Bennett, Jerome

    2016-01-01

    In this paper, we demonstrate a simple algorithm that projects low resolution (LR) images differing in subpixel shifts on a high resolution (HR) also called super resolution (SR) grid. The algorithm is very effective in accuracy as well as time efficiency. A number of spatial interpolation techniques using nearest neighbor, inverse-distance weighted averages, Radial Basis Functions (RBF) etc. used in projection yield comparable results. For best accuracy of reconstructing SR image by a factor of two requires four LR images differing in four independent subpixel shifts. The algorithm has two steps: i) registration of low resolution images and (ii) shifting the low resolution images to align with reference image and projecting them on high resolution grid based on the shifts of each low resolution image using different interpolation techniques. Experiments are conducted by simulating low resolution images by subpixel shifts and subsampling of original high resolution image and the reconstructing the high resolution images from the simulated low resolution images. The results of accuracy of reconstruction are compared by using mean squared error measure between original high resolution image and reconstructed image. The algorithm was tested on remote sensing images and found to outperform previously proposed techniques such as Iterative Back Projection algorithm (IBP), Maximum Likelihood (ML), and Maximum a posterior (MAP) algorithms. The algorithm is robust and is not overly sensitive to the registration inaccuracies.

  8. High resolution image reconstruction from projection of low resolution images differing in subpixel shifts

    NASA Astrophysics Data System (ADS)

    Mareboyana, Manohar; Le Moigne, Jacqueline; Bennett, Jerome

    2016-05-01

    In this paper, we demonstrate simple algorithms that project low resolution (LR) images differing in subpixel shifts on a high resolution (HR) also called super resolution (SR) grid. The algorithms are very effective in accuracy as well as time efficiency. A number of spatial interpolation techniques using nearest neighbor, inverse-distance weighted averages, Radial Basis Functions (RBF) etc. are used in projection. For best accuracy of reconstructing SR image by a factor of two requires four LR images differing in four independent subpixel shifts. The algorithm has two steps: i) registration of low resolution images and (ii) shifting the low resolution images to align with reference image and projecting them on high resolution grid based on the shifts of each low resolution image using different interpolation techniques. Experiments are conducted by simulating low resolution images by subpixel shifts and subsampling of original high resolution image and the reconstructing the high resolution images from the simulated low resolution images. The results of accuracy of reconstruction are compared by using mean squared error measure between original high resolution image and reconstructed image. The algorithm was tested on remote sensing images and found to outperform previously proposed techniques such as Iterative Back Projection algorithm (IBP), Maximum Likelihood (ML) algorithms. The algorithms are robust and are not overly sensitive to the registration inaccuracies.

  9. On the calibration of the IRAS low-resolution spectra

    NASA Technical Reports Server (NTRS)

    Volk, Kevin; Cohen, Martin

    1989-01-01

    The need for corrections to the LRS spectra based on a study of a number of normal stars observed by IRAS is discussed. The spectra of bright stars, such as alpha CMa, were found to be inconsistent with blackbody sources, this effect being generally observed in sources earlier than about K3. An attempt is made to correct the LRS spectra by changing the blackbody calibration temperature for Alpha Tau, assumed to be a 10,000-K blackbody source for the original LRS flux calibration. It is found that an anomalously low color temperature must be assumed for alpha Tau to produce reasonable results for earlier-type stars. Corrections based on a set of stars with well-determined effective temperatures are examined, as are the resulting color temperatures for 72 stars with Atlas spectra.

  10. CARMENES input catalogue of M dwarfs. I. Low-resolution spectroscopy with CAFOS

    NASA Astrophysics Data System (ADS)

    Alonso-Floriano, F. J.; Morales, J. C.; Caballero, J. A.; Montes, D.; Klutsch, A.; Mundt, R.; Cortés-Contreras, M.; Ribas, I.; Reiners, A.; Amado, P. J.; Quirrenbach, A.; Jeffers, S. V.

    2015-05-01

    Context. CARMENES is a stabilised, high-resolution, double-channel spectrograph at the 3.5 m Calar Alto telescope. It is optimally designed for radial-velocity surveys of M dwarfs with potentially habitable Earth-mass planets. Aims: We prepare a list of the brightest, single M dwarfs in each spectral subtype observable from the northern hemisphere, from which we will select the best planet-hunting targets for CARMENES. Methods: In this first paper on the preparation of our input catalogue, we compiled a large amount of public data and collected low-resolution optical spectroscopy with CAFOS at the 2.2 m Calar Alto telescope for 753 stars. We derived accurate spectral types using a dense grid of standard stars, a double least-squares minimisation technique, and 31 spectral indices previously defined by other authors. Additionally, we quantified surface gravity, metallicity, and chromospheric activity for all the stars in our sample. Results: We calculated spectral types for all 753 stars, of which 305 are new and 448 are revised. We measured pseudo-equivalent widths of Hα for all the stars in our sample, concluded that chromospheric activity does not affect spectral typing from our indices, and tabulated 49 stars that had been reported to be young stars in open clusters, moving groups, and stellar associations. Of the 753 stars, two are new subdwarf candidates, three are T Tauri stars, 25 are giants, 44 are K dwarfs, and 679 are M dwarfs. Many of the 261 investigated dwarfs in the range M4.0-8.0 V are among the brightest stars known in their spectral subtype. Conclusions: This collection of low-resolution spectroscopic data serves as a candidate target list for the CARMENES survey and can be highly valuable for other radial-velocity surveys of M dwarfs and for studies of cool dwarfs in the solar neighbourhood. Full Tables A.1, A.2, and A.3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc

  11. [The radial velocity measurement accuracy of different spectral type low resolution stellar spectra at different signal-to-noise ratio].

    PubMed

    Wang, Feng-Fei; Luo, A-Li; Zhao, Yong-Heng

    2014-02-01

    The radial velocity of the star is very important for the study of the dynamics structure and chemistry evolution of the Milky Way, is also an useful tool for looking for variable or special objects. In the present work, we focus on calculating the radial velocity of different spectral types of low-resolution stellar spectra by adopting a template matching method, so as to provide effective and reliable reference to the different aspects of scientific research We choose high signal-to-noise ratio (SNR) spectra of different spectral type stellar from the Sloan Digital Sky Survey (SDSS), and add different noise to simulate the stellar spectra with different SNR. Then we obtain theradial velocity measurement accuracy of different spectral type stellar spectra at different SNR by employing a template matching method. Meanwhile, the radial velocity measurement accuracy of white dwarf stars is analyzed as well. We concluded that the accuracy of radial velocity measurements of early-type stars is much higher than late-type ones. For example, the 1-sigma standard error of radial velocity measurements of A-type stars is 5-8 times as large as K-type and M-type stars. We discuss the reason and suggest that the very narrow lines of late-type stars ensure the accuracy of measurement of radial velocities, while the early-type stars with very wide Balmer lines, such as A-type stars, become sensitive to noise and obtain low accuracy of radial velocities. For the spectra of white dwarfs stars, the standard error of radial velocity measurement could be over 50 km x s(-1) because of their extremely wide Balmer lines. The above conclusion will provide a good reference for stellar scientific study. PMID:24822441

  12. [The radial velocity measurement accuracy of different spectral type low resolution stellar spectra at different signal-to-noise ratio].

    PubMed

    Wang, Feng-Fei; Luo, A-Li; Zhao, Yong-Heng

    2014-02-01

    The radial velocity of the star is very important for the study of the dynamics structure and chemistry evolution of the Milky Way, is also an useful tool for looking for variable or special objects. In the present work, we focus on calculating the radial velocity of different spectral types of low-resolution stellar spectra by adopting a template matching method, so as to provide effective and reliable reference to the different aspects of scientific research We choose high signal-to-noise ratio (SNR) spectra of different spectral type stellar from the Sloan Digital Sky Survey (SDSS), and add different noise to simulate the stellar spectra with different SNR. Then we obtain theradial velocity measurement accuracy of different spectral type stellar spectra at different SNR by employing a template matching method. Meanwhile, the radial velocity measurement accuracy of white dwarf stars is analyzed as well. We concluded that the accuracy of radial velocity measurements of early-type stars is much higher than late-type ones. For example, the 1-sigma standard error of radial velocity measurements of A-type stars is 5-8 times as large as K-type and M-type stars. We discuss the reason and suggest that the very narrow lines of late-type stars ensure the accuracy of measurement of radial velocities, while the early-type stars with very wide Balmer lines, such as A-type stars, become sensitive to noise and obtain low accuracy of radial velocities. For the spectra of white dwarfs stars, the standard error of radial velocity measurement could be over 50 km x s(-1) because of their extremely wide Balmer lines. The above conclusion will provide a good reference for stellar scientific study.

  13. Localization of MDMA-induced brain activity in healthy volunteers using low resolution brain electromagnetic tomography (LORETA).

    PubMed

    Frei, E; Gamma, A; Pascual-Marqui, R; Lehmann, D; Hell, D; Vollenweider, F X

    2001-11-01

    3,4-Methylenedioxymethamphetamine (MDMA; 'Ecstasy') is a psychostimulant drug producing heightened mood and facilitated social communication. In animal studies, MDMA effects are primarily mediated by serotonin (5-HT), but also by dopamine (DA) and possibly noradrenaline (NA). In humans, however, the neurochemical and neurophysiological basis of acute MDMA effects remains unknown. The distribution of active neuronal populations after administration of a single dose of MDMA (1.7 mg/kg) or placebo was studied in 16 healthy, MDMA-naïve volunteers. Thirty-one-channel scalp EEGs during resting with open and closed eyes was analyzed in the different EEG frequency bands. Scalp maps of power showed significant, global differences between MDMA and placebo in both eye conditions and all frequency bands. Low resolution brain electromagnetic tomography (LORETA) was used to compute 3D, functional images of electric neuronal activity from the scalp EEG data. MDMA produced a widespread decrease of slow and medium frequency activity and an increase of fast frequency activity in the anterior temporal and posterior orbital cortex, concomitant with a marked enhancement of mood, emotional arousal and increased extraversion. This activation of frontotemporal areas indicates that the observed enhancement of mood and possibly the increased extroversion rely on modulation of limbic orbitofrontal and anterotemporal structures known to be involved in emotional processes. Comparison of the MDMA-specific EEG pattern with that of various 5-HT, DA, and NA agonists indicates that serotonin, noradrenaline, and, to a lesser degree, dopamine, contribute to the effects of MDMA on EEG, and possibly also on mood and behavior.

  14. Low resolution scanning electron microscopy of cerebellar neurons and neuroglial cells of the granular layer.

    PubMed

    Castejón, O J

    1984-01-01

    Teleost fishes, Arius Spixii and Salmo trout and adult Swiss albino mice have been processed with the freeze-fracture technique for SEM to explore the inner cytoplasmic and nuclear surface details of neurons and neuroglial cells. The specimens were fixed by vascular perfusion with Karnovsky fixative and 2-3 mm thick cerebellar slices were subsequently fixed by immersion in the same fixative. They were postfixed in osmium tetroxide, dehydrated in ethanol, frozen in Freon 22, cooled by liquid nitrogen and fractured. After thawing in ethanol, they were critically point dried, coated with gold-palladium and viewed by SEM. The surface features of perikaryon were examined at low resolution and magnifications. The image of endoplasmic reticulum, GERL complex and chromatin were described in fractured cerebellar neurons (granule and Golgi cells). The fractured protoplasmic astrocytes displayed a characteristic glass surface appearance of cytoplasmic body and processes, which facilitated their recognition at the neuropile and perivascular region. The oligodendrocytes appeared as fusiform cells depicting a thin rim of perinuclear cytoplasm. The surface view of endoplasmic reticulum was well studied at the nuclear poles. Fine cytoplasmic beaded canaliculi appeared connecting the outer surface of nuclear envelope with the plasma membrane inner surface. The nucleus exhibited well developed peripheral heterochromatin masses forming anastomotic bands separated by vacuolar spaces. The SEM nerve and neuroglial cell fractographs were compared with similar images obtained by conventional transmission electron microscopy and freeze etching technique. PMID:6505621

  15. Low-Resolution Spectrum of the Extragalactic Background Light with the AKARI InfraRed Camera

    NASA Astrophysics Data System (ADS)

    Tsumura, Kohji; Matsumoto, Toshio; Matsuura, Shuji; Sakon, Itsuki; Wada, Takehiko

    2013-12-01

    The Extragalactic Background Light (EBL) as integrated light from outside of our Galaxy includes information about the early universe and the Dark Ages. We analyzed spectral data of the astrophysical diffuse emission obtained with the low-resolution spectroscopy mode on the AKARI Infra-Red Camera (IRC) in the 1.8-5.3μm wavelength region. Although previous EBL observations in this wavelength region were restricted to observations by DIRBE and IRTS, this study adds a new independent result with negligible contamination of Galactic stars owing to higher sensitivity for point sources. Two other major foreground components, zodiacal light (ZL) and diffuse Galactic light (DGL), were subtracted by taking correlations with ZL brightness estimated by the DIRBE ZL model and with the 100μm dust thermal emission, respectively. The isotropic emission was obtained as EBL, which shows significant excess over integrated light of galaxies at < 4μm. The obtained EBL is consistent with the previous measurements by IRTS and DIRBE.

  16. LAMOST OBSERVATIONS IN THE KEPLER FIELD. I. DATABASE OF LOW-RESOLUTION SPECTRA

    SciTech Connect

    Cat, P. De; Ren, A. B.; Yang, X. H.; Fu, J. N.; Shi, J. R.; Luo, A. L.; Yang, M.; Wang, J. L.; Zhang, H. T.; Shi, H. M.; Zhang, W.; Dong, Subo; Catanzaro, G.; Frasca, A.; Corbally, C. J.; Gray, R. O.; Żakowicz, J. Molenda-; Uytterhoeven, K.; Briquet, M.; Bruntt, H.; and others

    2015-09-15

    The nearly continuous light curves with micromagnitude precision provided by the space mission Kepler are revolutionizing our view of pulsating stars. They have revealed a vast sea of low-amplitude pulsation modes that were undetectable from Earth. The long time base of Kepler light curves allows for the accurate determination of the frequencies and amplitudes of pulsation modes needed for in-depth asteroseismic modeling. However, for an asteroseismic study to be successful, the first estimates of stellar parameters need to be known and they cannot be derived from the Kepler photometry itself. The Kepler Input Catalog provides values for the effective temperature, surface gravity, and metallicity, but not always with sufficient accuracy. Moreover, information on the chemical composition and rotation rate is lacking. We are collecting low-resolution spectra for objects in the Kepler field of view with the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (lamost, Xinglong observatory, China). All of the requested fields have now been observed at least once. In this paper, we describe those observations and provide a useful database for the whole astronomical community.

  17. Temperatures and metallicities of M giants in the Galactic bulge from low-resolution K-band spectra

    NASA Astrophysics Data System (ADS)

    Schultheis, M.; Ryde, N.; Nandakumar, G.

    2016-05-01

    Context. With the existing and upcoming large multifibre low-resolution spectrographs, the question arises of how precise stellar parameters such as Teff and [Fe/H] can be obtained from low-resolution K-band spectra with respect to traditional photometric temperature measurements. Until now, most of the effective temperatures in Galactic bulge studies come directly from photometric techniques. Uncertainties in interstellar reddening and in the assumed extinction law could lead to large systematic errors (>200 K). Aims: We obtain and calibrate the relation between Teff and the 12CO first overtone bands for M giants in the Galactic bulge covering a wide range in metallicity. Methods: We used low-resolution spectra for 20 M giants with well-studied parameters from photometric measurements covering the temperature range 3200 study the behaviour of Teff and [Fe/H] on the spectral indices. Results: We find a tight relation between Teff and the 12CO(2-0) band with a dispersion of 95 K and between Teff and the 12CO(3-1) with a dispersion of 120 K. We do not find any dependence of these relations on the metallicity of the star, which makes them attractive for Galactic bulge studies. This relation is also not sensitive to the spectral resolution, which allows this relation to be applied in a more general way. We also find a correlation between the combination of the Na i, Ca i, and the 12CO band with the metallicity of the star. However, this relation is only valid for subsolar metallicities. Conclusions: We show that low-resolution spectra provide a powerful tool for obtaining effective temperatures of M giants. We show that this relation does not depend on the metallicity of the star within the investigated range and is also applicable to different spectral resolutions making this relation in general useful for deriving effective temperatures in high-extinction regions where photometric temperatures

  18. Low-resolution mid-infrared reflection analysis for discernment of contaminants in seed cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Contaminants often decrease cotton quality, which subsequently decrease cotton profitability. In this research, a low-resolution mid-infrared reflection instrument was designed and constructed by using only four different wavelengths to accomplish good separation of cotton samples from 14 contaminan...

  19. How to beat the low resolution of multilayer mirror spectra (invited)

    SciTech Connect

    Regan, S.P.; Fournier, K.B.; May, M.J.; Soukhanovskii, V.; Finkenthal, M.; Moos, H.W.

    1997-01-01

    The soft x-ray and extreme ultraviolet (XUV) impurity emissions from tokamaks (10 {Angstrom}{lt}{lambda}{lt}304 {Angstrom}) have been extensively studied with high-resolution grazing incidence spectrographs, and atomic physics models predicting spectral line brightnesses have been benchmarked against these experimental data. This, together with the ability to perform large amounts of accurate atomic physics computations, enables the relaxation on the requirement for high resolution spectra. The multilayer mirror (MLM) is a low resolving power ({lambda}/{delta}{lambda}{lt}100) XUV dispersive/reflective optical element that obeys the Bragg law of reflection. MLM based monitors are compact, high-photon-throughput diagnostics capable of extracting XUV emissions of impurities from the harsh environment of large fusion reactor-type devices. We will show how atomic physics modeling can be used to extract the XUV spectral line brightnesses measured with low-resolution, high-photon-throughput, MLM-based devices. The Plasma Spectroscopy Group at The Johns Hopkins University has investigated the application of MLM based diagnostics for magnetically confined fusion plasmas: MLM based monitors have been constructed for and extensively used on DIII{endash}D, Alcator C-Mod, TEXT, Phaedrus-T, and CDX-U to study the impurity behavior of elements ranging from He to Mo. Experiments were also performed in which MLMs were irradiated to a fast neutron fluence of 1.1{times}10{sup 19} ncm{sup {minus}2} at 270{endash}300{degree}C, and the preliminary results indicate that MLMs would be a good first wall reflector for fusion plasmas. Future applications of MLM based devices to study divertor coolants (Ne, Ar, and Kr emissions) and {open_quotes}killer pellet{close_quotes} (W emissions) experiments will also be discussed. {copyright} {ital 1997 American Institute of Physics.}

  20. Structural Studies of Archaealthermophilic Adenylate Kinase

    SciTech Connect

    Konisky, J.

    2002-07-10

    Through this DOE-sponsored program Konisky has studied the evolution and molecular biology of microbes that live in extreme environments. The emphasis of this work has been the determination of the structural features of thermophilic enzymes that allow them to function optimally at near 100 C. The laboratory has focused on a comparative study of adenylate kinase (ADK), an enzyme that functions to interconvert adenine nucleotides. Because of the close phylogenetic relatedness of members of the Methanococci, differences in the structure of their ADKs will be dominated by structural features that reflect contributions to their optimal temperature for activity, rather than differences due to phylogenetic divergence. We have cloned, sequenced and modeled the secondary structure for several methanococcal ADKs. Using molecular modeling threading approaches that are based on the solved structure for the porcine ADK, we have also proposed a general low resolution three dimensional structure for each of the methanococcal enzymes. These analyses have allowed us to propose structural features that confer hyperthermoactivity to those enzymes functioning in the hyperthermophilic members of the Methanococci. Using protein engineering methodologies, we have tested our hypotheses by examining the effects of selective structural changes on thermoactivity. Despite possessing between 68-81% sequence identity, the methanococcal AKs had significantly different stability against thermal denaturation, with melting points ranging from 69-103 C. The construction of several chimerical AKs by linking regions of the MVO and MJA AKs demonstrated the importance of cooperative interactions between amino- and carboxyl-terminal regions in influencing thermostability. Addition of MJA terminal fragments to the MVO AK increased thermal stability approximately 20 C while maintaining 88% of the mesophilic sequence. Further analysis using structural models suggested that hydrophobic interactions are

  1. Pedestrian Detection and Tracking from Low-Resolution Unmanned Aerial Vehicle Thermal Imagery

    PubMed Central

    Ma, Yalong; Wu, Xinkai; Yu, Guizhen; Xu, Yongzheng; Wang, Yunpeng

    2016-01-01

    Driven by the prominent thermal signature of humans and following the growing availability of unmanned aerial vehicles (UAVs), more and more research efforts have been focusing on the detection and tracking of pedestrians using thermal infrared images recorded from UAVs. However, pedestrian detection and tracking from the thermal images obtained from UAVs pose many challenges due to the low-resolution of imagery, platform motion, image instability and the relatively small size of the objects. This research tackles these challenges by proposing a pedestrian detection and tracking system. A two-stage blob-based approach is first developed for pedestrian detection. This approach first extracts pedestrian blobs using the regional gradient feature and geometric constraints filtering and then classifies the detected blobs by using a linear Support Vector Machine (SVM) with a hybrid descriptor, which sophisticatedly combines Histogram of Oriented Gradient (HOG) and Discrete Cosine Transform (DCT) features in order to achieve accurate detection. This research further proposes an approach for pedestrian tracking. This approach employs the feature tracker with the update of detected pedestrian location to track pedestrian objects from the registered videos and extracts the motion trajectory data. The proposed detection and tracking approaches have been evaluated by multiple different datasets, and the results illustrate the effectiveness of the proposed methods. This research is expected to significantly benefit many transportation applications, such as the multimodal traffic performance measure, pedestrian behavior study and pedestrian-vehicle crash analysis. Future work will focus on using fused thermal and visual images to further improve the detection efficiency and effectiveness. PMID:27023564

  2. LRS2: the new facility low resolution integral field spectrograph for the Hobby-Eberly telescope

    NASA Astrophysics Data System (ADS)

    Chonis, Taylor S.; Hill, Gary J.; Lee, Hanshin; Tuttle, Sarah E.; Vattiat, Brian L.

    2014-07-01

    The second generation Low Resolution Spectrograph (LRS2) is a new facility instrument for the Hobby-Eberly Telescope (HET). Based on the design of the Visible Integral-field Replicable Unit Spectrograph (VIRUS), which is the new flagship instrument for carrying out the HET Dark Energy Experiment (HETDEX), LRS2 provides integral field spectroscopy for a seeing-limited field of 12" x 6". For LRS2, the replicable design of VIRUS has been leveraged to gain broad wavelength coverage from 370 nm to 1.0 μm, spread between two fiber-fed dual- channel spectrographs, each of which can operate as an independent instrument. The blue spectrograph, LRS2-B, covers 370 λ (nm) <= 470 and 460 <= λ (nm) <= 700 at fixed resolving powers of R = λ/δλ ≍ 1900 and 1100, respectively, while the red spectrograph, LRS2-R, covers 650 <= λ (nm) <= 842 and 818 <= λ (nm) <= 1050 with both of its channels having R ≍ 1800. In this paper, we present a detailed description of the instrument's design in which we focus on the departures from the basic VIRUS framework. The primary modifications include the fore-optics that are used to feed the fiber integral field units at unity fill-factor, the cameras' correcting optics and detectors, and the volume phase holographic grisms. We also present a model of the instrument's sensitivity and a description of specific science cases that have driven the design of LRS2, including systematically studying the spatially resolved properties of extended Lyα blobs at 2 < z < 3. LRS2 will provide a powerful spectroscopic follow-up platform for large surveys such as HETDEX.

  3. HETDEX: Developing the HET's Second Generation Low Resolution Spectrograph for Probing Lyman-alpha Emitting Galaxies

    NASA Astrophysics Data System (ADS)

    Chonis, Taylor S.; Hill, G. J.; Lee, H.; Tuttle, S. E.; Vattiat, B. L.; Gebhardt, K.; Finkelstein, S. L.; Adams, J. J.; HETDEX Collaboration

    2012-01-01

    HETDEX will map the power spectrum of 0.8 million blindly discovered Lyman-alpha Emitting Galaxies (LAE) using a revolutionary new array of massively replicated fiber-fed spectrographs dubbed the Visible Integral-Field Replicable Unit Spectrograph (VIRUS). In the era of the Hobby-Eberly Telescope wide-field upgrade and VIRUS, the current Low Resolution Spectrograph (LRS) must be replaced with a fiber instrument. We discuss the development of the second generation LRS (LRS2), which is a multi-channel instrument based on the VIRUS design. In its current design phase, it is fed by a 287 fiber microlens coupled integral field unit that covers 7” x 12” with 0.62” resolution. The instrument covers 3720 Å to 4700 Å at R ≈ 1900 and 4600 Å to 7000 Å at R ≈1200. With the purpose of making the instrument ideal for follow-up observations of LAE in the HETDEX survey, we discuss the science drivers for selecting the instrument's spectral resolution. We test the utility of the instrument and pilot a future study with LRS2 by presenting R ≈ 2000 spectra taken with the VIRUS prototype spectrograph (VIRUS-P) in a high-resolution mode at the McDonald Observatory Harlan J. Smith 2.7 m telescope. These LAE were originally discovered in the HETDEX Pilot Survey and their Lyman-alpha line profiles are constrained by near-infrared observations of rest-frame optical emission lines that set the systemic redshift of the galaxies. We discuss the velocity offsets of the Lyman-alpha line from the systemic line center and compare the line profiles to theoretical predictions and to similar observations for Lyman-break galaxies. Our observations provide an example of how LRS2 can be used to probe Lyman-alpha emission in 2 < z < 3 star forming galaxies.

  4. Calibration And Validation Of CryoSat-2 Low Resolution Mode Data

    NASA Astrophysics Data System (ADS)

    Naeije, M.; Schrama, E.; Scharroo, R.

    2011-02-01

    Running ahead of the continuously growing need for operational use of sea level products, TUDelft started off the Radar Altimeter Database System RADS many years ago. This system attends to a global international sea- level service. It supports, on one hand, science, like studies on ocean circulation, El Nio, sea level change, and ice topography, and on the other hand (offshore) operations, like delivery of ocean current information, wind and wave statistics, ice detection and ice classification. At present, the database is used by a large scientific community throughout the world, and is daily maintained and developed by Altimetrics LLC, TUDelft and NOAA. It contains all historic altimeter data, and now has to be up- dated with the data from ESAs ice mission CryoSat-2, which was launched successfully in April 2010. These new data are important to augment the data set and by that to improve the estimates of sea level change and its contributors. For this the data have to be validated and calibrated, necessary corrections added and improved (including modelling of corrections that are not directly available from the CryoSat-2 platform), and the orbit ac- curacy verified and if possible the orbits brushed up. Subsequently, value-added ocean and ice products need to be developed in synergy with all the other satellite altimeter data. During the commissioning phase we primarily looked at the sanity of the available level-1b and level-2 Low Resolution Mode (LRM) data. Here, for the 2011 CryoSat Validation Workshop, we present the results of our calibration and validation of LRM L2 data by internal comparison of CryoSat-2 and external comparison with other satellites. We have established a range bias of 3.77 (measurement range too long) and a timing bias of 8.2ms (measurement range too late).

  5. Pedestrian Detection and Tracking from Low-Resolution Unmanned Aerial Vehicle Thermal Imagery.

    PubMed

    Ma, Yalong; Wu, Xinkai; Yu, Guizhen; Xu, Yongzheng; Wang, Yunpeng

    2016-01-01

    Driven by the prominent thermal signature of humans and following the growing availability of unmanned aerial vehicles (UAVs), more and more research efforts have been focusing on the detection and tracking of pedestrians using thermal infrared images recorded from UAVs. However, pedestrian detection and tracking from the thermal images obtained from UAVs pose many challenges due to the low-resolution of imagery, platform motion, image instability and the relatively small size of the objects. This research tackles these challenges by proposing a pedestrian detection and tracking system. A two-stage blob-based approach is first developed for pedestrian detection. This approach first extracts pedestrian blobs using the regional gradient feature and geometric constraints filtering and then classifies the detected blobs by using a linear Support Vector Machine (SVM) with a hybrid descriptor, which sophisticatedly combines Histogram of Oriented Gradient (HOG) and Discrete Cosine Transform (DCT) features in order to achieve accurate detection. This research further proposes an approach for pedestrian tracking. This approach employs the feature tracker with the update of detected pedestrian location to track pedestrian objects from the registered videos and extracts the motion trajectory data. The proposed detection and tracking approaches have been evaluated by multiple different datasets, and the results illustrate the effectiveness of the proposed methods. This research is expected to significantly benefit many transportation applications, such as the multimodal traffic performance measure, pedestrian behavior study and pedestrian-vehicle crash analysis. Future work will focus on using fused thermal and visual images to further improve the detection efficiency and effectiveness. PMID:27023564

  6. Efficient simultaneous image deconvolution and upsampling algorithm for low-resolution microwave sounder data

    NASA Astrophysics Data System (ADS)

    Qin, Jing; Yanovsky, Igor; Yin, Wotao

    2015-01-01

    Microwave imaging has been widely used in the prediction and tracking of hurricanes, typhoons, and tropical storms. Due to the limitations of sensors, the acquired remote sensing data are usually blurry and have relatively low resolution, which calls for the development of fast algorithms for deblurring and enhancing the resolution. We propose an efficient algorithm for simultaneous image deconvolution and upsampling for low-resolution microwave hurricane data. Our model involves convolution, downsampling, and the total variation regularization. After reformulating the model, we are able to apply the alternating direction method of multipliers and obtain three subproblems, each of which has a closed-form solution. We also extend the framework to the multichannel case with the multichannel total variation regularization. A variety of numerical experiments on synthetic and real Advanced Microwave Sounding Unit and Microwave Humidity Sounder data were conducted. The results demonstrate the outstanding performance of the proposed method.

  7. Subspace-Based Holistic Registration for Low-Resolution Facial Images

    NASA Astrophysics Data System (ADS)

    Boom, B. J.; Spreeuwers, L. J.; Veldhuis, R. N. J.

    2010-12-01

    Subspace-based holistic registration is introduced as an alternative to landmark-based face registration, which has a poor performance on low-resolution images, as obtained in camera surveillance applications. The proposed registration method finds the alignment by maximizing the similarity score between a probe and a gallery image. We use a novel probabilistic framework for both user-independent as well as user-specific face registration. The similarity is calculated using the probability that the face image is correctly aligned in a face subspace, but additionally we take the probability into account that the face is misaligned based on the residual error in the dimensions perpendicular to the face subspace. We perform extensive experiments on the FRGCv2 database to evaluate the impact that the face registration methods have on face recognition. Subspace-based holistic registration on low-resolution images can improve face recognition in comparison with landmark-based registration on high-resolution images. The performance of the tested face recognition methods after subspace-based holistic registration on a low-resolution version of the FRGC database is similar to that after manual registration.

  8. Fast and precise iris localization for low-resolution facial images

    NASA Astrophysics Data System (ADS)

    Meng, Chun-Ning; Zhang, Tai-Ning; Zhang, Pin; Chang, Sheng-Jiang

    2012-07-01

    Fast and precise iris localization is a vital technique for face recognition, eye tracking, and gaze estimation. Low-resolution images bring about great difficulties for locating the iris precisely by traditional methods. In this paper, a fast and robust method to precisely detect the position and contour of the irises in low-resolution facial images is presented. A three-step coarse-to-fine strategy is employed. First, a gradient integral projection function is proposed to roughly detect the eye region, and the vertical integral projection function is adopted to select several possible vertical boundaries of the irises. Second, we have proposed a novel rectangular integro-variance operator to precisely locate both of the irises. Finally, the localization results are verified by two simple heuristic rules. A novel and more rigorous criterion is also proposed to evaluate the performance of the algorithm. Comparison experiments on images from the FERET and the Extended YaleB databases demonstrate that our method is more robust than traditional methods to scale variation, illumination changes, part occlusion, and limited changes of head poses in low-resolution facial images.

  9. Evaluating low-resolution tomography neurofeedback by single dissociation of mental grotation task from stop signal task performance.

    PubMed

    Getter, Nir; Kaplan, Zeev; Todder, Doron

    2015-10-01

    Electroencephalography source localization neurofeedback, i.e Standardized low-resolution tomography (sLORETA) neurofeedback are non-invasive method for altering region specific brain activity. This is an improvement over traditional neurofeedback which were based on recordings from a single scalp-electrode. We proposed three criteria clusters as a methodological framework to evaluate electroencephalography source localization neurofeedback and present relevant data. Our objective was to evaluate standardized low resolution EEG tomography neurofeedback by examining how training one neuroanatomical area effects the mental rotation task (which is related to the activity of bilateral Parietal regions) and the stop-signal test (which is related to frontal structures). Twelve healthy participants were enrolled in a single session sLORETA neurofeedback protocol. The participants completed both the mental rotation task and the stop-signal test before and after one sLORETA neurofeedback session. During sLORETA neurofeedback sessions participants watched one sitcom episode while the picture quality co-varied with activity in the superior parietal lobule. Participants were rewarded for increasing activity in this region only. Results showed a significant reaction time decrease and an increase in accuracy after sLORETA neurofeedback on the mental rotation task but not after stop signal task. Together with behavioral changes a significant activity increase was found at the left parietal brain after sLORETA neurofeedback compared with baseline. We concluded that activity increase in the parietal region had a specific effect on the mental rotation task. Tasks unrelated to parietal brain activity were unaffected. Therefore, sLORETA neurofeedback could be used as a research, or clinical tool for cognitive disorders.

  10. Merging raster meteorological data with low resolution satellite images for improved estimation of actual evapotranspiration

    NASA Astrophysics Data System (ADS)

    Cherif, Ines; Alexandridis, Thomas; Chambel Leitao, Pedro; Jauch, Eduardo; Stavridou, Domna; Iordanidis, Charalampos; Silleos, Nikolaos; Misopolinos, Nikolaos; Neves, Ramiro; Safara Araujo, Antonio

    2013-04-01

    ). A correlation analysis was performed at the common spatial resolution of 1km using selected homogeneous pixels (from the land cover point of view). A statistically significant correlation factor of 0.6 was found, and the RMSE was 0.92 mm/day. Using raster meteorological data the ITA-MyWater algorithms were able to catch the variability of weather patterns over the river basin and thus improved the spatial distribution of evapotranpiration estimations at low resolution. The work presented is part of the FP7-EU project "Merging hydrological models and Earth observation data for reliable information on water - MyWater".

  11. Use of evolutionary information in the fitting of atomic level protein models in low resolution cryo-EM map of a protein assembly improves the accuracy of the fitting.

    PubMed

    Joseph, Agnel P; Swapna, Lakshmipuram S; Rakesh, Ramachandran; Srinivasan, Narayanaswamy

    2016-09-01

    Protein-protein interface residues, especially those at the core of the interface, exhibit higher conservation than residues in solvent exposed regions. Here, we explore the ability of this differential conservation to evaluate fittings of atomic models in low-resolution cryo-EM maps and select models from the ensemble of solutions that are often proposed by different model fitting techniques. As a prelude, using a non-redundant and high-resolution structural dataset involving 125 permanent and 95 transient complexes, we confirm that core interface residues are conserved significantly better than nearby non-interface residues and this result is used in the cryo-EM map analysis. From the analysis of inter-component interfaces in a set of fitted models associated with low-resolution cryo-EM maps of ribosomes, chaperones and proteasomes we note that a few poorly conserved residues occur at interfaces. Interestingly a few conserved residues are not in the interface, though they are close to the interface. These observations raise the potential requirement of refitting the models in the cryo-EM maps. We show that sampling an ensemble of models and selection of models with high residue conservation at the interface and in good agreement with the density helps in improving the accuracy of the fit. This study indicates that evolutionary information can serve as an additional input to improve and validate fitting of atomic models in cryo-EM density maps. PMID:27444391

  12. Use of evolutionary information in the fitting of atomic level protein models in low resolution cryo-EM map of a protein assembly improves the accuracy of the fitting.

    PubMed

    Joseph, Agnel P; Swapna, Lakshmipuram S; Rakesh, Ramachandran; Srinivasan, Narayanaswamy

    2016-09-01

    Protein-protein interface residues, especially those at the core of the interface, exhibit higher conservation than residues in solvent exposed regions. Here, we explore the ability of this differential conservation to evaluate fittings of atomic models in low-resolution cryo-EM maps and select models from the ensemble of solutions that are often proposed by different model fitting techniques. As a prelude, using a non-redundant and high-resolution structural dataset involving 125 permanent and 95 transient complexes, we confirm that core interface residues are conserved significantly better than nearby non-interface residues and this result is used in the cryo-EM map analysis. From the analysis of inter-component interfaces in a set of fitted models associated with low-resolution cryo-EM maps of ribosomes, chaperones and proteasomes we note that a few poorly conserved residues occur at interfaces. Interestingly a few conserved residues are not in the interface, though they are close to the interface. These observations raise the potential requirement of refitting the models in the cryo-EM maps. We show that sampling an ensemble of models and selection of models with high residue conservation at the interface and in good agreement with the density helps in improving the accuracy of the fit. This study indicates that evolutionary information can serve as an additional input to improve and validate fitting of atomic models in cryo-EM density maps.

  13. Mapping permeability in low-resolution micro-CT images: A multiscale statistical approach

    NASA Astrophysics Data System (ADS)

    Botha, Pieter W. S. K.; Sheppard, Adrian P.

    2016-06-01

    We investigate the possibility of predicting permeability in low-resolution X-ray microcomputed tomography (µCT). Lower-resolution whole core images give greater sample coverage and are therefore more representative of heterogeneous systems; however, the lower resolution causes connecting pore throats to be represented by intermediate gray scale values and limits information on pore system geometry, rendering such images inadequate for direct permeability simulation. We present an imaging and computation workflow aimed at predicting absolute permeability for sample volumes that are too large to allow direct computation. The workflow involves computing permeability from high-resolution µCT images, along with a series of rock characteristics (notably open pore fraction, pore size, and formation factor) from spatially registered low-resolution images. Multiple linear regression models correlating permeability to rock characteristics provide a means of predicting and mapping permeability variations in larger scale low-resolution images. Results show excellent agreement between permeability predictions made from 16 and 64 µm/voxel images of 25 mm diameter 80 mm tall core samples of heterogeneous sandstone for which 5 µm/voxel resolution is required to compute permeability directly. The statistical model used at the lowest resolution of 64 µm/voxel (similar to typical whole core image resolutions) includes open pore fraction and formation factor as predictor characteristics. Although binarized images at this resolution do not completely capture the pore system, we infer that these characteristics implicitly contain information about the critical fluid flow pathways. Three-dimensional permeability mapping in larger-scale lower resolution images by means of statistical predictions provides input data for subsequent permeability upscaling and the computation of effective permeability at the core scale.

  14. Expectation values for low resolution flow slit scan prescreening: influence of nuclear shape and DNA density

    SciTech Connect

    Mullaney, P.F.; Mann, R.; Seger, G.; Achatz, M.

    1981-01-01

    High resolution fluorescent image analysis has been conducted with mithramycin stained cells from clinical gynecological specimens. Features characteristic of the usual, low resolution, one dimensional slit-scan flow cytometric measurements were extracted from 250 high resolution nuclear images. In addition to the measurement of the usual parameters, nuclear ellipticity and DNA density (DNA per unit nuclear size) were also determined. Preliminary results indicate both these features offer increased discrimination. When nuclear shape is included as a global feature, at least 77% of the diagnostic cells can be distinguished from normals, with no overlap. Both features hold promise for improving the discrimination possible with flow cytometry.

  15. Compound classification by computer treatment of low resolution mass spectra - Application to geochemical and environmental problems.

    NASA Technical Reports Server (NTRS)

    Smith, D. H.; Eglinton, G.

    1972-01-01

    A description is given of a development of computer analysis of low-resolution chromatographic-mass spectrometric data, which provides a preliminary classification of an unknown spectrum as a listing of candidate classes of compounds. This procedure, referred to as COMSOC (Classification of Mass Spectra on Computers), operates by converting an incoming unknown mass spectrum into a simplified key word which is then compared with each of the key words held in its reference file. The advantages of COMSOC in characterizing complex mixtures are emphasized.

  16. Monitoring the Continuing Spectral Evolution of Nova Delphini 2013 (V339 Del) with Low Resolution Spectroscopy

    NASA Astrophysics Data System (ADS)

    Mooers, H. D.; Wiethoff, W. S.; Evich, A.

    2016-06-01

    The continuing spectral evolution of Nova Delphini 2013 is presented with low-resolution spectroscopy collected with a 100 line per millimeter diffraction grating. Spectra were collected on 3 July, 2014 and 14 September, 2015, +321 and +759 days after peak visible brightness on 16 August, 2013. Imaging system was mounted on an equatorially-mounted, 14-inch Schmidt-Cassegrain telescope. The continuum is no longer visible in the spectra, however, Oiii (5007 Å) and Ha (6563 Å) are prominent and Nii (5755), Hg (4340 Å) and Ciii/Niii (4640 Å) can still be discerned at +759 days.

  17. A model-based approach for detection of objects in low resolution passive millimeter wave images

    NASA Technical Reports Server (NTRS)

    Kasturi, Rangachar; Tang, Yuan-Liang; Devadiga, Sadashiva

    1993-01-01

    A model-based vision system to assist the pilots in landing maneuvers under restricted visibility conditions is described. The system was designed to analyze image sequences obtained from a Passive Millimeter Wave (PMMW) imaging system mounted on the aircraft to delineate runways/taxiways, buildings, and other objects on or near runways. PMMW sensors have good response in a foggy atmosphere, but their spatial resolution is very low. However, additional data such as airport model and approximate position and orientation of aircraft are available. These data are exploited to guide our model-based system to locate objects in the low resolution image and generate warning signals to alert the pilots. Also analytical expressions were derived from the accuracy of the camera position estimate obtained by detecting the position of known objects in the image.

  18. Low Resolution Picture Transmission (LRPT) Demonstration System. Phase II; 1.0

    NASA Technical Reports Server (NTRS)

    Fong, Wai; Yeh, Pen-Shu; Duran, Steve; Sank, Victor; Nyugen, Xuan; Xia, Wei; Day, John H. (Technical Monitor)

    2002-01-01

    Low-Resolution Picture Transmission (LRPT) is a proposed standard for direct broadcast transmission of satellite weather images. This standard is a joint effort by the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and NOAA. As a digital transmission scheme, its purpose is to replace the current analog Automatic Picture Transmission (APT) system for use in the Meteorological Operational (METOP) satellites. GSFC has been tasked to build an LRPT Demonstration System (LDS). Its main objective is to develop or demonstrate the feasibility of a low-cost receiver utilizing a PC as the primary processing component and determine the performance of the protocol in the simulated Radio Frequency (RF) environment. The approach would consist of two phases.

  19. De Novo Correction of Mass Measurement Error in Low Resolution Tandem MS Spectra for Shotgun Proteomics

    NASA Astrophysics Data System (ADS)

    Egertson, Jarrett D.; Eng, Jimmy K.; Bereman, Michael S.; Hsieh, Edward J.; Merrihew, Gennifer E.; MacCoss, Michael J.

    2012-12-01

    We report an algorithm designed for the calibration of low resolution peptide mass spectra. Our algorithm is implemented in a program called FineTune, which corrects systematic mass measurement error in 1 min, with no input required besides the mass spectra themselves. The mass measurement accuracy for a set of spectra collected on an LTQ-Velos improved 20-fold from -0.1776 ± 0.0010 m/z to 0.0078 ± 0.0006 m/z after calibration (avg ± 95 % confidence interval). The precision in mass measurement was improved due to the correction of non-linear variation in mass measurement accuracy across the m/z range.

  20. Compact low resolution spectrograph, an imaging and long slit spectrograph for robotic telescopes

    SciTech Connect

    Rabaza, O.; Zeman, J.; Hudec, R.; Sabau-Graziati, L.

    2013-11-15

    The COmpact LOw REsolution Spectrograph (COLORES) is a compact and lightweight (13 kg) f/8 imaging spectrograph designed for robotic telescopes, now installed and operating on the TELMA, a rapid-slewing 60 cm telescope of the BOOTES-2 observatory in Málaga (Spain). COLORES is a multi-mode instrument that enables the observer to seamlessly switch between low-dispersion spectroscopy and direct imaging modes during an observation. In this paper, we describe the instrument and its development, from the initial scientific requirements through the optical design process to final configuration with theoretical performance calculations. The mechanical and electronic design is described, methods of calibration are discussed and early laboratory and scientific results are shown.

  1. Compact low resolution spectrograph, an imaging and long slit spectrograph for robotic telescopes.

    PubMed

    Rabaza, O; Jelinek, M; Castro-Tirado, A J; Cunniffe, R; Zeman, J; Hudec, R; Sabau-Graziati, L; Ruedas-Sánchez, J

    2013-11-01

    The COmpact LOw REsolution Spectrograph (COLORES) is a compact and lightweight (13 kg) f/8 imaging spectrograph designed for robotic telescopes, now installed and operating on the TELMA, a rapid-slewing 60 cm telescope of the BOOTES-2 observatory in Málaga (Spain). COLORES is a multi-mode instrument that enables the observer to seamlessly switch between low-dispersion spectroscopy and direct imaging modes during an observation. In this paper, we describe the instrument and its development, from the initial scientific requirements through the optical design process to final configuration with theoretical performance calculations. The mechanical and electronic design is described, methods of calibration are discussed and early laboratory and scientific results are shown.

  2. Compact low resolution spectrograph, an imaging and long slit spectrograph for robotic telescopes

    NASA Astrophysics Data System (ADS)

    Rabaza, O.; Jelinek, M.; Castro-Tirado, A. J.; Cunniffe, R.; Zeman, J.; Hudec, R.; Sabau-Graziati, L.; Ruedas-Sánchez, J.

    2013-11-01

    The COmpact LOw REsolution Spectrograph (COLORES) is a compact and lightweight (13 kg) f/8 imaging spectrograph designed for robotic telescopes, now installed and operating on the TELMA, a rapid-slewing 60 cm telescope of the BOOTES-2 observatory in Málaga (Spain). COLORES is a multi-mode instrument that enables the observer to seamlessly switch between low-dispersion spectroscopy and direct imaging modes during an observation. In this paper, we describe the instrument and its development, from the initial scientific requirements through the optical design process to final configuration with theoretical performance calculations. The mechanical and electronic design is described, methods of calibration are discussed and early laboratory and scientific results are shown.

  3. Solar Coronal Structure Study

    NASA Technical Reports Server (NTRS)

    Nitta, Nariaki; Bruner, Marilyn E.; Saba, Julia; Strong, Keith; Harvey, Karen

    2000-01-01

    The subject of this investigation is to study the physics of the solar corona through the analysis of the EUV and UV data produced by two flights (12 May 1992 and 25 April 1994) of the Lockheed Solar Plasma Diagnostics Experiment (SPDE) sounding rocket payload, in combination with Yohkoh and ground-based data. Each rocket flight produced both spectral and imaging data. These joint datasets are useful for understanding the physical state of various features in the solar atmosphere at different heights ranging from the photosphere to the corona at the time of the, rocket flights, which took place during the declining phase of a solar cycle, 2-4 years before the minimum. The investigation is narrowly focused on comparing the physics of small- and medium-scale strong-field structures with that of large-scale, weak fields. As we close th is investigation, we have to recall that our present position in the understanding of basic solar physics problems (such as coronal heating) is much different from that in 1995 (when we proposed this investigation), due largely to the great success of SOHO and TRACE. In other words, several topics and techniques we proposed can now be better realized with data from these missions. For this reason, at some point of our work, we started concentrating on the 1992 data, which are more unique and have more supporting data. As a result, we discontinued the investigation on small-scale structures, i.e., bright points, since high-resolution TRACE images have addressed more important physics than SPDE EUV images could do. In the final year, we still spent long time calibrating the 1992 data. The work was complicated because of the old-fashioned film, which had problems not encountered with more modern CCD detectors. After our considerable effort on calibration, we were able to focus on several scientific topics, relying heavily on the SPDE UV images. They include the relation between filaments and filament channels, the identification of hot

  4. From lows to highs: using low-resolution models to phase X-ray data

    SciTech Connect

    Stuart, David I.; Abrescia, Nicola G. A.

    2013-11-01

    An unusual example of how virus structure determination pushes the limits of the molecular replacement method is presented. The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ∼13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.

  5. From lows to highs: using low-resolution models to phase X-ray data

    PubMed Central

    Stuart, David I.; Abrescia, Nicola G. A.

    2013-01-01

    The study of virus structures has contributed to methodo­logical advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ∼13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis. PMID:24189238

  6. Cell Structure Study.

    ERIC Educational Resources Information Center

    Ekstrom, James V.

    2000-01-01

    Presents an activity in which students use microscopes and digital images to examine Elodea, a fresh water plant, before and after the process of plasmolysis, identify plant cellular structures before and after plasmolysis, and calculate the size of the plant's vacuole. (ASK)

  7. Towards a method to differentiate chronic disorder of consciousness patients' awareness: The Low-Resolution Brain Electromagnetic Tomography Analysis.

    PubMed

    Naro, Antonino; Bramanti, Placido; Leo, Antonino; Cacciola, Alberto; Bramanti, Alessia; Manuli, Alfredo; Calabrò, Rocco Salvatore

    2016-09-15

    Assessing residual signs of awareness in patients suffering from chronic disorders of consciousness (DOC) is a challenging issue. DOC patient behavioral assessment is often doubtful since some individuals may retain covert traces of awareness; thus, some Unresponsive Wakefulness Syndrome (UWS) patients may be misdiagnosed. The aim of our study was to explore possible differences between the source powers within poly-modal cortices to differentiate Minimally Conscious State (MCS) from UWS. To this end, we recorded an electroencephalogram (EEG) during awake resting state and performed a Low-Resolution Brain Electromagnetic Tomography (LORETA), which is a 3D source localization method allowing the visualization of the most probable neuroanatomical generators of EEG differences. MCS and UWS patients showed significant variations concerning the frontal source power of delta-band, frontal and parietal of theta, parietal and occipital of alpha, central of beta, and parietal of gamma, in correlation with the Coma Recovery Scale-Revised (CRS-R) score. The alpha-band was the most significant LORETA data correlating with the consciousness level. In addition, we observed a significant correlation between central beta-peaks and the motor abilities and a dissociation between theta and gamma bands within parietal regions. Our findings suggest that LORETA analysis may be useful in DOC differential diagnosis since distinct neurophysiological correlates in some UWS patients could be used to assess deeper the residual cerebral activity of brain areas responsible for covert awareness. PMID:27538628

  8. Quantitative EEG and Low-Resolution Electromagnetic Tomography (LORETA) Imaging of Patients Undergoing Methadone Treatment for Opiate Addiction.

    PubMed

    Wang, Grace Y; Kydd, Robert R; Russell, Bruce R

    2016-07-01

    Methadone maintenance treatment (MMT) has been used as a treatment for opiate dependence since the mid-1960s. Evidence suggests that methadone binds to mu opiate receptors as do other opiates and induces changes in neurophysiological function. However, little is known, about how neural activity within the higher frequency gamma band (>30 Hz) while at rest changes in those stabilized on MMT despite its association with the excitation-inhibition balance within pyramidal-interneuron networks. Our study investigated differences in resting gamma power (37-41 Hz) between patients undergoing MMT for opiate dependence, illicit opiate users, and healthy controls subjects. Electroencephalographic data were recorded from 26 sites according to the international 10-20 system. Compared with the healthy controls subjects, people either undergoing MMT (mean difference [MD] = 0.32, 95% CI = 0.09-0.55, P < .01) or currently using illicit opiates (MD = 0.31, 95% CI = 0.06-0.56, P = .01) exhibited significant increased gamma power. The sLORETA (standardized low-resolution electromagnetic tomography) between-group comparison revealed dysfunctional neuronal activity in the occipital, parietal, and frontal lobes in the patients undergoing MMT. A more severe profile of dysfunction was observed in those using illicit opiates. Our findings suggest that long-term exposure to opioids is associated with disrupted resting state network, which may be reduced after MMT.

  9. Laplace Inversion of Low-Resolution NMR Relaxometry Data Using Sparse Representation Methods

    PubMed Central

    Berman, Paula; Levi, Ofer; Parmet, Yisrael; Saunders, Michael; Wiesman, Zeev

    2013-01-01

    Low-resolution nuclear magnetic resonance (LR-NMR) relaxometry is a powerful tool that can be harnessed for characterizing constituents in complex materials. Conversion of the relaxation signal into a continuous distribution of relaxation components is an ill-posed inverse Laplace transform problem. The most common numerical method implemented today for dealing with this kind of problem is based on L2-norm regularization. However, sparse representation methods via L1 regularization and convex optimization are a relatively new approach for effective analysis and processing of digital images and signals. In this article, a numerical optimization method for analyzing LR-NMR data by including non-negativity constraints and L1 regularization and by applying a convex optimization solver PDCO, a primal-dual interior method for convex objectives, that allows general linear constraints to be treated as linear operators is presented. The integrated approach includes validation of analyses by simulations, testing repeatability of experiments, and validation of the model and its statistical assumptions. The proposed method provides better resolved and more accurate solutions when compared with those suggested by existing tools. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 72–88, 2013. PMID:23847452

  10. LRS2: a new low-resolution spectrograph for the Hobby-Eberly Telescope

    NASA Astrophysics Data System (ADS)

    Lee, Hanshin; Chonis, Taylor S.; Hill, Gary J.; DePoy, Darren L.; Marshall, Jennifer L.; Vattiat, Brian

    2010-07-01

    In the era of the Hobby-Eberly Telescope (HET) Wide-Field Upgrade (WFU), the current Low-Resolution Spectrograph (LRS) will be replaced with a more capable red-optimized fiber instrument, called LRS2. This new spectrograph will be based on the Visible Integral-field Replicable Unit Spectrograph (VIRUS) that was designed to be easily adapted to a wide range of spectral resolutions, and wavelength ranges. The current snapshot of LRS2, fed by a 7x12 sq. arcsec fiber integral-field unit (IFU), covers 350-1100 nm, simultaneously at a fixed resolving power R~1800, with the wavelength range split into two pairs of spectrographs, one for the blue to red wavelength range (350-630 nm) and the other for the red and far-red range (630-1100 nm). These units are designated LRS2-B and LRS2-R, respectively. Only minimal modification from the base VIRUS design in gratings (for both pairs) and in the detector (for the red pair only) is required. In addition to this flexibility, the generic nature and massively replicable characteristic of the instrument can allow us to adapt the instrument to a wide range of not only telescope diameters (1 m ~ 40 m), but also observing modes (single to multiple objects). We discuss the current snapshot of the LRS2 design.

  11. Laplace Inversion of Low-Resolution NMR Relaxometry Data Using Sparse Representation Methods.

    PubMed

    Berman, Paula; Levi, Ofer; Parmet, Yisrael; Saunders, Michael; Wiesman, Zeev

    2013-05-01

    Low-resolution nuclear magnetic resonance (LR-NMR) relaxometry is a powerful tool that can be harnessed for characterizing constituents in complex materials. Conversion of the relaxation signal into a continuous distribution of relaxation components is an ill-posed inverse Laplace transform problem. The most common numerical method implemented today for dealing with this kind of problem is based on L2-norm regularization. However, sparse representation methods via L1 regularization and convex optimization are a relatively new approach for effective analysis and processing of digital images and signals. In this article, a numerical optimization method for analyzing LR-NMR data by including non-negativity constraints and L1 regularization and by applying a convex optimization solver PDCO, a primal-dual interior method for convex objectives, that allows general linear constraints to be treated as linear operators is presented. The integrated approach includes validation of analyses by simulations, testing repeatability of experiments, and validation of the model and its statistical assumptions. The proposed method provides better resolved and more accurate solutions when compared with those suggested by existing tools. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 72-88, 2013.

  12. A distributed automatic target recognition system using multiple low resolution sensors

    NASA Astrophysics Data System (ADS)

    Yue, Zhanfeng; Lakshmi Narasimha, Pramod; Topiwala, Pankaj

    2008-04-01

    In this paper, we propose a multi-agent system which uses swarming techniques to perform high accuracy Automatic Target Recognition (ATR) in a distributed manner. The proposed system can co-operatively share the information from low-resolution images of different looks and use this information to perform high accuracy ATR. An advanced, multiple-agent Unmanned Aerial Vehicle (UAV) systems-based approach is proposed which integrates the processing capabilities, combines detection reporting with live video exchange, and swarm behavior modalities that dramatically surpass individual sensor system performance levels. We employ real-time block-based motion analysis and compensation scheme for efficient estimation and correction of camera jitter, global motion of the camera/scene and the effects of atmospheric turbulence. Our optimized Partition Weighted Sum (PWS) approach requires only bitshifts and additions, yet achieves a stunning 16X pixel resolution enhancement, which is moreover parallizable. We develop advanced, adaptive particle-filtering based algorithms to robustly track multiple mobile targets by adaptively changing the appearance model of the selected targets. The collaborative ATR system utilizes the homographies between the sensors induced by the ground plane to overlap the local observation with the received images from other UAVs. The motion of the UAVs distorts estimated homography frame to frame. A robust dynamic homography estimation algorithm is proposed to address this, by using the homography decomposition and the ground plane surface estimation.

  13. Low-Resolution Vehicle Image Recognition Technology by Frame-Composition of Moving Images

    NASA Astrophysics Data System (ADS)

    Kanzawa, Yusuke; Kobayashi, Hiroki; Ohkawa, Takenao; Ito, Toshio

    Developing on-board automotive driver assistance systems aiming to alert drivers about driving environments, and possible collision with other vehicles has attracted a lot of attention lately. Especially, many researchers have suggested the forward vehicle recognition technology by a camera on vehicle. In the forward vehicle recognition, however, it is difficult to detect the features of vehicle from a distant vehicle image by conventional methods because the image is too low-resolution (LR). This paper presents vehicle image recognition technology for detecting of the features of a distant vehicle by frame-composition of moving images. To detect the vehicle features of a distant LR vehicle image, we use the moving images obtained from the camera on the vehicle, and utilize super-resolution (SR) image reconstruction. SR image reconstruction is to use signal processing techniques to obtain a high-resolution (or sequence) image from observed multiple LR images. Use of this technique on real road image, we show the effectiveness of the proposed techniques.

  14. Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes

    PubMed Central

    Birmanns, Stefan; Rusu, Mirabela; Wriggers, Willy

    2011-01-01

    We describe an integrated software system called Sculptor that combines visualization capabilities with molecular modeling algorithms for the analysis of multi-scale data sets. Sculptor features extensive special purpose visualization techniques that are based on modern GPU programming and are capable of representing complex molecular assemblies in real-time. The integration of graphics and modeling offers several advantages. The user interface not only eases the usually steep learning curve of pure algorithmic techniques, but it also permits instant analysis and post-processing of results, as well as the integration of results from external software. Here, we implemented an interactive peak-selection strategy that enables the user to explore a preliminary score landscape generated by the colores tool of Situs. The interactive placement of components, one at a time, is advantageous for low-resolution or ambiguously shaped maps, which are sometimes difficult to interpret by the fully automatic peak selection of colores. For the subsequent refinement of the preliminary models resulting from both interactive and automatic peak selection, we have implemented a novel simultaneous multi-body docking in Sculptor and Situs that softly enforces shape complementarities between components using the normalization of the cross-correlation coefficient. The proposed techniques are freely available in Situs version 2.6 and Sculptor version 2.0. PMID:21078392

  15. Gold nanoparticle fluorescent molecular beacon for low-resolution DQ2 gene HLA typing.

    PubMed

    Beni, Valerio; Zewdu, Taye; Joda, Hamdi; Katakis, Ioanis; O'Sullivan, Ciara K

    2012-01-01

    Coeliac disease is an inflammation of the small intestine triggered by gluten ingestion. We present a fluorescent genosensor, exploiting molecular-beacon-functionalized gold nanoparticles, for the identification of human leukocyte antigen (HLA) DQ2 gene, a key genetic factor in coeliac disease. Optimization of sensor performance was achieved by tuning the composition of the oligonucleotide monolayer immobilized on the gold nanoparticle and the molecular beacon design. Co-immobilization of the molecular beacon with a spacing oligonucleotide (thiolated ten-thymine oligonucleotide) in the presence of ten-adenine oligonucleotides resulted in a significant increase of the sensor response owing to improved spacing of the molecular beacons and extension of the distance from the nanoparticle surface, which renders them more available for recognition. Further increase in the response (approximately 40%) was shown to be achievable when the recognition sequence of the molecular beacon was incorporated in the stem. Improvement of the specificity of the molecular beacons was also achieved by the incorporation within their recognition sequence of a one-base mismatch. Finally, gold nanoparticles functionalized with two molecular beacons targeting the DQA1*05* and DQB1*02* alleles allowed the low-resolution typing of the DQ2 gene at the nanomolar level.

  16. Low resolution 1H NMR assignment of proton populations in pound cake and its polymeric ingredients.

    PubMed

    Luyts, A; Wilderjans, E; Waterschoot, J; Van Haesendonck, I; Brijs, K; Courtin, C M; Hills, B; Delcour, J A

    2013-08-15

    Based on a model system approach, five different proton populations were distinguished in pound cake crumb using one dimensional low resolution (1)H NMR spectroscopy. In free induction decay (FID) measurements, proton populations were assigned to (i) non-exchanging CH protons of crystalline starch, proteins and crystalline fat and (ii) non-exchanging CH protons of amorphous starch and gluten, which are in little contact with water. In Carr-Purcell-Meiboom-Gill (CPMG) measurements, three proton populations were distinguished. The CPMG population with the lowest mobility and the FID population with the highest mobility represent the same proton population. The two CPMG proton populations with the highest mobility were assigned to exchanging protons (i.e., protons of water, starch, gluten, egg proteins and sugar) and protons of lipids (i.e., protons of egg yolk lipids and amorphous lipid fraction of margarine) respectively. Based on their spin-lattice relaxation times (T1), two dimensional (1)H NMR spectroscopy further resolved the two proton populations with the highest mobility into three and two proton populations, respectively. PMID:23561087

  17. Low resolution 1H NMR assignment of proton populations in pound cake and its polymeric ingredients.

    PubMed

    Luyts, A; Wilderjans, E; Waterschoot, J; Van Haesendonck, I; Brijs, K; Courtin, C M; Hills, B; Delcour, J A

    2013-08-15

    Based on a model system approach, five different proton populations were distinguished in pound cake crumb using one dimensional low resolution (1)H NMR spectroscopy. In free induction decay (FID) measurements, proton populations were assigned to (i) non-exchanging CH protons of crystalline starch, proteins and crystalline fat and (ii) non-exchanging CH protons of amorphous starch and gluten, which are in little contact with water. In Carr-Purcell-Meiboom-Gill (CPMG) measurements, three proton populations were distinguished. The CPMG population with the lowest mobility and the FID population with the highest mobility represent the same proton population. The two CPMG proton populations with the highest mobility were assigned to exchanging protons (i.e., protons of water, starch, gluten, egg proteins and sugar) and protons of lipids (i.e., protons of egg yolk lipids and amorphous lipid fraction of margarine) respectively. Based on their spin-lattice relaxation times (T1), two dimensional (1)H NMR spectroscopy further resolved the two proton populations with the highest mobility into three and two proton populations, respectively.

  18. A rapid and automated low resolution NMR method to analyze oil quality in intact oilseeds.

    PubMed

    Prestes, Rosilene Aparecida; Colnago, Luiz Alberto; Forato, Lucimara Aparecida; Vizzotto, Lucinéia; Novotny, Etelvino Henrique; Carrilho, Emanuel

    2007-07-23

    Oilseeds with modified fatty acid profiles have been the genetic alternative for high quality vegetable oil for food and biodiesel applications. They can provide stable, functional oils for the food industry, without the hydrogenation process that produces trans-fatty acid, which has been linked to cardiovascular disease. High yield and high quality oilseeds are also necessary for the success of biodiesel programs, as polyunsaturated or saturated fatty acid oil produces biofuel with undesirable properties. In this paper, a rapid and automated low resolution NMR method to select intact oilseeds with a modified fatty acid profile is introduced, based on 1H transverse relaxation time (T2). The T2 weighted NMR signal, obtained by a CPMG pulse sequence and processed by chemometric methods was able to determine the oil quality in intact seeds by its fatty composition, cetane number, iodine value and kinematic viscosity with a correlation coefficient r > 0.9. The automated system has the potential to analyze more than 1000 samples per hour and is a powerful tool to speed up the selection of high quality oilseeds for food and biodiesel applications.

  19. Registration of multitemporal low-resolution synthetic aperture radar images based on a new similarity measure

    NASA Astrophysics Data System (ADS)

    Ren, Weilong; Song, Jianshe; Zhang, Xiongmei; Cai, Xingfu

    2016-01-01

    Image registration is concerned with the precise overlap of two images. One challenging problem in this area is the registration of low-resolution synthetic aperture radar (SAR) images. In general, extracting feature points from such images is difficult due to the coarse observation and the severe speckle. The use of area similarity for image registration is another important branch to solve the problem. A similarity measure based on a conditional density function (cdf) is proposed. The cdf is specially tailored for SAR images, where the speckle is generally assumed as multiplicative gamma noise with unit mean. Additionally, a two-step procedure is devised for the registration of intro-model SAR images to improve the computational efficiency. First, the two images are roughly aligned considering only the translational difference. Then small blocks from the two images are accurately aligned and the center point of each block is treated as a control point, which is finally used to obtain the precise affine transformation between the two images. Five SAR image datasets are tested in the experiment part, and the results demonstrate the efficiency and accuracy of the proposed method.

  20. Low-resolution electromagnetic tomography and treatment response in obsessive-compulsive disorder.

    PubMed

    Fontenelle, Leonardo F; Mendlowicz, Mauro V; Ribeiro, Pedro; Piedade, Roberto A; Versiani, Marcio

    2006-02-01

    We investigated whether findings from pretreatment low-resolution electromagnetic tomography (LORETA) predicted response to drug treatment in patients with obsessive-compulsive disorder (OCD). The 3D intra-cerebral distribution of neuronal electrical activity from the scalp-recorded potential distribution of 17 drug-free patients with OCD was assessed with LORETA. They were treated with antidepressants in the maximum tolerated doses for at least 12 wk. Individuals were considered to be treatment responders if they displayed a reduction of at least 35% on the initial YBOCS scores and had a final CGI score of 1 or 2. The SPM-99 t test for independent samples was employed to compare, voxel-by-voxel, the brain electrical activities of responders (n = 10) and non-responders (n = 7). Responders exhibited significantly lower activities in beta band in the rostral anterior cingulate [Brodmann's area (BA) 24 and 32] (p = 0.002) and the medial frontal gyrus (BA 10) (p = 0.002), suggesting that a distinctive pattern of activity within the medial surface of the frontal lobe predicts therapeutic response in OCD.

  1. HUNTING THE PARENT OF THE ORPHAN STREAM: IDENTIFYING STREAM MEMBERS FROM LOW-RESOLUTION SPECTROSCOPY

    SciTech Connect

    Casey, Andrew R.; Da Costa, Gary; Keller, Stefan C.; Maunder, Elizabeth

    2013-02-10

    We present candidate K-giant members in the Orphan Stream that have been identified from low-resolution data taken with the AAOmega spectrograph on the Anglo-Australian Telescope. From modest signal-to-noise spectra and independent cuts in photometry, kinematics, gravity, and metallicity we yield self-consistent, highly probable stream members. We find a revised stream distance of 22.5 {+-} 2.0 kpc near the celestial equator and our kinematic signature peaks at V {sub GSR} = 82.1 {+-} 1.4 km s{sup -1}. The observed velocity dispersion of our most probable members is consistent with arising from the velocity uncertainties alone. This indicates that at least along this line of sight, the Orphan Stream is kinematically cold. Our data indicate an overall stream metallicity of [Fe/H] = -1.63 {+-} 0.19 dex which is more metal-rich than previously found and unbiased by spectral type. Furthermore, the significant metallicity dispersion displayed by our most probable members, {sigma}([Fe/H]) = 0.56 dex, suggests that the unidentified Orphan Stream parent is a dSph satellite. We highlight likely members for high-resolution spectroscopic follow-up.

  2. NEWLY IDENTIFIED CARBON STARS FROM SOURCES WITH UNUSUAL IRAS LOW-RESOLUTION SPECTRA

    SciTech Connect

    Chen, P. S.; Shan, H. G.

    2012-07-15

    The 11.2 {mu}m SiC feature in either emission or absorption in the infrared is an important indicator for identification of carbon stars. Sources whose infrared spectra are sorted in Group U of the Infrared Astronomical Satellite (IRAS) low-resolution spectrum (LRS) are good samples for finding objects with the 11.2 {mu}m SiC feature. Therefore, we have carefully checked all spectra in Group U of the LRS. We have found 13 new objects, which probably have SiC emission, sometimes with unusually broad features, that are presumed to be carbon-rich objects. In addition, their evolutionary types are also estimated from IRAS and Two Micron All Sky Survey two-color diagrams. Besides finding 13 new carbon-rich objects, another important result in this paper is that four sources are estimated as new extreme carbon stars (ECSs) and five previously known carbon stars sorted in the Group U of the IRAS LRS are also estimated as ECSs.

  3. The power of low-resolution spectroscopy: On the spectral classification of planet candidates in the ground-based CoRoT follow-up

    NASA Astrophysics Data System (ADS)

    Ammler-von Eiff, M.; Sebastian, D.; Guenther, E. W.; Stecklum, B.; Cabrera, J.

    2015-02-01

    Planetary transits detected by the CoRoT mission can be mimicked by a low-mass star in orbit around a giant star. Spectral classification helps to identify the giant stars and also early-type stars which are often excluded from further follow-up. We study the potential and the limitations of low-resolution spectroscopy to improve the photometric spectral types of CoRoT candidates. In particular, we want to study the influence of the signal-to-noise ratio (SNR) of the target spectrum in a quantitative way. We built an own template library and investigate whether a template library from the literature is able to reproduce the classifications. Including previous photometric estimates, we show how the additional spectroscopic information improves the constraints on spectral type. Low-resolution spectroscopy (R≈ 1000) of 42 CoRoT targets covering a wide range in SNR (1-437) and of 149 templates was obtained in 2012-2013 with the Nasmyth spectrograph at the Tautenburg 2 m telescope. Spectral types have been derived automatically by comparing with the observed template spectra. The classification has been repeated with the external CFLIB library. The spectral class obtained with the external library agrees within a few sub-classes when the target spectrum has a SNR of about 100 at least. While the photometric spectral type can deviate by an entire spectral class, the photometric luminosity classification is as close as a spectroscopic classification with the external library. A low SNR of the target spectrum limits the attainable accuracy of classification more strongly than the use of external templates or photometry. Furthermore we found that low-resolution reconnaissance spectroscopy ensures that good planet candidates are kept that would otherwise be discarded based on photometric spectral type alone.

  4. An adaptively generated feature set for low-resolution multifrequency sonar images

    NASA Astrophysics Data System (ADS)

    Arrieta, Rodolfo; Arrieta, Lisa L.; Stack, Jason R.

    2006-05-01

    Many small Unmanned Underwater Vehicles (UUVs) currently utilize inexpensive, low resolution sonars that are either mechanically or electronically steered as their main sensors. These sonars do not provide high quality images and are quite dissimilar from the broad area search sonars that will most likely be the source of the localization data given to the UUV in a reacquisition scenario. Therefore, the acoustic data returned by the UUV in its attempt to reacquire the target will look quite different from the original wide area image. The problem then becomes how to determine that the UUV is looking at the same object. Our approach is to exploit the maneuverability of the UUV and currently unused information in the echoes returned from these Commercial-Off-The-Shelf (COTS) sonars in order to classify a presumptive target as an object of interest. The approach hinges on the ability of the UUV to maneuver around the target in order to insonify the target at different frequencies of insonification, ranges, and aspects. We show how this approach would allow the UUV to extract a feature set derived from the inversion of simple physics-based models. These models predict echo time-of-arrival and inversion of these models using the echo data allows effective classification based on estimated surface and bulk material properties. We have simulated UUV maneuvers by positioning targets at different ranges and aspects to the sonar and have then interrogated the target at different frequencies. The properties that have been extracted include longitudinal, and shear speeds of the bulk, as well as longitudinal speed, Rayleigh speed, and density of the surface. The material properties we have extracted using this approach match the tabulated material values within 8%. We also show that only a few material properties are required to effectively segregate many classes of materials.

  5. RESEARCH PAPER: Automated estimation of stellar fundamental parameters from low resolution spectra: the PLS method

    NASA Astrophysics Data System (ADS)

    Zhang, Jian-Nan; Luo, A.-Li; Zhao, Yong-Heng

    2009-06-01

    PLS (Partial Least Squares regression) is introduced into an automatic estimation of fundamental stellar spectral parameters. It extracts the most correlative spectral component to the parameters (Teff, log g and [Fe/H]), and sets up a linear regression function from spectra to the corresponding parameters. Considering the properties of stellar spectra and the PLS algorithm, we present a piecewise PLS regression method for estimation of stellar parameters, which is composed of one PLS model for Teff, and seven PLS models for log g and [Fe/H] estimation. Its performance is investigated by large experiments on flux calibrated spectra and continuum normalized spectra at different signal-to-noise ratios (SNRs) and resolutions. The results show that the piecewise PLS method is robust for spectra at the medium resolution of 0.23 nm. For low resolution 0.5 nm and 1 nm spectra, it achieves competitive results at higher SNR. Experiments using ELODIE spectra of 0.23 nm resolution illustrate that our piecewise PLS models trained with MILES spectra are efficient for O ~ G stars: for flux calibrated spectra, the systematic offsets are 3.8%, 0.14 dex, and -0.09 dex for Teff, log g and [Fe/H], with error scatters of 5.2%, 0.44 dex and 0.38 dex, respectively; for continuum normalized spectra, the systematic offsets are 3.8%, 0.12dex, and -0.13dex for Teff, log g and [Fe/H], with error scatters of 5.2%, 0.49 dex and 0.41 dex, respectively. The PLS method is rapid, easy to use and does not rely as strongly on the tightness of a parameter grid of templates to reach high precision as Artificial Neural Networks or minimum distance methods do.

  6. Classification of Volcanic Eruptions on Io and Earth Using Low-Resolution Remote Sensing Data

    NASA Technical Reports Server (NTRS)

    Davies, A. G.; Keszthelyi, L. P.

    2005-01-01

    Two bodies in the Solar System exhibit high-temperature active volcanism: Earth and Io. While there are important differences in the eruptions on Earth and Io, in low-spatial-resolution data (corresponding to the bulk of available and foreseeable data of Io), similar styles of effusive and explosive volcanism yield similar thermal flux densities. For example, a square metre of an active pahoehoe flow on Io looks very similar to a square metre of an active pahoehoe flow on Earth. If, from observed thermal emission as a function of wavelength and change in thermal emission with time, the eruption style of an ionian volcano can be constrained, estimates of volumetric fluxes can be made and compared with terrestrial volcanoes using techniques derived for analysing terrestrial remotely-sensed data. In this way we find that ionian volcanoes fundamentally differ from their terrestrial counterparts only in areal extent, with Io volcanoes covering larger areas, with higher volumetric flux. Io outbursts eruptions have enormous implied volumetric fluxes, and may scale with terrestrial flood basalt eruptions. Even with the low-spatial resolution data available it is possible to sometimes constrain and classify eruption style both on Io and Earth from the integrated thermal emission spectrum. Plotting 2 and 5 m fluxes reveals the evolution of individual eruptions of different styles, as well as the relative intensity of eruptions, allowing comparison to be made from individual eruptions on both planets. Analyses like this can be used for interpretation of low-resolution data until the next mission to the jovian system. For a number of Io volcanoes (including Pele, Prometheus, Amirani, Zamama, Culann, Tohil and Tvashtar) we do have high/moderate resolution imagery to aid determination of eruption mode from analyses based only on low spatial-resolution data.

  7. Multi-object spectroscopy on the Hobby-Eberly Telescope low-resolution spectrograph

    NASA Astrophysics Data System (ADS)

    Wolf, Marsha J.; Hill, Gary J.; Mitsch, Wolfgang; Hessman, Frederic V.; Altmann, Werner; Thompson, Keith L.

    2000-08-01

    The low resolution spectrograph (LRS) is the first facility instrument on the 9.2m Hobby-Eberly Telescope (HET). The LRS has three operational modes: imaging, long-slit spectroscopy and multi-object spectroscopy (MOS). We present the design and early operations performance of the LRS MOS unit, which provides 13 slitless, each 1.3 arcsec by 15 arcsec, on 19.6 arcsec centers, within the 4 arcmin field of view of the HET. This type of remotely configurable unit was chosen over the more conventional slit masks due to the queue scheduling of the HET, and the instrument's remote location at the prime focus of the telescope. A restricted envelope around the HET focus at the LRS port forced a very compact design. The MOS unit has miniature mechanisms base don custom cross- roller stages and 0.25 mm pitch lead-screws. Geared stepper motors with 10 mm diameters drive the 13 axes at 0.8 micron per step. The precision of the mechanism is far greater than required by the HET plate scale of 205 microns per arcsec, but result in a robust unit. The slitlets were fabricated at the University of Texas by shadow-masking the slit area with a wire and vacuum depositing aluminum onto the silica substrates. Both sides are then coated with MgF2 which serves as an antireflection coating and a protective layer. Web-based software is available for optimizing the orientation of the MOS unit and the placement of slitlets on objects in the field. These setup scan be down loaded to the unit for configuration outside of the beam while the HET is slewing to its next target in the queue, or while the LRS is used in imaging mode for setup on faint objects. The preliminary results presented here are from one commissioning run with the MOS, where the unit appears to be meeting performance specifications.

  8. Studies of magnetopause structure

    NASA Technical Reports Server (NTRS)

    Speiser, Theodore W.

    1991-01-01

    From the International Sun-Earth Explorers (ISEE) 1 magnetopause crossings on November 10, 1977, three-dimensional distribution functions for energetic ions were studied in the magnetosphere, through the magnetopause, and in the magnetosheath (Speiser and Williams, 1982). The particle distributions were particularly examined at and near the times that Russell and Elphic (1978) identified as flux transfer events (FTE). Using a simple, one-dimensional, quasi-static model, particle orbits were followed numerically, from the magnetosphere into the sheath. The inner, trapped, distribution initializes the distribution function. Liouville's theorem allows the inner distribution to be mapped into the sheath following the orbits. This mapping is shown for four mangetosheath ion flows (MIF's) corresponding to four flux transfer events. Results from the studies are discussed. A brief discussion of current sheet particle motion is presented.

  9. Driving and braking control of PM synchronous motor based on low-resolution hall sensor for battery electric vehicle

    NASA Astrophysics Data System (ADS)

    Gu, Jing; Ouyang, Minggao; Li, Jianqiu; Lu, Dongbin; Fang, Chuan; Ma, Yan

    2013-01-01

    Resolvers are normally employed for rotor positioning in motors for electric vehicles, but resolvers are expensive and vulnerable to vibrations. Hall sensors have the advantages of low cost and high reliability, but the positioning accuracy is low. Motors with Hall sensors are typically controlled by six-step commutation algorithm, which brings high torque ripple. This paper studies the high-performance driving and braking control of the in-wheel permanent magnetic synchronous motor (PMSM) based on low-resolution Hall sensors. Field oriented control (FOC) based on Hall-effect sensors is developed to reduce the torque ripple. The positioning accuracy of the Hall sensors is improved by interpolation between two consecutive Hall signals using the estimated motor speed. The position error from the misalignment of the Hall sensors is compensated by the precise calibration of Hall transition timing. The braking control algorithms based on six-step commutation and FOC are studied. Two variants of the six-step commutation braking control, namely, half-bridge commutation and full-bridge commutation, are discussed and compared, which shows that the full-bridge commutation could better explore the potential of the back electro-motive forces (EMF), thus can deliver higher efficiency and smaller current ripple. The FOC braking is analyzed with the phasor diagrams. At a given motor speed, the motor turns from the regenerative braking mode into the plug braking mode if the braking torque exceeds a certain limit, which is proportional to the motor speed. Tests in the dynamometer show that a smooth control could be realized by FOC driving control and the highest efficiency and the smallest current ripple could be achieved by FOC braking control, compared to six-step commutation braking control. Therefore, FOC braking is selected as the braking control algorithm for electric vehicles. The proposed research ensures a good motor control performance while maintaining low cost and high

  10. Basic principles of static proton low-resolution spin diffusion NMR in nanophase-separated materials with mobility contrast.

    PubMed

    Schäler, Kerstin; Roos, Matthias; Micke, Peter; Golitsyn, Yury; Seidlitz, Anne; Thurn-Albrecht, Thomas; Schneider, Horst; Hempel, Günter; Saalwächter, Kay

    2015-11-01

    We review basic principles of low-resolution proton NMR spin diffusion experiments, relying on mobility differences in nm-sized phases of inhomogeneous organic materials such as block-co- or semicrystalline polymers. They are of use for estimates of domain sizes and insights into nanometric dynamic inhomogeneities. Experimental procedures and limitations of mobility-based signal decomposition/filtering prior to spin diffusion are addressed on the example of as yet unpublished data on semicrystalline poly(ϵ-caprolactone), PCL. Specifically, we discuss technical aspects of the quantitative, dead-time free detection of rigid-domain signals by aid of the magic-sandwich echo (MSE), and magic-and-polarization-echo (MAPE) and double-quantum (DQ) magnetization filters to select rigid and mobile components, respectively. Such filters are of general use in reliable fitting approaches for phase composition determinations. Spin diffusion studies at low field using benchtop instruments are challenged by rather short (1)H T1 relaxation times, which calls for simulation-based analyses. Applying these, in combination with domain sizes as determined by small-angle X-ray scattering, we have determined spin diffusion coefficients D for PCL (0.34, 0.19 and 0.032nm(2)/ms for crystalline, interphase and amorphous parts, respectively). We further address thermal-history effects related to secondary crystallization. Finally, the state of knowledge concerning the connection between D values determined locally at the atomic level, using (13)C detection and CP- or REDOR-based "(1)H hole burning" procedures, and those obtained by calibration experiments, is summarized. Specifically, the non-trivial dependence of D on the magic-angle spinning (MAS) frequency, with a minimum under static and a local maximum under moderate-MAS conditions, is highlighted.

  11. A low resolution model for the chromatin core particle by neutron scattering

    PubMed Central

    Suau, Pedro; Kneale, G.Geoff; Braddock, Gordon W.; Baldwin, John P.; Bradbury, E.Morton

    1977-01-01

    Neutron scattering studies have been applied to chromatin core particles in solution, using the contrast variation technique. On the basis of the contrast dependance of the radius of gyration and the radial distribution function it is shown that the core particle consists of a core containing most of the histone around which is wound the DNA helix,following a path with a mean radius of 4.5 nm,in association with a small proportion of the histones. Separation of the shape from the internal structure, followed by model calculations shows that the overall shape of the particle is that of a flat cylinder with dimensions ca. 11×11×6 nm. Further details of the precise folding of the DNA cannot be deduced from the data, but detailed model calculations support concurrent results from crystallographic studies25. Images PMID:593885

  12. Structural study of ammonium metatungstate

    SciTech Connect

    Christian, Joel B. Whittingham, M. Stanley

    2008-08-15

    Several techniques have been used to study the structure of the Keggin-type polyoxometalate salt ammonium metatungstate (AMT)-(NH{sub 4}){sub 6}[H{sub 2}W{sub 12}O{sub 40}]*nH{sub 2}O, a potential fuel cell catalyst. The dehydrated salt is comprised of a mixture of crystallites of different unit cells in a centered eutactic cubic configuration, with an average unit cell of a{approx_equal}12.295. Varied orientations of the Keggin ions in the cubic arrangement create the differences, and orientational variation within each unit cell size represents an energy well. Progressive hydration of each crystallite leads to expansion of the lattice, with the degree of expansion depending on the locations of the water added in relation to the Keggin ion, which is influenced by cation location and hydrogen bonding. The structural hypothesis is supported by electron diffraction of single and multicrystal samples, by powder density measurements, X-ray powder diffraction studies, synchrotron powder X-ray diffraction, and a priori structural modeling studies. Based on the structure, projected active site densities are compared with nanostructured platinum catalysts for fuel cell application. - Graphical abstract: The structure of ammonium metatungstate powders are highly dependent on hydration and POM molecule rotation, with cation and hydrogen bonding forces directing a mixture of structures that have been studied with bulk and single-crystal methods. The illustration shows Monte Carlo simulated anion structural disorder for the fully dehydrated form of the title compound.

  13. Low-resolution detergent tracing in protein crystals using xenon or krypton to enhance X-ray contrast.

    PubMed

    Sauer, Oliver; Roth, Michel; Schirmer, Tilman; Rummel, Gabriele; Kratky, Christoph

    2002-01-01

    Xenon and krypton show different solubilities in polar versus apolar solvents. Therefore, these noble gases should accumulate in apolar regions of protein crystals. Specifically, they should accumulate in lipid and detergent solvent regions within crystals of membrane proteins, which can be used as a basis for contrast-variation experiments to distinguish such apolar solvent regions from the aqueous phase by a low-resolution X-ray diffraction experiment. This possibility was explored with the OmpF porin, one of the general diffusion pores of the Escherichia coli outer membrane. Trigonal crystals were exposed to elevated pressures of the two noble gases (up to 10(7) Pa) for several minutes and subsequently flash-cooled to liquid-nitrogen temperatures. Both rare gases bind to a number of 'specific' sites, which can be classified as 'typical' noble-gas binding sites. Compared with a representative water-soluble protein, they are however much more abundant in OmpF. In addition, a very large number of weakly populated sites are observed which accumulate in the region of the 'detergent belt' for crystals exposed to xenon. After application of a Fourier-filtering protocol, low-resolution images of the detergent belt can be obtained. The resulting maps are similar to maps obtained from low-resolution neutron diffraction experiments on contrast-matched crystals.

  14. Structural dynamics verification facility study

    NASA Technical Reports Server (NTRS)

    Kiraly, L. J.; Hirchbein, M. S.; Mcaleese, J. M.; Fleming, D. P.

    1981-01-01

    The need for a structural dynamics verification facility to support structures programs was studied. Most of the industry operated facilities are used for highly focused research, component development, and problem solving, and are not used for the generic understanding of the coupled dynamic response of major engine subsystems. Capabilities for the proposed facility include: the ability to both excite and measure coupled structural dynamic response of elastic blades on elastic shafting, the mechanical simulation of various dynamical loadings representative of those seen in operating engines, and the measurement of engine dynamic deflections and interface forces caused by alternative engine mounting configurations and compliances.

  15. USANS study of wood structure

    NASA Astrophysics Data System (ADS)

    Garvey, Christopher J.; Knott, Robert B.; Searson, Matthew; Conroy, Jann P.

    2006-11-01

    Wood performs a vascular and structural function in trees. In this study we used the double-crystal diffractometer BT5 at the NIST Center for Neutron Scattering (Gaithersburg, USA) to study the pore structure inside wood sections. The slit-smeared intensity of scattered neutrons was measured from wood sections in directions parallel, orthogonal and transverse to the tree's trunk axis over a scattering vector range 0.00004-0.002 Å -1. The interpretation of the data in terms of a reductionist model consisting of infinitely long cylinders (cell lumens) is discussed.

  16. Quantitative treatment of coarsely binned low-resolution recordings in molecular absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Spietz, Peter; Martín, Juan Carlos Gómez; Burrows, John P.

    2006-06-01

    Optical multichannel detectors like photodiode arrays or CCD cameras combined with grating spectrometers are commonly used as detection systems in quantitative absorption spectroscopy. As a trade-off to broad spectral coverage, banded spectral features are sometimes recorded with insufficient spectral resolution and/or insufficiently fine detector binning. This renders the true physical spectrum of recorded intensities changed by instrumental and spectrum specific artefacts thus impeding comparability between results from different set-ups. In this work, it is demonstrated that in the case of a "well-behaved" - i.e. free of ro-vibronic structure - absorption band like the iodine monoxide IO(4 ← 0) transition, these effects can easily change the apparent peak absorption by up to 50%. Also deviations from the strict linearity (Beer-Lambert's law) between absorber concentration and apparent, i.e. pixelwise optical density occur. This can be critical in studies of chemical kinetics. It is shown that the observed non-linearity can cause errors of up to 50% in the determination of a second order rate coefficient for the IO self reaction. To overcome the problem, a consistent and rigorous integral approach for the treatment of intensity recordings is developed. Linearity between optical density and absorber concentration thereby is re-established. The method is validated using artificial test data as well as experimental data of the IO(4 ← 0) absorption transition, obtained in the context of I 2/O 3 photochemistry studies. The agreement is accurate to within ±2% (test data) and ±3% (experimental data) supporting the validity of the approach. Possible consequences for other spectroscopic work are indicated.

  17. Structural studies of ciliary components.

    PubMed

    Mizuno, Naoko; Taschner, Michael; Engel, Benjamin D; Lorentzen, Esben

    2012-09-14

    Cilia are organelles found on most eukaryotic cells, where they serve important functions in motility, sensory reception, and signaling. Recent advances in electron tomography have facilitated a number of ultrastructural studies of ciliary components that have significantly improved our knowledge of cilium architecture. These studies have produced nanometer-resolution structures of axonemal dynein complexes, microtubule doublets and triplets, basal bodies, radial spokes, and nexin complexes. In addition to these electron tomography studies, several recently published crystal structures provide insights into the architecture and mechanism of dynein as well as the centriolar protein SAS-6, important for establishing the 9-fold symmetry of centrioles. Ciliary assembly requires intraflagellar transport (IFT), a process that moves macromolecules between the tip of the cilium and the cell body. IFT relies on a large 20-subunit protein complex that is thought to mediate the contacts between ciliary motor and cargo proteins. Structural investigations of IFT complexes are starting to emerge, including the first three-dimensional models of IFT material in situ, revealing how IFT particles organize into larger train-like arrays, and the high-resolution structure of the IFT25/27 subcomplex. In this review, we cover recent advances in the structural and mechanistic understanding of ciliary components and IFT complexes. PMID:22683354

  18. Structural Studies of Ciliary Components

    PubMed Central

    Mizuno, Naoko; Taschner, Michael; Engel, Benjamin D.; Lorentzen, Esben

    2012-01-01

    Cilia are organelles found on most eukaryotic cells, where they serve important functions in motility, sensory reception, and signaling. Recent advances in electron tomography have facilitated a number of ultrastructural studies of ciliary components that have significantly improved our knowledge of cilium architecture. These studies have produced nanometer‐resolution structures of axonemal dynein complexes, microtubule doublets and triplets, basal bodies, radial spokes, and nexin complexes. In addition to these electron tomography studies, several recently published crystal structures provide insights into the architecture and mechanism of dynein as well as the centriolar protein SAS-6, important for establishing the 9-fold symmetry of centrioles. Ciliary assembly requires intraflagellar transport (IFT), a process that moves macromolecules between the tip of the cilium and the cell body. IFT relies on a large 20-subunit protein complex that is thought to mediate the contacts between ciliary motor and cargo proteins. Structural investigations of IFT complexes are starting to emerge, including the first three‐dimensional models of IFT material in situ, revealing how IFT particles organize into larger train-like arrays, and the high-resolution structure of the IFT25/27 subcomplex. In this review, we cover recent advances in the structural and mechanistic understanding of ciliary components and IFT complexes. PMID:22683354

  19. A Study in Structured Discussion.

    ERIC Educational Resources Information Center

    Gutzmer, Willard Ernest

    This study tested the hypothesis that group interaction skill and useful learning occur in a discussion group which is academically structured. A class procedure involving a cognitive map, member skills and roles, and group etiquette was incorporated into a class ("Education and the Contemporary Scene," Fall Quarter, 1968) at the University of…

  20. Development of an iterative reconstruction method to overcome 2D detector low resolution limitations in MLC leaf position error detection for 3D dose verification in IMRT.

    PubMed

    Visser, R; Godart, J; Wauben, D J L; Langendijk, J A; Van't Veld, A A; Korevaar, E W

    2016-05-21

    The objective of this study was to introduce a new iterative method to reconstruct multi leaf collimator (MLC) positions based on low resolution ionization detector array measurements and to evaluate its error detection performance. The iterative reconstruction method consists of a fluence model, a detector model and an optimizer. Expected detector response was calculated using a radiotherapy treatment plan in combination with the fluence model and detector model. MLC leaf positions were reconstructed by minimizing differences between expected and measured detector response. The iterative reconstruction method was evaluated for an Elekta SLi with 10.0 mm MLC leafs in combination with the COMPASS system and the MatriXX Evolution (IBA Dosimetry) detector with a spacing of 7.62 mm. The detector was positioned in such a way that each leaf pair of the MLC was aligned with one row of ionization chambers. Known leaf displacements were introduced in various field geometries ranging from  -10.0 mm to 10.0 mm. Error detection performance was tested for MLC leaf position dependency relative to the detector position, gantry angle dependency, monitor unit dependency, and for ten clinical intensity modulated radiotherapy (IMRT) treatment beams. For one clinical head and neck IMRT treatment beam, influence of the iterative reconstruction method on existing 3D dose reconstruction artifacts was evaluated. The described iterative reconstruction method was capable of individual MLC leaf position reconstruction with millimeter accuracy, independent of the relative detector position within the range of clinically applied MU's for IMRT. Dose reconstruction artifacts in a clinical IMRT treatment beam were considerably reduced as compared to the current dose verification procedure. The iterative reconstruction method allows high accuracy 3D dose verification by including actual MLC leaf positions reconstructed from low resolution 2D measurements. PMID:27100169

  1. Development of an iterative reconstruction method to overcome 2D detector low resolution limitations in MLC leaf position error detection for 3D dose verification in IMRT

    NASA Astrophysics Data System (ADS)

    Visser, R.; Godart, J.; Wauben, D. J. L.; Langendijk, J. A.; van't Veld, A. A.; Korevaar, E. W.

    2016-05-01

    The objective of this study was to introduce a new iterative method to reconstruct multi leaf collimator (MLC) positions based on low resolution ionization detector array measurements and to evaluate its error detection performance. The iterative reconstruction method consists of a fluence model, a detector model and an optimizer. Expected detector response was calculated using a radiotherapy treatment plan in combination with the fluence model and detector model. MLC leaf positions were reconstructed by minimizing differences between expected and measured detector response. The iterative reconstruction method was evaluated for an Elekta SLi with 10.0 mm MLC leafs in combination with the COMPASS system and the MatriXX Evolution (IBA Dosimetry) detector with a spacing of 7.62 mm. The detector was positioned in such a way that each leaf pair of the MLC was aligned with one row of ionization chambers. Known leaf displacements were introduced in various field geometries ranging from  -10.0 mm to 10.0 mm. Error detection performance was tested for MLC leaf position dependency relative to the detector position, gantry angle dependency, monitor unit dependency, and for ten clinical intensity modulated radiotherapy (IMRT) treatment beams. For one clinical head and neck IMRT treatment beam, influence of the iterative reconstruction method on existing 3D dose reconstruction artifacts was evaluated. The described iterative reconstruction method was capable of individual MLC leaf position reconstruction with millimeter accuracy, independent of the relative detector position within the range of clinically applied MU’s for IMRT. Dose reconstruction artifacts in a clinical IMRT treatment beam were considerably reduced as compared to the current dose verification procedure. The iterative reconstruction method allows high accuracy 3D dose verification by including actual MLC leaf positions reconstructed from low resolution 2D measurements.

  2. Development of an iterative reconstruction method to overcome 2D detector low resolution limitations in MLC leaf position error detection for 3D dose verification in IMRT

    NASA Astrophysics Data System (ADS)

    Visser, R.; Godart, J.; Wauben, D. J. L.; Langendijk, J. A.; van’t Veld, A. A.; Korevaar, E. W.

    2016-05-01

    The objective of this study was to introduce a new iterative method to reconstruct multi leaf collimator (MLC) positions based on low resolution ionization detector array measurements and to evaluate its error detection performance. The iterative reconstruction method consists of a fluence model, a detector model and an optimizer. Expected detector response was calculated using a radiotherapy treatment plan in combination with the fluence model and detector model. MLC leaf positions were reconstructed by minimizing differences between expected and measured detector response. The iterative reconstruction method was evaluated for an Elekta SLi with 10.0 mm MLC leafs in combination with the COMPASS system and the MatriXX Evolution (IBA Dosimetry) detector with a spacing of 7.62 mm. The detector was positioned in such a way that each leaf pair of the MLC was aligned with one row of ionization chambers. Known leaf displacements were introduced in various field geometries ranging from  ‑10.0 mm to 10.0 mm. Error detection performance was tested for MLC leaf position dependency relative to the detector position, gantry angle dependency, monitor unit dependency, and for ten clinical intensity modulated radiotherapy (IMRT) treatment beams. For one clinical head and neck IMRT treatment beam, influence of the iterative reconstruction method on existing 3D dose reconstruction artifacts was evaluated. The described iterative reconstruction method was capable of individual MLC leaf position reconstruction with millimeter accuracy, independent of the relative detector position within the range of clinically applied MU’s for IMRT. Dose reconstruction artifacts in a clinical IMRT treatment beam were considerably reduced as compared to the current dose verification procedure. The iterative reconstruction method allows high accuracy 3D dose verification by including actual MLC leaf positions reconstructed from low resolution 2D measurements.

  3. A structural study of gallstones.

    PubMed Central

    Bills, P M; Lewis, D

    1975-01-01

    A number of gallstones have been studied using methods which have not previously been applied to gallstones. In particular, the use of scanning electron microscopy and micro-x-radiography have allowed detailed observations to be made on the structure of the stones and the distribution of the various components within the stones. Large differences in structure have been shown to exist between stones having similar overall chemical compositions. In cholesterol gallstones containing calcium carbonate the crystalline nature, distribution and method of deposition of the calcium carbonate was studied and was found to vary from stone to stone. Evidence was found for the presence of fibrous material in the centre of many stones and it is possible that this material acted as a nucleus for the deposition of the other stone components. Images Fig 1 Fig 2 Fig 3 Fig 4 Fig 5 PMID:1183859

  4. Sr/Ca ratios in cold-water corals - a 'low-resolution' temperature archive?

    NASA Astrophysics Data System (ADS)

    Rüggeberg, Andres; Riethdorf, Jan-Rainer; Raddatz, Jacek; López Correa, Matthias; Montagna, Paolo; Dullo, Wolf-Christian; Freiwald, André

    2010-05-01

    One of the basic data to understand global change and past global changes is the measurement and the reconstruction of temperature of marine water masses. E.g. seawater temperature controls the density of seawater and in combination with salinity is the major driving force for the oceans circulation system. Geochemical investigations on cold-water corals Lophelia pertusa and Desmophyllum cristagalli indicated the potential of these organisms as high-resolution archives of environmental parameters from intermediate and deeper water masses (Adkins and Boyle 1997). Some studies tried to use cold-water corals as a high-resolution archive of temperature and salinity (Smith et al. 2000, 2002; Blamart et al. 2005; Lutringer et al. 2005). However, the fractionation of stable isotopes (delta18O and delta13C) and element ratios (Sr/Ca, Mg/Ca, U/Ca) are strongly influenced by vital effects (Shirai et al. 2005; Cohen et al. 2006), and difficult to interpret. Nevertheless, ongoing studies indicate the potential of a predominant temperature dependent fractionation of distinct isotopes and elements (e.g. Li/Ca, Montagna et al. 2008; U/Ca, Mg/Ca, delta18O, Lòpez Correa et al. 2008; delta88/86Sr, Rüggeberg et al. 2008). Within the frame of DFG-Project TRISTAN and Paläo-TRISTAN (Du 129/37-2 and 37-3) we investigated live-collected specimens of cold-water coral L. pertusa from all along the European continental margin (Northern and mid Norwegian shelves, Skagerrak, Rockall and Porcupine Bank, Galicia Bank, Gulf of Cadiz, Mediterranean Sea). These coral samples grew in waters characterized by temperatures between 6°C and 14°C. Electron Microprobe investigations along the growth direction of individual coral polyps were applied to determine the relationship between the incorporation of distinct elements (Sr, Ca, Mg, S). Cohen et al. (2006) showed for L. pertusa from the Kosterfjord, Skagerrak, that ~25% of the coral's Sr/Ca ratio is related to temperature, while 75% are influenced

  5. Sr/Ca ratios in cold-water corals - a 'low-resolution' temperature archive?

    NASA Astrophysics Data System (ADS)

    Rüggeberg, Andres; Riethdorf, Jan-Rainer; Raddatz, Jacek; López Correa, Matthias; Montagna, Paolo; Dullo, Wolf-Christian; Freiwald, André

    2010-05-01

    One of the basic data to understand global change and past global changes is the measurement and the reconstruction of temperature of marine water masses. E.g. seawater temperature controls the density of seawater and in combination with salinity is the major driving force for the oceans circulation system. Geochemical investigations on cold-water corals Lophelia pertusa and Desmophyllum cristagalli indicated the potential of these organisms as high-resolution archives of environmental parameters from intermediate and deeper water masses (Adkins and Boyle 1997). Some studies tried to use cold-water corals as a high-resolution archive of temperature and salinity (Smith et al. 2000, 2002; Blamart et al. 2005; Lutringer et al. 2005). However, the fractionation of stable isotopes (delta18O and delta13C) and element ratios (Sr/Ca, Mg/Ca, U/Ca) are strongly influenced by vital effects (Shirai et al. 2005; Cohen et al. 2006), and difficult to interpret. Nevertheless, ongoing studies indicate the potential of a predominant temperature dependent fractionation of distinct isotopes and elements (e.g. Li/Ca, Montagna et al. 2008; U/Ca, Mg/Ca, delta18O, Lòpez Correa et al. 2008; delta88/86Sr, Rüggeberg et al. 2008). Within the frame of DFG-Project TRISTAN and Paläo-TRISTAN (Du 129/37-2 and 37-3) we investigated live-collected specimens of cold-water coral L. pertusa from all along the European continental margin (Northern and mid Norwegian shelves, Skagerrak, Rockall and Porcupine Bank, Galicia Bank, Gulf of Cadiz, Mediterranean Sea). These coral samples grew in waters characterized by temperatures between 6°C and 14°C. Electron Microprobe investigations along the growth direction of individual coral polyps were applied to determine the relationship between the incorporation of distinct elements (Sr, Ca, Mg, S). Cohen et al. (2006) showed for L. pertusa from the Kosterfjord, Skagerrak, that ~25% of the coral's Sr/Ca ratio is related to temperature, while 75% are influenced

  6. Computational Studies of Flame Structures

    NASA Astrophysics Data System (ADS)

    Amin, Vaishali

    This thesis is concerned with computational studies of laminar flame structures using detailed and skeletal chemical kinetic mechanisms. Elementary reactions in these mechanisms control the observable combustion properties such as flame speed, autoignition temperature, ignition delay time, and extinction characteristics in nonpremixed and premixed flame phenomena. First part of thesis deals with computational investigations of influence of carbon monoxide and hydrogen addition on methane flames stabilized in counterflow configuration. Computations were performed employing detailed chemical kinetic mechanism---the San Diego mechanism. In case of nonpremixed flames, effect of carbon xvi monoxide addition on structure and critical condition of extinction were examined. Differences between addition on fuel and oxidizer sides were investigated and plausible explanation given for the differences. For premixed flames, effect of addition of hydrogen and carbon monoxide to reactant mixture was studied. Critical conditions of extinction were predicted using computations for various compositions. Rates of production and consumption of various species were calculated and flame structure was analyzed for nonpremixed and premixed flames. It was found that moderate amount of carbon monoxide addition to methane enhances flame reactivity. However, with large amount of carbon monoxide addition, additive chemistry dominates. Addition of increasing amounts of hydrogen in premixed reactant stream enhances methane flame reactivity. In second part of thesis, kinetic modeling was performed to elucidate the structure and mechanism of extinction and autoignition of nonpremixed toluene flames in counterflow configuration. Computations were performed using detailed chemistry to determine flame structure and to obtain values for critical conditions of extinction and autoignition. Sensitivity analysis of rate parameters, reaction pathway analysis, and spatial reaction rate profiles were used to

  7. Structural studies of bee melittin

    SciTech Connect

    Eisenberg, D.; Terwilliger, T.C.; Tsui, F.

    1980-10-01

    The question of how proteins refold in passing from an aqueous phase to an amphipathic environment such as a membrane is beig addressed by a structural study of bee melittin. Melittin is the toxic, main protein of bee venom, and has been shown by others to integrate into natural and synthetic membranes and to lyse a variety of cells. This function is presumably related to its unusual sequence. Except for charges at the N-terminus and at lysine 7, the first 20 residues are largely apolar. In contrast, the last six residues contain four charges and two polar residues.

  8. Structural studies of the formation of lipoplexes between siRNA and selected bis-imidazolium gemini surfactants.

    PubMed

    Andrzejewska, W; Pietralik, Z; Skupin, M; Kozak, M

    2016-10-01

    Dicationic (gemini) surfactants are agents that can be used for the preparation of stable complexes of nucleic acids, particularly siRNA for therapeutic purposes. In this study, we demonstrated that bis-imidazolium gemini surfactants with variable lengths of dioxyalkyl linker groups (from dioxyethyl to dioxydodecyl) and dodecyl side chains are excellent for the complexation of siRNA. All of these compounds effectively complexed siRNA in a charge ratio range (p/n) of 1.5-10. The low resolution structure of siRNA oligomers was characterised by small angle scattering of synchrotron radiation (SR-SAXS) and ab initio modelling. The structures of the formed complexes were also analysed using SR-SAXS, circular dichroism studies and electrophoretic mobility tests. The most promising agents for complexation with siRNA were the surfactants that contained dioxyethyl and dioxyhexyl spacer groups. PMID:27424091

  9. Comparative analysis of dioxins and furans by electron impact, high-resolution mass spectrometry and by electron capture, negative ionization, low-resolution mass spectrometry

    SciTech Connect

    Koester, C.J.; Harless, R.L.; Hites, R.A.

    1990-01-01

    Electron impact, high resolution mass spectrometry (HRMS) is currently the method of choice for the analysis of polychlorinated dibenso-p-dioxins and dibenzofurans (PCDD/F) because of its ability to detect PCDD/F in the presence of interfering compounds, such as polychlorinated biphenyls (PCB), which cannot be resolved by low resolution methods. The PDCC/F analyses may also be performed using electron capture, negative ionization (ECNI) low resolution mass spectrometry, providing extensive sample preparation is done to remove interferences. Before ECNI low resolution mass spectrometry (MS) can be accepted as a routine method for PCDD/F analysis, it is necessary to show that results generated by this method are comparable to those obtained by HRMS. Known mixtures and unknown air samples were analyzed by electron impact HRMS (Finnigan MAT 90 system) and by ECNI low resolution MS (Hewlett Packard 5985B). Both instruments were fitted with a gas chromatographic inlet. The PCDD/F concentrations determined by the two techniques compare favorably, typically within 20%. The major difference between these two methods is that the ECNI low resolution method shows poor sensitivity in detecting 2,3,7,8-tetrachlorodioxin. However, ECNI MS offers the advantage of lower detection limits (50-100 fg) than electron impact HRMS (0.1 to 0.5 pg). These results suggest that ECNI low resolution MS can be a simple, low cost alternative to the common high resolution methods used for PCDD/F analysis.

  10. Opportunities from low-resolution modelling of river morphology in remote parts of the world

    NASA Astrophysics Data System (ADS)

    Nones, M.; Guerrero, M.

    2013-10-01

    The study of rivers morphodynamics requires modelling of a variety of processes ranging from the typical small scale of fluid mechanics (e.g. flow turbulence dissipation) to the large scale of landscape evolution (e.g. fan deposition). However, simplifications inherent in the long-term modelling of large rivers derive from limited computational resource and the high level of processes detail (i.e. spatial and temporal resolution). These modelling results depend on processes parameterization and calibration over detailed field data (e.g. initial morphology). Thus, in these cases, simplified tools are attractive. Here, a simplified 1-D code is used for the modelling of very large rivers. A synthetic description of the variation of cross-sections shape is implemented on the basis of satellite images, typically available also in remote parts of the world. The model's flexibility is highlighted here, by presenting two applications. In the first case the model is used for analysing the long-term evolution of the Lower Zambezi (Africa) related to the construction of two reservoirs for hydropower exploitation; while, in the second case, the same code is applied for studying the evolution of the Middle and Lower Parana (Argentina) in light of climate variability. In both cases, having only basic data for boundary and initial conditions, the 1-D model provides results that are in agreement with past studies and that may be used to assist sediment management at watershed scale or at boundaries of more detailed modelling.

  11. The coelacanth rostral organ is a unique low-resolution electro-detector that facilitates the feeding strike

    PubMed Central

    Berquist, Rachel M.; Galinsky, Vitaly L.; Kajiura, Stephen M.; Frank, Lawrence R.

    2015-01-01

    The cartilaginous and non-neopterygian bony fishes have an electric sense typically comprised of hundreds or thousands of sensory canals distributed in broad clusters over the head. This morphology facilitates neural encoding of local electric field intensity, orientation, and polarity, used for determining the position of nearby prey. The coelacanth rostral organ electric sense, however, is unique in having only three paired sensory canals with distribution restricted to the dorsal snout, raising questions about its function. To address this, we employed magnetic resonance imaging methods to map electrosensory canal morphology in the extant coelacanth, Latimeria chalumnae, and a simple dipole ‘rabbit ears' antennae model with toroidal gain function to approximate their directional sensitivity. This identified a unique focal region of electrosensitivity directly in front of the mouth, and is the first evidence of a low-resolution electro-detector that solely facilitates prey ingestion. PMID:25758410

  12. A model-based approach for detection of objects in low resolution passive-millimeter wave images

    NASA Technical Reports Server (NTRS)

    Tang, Yuan-Liang; Devadiga, Sadashiva; Kasturi, Rangachar; Harris, Randall L., Sr.

    1993-01-01

    We describe a model-based vision system to assist pilots in landing maneuvers under restricted visibility conditions. The system was designed to analyze image sequences obtained from a Passive Millimeter Wave (PMMW) imaging system mounted on the aircraft to delineate runways/taxiways, buildings, and other objects on or near runways. PMMW sensors have good response in a foggy atmosphere; but, their spatial resolution is very low. However, additional data such as airport model and approximate position and orientation of aircraft are available. We exploit these data to guide our model-based system to locate objects in the low resolution image and generate warning signals to alert the pilots. We also derive analytical expressions for the accuracy of the camera position estimate obtained by detecting the position of known objects in the image.

  13. The coelacanth rostral organ is a unique low-resolution electro-detector that facilitates the feeding strike.

    PubMed

    Berquist, Rachel M; Galinsky, Vitaly L; Kajiura, Stephen M; Frank, Lawrence R

    2015-03-11

    The cartilaginous and non-neopterygian bony fishes have an electric sense typically comprised of hundreds or thousands of sensory canals distributed in broad clusters over the head. This morphology facilitates neural encoding of local electric field intensity, orientation, and polarity, used for determining the position of nearby prey. The coelacanth rostral organ electric sense, however, is unique in having only three paired sensory canals with distribution restricted to the dorsal snout, raising questions about its function. To address this, we employed magnetic resonance imaging methods to map electrosensory canal morphology in the extant coelacanth, Latimeria chalumnae, and a simple dipole 'rabbit ears' antennae model with toroidal gain function to approximate their directional sensitivity. This identified a unique focal region of electrosensitivity directly in front of the mouth, and is the first evidence of a low-resolution electro-detector that solely facilitates prey ingestion.

  14. The mid-infrared instrument for the James Webb Space Telescope: performance and operation of the Low-Resolution Spectrometer

    NASA Astrophysics Data System (ADS)

    Kendrew, Sarah; Scheithauer, Silvia; Bouchet, Patrice; Amiaux, Jerome; Azzollini, Ruymán.; Bouwman, Jeroen; Chen, Christine; Dubreuil, Didier; Fischer, Sebastian; Fox, Ori D.; Glasse, Alistair; Gordon, Karl; Greene, Tom; Hines, Dean C.; Lagage, Pierre-Olivier; Lahuis, Fred; Ronayette, Samuel; Wright, David; Wright, Gillian S.

    2016-07-01

    We describe here the performance and operational concept for the Low Resolution Spectrometer (LRS) of the mid-infrared instrument (MIRI) for the James Webb Space Telescope. The LRS will provide R˜100 slit and slitless spectroscopy from 5 to 12 micron, and its design is optimised for observations of compact sources, such as exoplanet host stars. We provide here an overview of the design of the LRS, and its performance as measured during extensive test campaigns, examining in particular the delivered image quality, dispersion, and resolving power, as well as spectrophotometric performance. The instrument also includes a slitless spectroscopy mode, which is optimally suited for transit spectroscopy of exoplanet atmospheres. We provide an overview of the operational procedures and the differences ahead of the JWST launch in 2018.

  15. The coelacanth rostral organ is a unique low-resolution electro-detector that facilitates the feeding strike.

    PubMed

    Berquist, Rachel M; Galinsky, Vitaly L; Kajiura, Stephen M; Frank, Lawrence R

    2015-01-01

    The cartilaginous and non-neopterygian bony fishes have an electric sense typically comprised of hundreds or thousands of sensory canals distributed in broad clusters over the head. This morphology facilitates neural encoding of local electric field intensity, orientation, and polarity, used for determining the position of nearby prey. The coelacanth rostral organ electric sense, however, is unique in having only three paired sensory canals with distribution restricted to the dorsal snout, raising questions about its function. To address this, we employed magnetic resonance imaging methods to map electrosensory canal morphology in the extant coelacanth, Latimeria chalumnae, and a simple dipole 'rabbit ears' antennae model with toroidal gain function to approximate their directional sensitivity. This identified a unique focal region of electrosensitivity directly in front of the mouth, and is the first evidence of a low-resolution electro-detector that solely facilitates prey ingestion. PMID:25758410

  16. Spectral irradiance calibration in the infrared. II - Alpha Tau and the recalibration of the IRAS low resolution spectrometer

    NASA Technical Reports Server (NTRS)

    Cohen, Martin; Walker, Russell G.; Witteborn, Fred C.

    1992-01-01

    A general process for creating complete, continuous, and absolutely calibrated 1-35 micron stellar spectra is described. The method is demonstrated by constructing an absolutely calibrated 1-35 micron spectrum of Alpha Tau and the method is independently validated using new observations. The absolute calibration of the IRAS low resolution spectrometer (LRS) data base is investigated by comparing the observed spectrum of Alpha Tau with that assumed in the original LRS calibration scheme. An analysis of asteroidal LRS spectra results in an independent assessment of the calibration problems with the LRS and provides a natural complement to the effort based on Alpha Tau. A direct comparison of LRS stellar spectra with independently calibrated long-wavelength airborne and ground-based spectra is made.

  17. Opportunities from low-resolution modelling of river morphology in remote parts of the world

    NASA Astrophysics Data System (ADS)

    Nones, M.; Guerrero, M.; Ronco, P.

    2014-01-01

    River morphodynamics are the result of a variety of processes, ranging from the typical small-scale of fluid mechanics (e.g. flow turbulence dissipation) to the large-scale of landscape evolution (e.g. fan deposition). However, problems inherent in the long-term modelling of large rivers derive from limited computational resources and the high level of process detail (i.e. spatial and temporal resolution). These modelling results depend on processes parameterization and calibrations based on detailed field data (e.g. initial morphology). Thus, for these cases, simplified tools are attractive. In this paper, a simplified 1-D approach is presented that is suited for modelling very large rivers. A synthetic description of the variations of cross-sections shapes is implemented on the basis of satellite images, typically also available for remote parts of the world. The model's flexibility is highlighted here by presenting two applications. In the first case, the model is used for analysing the long-term evolution of the lower Zambezi River (Africa) as it relates to the construction of two reservoirs for hydropower exploitation. In the second case, the same model is applied to study the evolution of the middle and lower Paraná River (Argentina), particularly in the context of climate variability. In both cases, having only basic data for boundary and initial conditions, the 1-D model provides results that are in agreement with past studies and therefore shows potential to be used to assist sediment management at the watershed scale or at boundaries of more detailed models.

  18. ELM: an Algorithm to Estimate the Alpha Abundance from Low-resolution Spectra

    NASA Astrophysics Data System (ADS)

    Bu, Yude; Zhao, Gang; Pan, Jingchang; Bharat Kumar, Yerra

    2016-01-01

    We have investigated a novel methodology using the extreme learning machine (ELM) algorithm to determine the α abundance of stars. Applying two methods based on the ELM algorithm—ELM+spectra and ELM+Lick indices—to the stellar spectra from the ELODIE database, we measured the α abundance with a precision better than 0.065 dex. By applying these two methods to the spectra with different signal-to-noise ratios (S/Ns) and different resolutions, we found that ELM+spectra is more robust against degraded resolution and ELM+Lick indices is more robust against variation in S/N. To further validate the performance of ELM, we applied ELM+spectra and ELM+Lick indices to SDSS spectra and estimated α abundances with a precision around 0.10 dex, which is comparable to the results given by the SEGUE Stellar Parameter Pipeline. We further applied ELM to the spectra of stars in Galactic globular clusters (M15, M13, M71) and open clusters (NGC 2420, M67, NGC 6791), and results show good agreement with previous studies (within 1σ). A comparison of the ELM with other widely used methods including support vector machine, Gaussian process regression, artificial neural networks, and linear least-squares regression shows that ELM is efficient with computational resources and more accurate than other methods.

  19. Monitoring environmental change in the Andes based on low resolution time series analysis

    NASA Astrophysics Data System (ADS)

    Tote, C.; Swinnen, E.; Beringhs, K.; Govers, G.

    2012-04-01

    Environmental change is an important issue in the Andes region and it is unknown to what extent the ongoing processes are a consequence of human impact and/or climate change. The objectives of this research are to study vegetation dynamics in the Andes region based on time series analysis of SPOT-Vegetation, NOAA-AVHRR and MODIS derived NDVI at low spatial but high temporal resolution, and to recognize to which extent this variability can be attributed to either climatic variability or human induced impacts through assimilation of satellite derived NDVI and rainfall data. Monthly rainfall estimates were available from the European Centre for Medium-Range Weather Forecasts (ECMWF) through MeteoConsult and the Monitoring Agricultural ResourceS (MARS) unit. Deviations from the 'average' situation were calculated for the NDVI time series using the Standardized Difference Vegetation Index (SDVI) and for the precipitation time series using the Standardized Precipitation Index (SPI). Correlation analysis between NDVI and SPI is performed in order to identify the temporal scale at which the environment is most sensitive to precipitation anomalies (best lag). Trends in SDVI and SPI are investigated using least square regression, taking into account the accumulated rainfall anomalies over the best lag. Hot spots of human induced environmental change are detected by subtraction of the precipitation induced signal on vegetation dynamics. The model can be used to predict possible effects of climate change in areas most sensible to trends in precipitation.

  20. Low-Resolution Electromagnetic Tomography (LORETA) of changed Brain Function Provoked by Pro-Dopamine Regulator (KB220z) in one Adult ADHD case

    PubMed Central

    Steinberg, Bruce; Blum, Kenneth; McLaughlin, Thomas; Lubar, Joel; Febo, Marcelo; Braverman, Eric R.; Badgaiyan, Rajendra D

    2016-01-01

    Attention Deficit-Hyperactivity Disorder (ADHD) often continues into adulthood. Recent neuroimaging studies found lowered baseline dopamine tone in the brains of affected individuals that may place them at risk for Substance Use Disorder (SUD). This is an observational case study of the potential for novel management of Adult ADHD with a non-addictive glutaminergic-dopaminergic optimization complex KB200z. Low-resolution electromagnetic tomography (LORETA) was used to evaluate the effects of KB220z on a 72-year-old male with ADHD, at baseline and one hour following administration. The resultant z-scores, averaged across Eyes Closed, Eyes Open and Working Memory conditions, increased for each frequency band, in the anterior, dorsal and posterior cingulate regions, as well as the right dorsolateral prefrontal cortex during Working Memory, with KB220z. These scores are consistent with other human and animal neuroimaging studies that demonstrated increased connectivity volumes in reward circuitry and may offer a new approach to ADHD treatment. However, larger randomized trials to confirm these results are required.

  1. Low-Resolution Electromagnetic Tomography (LORETA) of changed Brain Function Provoked by Pro-Dopamine Regulator (KB220z) in one Adult ADHD case

    PubMed Central

    Steinberg, Bruce; Blum, Kenneth; McLaughlin, Thomas; Lubar, Joel; Febo, Marcelo; Braverman, Eric R.; Badgaiyan, Rajendra D

    2016-01-01

    Attention Deficit-Hyperactivity Disorder (ADHD) often continues into adulthood. Recent neuroimaging studies found lowered baseline dopamine tone in the brains of affected individuals that may place them at risk for Substance Use Disorder (SUD). This is an observational case study of the potential for novel management of Adult ADHD with a non-addictive glutaminergic-dopaminergic optimization complex KB200z. Low-resolution electromagnetic tomography (LORETA) was used to evaluate the effects of KB220z on a 72-year-old male with ADHD, at baseline and one hour following administration. The resultant z-scores, averaged across Eyes Closed, Eyes Open and Working Memory conditions, increased for each frequency band, in the anterior, dorsal and posterior cingulate regions, as well as the right dorsolateral prefrontal cortex during Working Memory, with KB220z. These scores are consistent with other human and animal neuroimaging studies that demonstrated increased connectivity volumes in reward circuitry and may offer a new approach to ADHD treatment. However, larger randomized trials to confirm these results are required. PMID:27610420

  2. Field-structured composite studies.

    SciTech Connect

    Martin, James Ellis; Williamson, Rodney L.

    2004-04-01

    Field-structured composites (FSCs) were produced by hosting micron-sized gold-coated nickel particles in a pre-polymer and allowing the mixture to cure in a magnetic field environment. The feasibility of controlling a composite's electrical conductivity using feedback control applied to the field coils was investigated. It was discovered that conductivity in FSCs is primarily determined by stresses in the polymer host matrix due to cure shrinkage. Thus, in cases where the structuring field was uniform and unidirectional so as to produce chainlike structures in the composite, no electrical conductivity was measured until well after the structuring field was turned off at the gel point. In situations where complex, rotating fields were used to generate complex, three-dimensional structures in a composite, very small, but measurable, conductivity was observed prior to the gel point. Responsive, sensitive prototype chemical sensors were developed based on this technology with initial tests showing very promising results.

  3. Structural studies in limestone sulfidation

    SciTech Connect

    Fenouil, L.A.; Lynn, S.

    1993-05-01

    This study investigates the sulfidation of limestone at high temperatures (700--900{degree}C) as the first step in the design of a High-Temperature Coal-Gas Clean-Up system using millimeter-size limestone particles. Several workers have found that the rate of this reaction significantly decreases after an initial 10 to 15% conversion of CaCO{sub 3} to CaS. The present work attempts to explain this feature. It is first established that millimeter-size limestone particles do not sinter at temperatures up to the CaCO{sub 3} calcination point (899{degree}C at 1.03 bar CO{sub 2} partial pressure). It is then shown that CaS sinters rapidly at 750 to 900{degree}C if CO{sub 2} is present in the gas phase. Scanning Electron Microscope (SEM) photographs and Electron Dispersive Spectroscopy (EDS) data reveal that the CaS product layer sinters and forms a quasi-impermeable coating around the CaCO{sub 3} grains that greatly hinders more H{sub 2}S from reaching the still unreacted parts of the stone. Moreover, most of the pores initially present within the limestone structure begin to disappear or, at least, are significantly reduced in size. From then on, subsequent conversion is limited by diffusion of H{sub 2}S through the CaS layer, possibly by S{sup 2{minus}} ionic diffusion. The kinetics is then adequately described by a shrinking-core model, in which a sharp front of completely converted limestone is assumed to progress toward the center of the pellet. Finally, experimental evidence and computer simulations using simple sintering models suggest that the CaS sintering, responsible for the sharp decrease in the sulfidation rate, is surface-diffusion controlled.

  4. The study on large space structure assembly technology: The study on deployable truss structure, part 1

    NASA Astrophysics Data System (ADS)

    1993-03-01

    An overview of the results of the study on large structure assembly technology is presented. The following aspects of the study are outlined: (1) placement and scope of the study; (2) study on large structure assembly technology, establishment of the dimensional requirements for the deployable structure, and extraction of critical elements in deployable structure system technology; (3) design study on critical elements, including study on the deployable structure systems, design study on one dimensional deployable truss structure and element technologies, and study on deployment simulation software and deployment test equipment; (4) planning of the trial production and test program; and (5) WBS (Work Breakdown Structure) for the deployable assembly structure study.

  5. Potential radionuclide emissions from stacks on the Hanford site, Part 2: Dose assessment methodology using portable low-resolution gamma spectroscopy

    SciTech Connect

    Barnett, J.M.

    1995-02-01

    In September 1992, the Westinghouse Hanford Company began developing an in situ measurement method to assess gamma radiation emanating from high-efficiency particulate air filters using portable low-resolution gamma spectroscopy. The purpose of the new method was to assess radioactive exhaust stack air emissions from empirical data rather than from theoretical models and to determine the potential unabated dose to an offsite theoretical maximally exposed individual. In accordance with Title 40, Code of Federal Regulations, Part 61, Subpart H, {open_quotes}National Emission Standards for Hazardous Air Pollutants{close_quotes}, stacks that have the potential to emit {ge} 1 {mu}Sv y{sup {minus}1} (0.1 mrem y{sup {minus}1}) to the maximally exposed individual are considered {open_quotes}major{close_quotes} and must meet the continuous monitoring requirements. After the method was tested and verified, the U.S. Environmental Protection Agency, Region 10, approved its use in June 1993. Of the 125 stacks operated by the Westinghouse Hanford Company, 22 were targeted for evaluation by this method, and 15 were assessed. (The method could not be applied at seven stacks because of excessive background radiation or because no gamma emitting particles appear in the emission stream.) The most significant result from this study was the redesignation of the T Plant main stack. The stack was assessed as being {open_quotes}minor{close_quotes}, and it now only requires periodic confirmatory measurements and meets federally imposed sampling requirements.

  6. LOW-RESOLUTION SPECTROSCOPY FOR THE GLOBULAR CLUSTERS WITH SIGNS OF SUPERNOVA ENRICHMENT: M22, NGC 1851, AND NGC 288

    SciTech Connect

    Lim, Dongwook; Han, Sang-Il; Lee, Young-Wook; Roh, Dong-Goo; Sohn, Young-Jong; Chun, Sang-Hyun; Lee, Jae-Woo; Johnson, Christian I.

    2015-01-01

    There is increasing evidence for the presence of multiple red giant branches (RGBs) in the color-magnitude diagrams of massive globular clusters (GCs). In order to investigate the origin of this split on the RGB, we have performed new narrow-band Ca photometry and low-resolution spectroscopy for M22, NGC 1851, and NGC 288. We find significant differences (more than 4σ) in calcium abundance from the spectroscopic HK' index for M22 and NGC 1851. We also find more than 8σ differences in CN-band strength between the Ca-strong and Ca-weak subpopulations for these GCs. For NGC 288, however, a large difference is detected only in the CN strength. The calcium abundances of RGB stars in this GC are identical to within the errors. This is consistent with the conclusion from our new Ca photometry where the RGB splits are confirmed in M22 and NGC 1851, but not in NGC 288. We also find interesting differences in the CN-CH correlations among these GCs. While CN and CH are anti-correlated in NGC 288, they show a positive correlation in M22. NGC 1851, however, shows no difference in CH between the two groups of stars with different CN strengths. We suggest that all of these systematic differences would be best explained by how strongly Type II supernovae enrichment has contributed to the chemical evolution of these GCs.

  7. A method of discriminating transuranic radionuclides from radon progeny using low-resolution alpha spectroscopy and curve-fitting techniques.

    PubMed

    Konzen, Kevin; Brey, Richard

    2012-05-01

    ²²²Rn (radon) and ²²⁰Rn (thoron) progeny are known to interfere with determining the presence of long-lived transuranic radionuclides, such as plutonium and americium, and require from several hours up to several days for conclusive results. Methods are proposed that should expedite the analysis of air samples for determining the amount of transuranic radionuclides present using low-resolution alpha spectroscopy systems available from typical alpha continuous air monitors (CAMs) with multi-channel analyzer (MCA) capabilities. An alpha spectra simulation program was developed in Microsoft Excel visual basic that employed the use of Monte Carlo numerical methods and serial-decay differential equations that resembled actual spectra. Transuranic radionuclides were able to be quantified with statistical certainty by applying peak fitting equations using the method of least squares. Initial favorable results were achieved when samples containing radon progeny were decayed 15 to 30 min, and samples containing both radon and thoron progeny were decayed at least 60 min. The effort indicates that timely decisions can be made when determining transuranic activity using available alpha CAMs with alpha spectroscopy capabilities for counting retrospective air samples if accompanied by analyses that consider the characteristics of serial decay.

  8. Preliminary shuttle structural dynamics modeling design study

    NASA Technical Reports Server (NTRS)

    1972-01-01

    The design and development of a structural dynamics model of the space shuttle are discussed. The model provides for early study of structural dynamics problems, permits evaluation of the accuracy of the structural and hydroelastic analysis methods used on test vehicles, and provides for efficiently evaluating potential cost savings in structural dynamic testing techniques. The discussion is developed around the modes in which major input forces and responses occur and the significant structural details in these modes.

  9. Wayfinding with simulated prosthetic vision: performance comparison with regular and structure-enhanced renderings.

    PubMed

    Vergnieux, Victor; Macé, Marc J-M; Jouffrais, Christophe

    2014-01-01

    In this study, we used a simulation of upcoming low-resolution visual neuroprostheses to evaluate the benefit of embedded computer vision techniques in a wayfinding task. We showed that augmenting the classical phosphene rendering with the basic structure of the environment - displaying the ground plane with a different level of brightness - increased both wayfinding performance and cognitive mapping. In spite of the low resolution of current and upcoming visual implants, the improvement of these cognitive functions may already be possible with embedded artificial vision algorithms.

  10. Large space erectable structures - building block structures study

    NASA Technical Reports Server (NTRS)

    Armstrong, W. H.; Skoumal, D. E.; Straayer, J. W.

    1977-01-01

    A modular planar truss structure and a long slender boom concept identified as building block approaches to construction of large spacecraft configurations are described. The concepts are compatible in weight and volume goals with the Space Transportation System, use standard structural units, and represent high on-orbit productivity in terms of structural area or beam length. Results of structural trade studies involving static and dynamic analyses of a single module and rigid body deployment analyses to assess kinetics and kinematics of automatic deployment of the building block modules are presented.

  11. Use of a shielded low resolution gamma spectrometer for segregation of free release and low level waste

    SciTech Connect

    Wilkins, C.G.; Alvarez, E.; Cocks, J.; Davison, L.; Mattinson, A.

    2007-07-01

    In the UK, low level radioactive waste (LLW) is sent to the national Low Level Waste Repository (LLWR) at Drigg in Cumbria. Strict rules limit the specific activity of waste that is sent to the LLW Repository and waste producers and consignors have to demonstrate that the waste they send to the repository meets its conditions for acceptance. However, the limited capacity of the Low Level Waste Repository means that it is just as important for waste consignees to ensure that inactive 'free release' or 'exempt' waste is not inadvertently sent to the repository. Incorrect segregation of waste in a decommissioning activity can mean that large amounts of the waste produced is below the exemption limit and could therefore be disposed of in conventional landfill. Sellafield Ltd. is using a pair of Canberra WM2750 Clearance Monitors to assay 100 litre packages of soft waste produced in some of their decommissioning activities at Sellafield. The WM2750 uses low resolution gamma spectrometry (LRGS) to determine the radionuclide content of packages or drums of LLW up to a maximum of 140 litre capacity. It uses a lead shielded measurement chamber to reduce the local radiation background along with high efficiency sodium iodide (NaI) detectors in order to obtain the measurement sensitivity required to be able to distinguish between LLW and exempt waste in a measurement time of less than 1 minute per package. This paper describes the waste monitoring process and the design of the clearance monitor - in particular how it was calibrated and the performance testing that was carried out to ensure that waste items identified by the monitors as being exempt waste are suitable for disposal to a conventional landfill site. (authors)

  12. Three-Dimensional Electroencephalographic Changes on Low-Resolution Brain Electromagnetic Tomography (LORETA) During the Sleep Onset Period.

    PubMed

    Park, Doo-Heum; Ha, Jee Hyun; Ryu, Seung-Ho; Yu, Jaehak; Shin, Chul-Jin

    2015-10-01

    Electroencephalographic (EEG) patterns during sleep are markedly different from those measured during the waking state, but the process of falling asleep is not fully understood in terms of biochemical and neurophysiological aspects. We sought to investigate EEG changes that occur during the transitional period from wakefulness to sleep in a 3-dimensional manner to gain a better understanding of the physiological meaning of sleep for the brain. We examined EEG 3-dimensionally using LORETA (low-resolution electromagnetic tomography), to localize the brain region associated with changes that occur during the sleep onset period (SOP). Thirty-channel EEG was recorded in 61 healthy subjects. EEG power spectra and intracortical standardized LORETA were compared between 4 types of 30-second states, including the wakeful stage, transition stage, early sleep stage 1, and late sleep stage 1. Sleep onset began with increased delta and theta power and decreased alpha-1 power in the occipital lobe, and increased theta power in the parietal lobe. Thereafter, global reductions of alpha-1 and alpha-2 powers and greater increases of theta power in the occipito-parietal lobe occurred. As sleep became deeper in sleep stage 1, beta-2 and beta-3, powers decreased mainly in the frontal lobe and some regions of the parieto-temporo-limbic area. These findings suggest that sleep onset includes at least 3 steps in a sequential manner, which include an increase in theta waves in the posterior region of the brain, a global decrease in alpha waves, and a decrease in beta waves in the fronto-central area.

  13. Nuclear structure studies with intermediate energy probes

    SciTech Connect

    Lee, T.S.H.

    1993-10-01

    Nuclear structure studies with pions are reviewed. Results from a recent study of 1 p-shell nuclei using (e,e{prime}), ({pi}, {pi}{prime}), and ({gamma},{pi}) reactions are reported. Future nuclear structure studies with GeV electrons at CEBAF are also briefly discussed.

  14. Structural studies of hydrodesulfurization catalysts

    SciTech Connect

    Sanchez, A.

    1983-01-01

    Hydrodesulfurization (HDS) is a catalytic process used to remove sulfur from S-containing compounds by converting it to hdyrogen sulfide in the presence of dihydrogen. Catalysts used in HDS are mainly made of molybdenum and cobalt sulfides supported on ..gamma..-alumina. The objective of this work was to correlate changes in the HDS activity of these catalysts with structural information obtained by X-ray absorption spectroscopy (XAS). Two series of catalysts were prepared, one by incipient wetness impregnation and the other by bulk impregnation. The catalysts had approximately the same Mo content and varying Co content, and were tested for thiophene HDS in a fixed bed reactor at 573 K and atmospheric pressure. Extended X-ray absorption fine structure (EXAFS) and X-ray absorption edge spectroscopy (XAES) were used at the Mo and Co K-edges. The catalysts were treated in a mixture of hydrogen sulfide/dihydrogen. For both series of catalysts, HDS activity increased with atomic ratio r = Co/(Co + Mo), reached a maximum and declined with further increase in r. Catalysts prepared by incipient wetness impregnation showed higher HDS activity. From EXAFS and XAES, it appears that molybdenum has a local environment similar to that of molybdenum disulfide, very dispersed on the surface of the alumina. Cobalt has sulfur atoms as nearest neighbors. The number N(S) of sulfur neighbors of Mo, determined from EXAFS, depends on r like HDS activity, and shows a linear correlation with HDS activity that holds for both series of catalysts. It seems reasonable that as r increases, the sulfur binding energy of Mo increases until the maximum value of N(S) is reached, and then declines.

  15. Spitzer/infrared spectrograph investigation of mipsgal 24 μm compact bubbles: low-resolution observations

    SciTech Connect

    Nowak, M.; Flagey, N.; Noriega-Crespo, A.; Carey, S. J.; Van Dyk, S. D.; Billot, N.; Paladini, R.

    2014-12-01

    We present Spitzer/InfraRed Spectrograph (IRS) low-resolution observations of 11 compact circumstellar bubbles from the MIPSGAL 24 μm Galactic plane survey. We find that this set of MIPSGAL bubbles (MBs) is divided into two categories and that this distinction correlates with the morphologies of the MBs in the mid-infrared (IR). The four MBs with central sources in the mid-IR exhibit dust-rich, low-excitation spectra, and their 24 μm emission is accounted for by the dust continuum. The seven MBs without central sources in the mid-IR have spectra dominated by high-excitation gas lines (e.g., [O IV] 26.0 μm, [Ne V] 14.3 and 24.3 μm, and [Ne III] 15.5 μm), and the [O IV] line accounts for 50% to almost 100% of the 24 μm emission in five of them. In the dust-poor MBs, the [Ne V] and [Ne III] line ratios correspond to high-excitation conditions. Based on comparisons with published IRS spectra, we suggest that the dust-poor MBs are highly excited planetary nebulae (PNs) with peculiar white dwarfs (e.g., Wolf-Rayet [WR] and novae) at their centers. The central stars of the four dust-rich MBs are all massive star candidates. Dust temperatures range from 40 to 100 K in the outer shells. We constrain the extinction along the lines of sight from the IRS spectra. We then derive distance, dust masses, and dust production rate estimates for these objects. These estimates are all consistent with the nature of the central stars. We summarize the identifications of MBs made to date and discuss the correlation between their mid-IR morphologies and natures. Candidate Be/B[e]/luminous blue variable and WR stars are mainly 'rings' with mid-IR central sources, whereas PNs are mostly 'disks' without mid-IR central sources. Therefore we expect that most of the 300 remaining unidentified MBs will be classified as PNs.

  16. Design and construction progress of LRS2-B: a new low resolution integral-field spectrograph for the Hobby-Eberly Telescope

    NASA Astrophysics Data System (ADS)

    Chonis, Taylor S.; Lee, Hanshin; Hill, Gary J.; Cornell, Mark E.; Tuttle, Sarah E.; Vattiat, Brian L.

    2012-09-01

    The upcoming Wide-Field Upgrade (WFU) has ushered in a new era of instrumentation for the Hobby-Eberly Telescope (HET). Here, we present the design, construction progress, and lab tests completed to date of the blue-optimized second generation Low Resolution Spectrograph (LRS2-B). LRS2-B is a dual-channel, fiber fed instrument that is based on the design of the Visible Integral Field Replicable Unit Spectrograph (VIRUS), which is the new flagship instrument for carrying out the HET Dark Energy eXperiment (HETDEX). LRS2-B utilizes a microlens-coupled integral field unit (IFU) that covers a 7"x12" area on the sky having unity fill-factor with ~300 spatial elements that subsample the median HET image quality. The fiber feed assembly includes an optimized dichroic beam splitter that allows LRS2-B to simultaneously observe 370 <λ(nm) < 470 and 460 < λ(nm) < 700 at fixed resolving powers of R ≍ λ/Δλ ≍ 1900 and 1200, respectively. We discuss the departures from the nominal VIRUS design, which includes the IFU, fiber feed, camera correcting optics, and volume phase holographic grisms. Additionally, the motivation for the selection of the wavelength coverage and spectral resolution of the two channels is briefly discussed. One such motivation is the follow-up study of spectrally and (or) spatially resolved Lyα emission from z ≍ 2.5 star-forming galaxies in the HETDEX survey. LRS2-B is planned to be a commissioning instrument for the HET WFU and should be on-sky during quarter 4 of 2013. Finally, we mention the current state of LRS2-R, the red optimized sister instrument of LRS2-B.

  17. Comparison of sensitivity between gas chromatography-low-resolution mass spectrometry and gas chromatography-high-resolution mass spectrometry for determining metandienone metabolites in urine.

    PubMed

    Kokkonen, J; Leinonen, A; Tuominen, J; Seppälä, T

    1999-11-12

    In doping control laboratories the misuse of anabolic androgenic steroids is commonly investigated in urine by gas chromatography-low-resolution mass spectrometry with selected ion monitoring (GC-LRMS-SIM). By using high-resolution mass spectrometry (HRMS) detection sensitivity is improved due to reduction of biological background. In our study HRMS and LRMS methods were compared to each other. Two different sets were measured both with HRMS and LRMS. In the first set metandienone (I) metabolites 17alpha-methyl-5beta-androstan-3alpha,17beta-dio l (II), 17-epimetandienone (III), 17beta-methyl-5beta-androst-1-ene-3alpha,17alpha-diol (IV) and 6beta-hydroxymetandienone (V) were spiked in urine extract prepared by solid-phase extraction, hydrolysis with beta-glucuronidase from Escherichia coli and liquid-liquid extraction. In the second set the metabolites were first spiked in blank urine samples of four male persons before pretreatment. Concentration range of the spiked metabolites was 0.1-10 ng/ml in both sets. With HRMS (resolution of 5000) detection limits were 2-10 times lower than with LRMS. However, also with the HRMS method the biological background hampered detection and compounds from matrix were coeluted with some metabolites. For this reason the S/N values of the metabolites spiked had to be first compared to S/N values of coeluted matrix compounds to get any idea of detection limits. At trace concentrations selective isolation procedures should be implemented in order to confirm a positive result. The results suggest that metandienone misuse can be detected by HRMS for a prolonged period after stopping the intake of metandienone. PMID:10595716

  18. Electromagnetic studies of nuclear structure and reactions

    SciTech Connect

    Hersman, F.W.; Dawson, J.F.; Heisenberg, J.H.; Calarco, J.R.

    1990-06-01

    This report contains papers on the following topics: giant resonance studies; deep inelastic scattering studies; high resolution nuclear structure work; and relativistic RPA; and field theory in the Schroedinger Representation.

  19. Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models.

    PubMed

    Frank, Aaron T; Law, Sean M; Ahlstrom, Logan S; Brooks, Charles L

    2015-01-13

    Given the demonstrated utility of coarse-grained modeling and simulations approaches in studying protein structure and dynamics, developing methods that allow experimental observables to be directly recovered from coarse-grained models is of great importance. In this work, we develop one such method that enables protein backbone chemical shifts (1HN, 1Hα, 13Cα, 13C, 13Cβ, and 15N) to be predicted from Cα coordinates. We show that our Cα-based method, LARMORCα, predicts backbone chemical shifts with comparable accuracy to some all-atom approaches. More importantly, we demonstrate that LARMORCα predicted chemical shifts are able to resolve native structure from decoy pools that contain both native and non-native models, and so it is sensitive to protein structure. As an application, we use LARMORCα to characterize the transient state of the fast-folding protein gpW using recently published NMR relaxation dispersion derived backbone chemical shifts. The model we obtain is consistent with the previously proposed model based on independent analysis of the chemical shift dispersion pattern of the transient state. We anticipate that LARMORCα will find utility as a tool that enables important protein conformational substates to be identified by “parsing” trajectories and ensembles generated using coarse-grained modeling and simulations.

  20. (High-pressure structural studies of promethium)

    SciTech Connect

    Haire, R.G.

    1988-11-15

    The primary object of the foreign travel was to carry out collaborative high-pressure structural studies at the European Institute for Transuranium Elements (EITU), Karlsruhe, Federal Republic of Germany. These studies reestablished previous collaborative investigations by ORNL and EITU that have been very productive scientifically during the past few years. The study during the present travel period was limited to a structural study of promethium metal under pressure.

  1. Experimental Study of Nucleon Structure and QCD

    SciTech Connect

    Jian-Ping Chen

    2012-03-01

    Overview of Experimental Study of Nucleon Structure and QCD, with focus on the spin structure. Nucleon (spin) Structure provides valuable information on QCD dynamics. A decade of experiments from JLab yields these exciting results: (1) valence spin structure, duality; (2) spin sum rules and polarizabilities; (3) precision measurements of g{sub 2} - high-twist; and (4) first neutron transverse spin results - Collins/Sivers/A{sub LT}. There is a bright future as the 12 GeV Upgrade will greatly enhance our capability: (1) Precision determination of the valence quark spin structure flavor separation; and (2) Precision extraction of transversity/tensor charge/TMDs.

  2. Structural studies on HCN oligomers.

    PubMed

    Ferris, J P; Edelson, E H; Auyeung, J M; Joshi, P C

    1981-01-01

    NMR spectral studies on the HCN oligomers suggest the presence of carboxamide and urea groupings. The release of CO2, H2O, HCN, CH3CN, HCONH2 and pyridine on pyrolysis is consistent with the presence of these groupings as well as carboxylic acid groups. No basic primary amine groupings could be detected with fluorescamine. Hydrazinolysis of the HCN oligomers releases 10% of the amino acids normally released by acid hydrolysis. The oligomers give a positive biuret test but this is not due to the presence of peptide bonds. There is no conclusive evidence for the presence of peptide bonds in the HCN oligomers. No diglycine was detected on partial hydrolysis of the HCN oligomers at pH 8.5 suggesting that HCN oligomers were not a source of prebiotic peptides.

  3. Structural damping studies at cryogenic temperatures

    NASA Technical Reports Server (NTRS)

    Young, Clarence P., Jr.; Buehrle, Ralph D.

    1994-01-01

    Results of an engineering study to measure changes in structural damping properties of two cryogenic wind tunnel model systems and two metallic test specimens at cryogenic temperatures are presented. Data are presented which indicate overall, a trend toward reduced structural damping at cryogenic temperatures (-250 degrees F) when compared with room temperature damping properties. The study was focused on structures and materials used for model systems tested in the National Transonic Facility (NTF). The study suggests that the significant reductions in damping at extremely cold temperatures are most likely associated with changes in mechanical joint compliance damping rather than changes in material (solid) damping.

  4. Structures performance, benefit, cost-study

    NASA Technical Reports Server (NTRS)

    Woike, O. G.; Salemme, C.; Stearns, E.; Oritz, P.; Roberts, M. L.; Baughman, J. L.; Johnston, R. P.; Demel, H. F.; Stabrylla, R. G.; Coffinberry, G. A.

    1981-01-01

    New technology concepts and structural analysis development needs which could lead to improved life cycle cost for future high-bypass turbofans were studied. The NASA-GE energy efficient engine technology is used as a base to assess the concept benefits. Recommended programs are identified for attaining these generic structural and other beneficial technologies.

  5. Displaying a high-resolution digital hologram on a low-resolution spatial light modulator with the same resolution obtained from the hologram.

    PubMed

    Tsang, P W M; Poon, T-C; Zhou, C

    2013-07-29

    In this paper, a fast method for displaying a digital, real and off-axis Fresnel hologram on a lower resolution device is reported. Preserving the original resolution of the hologram upon display is one of the important attributes of the proposed method. Our method can be divided into 3 stages. First, a digital hologram representing a given three dimensional (3D) object is down-sampled based on a fix, jitter down-sampling lattice. Second, the down-sampled hologram is interpolated, through pixel duplication, into a low resolution hologram that can be displayed with a low-resolution spatial light modulator (SLM). Third, the SLM is overlaid with a grating which is generated based on the same jitter down-sampling lattice that samples the hologram. The integration of the grating and the low-resolution hologram results in, to a good approximation, the resolution of the original hologram. As such, our proposed method enables digital holograms to be displayed with lower resolution SLMs, paving the way for the development of low-cost holographic video display.

  6. Structural Studies of Biological Solids Using NMR

    NASA Astrophysics Data System (ADS)

    Ramamoorthy, Ayyalusamy

    2011-03-01

    High-resolution structure and dynamics of biological molecules are important in understanding their function. While studies have been successful in solving the structures of water-soluble biomolecules, it has been proven difficult to determine the structures of membrane proteins and fibril systems. Recent studies have shown that solid-state NMR is a promising technique and could be highly valuable in studying such non-crystalline and non-soluble biosystems. I will present strategies to study the structures of such challenging systems and also about the applications of solid-state NMR to study the modes of membrane-peptide interactions for a better assessment of the prospects of antimicrobial peptides as substitutes to antibiotics in the control of human disease. Our studies on the mechanism of membrane disruption by LL-37 (a human antimicrobial peptide), analogs of the naturally occurring antimicrobial peptide magainin2 extracted from the skin of the African frog Xenopus Laevis, and pardaxin will be presented. Solid-state NMR experiments were used to determine the secondary structure, dynamics and topology of these peptides in lipid bilayers. Similarities and difference in the cell-lysing mechanism, and their dependence on the membrane composition, of these peptides will be discussed. Atomic-level resolution NMR structures of amyloidogenic proteins revealing the misfolding pathway and early intermediates that play key roles in amyloid toxicity will also be presented.

  7. Shape and Albedo from Shading (SAfS) for Pixel-Level dem Generation from Monocular Images Constrained by Low-Resolution dem

    NASA Astrophysics Data System (ADS)

    Wu, Bo; Chung Liu, Wai; Grumpe, Arne; Wöhler, Christian

    2016-06-01

    ) Narrow Angle Camera (NAC) (0.5 m spatial resolution), constrained by the SELENE and LRO Elevation Model (SLDEM 2015) of 60 m spatial resolution. The results indicate that local details are largely recovered by the algorithm while low frequency topographic consistency is affected by the low-resolution DEM.

  8. Electromagnetic studies of nucleon and nuclear structure

    SciTech Connect

    Heisenberg, J.H.; Calarco, J.R.; Hersman, F.W.; Dawson, J.F.

    1993-06-01

    Important objectives of the group are the study of subatomic structure through experimental measurements and the interpretation of the data through modeling. The common theme that unifies the studies of strong interactions and hadronic systems is the effort to determine the electromagnetic response as completely as possible. The general approach is coincidence detection of exclusive final states and determination of the dependence on the spin variables using polarized beams and targets and outgoing nucleon polarimetry. Direct reaction and giant resonance studies of electron quasi-elastic scattering on {sup 12}C and {sup 16}O are reported, as well as work on nuclear structure models and instrumentation development.

  9. Structural methods for studying IRES function.

    PubMed

    Kieft, Jeffrey S; Costantino, David A; Filbin, Megan E; Hammond, John; Pfingsten, Jennifer S

    2007-01-01

    Internal ribosome entry sites (IRESs) substitute RNA sequences for some or all of the canonical translation initiation protein factors. Therefore, an important component of understanding IRES function is a description of the three-dimensional structure of the IRES RNA underlying this mechanism. This includes determining the degree to which the RNA folds, the global RNA architecture, and higher resolution information when warranted. Knowledge of the RNA structural features guides ongoing mechanistic and functional studies. In this chapter, we present a roadmap to structurally characterize a folded RNA, beginning from initial studies to define the overall architecture and leading to high-resolution structural studies. The experimental strategy presented here is not unique to IRES RNAs but is adaptable to virtually any RNA of interest, although characterization of RNA-protein interactions requires additional methods. Because IRES RNAs have a specific function, we present specific ways in which the data are interpreted to gain insight into that function. We provide protocols for key experiments that are particularly useful for studying IRES RNA structure and that provide a framework onto which additional approaches are integrated. The protocols we present are solution hydroxyl radical probing, RNase T1 probing, native gel electrophoresis, sedimentation velocity analytical ultracentrifugation, and strategies to engineer RNA for crystallization and to obtain initial crystals. PMID:17913644

  10. Structural studies of Hollandite based radioactive wasteformd

    NASA Astrophysics Data System (ADS)

    Whittle, K. R.; Maddrell, E. R.; Ashbrook, S. E.; Sartbaeva, A.; Attfield, J. P.; Dove, M. T.; Farnan, I.; Redfern, S. A. T.

    2003-04-01

    Materials based on the hollandite-type structure, Ba1.2-xCs_x(Al,Mg,Ti)_8O16 (x=0,0.1,0.25) have been studied as a basis for 135Cs and 137Cs active waste immobilisation. Powders have been prepared using a modified 2-stage isopropoxide-gel route. The samples have been consolidated using both Hot Isostatic Pressing (HIP) and Cold Uniaxial Pressing prior to sintering.. The structures of these materials have been determined using X-ray diffraction techniques, and Magic-Angle Spinning Nuclear Magnetic Resonance (MAS-NMR). Dielectric spectroscopy has been measured for these systems to determine mobility of the Cs^+ ion in the structure. The structural data is compared for both pressing techniques and by direct comparison with the pseudo-amorphous precursor. The dielectric spectroscopy data has been collected for the pressed and fired samples.

  11. Parametric study of double cellular detonation structure

    NASA Astrophysics Data System (ADS)

    Khasainov, B.; Virot, F.; Presles, H.-N.; Desbordes, D.

    2013-05-01

    A parametric numerical study is performed of a detonation cellular structure in a model gaseous explosive mixture whose decomposition occurs in two successive exothermic reaction steps with markedly different characteristic times. Kinetic and energetic parameters of both reactions are varied in a wide range in the case of one-dimensional steady and two-dimensional (2D) quasi-steady self-supported detonations. The range of governing parameters of both exothermic steps is defined where a "marked" double cellular structure exists. It is shown that the two-level cellular structure is completely governed by the kinetic parameters and the local overdrive ratio of the detonation front propagating inside large cells. Furthermore, since it is quite cumbersome to use detailed chemical kinetics in unsteady 2D case, the proposed work should help to identify the mixtures and the domain of their equivalence ratio where double detonation structure could be observed.

  12. Computer programs for the interpretation of low resolution mass spectra: Program for calculation of molecular isotopic distribution and program for assignment of molecular formulas

    NASA Technical Reports Server (NTRS)

    Miller, R. A.; Kohl, F. J.

    1977-01-01

    Two FORTRAN computer programs for the interpretation of low resolution mass spectra were prepared and tested. One is for the calculation of the molecular isotopic distribution of any species from stored elemental distributions. The program requires only the input of the molecular formula and was designed for compatability with any computer system. The other program is for the determination of all possible combinations of atoms (and radicals) which may form an ion having a particular integer mass. It also uses a simplified input scheme and was designed for compatability with any system.

  13. Structural studies on leukaemia inhibitory factor

    SciTech Connect

    Norton, R.S.; Maurer, T.; Smith, D.K.; Nicola, N.A.

    1994-12-01

    Leukaemia Inhibitory Factor (LIF) is a pleiotropic cytokine that acts on a wide range of target cells, including mega-karyocytes, osteoblasts, hepatocytes, adipocytes, neurons, embryonic stem cells, and primordial germ cells. Many of its activities are shared with other cytokines, particularly interleukin-6, oncostatin-M, ciliary neurotrophic factor, and granulocyte colony-stimulating factor (G-CSF). Although secreted in vivo as a glycoprotein, nonglycosylated recombinant protein expressed in E. coli is fully active and has been used in our nuclear magnetic resonance (NMR) studies of the three-dimensional structure and structure-function relationships of LIF. With 180 amino acids and a molecular mass of about 20 kDa, OF is too large for direct structure determination by two-dimensional and three-dimensional {sup 1}HNMR. It is necessary to label the protein with the stable isotopes {sup 15}N and {sup 13}C and employ heteronuclear three-dimensional NMR in order to resolve and interpret the spectral information required for three-dimensional structure determination. This work has been undertaken with both human LIF and a mouse-human chimaera that binds to the human LIF receptor with the same affinity as the human protein and yet expresses in E. coli at much higher levels. Sequence-specific resonance assignments and secondary structure elements for these proteins will be presented and progress towards determination of their three-dimensional structures described.

  14. Experimental and computational study of thaumasite structure

    SciTech Connect

    Scholtzová, Eva; Kucková, Lenka; Kožíšek, Jozef; Pálková, Helena; Tunega, Daniel

    2014-05-01

    The structure of thaumasite has been studied experimentally by means of a single crystal X-ray diffraction and FTIR methods, and theoretically using density functional theory (DFT) method. Very good agreement was achieved between calculated and experimental structural parameters. In addition, calculations offered the refinement of the positions of the hydrogen atoms. The detailed analysis of the hydrogen bonds existing in the thaumasite structure has been performed. Several types of hydrogen bonds have been classified. The water molecules coordinating Ca{sup 2+} cation act as proton donors in moderate O-H···O hydrogen bonds formed with CO₃⁻²and SO₄⁻² anions. The multiple O-H···O hydrogen bonds exist among water molecules themselves. Finally, relatively weak hydrogen bonds form water molecules with the OH groups from the coordination sphere of the Si(OH)₆⁻² anion. Further, calculated vibrational spectrum allowed complete assignment of all vibrational modes which are not available from the experimental spectrum that has a complex structure with overlapped bands, especially below 1500 cm⁻¹. Highlights: • The thaumasite structure was studied experimentally and using DFT method. • We used DFT method for the refinement of the positions of hydrogen atoms. • A detailed analysis of the hydrogen bonds was done. • A complete assignment of all bands to particular types of vibrations was done.

  15. Revolutionary opportunities for materials and structures study

    NASA Technical Reports Server (NTRS)

    Schweiger, F. A.

    1987-01-01

    The revolutionary opportunities for materials and structures study was performed to provide Government and Industry focus for advanced materials technology. Both subsonic and supersonic engine studies and aircraft fuel burn and DOC evaluation are examined. Year 2010 goal materials were used in the advanced engine studies. These goal materials and improved component aero yielded subsonic fuel burn and DOC improvements of 13.4 percent and 5 percent, respectively and supersonic fuel burn and DOC improvements of 21.5 percent and 18 percent, respectively. Conclusions are that the supersonic study engine yielded fuel burn and DOC improvements well beyond the program goals; therefore, it is appropriate that advanced material programs be considered.

  16. A study of the Lute Metering Structure

    NASA Technical Reports Server (NTRS)

    Foreman, James W.

    1992-01-01

    Two Metering Structure configurations were investigated. The first case was the traditional style metering structure which is larger than the outside diameter of the primary mirror. The second case investigated was the center support concept in which the outside diameter of the structure is less than the inside diameter of the primary mirror. Beryllium was used as the baseline material for this study. Four other materials were considered as candidates for the metering structure. These materials are: Graphite Epoxy, Aluminum, Titanium, and Invar. The loading conditions used for this study were estimated to be: Quasi Static: 6.0 G (all three directions); and Random Vibration: 30.0 G (applied 1 axis at a time). Taking advantage of symmetry, it was necessary to apply the lateral loading to only one axis. These loads were applied to both concepts and to all material configurations. The loadings as described above were based on the best available information and is felt to be adequate for this study since it was consistently used for all configurations. A load factor 2.00 was applied to both quasi static and random vibration loads. The allowable stresses are conservatively based yield strength of the material, except for the struts which are controlled by elastic stability. The stresses determined from each individual loading direction were conservatively combined by the absolute sum method.

  17. A study of the Lute Metering Structure

    NASA Astrophysics Data System (ADS)

    Foreman, James W.

    1992-12-01

    Two Metering Structure configurations were investigated. The first case was the traditional style metering structure which is larger than the outside diameter of the primary mirror. The second case investigated was the center support concept in which the outside diameter of the structure is less than the inside diameter of the primary mirror. Beryllium was used as the baseline material for this study. Four other materials were considered as candidates for the metering structure. These materials are: Graphite Epoxy, Aluminum, Titanium, and Invar. The loading conditions used for this study were estimated to be: Quasi Static: 6.0 G (all three directions); and Random Vibration: 30.0 G (applied 1 axis at a time). Taking advantage of symmetry, it was necessary to apply the lateral loading to only one axis. These loads were applied to both concepts and to all material configurations. The loadings as described above were based on the best available information and is felt to be adequate for this study since it was consistently used for all configurations. A load factor 2.00 was applied to both quasi static and random vibration loads. The allowable stresses are conservatively based yield strength of the material, except for the struts which are controlled by elastic stability. The stresses determined from each individual loading direction were conservatively combined by the absolute sum method.

  18. In-house phase determination of the lima bean trypsin inhibitor: a low-resolution sulfur-SAD case.

    PubMed

    Debreczeni, Judit E; Bunkóczi, Gábor; Girmann, Beatrix; Sheldrick, George M

    2003-02-01

    SAD (single-wavelength anomalous diffraction) has enormous potential for phasing proteins using only the anomalous signal of the almost ubiquitous native sulfur, but requires extremely precise data. The previously unknown structure of the lima bean trypsin inhibitor (LBTI) was solved using highly redundant data collected to 3 A using a CCD detector with a rotating-anode generator and three-circle goniometer. The seven 'super-S' atoms (disulfide bridges) were located by dual-space recycling with SHELXD and the high solvent content enabled the density-modification program SHELXE to generate high-quality maps despite the modest resolution. Subsequently, a 2.05 A synchrotron data set was collected and used for further phase extension and structure refinement.

  19. Structural Studies of Protein-Surfactant Complexes

    SciTech Connect

    Chodankar, S. N.; Aswal, V. K.; Wagh, A. G.

    2008-03-17

    The structure of protein-surfactant complexes of two proteins bovine serum albumin (BSA) and lysozyme in presence of anionic surfactant sodium dodecyl sulfate (SDS) has been studied using small-angle neutron scattering (SANS). It is observed that these two proteins form different complex structures with the surfactant. While BSA protein undergoes unfolding on addition of surfactant, lysozyme does not show any unfolding even up to very high surfactant concentrations. The unfolding of BSA protein is caused by micelle-like aggregation of surfactant molecules in the complex. On the other hand, for lysozyme protein there is only binding of individual surfactant molecules to protein. Lysozyme in presence of higher surfactant concentrations has protein-surfactant complex structure coexisting with pure surfactant micelles.

  20. IMPROVING THE ACCURACY OF HISTORIC SATELLITE IMAGE CLASSIFICATION BY COMBINING LOW-RESOLUTION MULTISPECTRAL DATA WITH HIGH-RESOLUTION PANCHROMATIC DATA

    SciTech Connect

    Getman, Daniel J

    2008-01-01

    Many attempts to observe changes in terrestrial systems over time would be significantly enhanced if it were possible to improve the accuracy of classifications of low-resolution historic satellite data. In an effort to examine improving the accuracy of historic satellite image classification by combining satellite and air photo data, two experiments were undertaken in which low-resolution multispectral data and high-resolution panchromatic data were combined and then classified using the ECHO spectral-spatial image classification algorithm and the Maximum Likelihood technique. The multispectral data consisted of 6 multispectral channels (30-meter pixel resolution) from Landsat 7. These data were augmented with panchromatic data (15m pixel resolution) from Landsat 7 in the first experiment, and with a mosaic of digital aerial photography (1m pixel resolution) in the second. The addition of the Landsat 7 panchromatic data provided a significant improvement in the accuracy of classifications made using the ECHO algorithm. Although the inclusion of aerial photography provided an improvement in accuracy, this improvement was only statistically significant at a 40-60% level. These results suggest that once error levels associated with combining aerial photography and multispectral satellite data are reduced, this approach has the potential to significantly enhance the precision and accuracy of classifications made using historic remotely sensed data, as a way to extend the time range of efforts to track temporal changes in terrestrial systems.

  1. CARMENES science preparation: characterisation of M dwarfs with low-resolution spectroscopy and search for low-mass wide companions to young stars

    NASA Astrophysics Data System (ADS)

    Alonso-Floriano, F. J.

    2015-11-01

    This thesis is focused on the study of low-mass objects that can be targets of exoplanet searches with near-infrared spectrographs in general and CARMENES (Calar Alto high-Resolution search for M dwarfs with Exo-earths with Near-infrared and optical Echelle Spectrographs; see Quirrenbach et al. 2014) in particular. The CARMENES consortium comprises 11 institutions from Germany and Spain that are building a high-resolution spectrograph (R=82,000) with two channels, visible (0.55 - 1.05 um) and infrared (0.95 - 1.7 um), for the 3.5 m Calar Alto telescope. It will observe a sample of 300 M dwarfs in 600 nights of guaranteed time during at least three years, starting in January 2016. The final sample will be chosen from the 2200 M dwarfs included in the CARMENCITA input catalogue. For these stars, we have obtained and collected a large amount of data: spectral types, radial and rotational velocities, photometry in several bands, etc. Part of the e effort of the science preparation necessary for the final selection of targets for CARMENES and other near-infrared spectrographs has been collected in two publications, which are presented in this PhD thesis. In the first publication (Alonso-Floriano et al., 2015A&A...577A.128A), we obtained low-resolution spectra for 753 stars using the CAFOS spectrograph at the 2.2 m Calar Alto telescope. The main goal was to derive accurate spectral types, which are fundamental parameters for the sample selection. We used a grid of 49 standard stars, from spectral types K3V to M8V, together with a double least-square minimisation technique and 31 spectral indices previously defined by other authors. In addition, we quantified the surface gravity, metallicity and chromospheric activity of the sample, in order to detect low-gravity stars (giants and very young), metal-poor and very metal-poor stars (subdwarfs), and very active stars. In the second publication (Alonso-Floriano et al., 2015A&A...583A..85A), we searched for common proper

  2. Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1.

    PubMed

    Akey, David L; Brown, W Clay; Konwerski, Jamie R; Ogata, Craig M; Smith, Janet L

    2014-10-01

    An emergent challenge in macromolecular crystallography is the identification of the substructure from native anomalous scatterers in crystals that diffract to low to moderate resolution. Increasing the multiplicity of data sets has been shown to make previously intractable phasing problems solvable and to increase the useful resolution in model refinement. For the West Nile virus nonstructural protein 1 (NS1), a protein of novel fold, the utility of exceptionally high multiplicity data is demonstrated both in solving the crystal structure from the anomalous scattering of the native S atoms and in extending the useful limits of resolution during refinement. A high-multiplicity data set from 18 crystals had sufficient anomalous signal to identify sulfur sites using data to 5.2 Å resolution. Phases calculated to 4.5 Å resolution and extended to 3.0 Å resolution were of sufficient quality for automated building of three-quarters of the final structure. Crystallographic refinement to 2.9 Å resolution proceeded smoothly, justifying the increase in resolution that was made possible by combining multiple data sets. The identification and exclusion of data from outlier crystals is shown to result in more robust substructure determination.

  3. Electronic structure studies of topological materials

    NASA Astrophysics Data System (ADS)

    Zhou, Shuyun

    Three-dimensional (3D) Dirac fermions are a new class of topological quantum materials. In 3D Dirac semimetals, the conduction and valence bands touch each other at discrete points in the momentum space and show linear dispersions along all momentum directions, forming 3D Dirac cones which are protected by the crystal symmetry. Here I will present our recent studies of the electronic structures of novel materials which host 3D Dirac fermions by using angle-resolved photoemission spectroscopy.

  4. Studies of Flame Structure in Microgravity

    NASA Technical Reports Server (NTRS)

    Law, C. K.; Sung, C. J.; Zhu, D. L.

    1997-01-01

    The present research endeavor is concerned with gaining fundamental understanding of the configuration, structure, and dynamics of laminar premixed and diffusion flames under conditions of negligible effects of gravity. Of particular interest is the potential to establish and hence study the properties of spherically- and cylindrically-symmetric flames and their response to external forces not related to gravity. For example, in an earlier experimental study of the burner-stabilized cylindrical premixed flames, the possibility of flame stabilization through flow divergence was established, while the resulting one-dimensional, adiabatic, stretchless flame also allowed an accurate means of determining the laminar flame speeds of combustible mixtures. We have recently extended our studies of the flame structure in microgravity along the following directions: (1) Analysis of the dynamics of spherical premixed flames; (2) Analysis of the spreading of cylindrical diffusion flames; (3) Experimental observation of an interesting dual luminous zone structure of a steady-state, microbuoyancy, spherical diffusion flame of air burning in a hydrogen/methane mixture environment, and its subsequent quantification through computational simulation with detailed chemistry and transport; (4) Experimental quantification of the unsteady growth of a spherical diffusion flame; and (5) Computational simulation of stretched, diffusionally-imbalanced premixed flames near and beyond the conventional limits of flammability, and the substantiation of the concept of extended limits of flammability. Motivation and results of these investigations are individually discussed.

  5. NMR Studies of Protein Structure and Dynamics

    NASA Astrophysics Data System (ADS)

    Li, Xiang

    Available from UMI in association with The British Library. Requires signed TDF. This thesis describes applications of 2D homonuclear NMR techniques to the study of protein structure and dynamics in solution. The sequential assignments for the 3G-residue bovine Pancreatic Polypeptide (bPP) are reported. The secondary and tertiary structure of bPP in solution has been determined from experimental NMR data. bPP has a well defined C-terminal alpha-helix and a rather ordered conformation in the N-terminal region. The two segments are joined by a turn which is poorly defined. Both the N- and the C-terminus are highly disordered. The mean solution structure of bPP is remarkably similar to the crystal structure of avian Pancreatic Polypeptide (aPP). The average conformations of most side-chains from the alpha-helix of bPP in solution are closely similar to those of aPP in the crystalline state. A large number of side-chains of bPP, however, show significant conformational averaging in solution. The 89-residue kringle domain of urokinase from both human and recombinant sources has been investigated. Sequential assignments based primarily on the recombinant sample and the determination of secondary structure are presented. Two helices have been identified; one of these corresponds to that reported for t-PA kringle 2, but does not exist in other kringles with known structures. The second helix is thus far unique to the urokinase kringle. Three antiparallel beta-sheets and three tight turns have also been identified. The tertiary fold of the molecule conforms broadly to that found for other kringles. Three regions in the urokinase kringle exhibit high local mobility; one of these, the Pro56-Pro62 segment, forms part of the proposed binding site. The other two mobile regions are the N- and C-termini which are likely to form the interfaces between the kringle and the other two domains (EGF and protease) in urokinase. The differential dynamic behaviours of the kringle and

  6. The structure of circumstellar shells

    NASA Technical Reports Server (NTRS)

    Fix, John D.

    1993-01-01

    This document provides a report on research activities carried out with the support of NASA grant NAG 5-1174, the Structure of Circumstellar Shells, funded under the Astrophysics Data Program. The research carried out with the support of this grant is a study of the properties of circumstellar dust shells for which spectra are available through IRAS low resolution spectrometry (LRS). This research consisted of the development and application of models of axisymmetric circumstellar shells and a preliminary survey of the applicability of neural nets for analysis of the IRAS LRS spectra of circumstellar dust shells.

  7. Structural studies of the Sputnik virophage.

    PubMed

    Sun, Siyang; La Scola, Bernard; Bowman, Valorie D; Ryan, Christopher M; Whitelegge, Julian P; Raoult, Didier; Rossmann, Michael G

    2010-01-01

    The virophage Sputnik is a satellite virus of the giant mimivirus and is the only satellite virus reported to date whose propagation adversely affects its host virus' production. Genome sequence analysis showed that Sputnik has genes related to viruses infecting all three domains of life. Here, we report structural studies of Sputnik, which show that it is about 740 A in diameter, has a T=27 icosahedral capsid, and has a lipid membrane inside the protein shell. Structural analyses suggest that the major capsid protein of Sputnik is likely to have a double jelly-roll fold, although sequence alignments do not show any detectable similarity with other viral double jelly-roll capsid proteins. Hence, the origin of Sputnik's capsid might have been derived from other viruses prior to its association with mimivirus. PMID:19889775

  8. TEM-nanoindentation studies of semiconducting structures.

    PubMed

    Le Bourhis, E; Patriarche, G

    2007-01-01

    This paper reviews the application of nanoindentation coupled with transmission electron microscopy (TEM) to investigations of the plastic behaviour of semiconducting structures and its implication for device design. Instrumented nanoindentation has been developed to extract the mechanical behaviour of small volumes scaled to those encountered in semiconductor heterostructures. We illustrate that TEM is a powerful complementary tool for the study of local plasticity induced by nanoindentation. TEM-nanoindentation allows for detailed understanding of the plastic deformation in semiconducting structures and opens practical routes for improvement of devices. Performances of heterostructures are deteriously affected by dislocations that relax the lattice mismatched layers. Different ways to obtain compliant substructures are being developed in order to concentrate the plastic relaxation underneath the heterostructure. Such approaches allow for mechanical design of micro- and opto-electronic devices to be considered throughout the fabrication process. PMID:16901706

  9. Structure of giant muscle proteins

    PubMed Central

    Meyer, Logan C.; Wright, Nathan T.

    2013-01-01

    Giant muscle proteins (e.g., titin, nebulin, and obscurin) play a seminal role in muscle elasticity, stretch response, and sarcomeric organization. Each giant protein consists of multiple tandem structural domains, usually arranged in a modular fashion spanning 500 kDa to 4 MDa. Although many of the domains are similar in structure, subtle differences create a unique function of each domain. Recent high and low resolution structural and dynamic studies now suggest more nuanced overall protein structures than previously realized. These findings show that atomic structure, interactions between tandem domains, and intrasarcomeric environment all influence the shape, motion, and therefore function of giant proteins. In this article we will review the current understanding of titin, obscurin, and nebulin structure, from the atomic level through the molecular level. PMID:24376425

  10. IRAS observations of the exciting stars of Herbig-Haro objects. II - The Reipurth and Graham sample and low-resolution spectra

    NASA Technical Reports Server (NTRS)

    Cohen, Martin

    1990-01-01

    Using IRAS COADDed images, candidates are suggested for the exciting stars of Herbig-Haro objects from the Reipurth and Graham sample. The IRAS low-resolution spectrometer provides spectra for 20 of the 46 candidate stars so far identified as exciting young, unevolved H-H systems. These reveal 10-micron silicate absorption features, or are too red to show detectable flux near 10 microns. The histogram of bolometric luminosities for 46 young Herbig-Haro exciting stars has a median of 13 solar luminosities and a mode between 16 and 32 solar luminosities. Although the enlarged sample of known exciting stars has more of the higher luminosity objects than an earlier sample, the histogram still represents a generally low-luminosity distribution.

  11. Quantum mechanical studies of carbon structures

    SciTech Connect

    Bartelt, Norman Charles; Ward, Donald; Zhou, Xiaowang; Foster, Michael E.; Schultz, Peter A.; Wang, Bryan M.; McCarty, Kevin F.

    2015-10-01

    Carbon nanostructures, such as nanotubes and graphene, are of considerable interest due to their unique mechanical and electrical properties. The materials exhibit extremely high strength and conductivity when defects created during synthesis are minimized. Atomistic modeling is one technique for high resolution studies of defect formation and mitigation. To enable simulations of the mechanical behavior and growth mechanisms of C nanostructures, a high-fidelity analytical bond-order potential for the C is needed. To generate inputs for developing such a potential, we performed quantum mechanical calculations of various C structures.

  12. Structural study of supercooled liquid silicon

    SciTech Connect

    Kim, T.H.; Goldman, A.I.; Kelton, K.F.

    2007-11-06

    For many years, theoretical studies using model and ab initio potentials have predicated the existence of a liquid/liquid phase transition in silicon, based on a continuous change of the liquid A5 structure to A4. In contrast, we report here a quantitative analysis of data from high-energy X-ray diffraction measurements of containerlessly-processed supercooled liquid silicon that demonstrates that the fractions of regions with A5 and A4 order instead remain essentially constant with supercooling, but that the coherence length of the A5 order increases.

  13. Seasonal predictions of equatorial Atlantic SST in a low-resolution CGCM with surface heat flux correction

    NASA Astrophysics Data System (ADS)

    Dippe, Tina; Greatbatch, Richard; Ding, Hui

    2016-04-01

    The dominant mode of interannual variability in tropical Atlantic sea surface temperatures (SSTs) is the Atlantic Niño or Zonal Mode. Akin to the El Niño-Southern Oscillation in the Pacific sector, it is able to impact the climate both of the adjacent equatorial African continent and remote regions. Due to heavy biases in the mean state climate of the equatorial-to-subtropical Atlantic, however, most state-of-the-art coupled global climate models (CGCMs) are unable to realistically simulate equatorial Atlantic variability. In this study, the Kiel Climate Model (KCM) is used to investigate the impact of a simple bias alleviation technique on the predictability of equatorial Atlantic SSTs. Two sets of seasonal forecasting experiments are performed: An experiment using the standard KCM (STD), and an experiment with additional surface heat flux correction (FLX) that efficiently removes the SST bias from simulations. Initial conditions for both experiments are generated by the KCM run in partially coupled mode, a simple assimilation technique that forces the KCM with observed wind stress anomalies and preserves SST as a fully prognostic variable. Seasonal predictions for both sets of experiments are run four times yearly for 1981-2012. Results: Heat flux correction substantially improves the simulated variability in the initialization runs for boreal summer and fall (June-October). In boreal spring (March-May), however, neither the initialization runs of the STD or FLX-experiments are able to capture the observed variability. FLX-predictions show no consistent enhancement of skill relative to the predictions of the STD experiment over the course of the year. The skill of persistence forecasts is hardly beat by either of the two experiments in any season, limiting the usefulness of the few forecasts that show significant skill. However, FLX-forecasts initialized in May recover skill in July and August, the peak season of the Atlantic Niño (anomaly correlation

  14. LAMOST Observations in the Kepler Field. Analysis of the Stellar Parameters Measured with LASP Based on Low-resolution Spectra

    NASA Astrophysics Data System (ADS)

    Ren, Anbing; Fu, Jianning; De Cat, Peter; Wu, Yue; Yang, Xiaohu; Shi, Jianrong; Luo, Ali; Zhang, Haotong; Dong, Subo; Zhang, Ruyuan; Zhang, Yong; Hou, Yonghui; Wang, Yuefei; Cao, Zihuang; Du, Bing

    2016-08-01

    All 14 subfields of the Kepler field were observed at least once with the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (lamost, Xinglong Observatory, China) during the 2012–2014 observation seasons. There are 88,628 reduced spectra with a signal-to-noise ratio in the g band (S/N g ) ≥ 6 after the first round (2012–2014) of observations of the lamost– Kepler project (LK-project). By adopting the upgraded version of the lamost Stellar Parameter pipeline (lasp), we have determined the atmospheric parameters ({T}{eff}, {log}g, and [Fe/H]) and heliocentric radial velocity v rad for 51,406 stars with 61,226 spectra. Compared with the atmospheric parameters derived from both high-resolution spectroscopy and asteroseismology for common stars in Huber et al., an external calibration of lasp atmospheric parameters was made, leading to the determination of the external errors for giants and dwarfs. Multiple spectroscopic observations of the same objects in the LK-project were used to estimate the internal uncertainties of the atmospheric parameters as a function of S/N g with the unbiased estimation method. The lasp atmospheric parameters were calibrated based on both the external and internal uncertainties for the giants and dwarfs. A general statistical analysis of the stellar parameters leads to the discovery of 106 candidate metal-poor stars, 9 candidate very metal-poor stars, and 18 candidate high-velocity stars. Fitting formulae were obtained segmentally for both the calibrated atmospheric parameters of the LK-project and the Kepler Input Catalog (KIC) parameters with common stars. The calibrated atmospheric parameters and radial velocities of the LK-project will be useful for studying stars in the Kepler field. ) located at the Xinglong Observatory, China.

  15. LAMOST Observations in the Kepler Field. Analysis of the Stellar Parameters Measured with LASP Based on Low-resolution Spectra

    NASA Astrophysics Data System (ADS)

    Ren, Anbing; Fu, Jianning; De Cat, Peter; Wu, Yue; Yang, Xiaohu; Shi, Jianrong; Luo, Ali; Zhang, Haotong; Dong, Subo; Zhang, Ruyuan; Zhang, Yong; Hou, Yonghui; Wang, Yuefei; Cao, Zihuang; Du, Bing

    2016-08-01

    All 14 subfields of the Kepler field were observed at least once with the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (lamost, Xinglong Observatory, China) during the 2012-2014 observation seasons. There are 88,628 reduced spectra with a signal-to-noise ratio in the g band (S/N g ) ≥ 6 after the first round (2012-2014) of observations of the lamost- Kepler project (LK-project). By adopting the upgraded version of the lamost Stellar Parameter pipeline (lasp), we have determined the atmospheric parameters ({T}{eff}, {log}g, and [Fe/H]) and heliocentric radial velocity v rad for 51,406 stars with 61,226 spectra. Compared with the atmospheric parameters derived from both high-resolution spectroscopy and asteroseismology for common stars in Huber et al., an external calibration of lasp atmospheric parameters was made, leading to the determination of the external errors for giants and dwarfs. Multiple spectroscopic observations of the same objects in the LK-project were used to estimate the internal uncertainties of the atmospheric parameters as a function of S/N g with the unbiased estimation method. The lasp atmospheric parameters were calibrated based on both the external and internal uncertainties for the giants and dwarfs. A general statistical analysis of the stellar parameters leads to the discovery of 106 candidate metal-poor stars, 9 candidate very metal-poor stars, and 18 candidate high-velocity stars. Fitting formulae were obtained segmentally for both the calibrated atmospheric parameters of the LK-project and the Kepler Input Catalog (KIC) parameters with common stars. The calibrated atmospheric parameters and radial velocities of the LK-project will be useful for studying stars in the Kepler field. ) located at the Xinglong Observatory, China.

  16. Energetic and Structural Study of Diphenylpyridine Isomers

    NASA Astrophysics Data System (ADS)

    Rocha, Marisa A. A.; Gomes, Lígia R.; Low, John N.; Santos, Luís M. N. B. F.

    2009-09-01

    The energetic and structural study of three diphenylpyridine isomers is presented in detail. The three isomers, 2,6-, 2,5-, and 3,5-diphenylpyridines, were synthesized via Suzuki-Miyaura methodology based on palladium catalysis, and the crystal structures of the isomers were obtained by X-ray diffraction. The relative energetic stabilities in the condensed and gaseous phases as well as volatilities and structures of the three studied isomers were evaluated, regarding the position of the phenyl groups relative to the nitrogen atom of the pyridine ring. The temperature, standard molar enthalpies, and entropies of fusion were measured and derived by differential scanning calorimetry. The vapor pressures of the considered isomers were determined by a static apparatus based on a MKS capacitance diaphragm manometer. The standard molar enthalpies, entropies, and Gibbs energies of sublimation, at T = 298.15 K, were derived, and the phase diagram near the triple point coordinates were determined for all isomers. The standard (p° = 0.1 MPa) molar enthalpies of combustion of all crystalline isomers were determined, at T = 298.15 K, by static bomb combustion calorimetry. The standard molar enthalpies of formation, in the crystalline and gaseous phases, at T = 298.15 K, were derived. The experimental results for the energetics in the gaseous phase of the three compounds were compared and assessed with the values obtained by ab initio calculations at different levels of theory (DFT and MP2) showing that, at this level of theory, the computational methods underestimate the energetic stability, in the gaseous phase, for these molecules. In order to understand the aromaticity in the central ring of each isomer, calculations of NICS (B3LYP/6-311G++(d,p) level of theory) values on the pyridine ring were also performed.

  17. Nucleon spin structure studies at COMPASS

    SciTech Connect

    Marchand, Claude

    2006-02-11

    One of the main goal of the COMPASS experiment at CERN is the study of the spin structure of the nucleon in DIS, by scattering 160 GeV polarized muon beam on a longitudinally (or transversely) polarized 6LiD target. Besides the scattered muon, the particles produced in the deep inelastic scattering are detected by a two stage magnetic spectrometer equipped with state of the art tracking and particle ID detectors.The emphasis of COMPASS muon program is the direct determination of the gluon polarization {delta}G/G, accessed via asymmetries involving photon-gluon fusion mechanism (PGF). Both open charm production (detecting D0's), as well as production of height pT hadron pairs are used to tag PGF. Preliminary results for {delta}G/G based on the analysis of 2002 and 2003 data are shown. In addition, improved measurement of the deuteron structure function g{sub 1}{sup d} at small x, as well as studies of transverse distribution functions in the deuteron by measuring Collins and Sivers azimuthal asymmetries, are reported.

  18. Micromechanical study of mitotic chromosome structure

    NASA Astrophysics Data System (ADS)

    Marko, John

    2011-03-01

    Our group has developed micromanipulation techniques for study of the highly compacted mitotic form of chromosome found in eukaryote cells during cell division. Each metaphase chromosome contains two duplicate centimeter-long DNA molecules, folded up by proteins into cylindrical structures several microns in length. Native chromosomes display linear and reversible stretching behavior over a wide range of extensions (up to 5x native length for amphibian chromosomes), described by a Young modulus of about 300 Pa. Studies using DNA-cutting and protein-cutting enzymes have revealed that metaphase chromosomes behave as a network of chromatin fibers held together by protein-based isolated crosslinks. Our results are not consistent with the more classical model of loops of chromatin attached to a protein-based structural organizer or ``scaffold". In short, our experiments indicate that metaphase chromosomes can be considered to be ``gels" of chromatin; the stretching modulus of a whole chromosome is consistent with stretching of the chromatin fibers contained within it. Experiments using topoisomerases suggest that topological constraints may play an appreciable role in confining chromatin in the metaphase chromosome. Finally, recent experiments on human chromosomes will be reviewed, including results of experiments where chromosome-folding proteins are specifically depleted using siRNA methods. Supported by NSF-MCB-1022117, DMR-0715099, PHY-0852130, DMR-0520513, NCI 1U54CA143869-01 (NU-PS-OC), and the American Heart Association.

  19. Studying the Nucleon Structure with Spin

    SciTech Connect

    Hasell, D. K.

    2007-10-26

    The BLAST (Bates Large Acceptance Spectrometer Toroid) collaboration is finalizing the analysis of a systematic study of the spin-dependent, electromagnetic interaction on hydrogen and deuterium. The experiment utilized: the highly polarized electron beam of the MIT-Bates Linear Accelerator Center stored in the South Hall Ring; an internal gas target of isotopically pure and highly polarized hydrogen or deuterium provided by an atomic beam source; and the symmetric, general purpose BLAST spectrometer. By making simultaneous measurements of many reaction channels for different combinations of beam helicity and target polarization BLAST is providing new, precise measurements for the nucleon and deuteron elastic form factors as well as studying the structure of deuterium and pion production from hydrogen and deuterium. A brief overview of the experiment will be presented together with a selection results.

  20. Studies on metal-dielectric plasmonic structures.

    SciTech Connect

    Chettiar, Uday K.; Liu, Zhengtong; Thoreson, Mark D.; Shalaev, Vladimir M.; Drachev, Vladimir P.; Pack, Michael Vern; Kildishev, Alexander V.; Nyga, Piotr

    2010-01-01

    The interaction of light with nanostructured metal leads to a number of fascinating phenomena, including plasmon oscillations that can be harnessed for a variety of cutting-edge applications. Plasmon oscillation modes are the collective oscillation of free electrons in metals under incident light. Previously, surface plasmon modes have been used for communication, sensing, nonlinear optics and novel physics studies. In this report, we describe the scientific research completed on metal-dielectric plasmonic films accomplished during a multi-year Purdue Excellence in Science and Engineering Graduate Fellowship sponsored by Sandia National Laboratories. A variety of plasmonic structures, from random 2D metal-dielectric films to 3D composite metal-dielectric films, have been studied in this research for applications such as surface-enhanced Raman sensing, tunable superlenses with resolutions beyond the diffraction limit, enhanced molecular absorption, infrared obscurants, and other real-world applications.

  1. Southern Africa seismic structure and source studies

    NASA Astrophysics Data System (ADS)

    Zhao, Ming

    1998-09-01

    The upper mantle seismic velocity structure beneath southern Africa is investigated using travel time and waveform data. Waveform and travel time data used in this study come mainly from a large mine tremor in South Africa (msb{b} 5.6) recorded on stations of the southern Africa and the Tanzania Broadband Seismic Experiment. Auxiliary data along similar profiles are obtained from other moderate events within eastern and southern Africa. The waveform data from the large tremor show upper mantle triplications for both the 400 and 670-km discontinuities between 18sp° and 27sp° distance. The most notable feature of the data is a large, late P phase that propagates to at least 27sp°. This phase is striking because of its late arrival time (as much as 15 seconds after direct P at 27sp°) and high amplitude relative to the first arrival. Travel times from all available stations are used to invert for the P wave velocity structure down to 800 km depth and S wave velocity structure down to 200 km using the Wiechert-Herglotz (W-H) inversion technique. The P wave velocities from the uppermost mantle down to 300 km are as much as 3% higher than the global average and are slightly slower than the global average between 300 and 400 km depths. The velocity gradient between 300 and 400 km is 0.0015 1/s. The S wave travel time data yield fast velocities above 200-km depth. The S wave velocity structure appears inconsistent with the P wave structure model indicating varying Poisson's ratio in the upper mantle. Little evidence is found for a pronounced upper mantle low velocity zone. Both sharp and gradual-change 400-km discontinuities are favored by the waveform data. The 670-km discontinuity appears as a gradual-change zone. The source mechanism of the mb 5.6 mining tremor itself is important for seismic discrimination and insight into mining tremor sources. Source parameters for this event as well as some other large mining tremors from the South African gold mines are studied

  2. Structural studies on ferroelectric and ferrodistortive materials

    NASA Astrophysics Data System (ADS)

    Zou, Mingqin

    The structure of the piezoelectric material 0.68PbMg1/3Nb 2/3O3-0.32PbTiO3 have been studied by single crystal, powder x-ray diffraction techniques over the temperature range from 25°C to 200°C. The existence of twinned structures or coexistence of rhombohedral and tetragonal phases has been shown by the peak distortion of Bragg reflections. Superlattice structure was observed for all experimental PMN-PT crystals. Refinement results showed that the 2 x 2 x 2 superlattice resulted from anti-parallel displacement of oxygen in the adjacent conventional perovskite unit cells. No cation displacement in the paraelectric phase and little in the ferroelectric phase were shown by the refinement results. This unique feature associated with the ferroelectric mechanism of the material was explained by comparison with PbMg1/3Nb2/3O3. The crystals were extensively characterized by using powder x-ray diffraction, Laue back-reflection and electron backscatter diffraction (EBSD) techniques. The detailed orientation information such as misorientation of grains, location of grain boundaries and the orientation distribution was obtained from the automatic orientation mapping with the EBSD technique. The uniform orientation was confirmed for crystals with a "cellular-like" structure. A crystal growth model, the two-dimensional layer mechanism, was proposed by orientation analysis. Based on the model, some important comments were made on orientation problems under general growth conditions. The ferrodistortive phase transitions of tertramethylphosphonium tetrabromozincate [P(CH3)4]2ZnBr4 and tertramethylphosphonium tetraiodonzincate [P(CH3)4]2ZnI4 were thoroughly studied by a single crystal x-ray diffraction technique. An order parameter analysis by application of Landau theory showed that the two compounds undergo first-order phase transitions near a tricritical Lifshitz point. Transitions for both compounds appear to be first order, but with the iodo salt the transition is nearly

  3. Increasing association mapping power and resolution in mouse genetic studies through the use of meta-analysis for structured populations.

    PubMed

    Furlotte, Nicholas A; Kang, Eun Yong; Van Nas, Atila; Farber, Charles R; Lusis, Aldons J; Eskin, Eleazar

    2012-07-01

    Genetic studies in mouse models have played an integral role in the discovery of the mechanisms underlying many human diseases. The primary mode of discovery has been the application of linkage analysis to mouse crosses. This approach results in high power to identify regions that affect traits, but in low resolution, making it difficult to identify the precise genomic location harboring the causal variant. Recently, a panel of mice referred to as the hybrid mouse diversity panel (HMDP) has been developed to overcome this problem. However, power in this panel is limited by the availability of inbred strains. Previous studies have suggested combining results across multiple panels as a means to increase power, but the methods employed may not be well suited to structured populations, such as the HMDP. In this article, we introduce a meta-analysis-based method that may be used to combine HMDP studies with F2 cross studies to gain power, while increasing resolution. Due to the drastically different genetic structure of F2s and the HMDP, the best way to combine two studies for a given SNP depends on the strain distribution pattern in each study. We show that combining results, while accounting for these patterns, leads to increased power and resolution. Using our method to map bone mineral density, we find that two previously implicated loci are replicated with increased significance and that the size of the associated is decreased. We also map HDL cholesterol and show a dramatic increase in the significance of a previously identified result. PMID:22505625

  4. Spacecraft control/flexible structures interaction study

    NASA Technical Reports Server (NTRS)

    Kaplan, M. H.; Hillard, S. E.

    1974-01-01

    An initial study to begin development of a flight experiment to measure spacecraft control/flexible structure interactions was completed. The approach consisted of developing the equations of motion for a vehicle possessing a flexible solar array, then linearizing about some nominal motion of the craft. A set of solutions is assumed for array deflection using a continuous normal mode method and important parameters are identified. Interrelationships between these parameters, measurement techniques, and input requirements are discussed which assure minimization of special vehicle maneuvers and optimization of data to be obtained during the normal flight sequence. Limited consideration is given to flight data retrieval and processing techniques as correlated with the requirements imposed by the measurement system. Results indicate that inflight measurement of the bending and torsional mode shapes and respective frequencies, and damping ratios, is necessary. Other parameters may be measured from design data.

  5. Nuclease digestion studies of chromatin structure

    SciTech Connect

    Deutsch, S.M.

    1987-01-01

    Micrococcal nuclease, which preferentially cleaves linker DNA in chromatin, was immobilized by covalent attachment to CNBr-activated agarose beads and used to study the accessibility of linker DNA in chromatin fibers prepared from chicken erythrocyte nuclei. This immobilized nuclease was able to cleave chromatin fibers into the typical pattern of fragments corresponding to multiples of mononucleosomes. Cleavage from only the ends of the fibers was ruled out by examining the products of cleavage of fibers end-labelled with /sup 35/P. Comparison of the rate of digestion by immobilized and soluble micrococcal nuclease indicated that the fiber structure does not significantly affect access to linker DNA. The absence of an effect of reducing temperatures on the rate of digestion of fibers, as compared to short oligonucleosomes, indicated that breathing motions to allow access to the fiber interior were not required for cleavage of linker DNA.

  6. Nuclear structure studies of 24F

    NASA Astrophysics Data System (ADS)

    Cáceres, L.; Lepailleur, A.; Sorlin, O.; Stanoiu, M.; Sohler, D.; Dombrádi, Zs.; Bogner, S. K.; Brown, B. A.; Hergert, H.; Holt, J. D.; Schwenk, A.; Azaiez, F.; Bastin, B.; Borcea, C.; Borcea, R.; Bourgeois, C.; Elekes, Z.; Fülöp, Zs.; Grévy, S.; Gaudefroy, L.; Grinyer, G. F.; Guillemaud-Mueller, D.; Ibrahim, F.; Kerek, A.; Krasznahorkay, A.; Lewitowicz, M.; Lukyanov, S. M.; Mrázek, J.; Negoita, F.; de Oliveira, F.; Penionzhkevich, Yu.-E.; Podolyák, Zs.; Porquet, M. G.; Rotaru, F.; Roussel-Chomaz, P.; Saint-Laurent, M. G.; Savajols, H.; Sletten, G.; Thomas, J. C.; Timàr, J.; Timis, C.; Vajta, Zs.

    2015-07-01

    The structure of the 24F nucleus has been studied at GANIL using the β decay of 24O and the in-beam γ -ray spectroscopy from the fragmentation of Na,2827,25,26Ne, and 29,30

  7. Structured Controversy: A Case Study Strategy.

    ERIC Educational Resources Information Center

    Herreid, Clyde Freeman

    1996-01-01

    Introduces a dynamic form of the case instruction method that involves debate and compromise. Discusses two versions of structured controversy and presents an example of structured controversy that involves the use of DNA fingerprinting in forensic medicine. (JRH)

  8. Studies of coal structure using carbene chemistry

    SciTech Connect

    Not Available

    1990-01-01

    The object of this grant was to react coal, derivatized forms of coal, and solvent swelled coal with carbenes (divalent carbon species) under mild conditions. These carbenes were to be prepared by treating the coal with several diazo compounds and then thermally decomposing them at relatively low temperatures (80--130{degree}C). The carbenes were to be chosen to show varying selectively toward aromatic rings containing heteroatom functionalities and toward polynuclear aromatic systems. In some instances, where selectivities toward aromatic and heteroaromatic ring systems were not known, model studies were to be carried out. Because of the generally mild conditions employed and the good selectivity anticipated, and actually observed with one particular system, it was expected that this methodology would provide structural information about the coal, along with data on the extent of occurrence and type of aromatic systems. After carbene reactions, treatment of the coal samples was to include extractions and thermolysis. Physical studies included thermogravimetric analysis, diffuse reflectance FT-IR spectroscopy, NMR ({sup 1}H and {sup 13}C) spectroscopy, gas chromatography, GC/MS and GC/FT-IR. 7 figs., 10 tabs.

  9. Study of joint designing on composite structures

    NASA Astrophysics Data System (ADS)

    Kazushi, Haruna

    In this paper, strength design techniques of CFRP mechanical joints and adhesively bonded joints were examined. Remarkable stress concentration generates at the mechanical hole edge and the adhesive edge, therefore an unskillful design of joints often causes a reduction in the strength of composite structures. In mechanical joints, a study on predicting the joint strength has been performed, but bearing failure that is most important failure mode for designing joints can not be predicted. So in this paper, the strength prediction method in consideration with bearing failure was examined. On the other hand, the criterion using the intensity of stress singularity was suggested in adhesive joints, but it was clarified in this paper, that this method can not be applied the prediction of the final failure strength. So the critical stress distribution of single-lap adhesive bonded carbon/epoxy joints was examined to obtain the failure criterion of the final failure. Moreover the simulation method for an internal stress generated by cure shrinkage of adhesive was also examined. In the proposed method for mechanical joint, 2-parameter criterion, that is combined the characteristic length with the Yamada-Sun criterion, was applied and the characteristic length for compression was determined from "bearing failure test" that was newly conceived to take bearing failure into consideration. In case of adhesive joints, it was thought that 2-parameter criterion was effective. So the prediction method using 2-parameter criterion was applied to other adhesive joints. Good agreement was obtained between predicted and experimental results in both mechanical and adhesive joints. And it was cleared that an internal stress could be simulated by the proposed method. Moreover, in mechanical joints, the most suitable stacking sequence, the reduction technique of interlaminar stress, and the elevation of joint strength by application of high toughness matrix were also shown. Consequently

  10. Structural efficiency study of composite wing rib structures

    NASA Technical Reports Server (NTRS)

    Swanson, Gary D.; Gurdal, Zafer; Starnes, James H., Jr.

    1988-01-01

    A series of short stiffened panel designs which may be applied to a preliminary design assessment of an aircraft wing rib is presented. The computer program PASCO is used as the primary design and analysis tool to assess the structural efficiency and geometry of a tailored corrugated panel, a corrugated panel with a continuous laminate, a hat stiffened panel, a blade stiffened panel, and an unstiffened flat plate. To correct some of the shortcomings in the PASCO analysis when shear is present, a two step iterative process using the computer program VICON is used. The loadings considered include combinations of axial compression, shear, and lateral pressure. The loading ranges considered are broad enough such that the designs presented may be applied to other stiffened panel applications. An assessment is made of laminate variations, increased spacing, and nonoptimum geometric variations, including a beaded panel, on the design of the panels.

  11. Food peptidomics of in vitro gastrointestinal digestions of partially purified bovine hemoglobin: low-resolution versus high-resolution LC-MS/MS analyses.

    PubMed

    Caron, Juliette; Chataigné, Gabrielle; Gimeno, Jean-Pascal; Duhal, Nathalie; Goossens, Jean-François; Dhulster, Pascal; Cudennec, Benoit; Ravallec, Rozenn; Flahaut, Christophe

    2016-07-01

    Consumers and governments have become aware how the daily diet may affect the human health. All proteins from both plant and animal origins are potential sources of a wide range of bioactive peptides and the large majority of those display health-promoting effects. In the meat production food chain, the slaughterhouse blood is an inevitable co-product and, today, the blood proteins remain underexploited despite their bioactive potentiality. Through a comparative food peptidomics approach we illustrate the impact of resolving power, accuracy, sensitivity, and acquisition speed of low-resolution (LR)- and high-resolution (HR)-LC-ESI-MS/MS on the obtained peptide mappings and discuss the limitations of MS-based peptidomics. From in vitro gastrointestinal digestions of partially purified bovine hemoglobin, we have established the peptide maps of each hemoglobin chain. LR technique (normal bore C18 LC-LR-ESI-MS/MS) allows us to identify without ambiguity 75 unique peptides while the HR approach (nano bore C18 LC-HR-ESI-MS/MS) unambiguously identify more than 950 unique peptides (post-translational modifications included). Herein, the food peptidomics approach using the most performant separation methods and mass spectrometers with high-resolution capabilities appears as a promising source of information to assess the health potentiality of proteins.

  12. The SpeX Prism Library: 1000+ low-resolution, near-infrared spectra of ultracool M, L, T and Y dwarfs

    NASA Astrophysics Data System (ADS)

    Burgasser, Adam J.

    The SpeX Prism Library (SPL) is a uniform compilation of low-resolution (λ/Δλ ≈ 75-120), near-infrared (0.8--2.5 μm) spectra spanning a decade of observations with the IRTF SpeX spectrograph. Primarily containing ultracool M, L, T and Y dwarfs, this spectral library has been used in over 100 publications to date, facilitating a broad range of science on low mass stars, exoplanets, high redshift sources and instrument/survey design. I summarize the contents of the SPL and highlight a few of the key scientific results that have made use of this resource, as well as applications in education, outreach and art. I also outline the future plans of the SPL, which include a reanalysis of early data, better integration and dissemination of source and spectral metadata, conversion to Virtual Observatory formats, development of a Python software package for community analysis, and a design for a node-based visual programming platform that can facilitate citizen science and project-based learning in stellar spectroscopy. http://www.browndwarfs.org/spexprism

  13. Low-Resolution Spectrum of the Diffuse Galactic Light and 3.3 μm PAH Emission with the AKARI InfraRed Camera

    NASA Astrophysics Data System (ADS)

    Tsumura, Kohji; Matsumoto, Toshio; Matsuura, Shuji; Sakon, Itsuki; Tanaka, Masahiro; Wada, Takehiko

    2013-12-01

    We first obtained the spectrum of the diffuse Galactic light (DGL) at general interstellar space in the 1.8-5.3μm wavelength region with the low-resolution prism spectroscopy mode of the AKARI Infra-Red Camera (IRC) NIR channel. The 3.3μm m PAH band is detected in the DGL spectrum at Galactic latitude |b| < 15˚, and its correlations with the Galactic dust and gas are confirmed. The correlation between the 3.3μm PAH band and the thermal emission from the Galactic dust is expressed not by a simple linear correlation, but by a relation with extinction. Using this correlation, the spectral shape of DGL at an optically thin region (5˚ < |b| < 15˚) was derived as a template spectrum. Assuming that the spectral shape of this template spectrum is uniform at any position, the DGL spectrum can be estimated by scaling this template spectrum using the correlation between the 3.3μm PAH band and the thermal emission from the Galactic dust.

  14. Raman structural studies of the nickel electrode

    NASA Technical Reports Server (NTRS)

    Cornilsen, B. C.

    1985-01-01

    Raman spectroscopy is sensitive to empirically controlled nickel electrode structural variations, and has unique potential for structural characterization of these materials. How the structure relates to electrochemical properties is examined so that the latter can be more completely understood, controlled, and optimized. Electrodes were impregnated and cycled, and cyclic voltammetry is being used for electrochemical characterization. Structural variation was observed which has escaped detection using other methods. Structural changes are induced by: (1) cobalt doping, (2) the state of change or discharge, (3) the preparation conditions and type of buffer used, and (4) the formation process. Charged active mass has an NiOOH-type structure, agreeing with X-ray diffraction results. Discharged active mass, however, is not isostructural with beta-Ni(OH)2. Chemically prepared alpha phases are not isostructural either. A disordered structural model, containing point defects, is proposed for the cycled materials. This model explains K(+) incorporation. Band assignments were made and spectra interpreted for beta-Ni(OH)2, electrochemical NiOOH and chemically precipitated NiOOH.

  15. Raman structural studies of the nickel electrode

    NASA Technical Reports Server (NTRS)

    Cornilsen, Bahne C.

    1994-01-01

    The objectives of this investigation have been to define the structures of charged active mass, discharged active mass, and related precursor materials (alpha-phases), with the purpose of better understanding the chemical and electrochemical reactions, including failure mechanisms and cobalt incorporation, so that the nickel electrode may be improved. Although our primary tool has been Raman spectroscopy, the structural conclusions drawn from the Raman data have been supported and augmented by three other analysis methods: infrared spectroscopy, powder X-ray Diffraction (XRD), and x-ray absorption spectroscopy (in particular EXAFS, Extended X-ray Absorption Fine Structure spectroscopy).

  16. Artificially Structured Boundary For Antihydrogen Studies

    SciTech Connect

    Ordonez, C. A.

    2011-06-01

    It may be possible to confine antiprotons using an artificially structured boundary, as part of a process for synthesizing antihydrogen. An artificially structured boundary is defined at present as one that produces a spatially periodic static field, such that the spatial period and range of the field is much smaller than the dimensions of a cloud, plasma or beam of charged particles that is confined by the boundary. A modified Kingdon trap could employ an artificially structured boundary at the location of inner electrodes. The artificially structured boundary would produce a multipole magnetic field that keeps confined particles from reaching the inner electrodes. The magnetic field would be sufficiently short in range to affect the particle trajectories only in close proximity to the inner electrodes. The conditions for producing such a magnetic field have been assessed. The results indicate that the magnetic field must be an octupole or higher order field.

  17. Distillation tray structural parameter study: Phase 1

    NASA Technical Reports Server (NTRS)

    Winter, J. Ronald

    1991-01-01

    The purpose here is to identify the structural parameters (plate thickness, liquid level, beam size, number of beams, tray diameter, etc.) that affect the structural integrity of distillation trays in distillation columns. Once the sensitivity of the trays' dynamic response to these parameters has been established, the designer will be able to use this information to prepare more accurate specifications for the construction of new trays. Information is given on both static and dynamic analysis, modal response, and tray failure details.

  18. In Silico Analysis for the Study of Botulinum Toxin Structure

    NASA Astrophysics Data System (ADS)

    Suzuki, Tomonori; Miyazaki, Satoru

    2010-01-01

    Protein-protein interactions play many important roles in biological function. Knowledge of protein-protein complex structure is required for understanding the function. The determination of protein-protein complex structure by experimental studies remains difficult, therefore computational prediction of protein structures by structure modeling and docking studies is valuable method. In addition, MD simulation is also one of the most popular methods for protein structure modeling and characteristics. Here, we attempt to predict protein-protein complex structure and property using some of bioinformatic methods, and we focus botulinum toxin complex as target structure.

  19. Nucleon Spin And Structure Studies With COMPASS

    SciTech Connect

    Platchkov, Stephane

    2006-07-11

    The COMPASS experiment at CERN investigates nucleon structure and spectroscopy with high-intensity muon and hadron beams. Between 2002 and 2004 COMPASS has mainly concentrated on the spin structure of the nucleon via deep-inelastic scattering of polarized muons on polarized nucleons. First results include measurements of the gluon contribution to the nucleon spin via charm production and high-pt pairs, {lambda} polarization, vector-meson production, Collins and Sivers asymmetries, inclusive and semi-inclusive deep-inelastic scattering asymmetries and a search for pentaquark states. A short overview of these results is presented.

  20. Teacher's Guide for Structures. Elementary Science Study.

    ERIC Educational Resources Information Center

    Watt, Daniel H.; And Others

    Presented are building activities, for elementary school children, using a variety of different materials. Weak materials, such as clay, straws and pins, paper tubes and index cards, are used as examples; structures built with these materials are displayed in photographs and discussed. Problems are suggested from which additional activities can be…

  1. Structural equation modeling for observational studies

    USGS Publications Warehouse

    Grace, J.B.

    2008-01-01

    Structural equation modeling (SEM) represents a framework for developing and evaluating complex hypotheses about systems. This method of data analysis differs from conventional univariate and multivariate approaches familiar to most biologists in several ways. First, SEMs are multiequational and capable of representing a wide array of complex hypotheses about how system components interrelate. Second, models are typically developed based on theoretical knowledge and designed to represent competing hypotheses about the processes responsible for data structure. Third, SEM is conceptually based on the analysis of covariance relations. Most commonly, solutions are obtained using maximum-likelihood solution procedures, although a variety of solution procedures are used, including Bayesian estimation. Numerous extensions give SEM a very high degree of flexibility in dealing with nonnormal data, categorical responses, latent variables, hierarchical structure, multigroup comparisons, nonlinearities, and other complicating factors. Structural equation modeling allows researchers to address a variety of questions about systems, such as how different processes work in concert, how the influences of perturbations cascade through systems, and about the relative importance of different influences. I present 2 example applications of SEM, one involving interactions among lynx (Lynx pardinus), mongooses (Herpestes ichneumon), and rabbits (Oryctolagus cuniculus), and the second involving anuran species richness. Many wildlife ecologists may find SEM useful for understanding how populations function within their environments. Along with the capability of the methodology comes a need for care in the proper application of SEM.

  2. CGEL-2: Structural Studies of Colloidal Suspensions

    NASA Technical Reports Server (NTRS)

    2004-01-01

    These are images of CGEL-2 samples taken during STS-95. They show binary colloidal suspensions that have formed ordered crystalline structures in microgravity. In sample 5, there are more particles therefore, many, many crystallites (small crystals) form. In sample 6, there are less particles therefore, the particles are far apart and few, much larger crystallites form. The white object in the right corner of sample 5 is the stir bar used to mix the sample at the begirning of the mission.

  3. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers

    SciTech Connect

    Vandavasi, Venu Gopal; Putnam, Daniel K.; Zhang, Qiu; Petridis, Loukas; Heller, William T.; Nixon, B. Tracy; Haigler, Candace H.; Kalluri, Udaya; Coates, Leighton; Langan, Paul; Smith, Jeremy C.; Meiler, Jens; O’Neill, Hugh

    2015-11-10

    In a cellulose synthesis complex a "rosette" shape is responsible for the synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. Our work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer in solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. Moreover, the conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. Finally, this study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.

  4. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers.

    PubMed

    Vandavasi, Venu Gopal; Putnam, Daniel K; Zhang, Qiu; Petridis, Loukas; Heller, William T; Nixon, B Tracy; Haigler, Candace H; Kalluri, Udaya; Coates, Leighton; Langan, Paul; Smith, Jeremy C; Meiler, Jens; O'Neill, Hugh

    2016-01-01

    A cellulose synthesis complex with a "rosette" shape is responsible for synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. This work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer in solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. The conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. This study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.

  5. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers

    DOE PAGESBeta

    Vandavasi, Venu Gopal; Putnam, Daniel K.; Zhang, Qiu; Petridis, Loukas; Heller, William T.; Nixon, B. Tracy; Haigler, Candace H.; Kalluri, Udaya; Coates, Leighton; Langan, Paul; et al

    2015-11-10

    In a cellulose synthesis complex a "rosette" shape is responsible for the synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. Our work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer inmore » solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. Moreover, the conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. Finally, this study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.« less

  6. Structural Studies of Human Pyruvate Dehydrogenase

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Korotchkina, Lioubov G.; Dominiak, Paulina; Sidhu, Sukhdeep; Patel, Mulchand S.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    Human pyruvate dehydrogenase (E1) catalyzes the irreversible decarboxylation of pyruvate in the presence of Mg(2+) and thiamin pyrophosphate (TPP) followed by the rate-limiting reductive acetylation of the lipoyl moiety linked to dihydrolipoamide acetyltransferase. The three-dimensional structure of human E1 is elucidated using the methods of macromolecular X-ray crystallography. The structure is an alpha, alpha', beta and beta' tetramer with the protein units being in the tetrahedral arrangement. Each 361-residue alpha-subunit and 329-residue beta-subunit is composed of a beta-sheet core surrounded by alpha-helical domains. Each subunit is in extensive contact with all the three subunits involving TPP and magnesium cofactors, and potassium ions. The two binding sites for TPP are at the alpha-beta' and alpha'-beta interfaces, each involving a magnesium ion and Phe6l, His63, Tyr89, and Met200 from the alpha-subunit (or alpha'-subunit), and Met81 Phe85, His128 from the beta-subunit (or beta'-subunit). K+ ions are nestled between two beta-sheets and the end of an alpha-helix in each beta-subunit, where they are coordinated by four carbonyl oxygen groups from Ile12, Ala160, Asp163, and Asnl65, and a water molecule. The catalytic C2 carbon of thiazolium ring in this structure forms a 3.2 A contact with a water molecule involved in a series of H-bonds with other water molecules, and indirectly with amino acids including those involved in the catalysis and regulation of the enzyme.

  7. Structural and spectroscopic studies of fluoroprotactinates.

    PubMed

    De Sio, Stéphanie M; Wilson, Richard E

    2014-02-01

    Seven protactinium(V) fluoride compounds have been synthesized, and their crystal structures and Raman spectra are reported. (NH4)2PaF7, K2PaF7, Rb2PaF7, and Cs2PaF7 were found to crystallize in the monoclinic space group P21/c for the ammonium compound and C2/c for the K(+)-, Rb(+)-, and Cs(+)-containing compounds, with nine-coordinate Pa forming infinite chains through fluorine bridges. Na3PaF8 crystallizes in the tetragonal space group I4/mmm with eight-coordinate Pa in tetragonal geometry, while tetramethylammonium fluoroprotactinate shows two different structures: (Me4N)2(H3O)PaF8, an eight-coordinate molecular compound crystallizing in the monoclinic space group C2/c, and (Me4N)PaF6, an eight-coordinate Pa compound forming infinite chains and crystallizing in the orthorhombic space group Pnnm. A comparison of solid- and solution-state Raman data indicates that the PaF8(-) anion could be the predominant Pa(V) complex in concentrated solutions of aqueous HF.

  8. Structural and spectroscopic studies of fluoroprotactinates.

    PubMed

    De Sio, Stéphanie M; Wilson, Richard E

    2014-02-01

    Seven protactinium(V) fluoride compounds have been synthesized, and their crystal structures and Raman spectra are reported. (NH4)2PaF7, K2PaF7, Rb2PaF7, and Cs2PaF7 were found to crystallize in the monoclinic space group P21/c for the ammonium compound and C2/c for the K(+)-, Rb(+)-, and Cs(+)-containing compounds, with nine-coordinate Pa forming infinite chains through fluorine bridges. Na3PaF8 crystallizes in the tetragonal space group I4/mmm with eight-coordinate Pa in tetragonal geometry, while tetramethylammonium fluoroprotactinate shows two different structures: (Me4N)2(H3O)PaF8, an eight-coordinate molecular compound crystallizing in the monoclinic space group C2/c, and (Me4N)PaF6, an eight-coordinate Pa compound forming infinite chains and crystallizing in the orthorhombic space group Pnnm. A comparison of solid- and solution-state Raman data indicates that the PaF8(-) anion could be the predominant Pa(V) complex in concentrated solutions of aqueous HF. PMID:24437929

  9. Fatigue studies of polyurethane sandwich structures

    NASA Astrophysics Data System (ADS)

    Sharma, S. C.; Krishna, M.; Narasimha Murthy, H. N.; Sathyamoorthy, M.; Bhattacharya, Debes

    2004-10-01

    The fatigue characteristics of polyurethane foam-cored (PUF) composite sandwich structures were investigated using three-point bending tests carried out according to ASTM C 393. Three types of specimens (epoxy/glass-PUF-epoxy/glass, polyester/glass-PUF-polyester/glass, and epoxy/glass-PUF-polyester/glass) were considered for investigation. Experimental results indicate that degradation of stiffness occurs due to debonding and sliding between the skin and the foam during fatigue cycles. Epoxy/glass-PUF-epoxy/glass sandwich structures exhibit higher bending strength along with higher stiffness degradation than the other two types of sandwich panels, due to higher initial fatigue loading. The lowest fatigue properties have been obtained for the polyester/glass-PUF-polyester/glass sandwich panel specimens. Better performance of the epoxy/glass-PUF-epoxy/glass sandwich panels is most likely due to the superior properties of the outer thin skins. Most of the specimens fail within the foam region and not at the skin level. This situation is possibly due to debonding between the foam and the skin. The fatigue damage development in the foam and skin has been investigated using scanning electron microscopy.

  10. Lunar surface structural concepts and construction studies

    NASA Technical Reports Server (NTRS)

    Mikulas, Martin

    1991-01-01

    The topics are presented in viewgraph form and include the following: lunar surface structures construction research areas; lunar crane related disciplines; shortcomings of typical mobile crane in lunar base applications; candidate crane cable suspension systems; NIST six-cable suspension crane; numerical example of natural frequency; the incorporation of two new features for improved performance of the counter-balanced actively-controlled lunar crane; lunar crane pendulum mechanics; simulation results; 1/6 scale lunar crane testbed using GE robot for global manipulation; basic deployable truss approaches; bi-pantograph elevator platform; comparison of elevator platforms; perspective of bi-pantograph beam; bi-pantograph synchronously deployable tower/beam; lunar module off-loading concept; module off-loader concept packaged; starburst deployable precision reflector; 3-ring reflector deployment scheme; cross-section of packaged starburst reflector; and focal point and thickness packaging considerations.

  11. A study of the mechanical and structural properties ofpolonium

    SciTech Connect

    Kraig, Robert E.; Roundy, David; Cohen, Marvin L.

    2003-05-15

    We have performed an ab initio study of the structure of polonium. By calculating total energies in a number of tetragonal lattice configurations, we have shown that the simple cubic structure is preferred by the system. The other two zero-stress structures, bcc and fcc, correspond to inflection points along this path. These calculations agree with experimental evidence that polonium is the only known element to assume the simple cubic structure at room temperature.

  12. Simplified environmental study on innovative bridge structure.

    PubMed

    Bouhaya, Lina; Le Roy, Robert; Feraille-Fresnet, Adélaïde

    2009-03-15

    The aim of this paper is to present a simplified life cycle assessment on an innovative bridge structure, made of wood and ultra high performance concrete, which combines mechanical performance with minimum environmental impact. The environmental analysis was conducted from cradle to grave using the Life Cycle Assessment method. It was restricted to energy release and greenhouse gas emissions. Assumptions are detailed for each step of the analysis. For the wood end-of-life, three scenarios were proposed: dumping, burning, and recycling. Results show that the most energy needed is in the production phase, which represents 73.4% of the total amount. Analysis shows that the renewable energy is about 70% of the production energy. Wood, through its biomass CO2, contributes positively to the environmental impact. It was concluded that no scenario can be the winner on both impacts. Indeed, the end-of-life wood recycling gives the best impact on CO2 release, whereas burning wood, despite its remarkable energy impact is the worst. According to the emphasis given to each impact, designers will be able to choose one or the other. PMID:19368215

  13. Structure Property Studies for Additively Manufactured Parts

    SciTech Connect

    Milenski, Helen M; Schmalzer, Andrew Michael; Kelly, Daniel

    2015-08-17

    Since the invention of modern Additive Manufacturing (AM) processes engineers and designers have worked hard to capitalize on the unique building capabilities that AM allows. By being able to customize the interior fill of parts it is now possible to design components with a controlled density and customized internal structure. The creation of new polymers and polymer composites allow for even greater control over the mechanical properties of AM parts. One of the key reasons to explore AM, is to bring about a new paradigm in part design, where materials can be strategically optimized in a way that conventional subtractive methods cannot achieve. The two processes investigated in my research were the Fused Deposition Modeling (FDM) process and the Direct Ink Write (DIW) process. The objectives of the research were to determine the impact of in-fill density and morphology on the mechanical properties of FDM parts, and to determine if DIW printed samples could be produced where the filament diameter was varied while the overall density remained constant.

  14. Study of excited nucleons and their structure

    SciTech Connect

    Burkert, Volker D.

    2014-01-01

    Recent advances in the study of excited nucleons are discussed. Much of the progress has been achieved due to the availability of high precision meson production data in the photoproduction and electroproduction sectors, the development of multi-channel partial wave analysis techniques, and advances in Lattice QCD with predictions of the full excitation spectrum.

  15. CASP11--An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline.

    PubMed

    Fischer, Axel W; Heinze, Sten; Putnam, Daniel K; Li, Bian; Pino, James C; Xia, Yan; Lopez, Carlos F; Meiler, Jens

    2016-01-01

    In silico prediction of a protein's tertiary structure remains an unsolved problem. The community-wide Critical Assessment of Protein Structure Prediction (CASP) experiment provides a double-blind study to evaluate improvements in protein structure prediction algorithms. We developed a protein structure prediction pipeline employing a three-stage approach, consisting of low-resolution topology search, high-resolution refinement, and molecular dynamics simulation to predict the tertiary structure of proteins from the primary structure alone or including distance restraints either from predicted residue-residue contacts, nuclear magnetic resonance (NMR) nuclear overhauser effect (NOE) experiments, or mass spectroscopy (MS) cross-linking (XL) data. The protein structure prediction pipeline was evaluated in the CASP11 experiment on twenty regular protein targets as well as thirty-three 'assisted' protein targets, which also had distance restraints available. Although the low-resolution topology search module was able to sample models with a global distance test total score (GDT_TS) value greater than 30% for twelve out of twenty proteins, frequently it was not possible to select the most accurate models for refinement, resulting in a general decay of model quality over the course of the prediction pipeline. In this study, we provide a detailed overall analysis, study one target protein in more detail as it travels through the protein structure prediction pipeline, and evaluate the impact of limited experimental data.

  16. Study made of interaction between sound fields and structural vibrations

    NASA Technical Reports Server (NTRS)

    Lyon, R. H.; Smith, P. W., Jr.

    1967-01-01

    Study analyzes structural vibrations and the interactions between them and sound fields. It outlines a conceptual framework to analyze the vibrations of systems and their interactions, incorporating the results of earlier studies and establishing a unified basis for continuing research.

  17. Low-resolution spectroscopy of main sequence stars belonging to 12 Galactic globular clusters. I. CH and CN band strength variations

    NASA Astrophysics Data System (ADS)

    Pancino, E.; Rejkuba, M.; Zoccali, M.; Carrera, R.

    2010-12-01

    Context. Globular clusters show star-to-star abundance variations for light elements that are not yet well understood. The preferred explanation involves a self-enrichment scenario, within which two subsequent generations of stars co-exist in globular clusters. Observations of chemical abundances in the main sequence and sub-giant branch stars allow us to investigate the signature of this chemically processed material without the complicating effects caused by stellar evolution and internal mixing. Aims: Our main goal is to investigate the carbon-nitrogen anti-correlation with low-resolution spectroscopy of 20-50 stars fainter than the first dredge-up in seven Galactic globular clusters (NGC 288, NGC 1851, NGC 5927, NGC 6352, NGC 6388, and Pal 12) with different properties. We complemented our observations with 47 Tuc archival data, with four additional clusters from the literature (M 15, M 22, M 55, NGC 362), and with additional literature data on NGC 288. Methods: In this first paper, we measured the strengh of the CN and CH band indices, which correlate with the N and C abundances, and we investigated the anti-correlation and bimodality of these indices. We compared rCN, the ratio of stars belonging to the CN-strong and weak groups, with 15 different cluster parameters. Results: We clearly see bimodal anti-correlation of the CH and CN band stregths in the metal-rich clusters (Pal 12, 47 Tuc, NGC 6352, NGC 5927). Only M 15 among the metal-poor clusters shows a clearly bimodal anti-correlation. We found weak correlations (sligthly above 1σ) of rCN with the cluster orbital parameters, present-day total mass, cluster concentration, and age. Conclusions: Our findings support the self-enrichment scenario, and suggest that the occurrence of more than two major generations of stars in a GGC should be rare. Small additional generations (<10-20% of the total) would be difficult to detect with our samples. The first generation, which corresponds to the CN-weak stars

  18. Modularity in protein structures: study on all-alpha proteins.

    PubMed

    Khan, Taushif; Ghosh, Indira

    2015-01-01

    Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

  19. A theoretical study of structural acoustic silencers for hydraulic systems.

    PubMed

    Ramamoorthy, Sripriya; Grosh, Karl; Dodson, John M

    2002-05-01

    Theoretical studies show that the introduction of an in-line structural acoustic silencer into a hydraulic system can achieve broadband quieting (i.e., high transmission loss). Strategies for using structural acoustic filters for simultaneously reducing reflection and transmission by tailoring the material properties are studied. A structural acoustic silencer consists of a flexible layer inserted into nominally rigid hydraulic piping. Transmission loss is achieved by two mechanisms--reflection of energy due to an impedance mismatch, and coupling of the incoming acoustic fluctuations to structural vibrations thereby allowing for the extraction of energy through losses in the structure. Structural acoustic finite element simulations are used to determine the transmission loss and evaluate designs. Results based on the interaction of orthotropic and isotropic plates with variable geometry, operating in heavy fluids like water and oil, are presented.

  20. Recombinant Thermus aquaticus RNA Polymerase for Structural Studies

    SciTech Connect

    Juznedelov,K.; Lamour, V.; Patikoglou, G.; Chlenov, M.; Darst, S.; Severinov, K.

    2006-01-01

    Advances in the structural biology of bacterial transcription have come from studies of RNA polymerases (RNAPs) from the thermophilic eubacteria Thermus aquaticus (Taq) and Thermus thermophilus (Tth). These structural studies have been limited by the fact that only endogenous Taq or Tth RNAP, laboriously purified from large quantities of Taq or Tth cell paste and offering few options for genetic modification, is suitable for structural studies. Recombinant systems for the preparation of Taq RNAP by co-overexpression and assembly in the heterologous host, Escherichia coli, have been described, but these did not yield enzyme suitable for crystallographic studies. Here we describe recombinant systems for the preparation of Taq RNAP harboring full or partial deletions of the Taq {beta}' non-conserved domain (NCD), yielding enzyme suitable for crystallographic studies. This opens the way for structural studies of genetically manipulated enzymes, allowing the preparation of more crystallizable enzymes and facilitating detailed structure/function analysis. Characterization of the Taq{beta}'NCD deletion mutants generated in this study showed that the {beta}'NCD is important for the efficient binding of the s subunit, confirming previous hypotheses. Finally, preliminary structural analysis (at 4.1 Angstroms resolution) of one of the recombinant mutants revealed a previously unobserved conformation of the {beta}-flap, further defining the range of conformations accessible to this flexible structural element.

  1. THE CROSS-CULTURAL STUDY OF SEMANTIC STRUCTURE. FINAL REPORT.

    ERIC Educational Resources Information Center

    BURLING, ROBBINS; FRIEDRICH, PAUL

    SEVERAL EXPLORATIONS WERE MADE INTO THE STRUCTURE OF MEANING IN BURMESE AND RUSSIAN. VARIOUS KINDS OF LINGUISTIC INFORMATION WERE ISOLATED BY TEXTUAL STUDY AND INTERVIEWS WITH NATIVE SPEAKERS. DISCUSSION COVERED SUCH THEORETICAL QUESTIONS AS (1) SYNCHRONY AND DIACHRONY, (2) SEMANTICS AND GRAMMAR, (3) SEMANTICS AND SOCIAL STRUCTURE, (4) SEMANTICS…

  2. Experimental studies of the structure of grain boundaries

    SciTech Connect

    Sass, S.L.

    1993-04-01

    Goals are to understand factors affecting structure of grain boundaries in intermetallic compounds, understand how solute segregation affects grain boundary structure and causes embrittlement in Fe-base alloys, and explore control of grain boundary properties. Fe and boron-doped Ni[sub 3]Al and NiAl were studied. 7 figs, 1 tab, 18 refs.

  3. Electron crystallography for structural and functional studies of membrane proteins.

    PubMed

    Fujiyoshi, Yoshinori

    2011-01-01

    Membrane proteins are important research targets for basic biological sciences and drug design, but studies of their structure and function are considered difficult to perform. Studies of membrane structures have been greatly facilitated by technological and instrumental advancements in electron microscopy together with methodological advancements in biology. Electron crystallography is especially useful in studying the structure and function of membrane proteins. Electron crystallography is now an established method of analyzing the structures of membrane proteins in lipid bilayers, which resembles their natural biological environment. To better understand the neural system function from a structural point of view, we developed the cryo-electron microscope with a helium-cooled specimen stage, which allows for analysis of the structures of membrane proteins at a resolution higher than 3 Å. This review introduces recent instrumental advances in cryo-electron microscopy and presents some examples of structure analyses of membrane proteins, such as bacteriorhodopsin, water channels and gap junction channels. This review has two objectives: first, to provide a personal historical background to describe how we came to develop the cryo-electron microscope and second, to discuss some of the technology required for the structural analysis of membrane proteins based on cryo-electron microscopy.

  4. Band Structure of SnTe Studied by Photoemission Spectroscopy

    NASA Astrophysics Data System (ADS)

    Littlewood, P. B.; Mihaila, B.; Schulze, R. K.; Safarik, D. J.; Gubernatis, J. E.; Bostwick, A.; Rotenberg, E.; Opeil, C. P.; Durakiewicz, T.; Smith, J. L.; Lashley, J. C.

    2010-08-01

    We present an angle-resolved photoemission spectroscopy study of the electronic structure of SnTe and compare the experimental results to ab initio band structure calculations as well as a simplified tight-binding model of the p bands. Our study reveals the conjectured complex Fermi surface structure near the L points showing topological changes in the bands from disconnected pockets, to open tubes, and then to cuboids as the binding energy increases, resolving lingering issues about the electronic structure. The chemical potential at the crystal surface is found to be 0.5 eV below the gap, corresponding to a carrier density of p=1.14×1021cm-3 or 7.2×10-2 holes per unit cell. At a temperature below the cubic-rhombohedral structural transition a small shift in spectral energy of the valance band is found, in agreement with model predictions.

  5. Band structure of SnTe studied by photoemission spectroscopy.

    PubMed

    Littlewood, P B; Mihaila, B; Schulze, R K; Safarik, D J; Gubernatis, J E; Bostwick, A; Rotenberg, E; Opeil, C P; Durakiewicz, T; Smith, J L; Lashley, J C

    2010-08-20

    We present an angle-resolved photoemission spectroscopy study of the electronic structure of SnTe and compare the experimental results to ab initio band structure calculations as well as a simplified tight-binding model of the p bands. Our study reveals the conjectured complex Fermi surface structure near the L points showing topological changes in the bands from disconnected pockets, to open tubes, and then to cuboids as the binding energy increases, resolving lingering issues about the electronic structure. The chemical potential at the crystal surface is found to be 0.5 eV below the gap, corresponding to a carrier density of p=1.14 × 10(21)  cm(-3) or 7.2 × 10(-2) holes per unit cell. At a temperature below the cubic-rhombohedral structural transition a small shift in spectral energy of the valance band is found, in agreement with model predictions. PMID:20868120

  6. An algorithm for generalizing topography to grids while preserving subscale morphologic characteristics—creating a glacier bed DEM for Jakobshavn trough as low-resolution input for dynamic ice-sheet models

    NASA Astrophysics Data System (ADS)

    Herzfeld, Ute C.; Wallin, Bruce F.; Leuschen, Carlton J.; Plummer, Joel

    2011-11-01

    The objective of this paper is to derive an algorithm for preserving important subscale morphologic characteristics at grids of lower-resolution, in particular for linear features such as canyons and ridge lines. The development of such an algorithm is necessitated by applications that require reduced spatial resolution, as is common in cartographic generalization, GIS applications, and geophysical modeling. Since any algorithm that results in weighted averages, including optimum interpolation and ordinary kriging, cannot reproduce correct depths, a new algorithm is designed based on principles of mathematical morphology. The algorithm described here is applied to derive a subglacial bed of the Greenland Ice Sheet that includes the trough of Jakobshavn Isbræ as a continuous canyon at correct depth in a low-resolution (5-km) digital elevation model (DEM). Data from recent airborne radar measurements of the elevation of the subglacial bed as part of the CReSIS project are utilized. The morphologic algorithm is designed with geophysical ice-sheet modeling in mind, in the following context. Currently occurring changes in the Earth's climate and the cryosphere cause changes in sea level, and the societal relevance of these natural processes motivates estimation of maximal sea-level rise in the medium-term future. The fast-moving outlet glaciers are more sensitive to climatic change than other parts of the Greenland ice sheet. Jakobshavn Isbrae, the fastest-moving ice stream in Greenland, follows a subglacial geologic trough. Since the existence of the trough causes the acceleration of the slow-moving inland ice in the Jakobshavn region and the formation of the ice stream, correct representation of the trough in a DEM is essential to model changes in the dynamics of the ice sheet and resultant sea-level predictions, even if current ice-sheet models can typically be run only at 5-km resolution. The DEM resultant from this study helps to bridge the conceptual gap between

  7. Structural and Aggregation Study of Protic Ionic Liquids

    NASA Astrophysics Data System (ADS)

    Mattedi, S.; Martin-Pastor, M.; Iglesias, M.

    2011-12-01

    In this work there were studied structural and agreggation aspects of ionic liquids formed by the reaction between ethanolamines with low chain organic acids using NMR techniques. Three ionic liquids composed of pentanoic acid and (mono-, di- and tri-) ethanol amine were studied by 1H, and 13C solution NMR methods. NMR assisted the chemical and quantitative characterization of these three ionic liquids and provided insight in their structural arrangement of their components in the ionic liquid medium. The obtained results could be used to understand the structure and aggregation pattern of these ionic liquids and helps in the development of possible industrial applications.

  8. Selection process for trade study: Graphite Composite Primary Structure (GCPS)

    NASA Technical Reports Server (NTRS)

    Greenberg, H. S.

    1994-01-01

    This TA 2 document describes the selection process that will be used to identify the most suitable structural configuration for an SSTO winged vehicle capable of delivering 25,000 lbs to a 220 nm circular orbit at 51.6 degree inclination. The most suitable unpressurized graphite composite structures and material selections is within this configuration and will be the prototype design for subsequent design and analysis and the basis for the design and fabrication of payload bay, wing, and thrust structure full scale test articles representing segments of the prototype structures. The selection process for this TA 2 trade study is the same as that for the TA 1 trade study. As the trade study progresses additional insight may result in modifications to the selection criteria within this process. Such modifications will result in an update of this document as appropriate.

  9. Trade study plan for Graphite Composite Primary Structure (GCPS)

    NASA Technical Reports Server (NTRS)

    Greenberg, H. S.

    1994-01-01

    This TA 2 document (with support from TA 1) describes the trade study plan that will identify the most suitable structural configuration for an SSTO winged vehicle capable of delivering 25,000 lbs to a 220 nm circular orbit at 51.6 degree inclination For this most suitable configuration the structural attachment of the wing, and the most suitable GCPS composite materials for intertank, wing, tail and thrust structure are identified. This trade study analysis uses extensive information derived in the TA 1 trade study plan and is identified within the study plan. In view of this, for convenience, the TA 1 study plan is included as an appendix to this document.

  10. Structure and dynamics in Photosystem I

    NASA Astrophysics Data System (ADS)

    Jolley, Craig Charles

    Photosystem I (PSI) is a transmembrane protein complex that uses incident light energy to drive an energetically unfavorable electron transfer reaction across a membrane in the early steps of oxygenic photosynthesis. This electron transfer reaction provides energy for the fixing of carbon dioxide and for the subsequent synthesis of nearly all biological material on Earth. Despite the morphological variety of oxygenic photosynthetic organisms---ranging from single-celled aquatic cyanobacteria to large, complex terrestrial plants---the structure and function of PSI are remarkably well-conserved across phyla. PSI has been the subject of extensive interdisciplinary research involving fields ranging from molecular genetics to condensed matter physics, and many aspects of its function still remain unclear. This study presents a variety of theoretical and experimental approaches to aspects of PSI structure and dynamics. An atomic-level structural model of higher plant PSI has been constructed based on recent protein crystal structures, and provides insight into the evolution of eukaryotic PSI. Time-resolved optical spectroscopic studies of PSI supercomplexes from the green freshwater alga Chlamydomonas reinhardtii illustrate how this organism adapts its photosynthetic apparatus to deal with changing environmental conditions and highlight the importance of structure-function relationships in light-harvesting systems. A novel computational approach using constrained geometric simulations has been used to model a portion of the PSI assembly process, shedding some light on how the heterodimeric PSI reaction center evolved from the more ancient homodimeric photosynthetic reaction centers found in green sulfur bacteria and heliobacteria. A new method is also demonstrated in which constrained geometric simulations are used to flexibly fit a high-resolution protein structure to a low-resolution density map obtained with cryo-electron microscopy (cryo-EM) or low-resolution x

  11. Structural Studies of Pterin-Based Inhibitors of Dihydropteroate Synthase

    SciTech Connect

    Hevener, Kirk E.; Yun, Mi-Kyung; Qi, Jianjun; Kerr, Iain D.; Babaoglu, Kerim; Hurdle, Julian G.; Balakrishna, Kanya; White, Stephan W.; Lee, Richard E.

    2010-01-12

    Dihydropteroate synthase (DHPS) is a key enzyme in bacterial folate synthesis and the target of the sulfonamide class of antibacterials. Resistance and toxicities associated with sulfonamides have led to a decrease in their clinical use. Compounds that bind to the pterin binding site of DHPS, as opposed to the p-amino benzoic acid (pABA) binding site targeted by the sulfonamide agents, are anticipated to bypass sulfonamide resistance. To identify such inhibitors and map the pterin binding pocket, we have performed virtual screening, synthetic, and structural studies using Bacillus anthracis DHPS. Several compounds with inhibitory activity have been identified, and crystal structures have been determined that show how the compounds engage the pterin site. The structural studies identify the key binding elements and have been used to generate a structure-activity based pharmacophore map that will facilitate the development of the next generation of DHPS inhibitors which specifically target the pterin site.

  12. Experimental study on wake structure of single rising clean bubble

    NASA Astrophysics Data System (ADS)

    Sato, Ayaka; Takedomi, Yuta; Shirota, Minori; Sanada, Toshiyuki; Watanabe, Masao

    2007-11-01

    Wake structure of clean bubble rising in quiescent silicone oil solution of photochromic dye is experimentally studied. A single bubble is generated, immediately after UV sheet light illuminates the part of the liquid just above the bubble generation nozzle in order to activate photochromic dye. Once the bubble passes across the colored part of the liquid, the bubble is accompanied by some portion of activated dye tracers; hence the flow structure in the rear of the single rising bubble is visualized. We capture stereo images of both wake structure and bubble motion. We study how wake structure changes with the increase in bubble size. We observe the stable axisymmetric wake structure, which is called `standing eddy' when bubble size is relatively small, and then wake structure becomes unstable and starts to oscillate with the increase in bubble size. With further increase in bubble size, a pair of streamwise vortices, which is called `double thread', is observed. We discuss in detail this transition from the steady wake to unsteady wake structure, especially double thread wake development and hairpin vortices shedding, in relation to the transition from rectilinear to spiral or zigzag bubble motions.

  13. Further Geophysical Studies of the Haughton Impact Structure

    NASA Technical Reports Server (NTRS)

    Glass, B. J.; Domville, S.; Lee, P.

    2005-01-01

    The approximately 23 Ma Haughton impact structure, located at 75 deg 23 min N, 89 deg 39 min W in the Canadian Arctic, on Devon Island, Nunavut, Canada is a well-preserved impact structure with an original rim diameter estimated at about 23 - 24 km. Past studies, in the 1980s, did an initial survey of the Haughton structure, looking at its surface units, exposures, map surface geology, topographic and initial surveys of gravity and magnetic fields in profiles across the impact structure. A topological outer ring and the lack of a well-defined central peak was cited as evidence that Haughton was a multi-ring structure. However other authors consider it more likely that the Haughton structure is a central-peak basin with simply a limited extent, and/or full peak features having been removed through glaciations and subsequent years. The impact structure is located in approximately 2 km thickness of carbonate material on top of a gneissic basement. The impact structure itself can be described in terms of uplifted and moved blocks of altered gneissic and carbonate material with areas in the center of the crater covered with impact carbonate melts and/or reworked impact breccias. Additional information is included in the original extended abstract.

  14. Structures, performance, benefit, cost study. [gas turbine engines

    NASA Technical Reports Server (NTRS)

    Feder, E.

    1981-01-01

    Aircraft engine structures were studied to identify the advanced structural technologies that would provide the most benefits to future aircraft operations. A series of studies identified engine systems with the greatest potential for improvements. Based on these studies, six advanced generic structural concepts were selected and conceptually designed. The benefits of each concept were quantitatively assessed in terms of thrust specific fuel consumption, weight, cost, maintenance cost, fuel burned and direct operating cost plus interest. The probability of success of each concept was also determined. The concepts were ranked and the three most promising were selected for further study which consisted of identifying and comprehensively outlining the advanced technologies required to develop these concepts for aircraft engine application. Analytic, fabrication, and test technology developments are required. The technology programs outlined emphasize the need to provide basic, fundamental understanding of technology to obtain the benefit goals.

  15. The evolution of structured illumination microscopy in studies of HIV.

    PubMed

    Marno, Kelly; Al'Zoubi, Lara; Pearson, Matthew; Posch, Markus; McKnight, Áine; Wheeler, Ann P

    2015-10-15

    The resolution limit of conventional light microscopy has proven to be limiting for many biological structures such as viruses including Human immunodeficiency virus (HIV). Individual HIV virions are impossible to study using confocal microscopy as they are well below the 200 nm resolution limit of conventional light microscopes. Structured illumination microscopy (SIM) allows a twofold enhancement in image resolution compared to standard widefield illumination and so provides an excellent tool for study of HIV. Viral capsids (CAs) vary between 110 and 146 nm so this study challenges the performance of SIM microscopes. SIM microscopy was first developed in 2000, commercialised in 2007 and rapidly developed. Here we present the changes in capabilities of the SIM microscopes for study of HIV localisation as the instrumentation for structured illumination microscopy has evolved over the past 8 years.

  16. Structural study of surfactant-dependent interaction with protein

    SciTech Connect

    Mehan, Sumit; Aswal, Vinod K.; Kohlbrecher, Joachim

    2015-06-24

    Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

  17. Neutron Scattering Studies of Nanomagnetism and Artificially Structured Materials

    SciTech Connect

    Fitzsimmons, M.R.; Bader, S.D.; Borchers, J.A.; Felcher, G.P.; Furdyna, J.K.; Hoffmann, A.; Kortright, J.B.; Schuller, Ivan K.; Schulthess, T.C.; Sinha, S.K.; Toney, M.F.; Weller, D.; Wolf, S.

    2003-02-01

    Nanostructured magnetic materials are intensively studied due to their unusual properties and promise for possible applications. The key issues in these materials relate to the connection between their physical properties (transport, magnetism, mechanical, etc.) and their chemical-physical structure. In principle, a detailed knowledge of the chemical and physical structure allows calculation of their physical properties. Theoretical and computational methods are rapidly evolving so that magnetic properties of nanostructured materials might soon be predicted. Success in this endeavor requires detailed quantitative understanding of the magnetic structure and properties.

  18. Structural study of surfactant-dependent interaction with protein

    NASA Astrophysics Data System (ADS)

    Mehan, Sumit; Aswal, Vinod K.; Kohlbrecher, Joachim

    2015-06-01

    Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

  19. Structure of overheated metal clusters: MD simulation study

    SciTech Connect

    Vorontsov, Alexander

    2015-08-17

    The structure of overheated metal clusters appeared in condensation process was studied by computer simulation techniques. It was found that clusters with size larger than several tens of atoms have three layers: core part, intermediate dense packing layer and a gas- like shell with low density. The change of the size and structure of these layers with the variation of internal energy and the size of cluster is discussed.

  20. Modelling molecular structures for computer-assisted studies of drug structure-activity relations

    SciTech Connect

    Jerman-Blazic, B.; Randic, M.

    1983-01-01

    The characterizations of structure by selected graph invariant is used as an element for model building in the study of quantitative structure activity relations. The path numbers Pi were adopted as the basic graph invariants. Euclidian distance between two sequences of path numbers, which are considered as position vectors in an n-dimensional space, was the measure of similarity between the two structures. The results, which proceeded from the application of the method on a set of 38 substituted barbituratic acids show that path enumeration model offer suitable basis for QSAR analysis and deserve further attention.

  1. Feasibility study of archaeological structures scanning by muon tomography

    NASA Astrophysics Data System (ADS)

    Gómez, H.; Carloganu, C.; Gibert, D.; Marteau, J.; Niess, V.; Katsanevas, S.; Tonazzo, A.

    2015-08-01

    One of the main concerns in archaeology is to find of a method to study precisely archaeological structures in the least invasive way possible to avoid damage. The requirement of preserving the structures integrity prevents, in the case of pyramids or tumuli, the study of any internal structure (halls or tombs) which are not reachable by existing corridors. One non-invasive method is the muon tomography. By placing a detector which allows to register the muon direction after the structure, it is possible to have an idea of its composition based on the attenuation of the muon flux, which depends on the material length and density that muons have crossed. This technique, alone or together with other exploration techniques as seismic tomography or electrical resistivity tomography, can provide useful information about the internal structure of the archaeological form that can not be obtained by conventional archaeological methods. In this work, the time measurement necessary to obtain a significant result about the composition of an archaeological structure is estimated. To do that, a Monte Carlo simulation framework based on the MUSIC software, properly tuned for this study, has been developed. The particular case of the Kastas Amfipoli Macedonian tumulus has been considered to perform the simulations.

  2. Feasibility study of archaeological structures scanning by muon tomography

    SciTech Connect

    Gómez, H.; Katsanevas, S.; Tonazzo, A.; Carloganu, C.; Niess, V.; Gibert, D.; Marteau, J.

    2015-08-17

    One of the main concerns in archaeology is to find of a method to study precisely archaeological structures in the least invasive way possible to avoid damage. The requirement of preserving the structures integrity prevents, in the case of pyramids or tumuli, the study of any internal structure (halls or tombs) which are not reachable by existing corridors. One non-invasive method is the muon tomography. By placing a detector which allows to register the muon direction after the structure, it is possible to have an idea of its composition based on the attenuation of the muon flux, which depends on the material length and density that muons have crossed. This technique, alone or together with other exploration techniques as seismic tomography or electrical resistivity tomography, can provide useful information about the internal structure of the archaeological form that can not be obtained by conventional archaeological methods. In this work, the time measurement necessary to obtain a significant result about the composition of an archaeological structure is estimated. To do that, a Monte Carlo simulation framework based on the MUSIC software, properly tuned for this study, has been developed. The particular case of the Kastas Amfipoli Macedonian tumulus has been considered to perform the simulations.

  3. Imidate-Based Cross-Linkers for Structural Proteomics: Increased Charge of Protein and Peptide Ions and CID and ECD Fragmentation Studies

    NASA Astrophysics Data System (ADS)

    Koolen, Hector H. F.; Gomes, Alexandre F.; Schwab, Nicolas V.; Eberlin, Marcos N.; Gozzo, Fabio C.

    2014-07-01

    Chemical cross-linking is an attractive low-resolution technique for structural studies of protein complexes. Distance constraints obtained from cross-linked peptides identified by mass spectrometry (MS) are used to construct and validate protein models. Amidinating cross-linkers such as diethyl suberthioimidate (DEST) have been used successfully in chemical cross-linking experiments. In this work, the application of a commercial diimidate cross-linking reagent, dimethyl suberimidate (DMS), was evaluated with model peptides and proteins. The peptides were designed with acetylated N-termini followed by random sequences containing two Lys residues separated by an Arg residue. After cross-linking reactions, intra- and intermolecular cross-linked species were submitted to CID and ECD dissociations to study their fragmentation features in the gas phase. Fragmentation of intramolecular peptides by collision induced dissociation (CID) demonstrates a unique two-step fragmentation pathway involving formation of a ketimine as intermediate. Electron capture and electron transfer dissociation (ECD and ETD) experiments demonstrated that the cyclic moiety is not dissociated. Intermolecular species demonstrated previously described fragmentation behavior in both CID and ECD experiments. The charge state distributions (CSD) obtained after reaction with DMS were compared with those obtained with disuccinimidyl suberate (DSS). CSDs for peptides and proteins were increased after their reaction with DMS, owing to the higher basicity of DMS modified species. These features were also observed in LC-MS experiments with bovine carbonic anhydrase II (BCA) after cross-linking with DMS and tryptic proteolysis. Cross-linked peptides derived from this protein were identified at high confidence and those species were in agreement with the crystal structure of BCA.

  4. Geological-structural interpretation using products of remote sensing in the region of Carrancas, Minas Gerais, Brazil

    NASA Technical Reports Server (NTRS)

    Parada, N. D. J. (Principal Investigator); Dossantos, A. R.; Dosanjos, C. E.; Barbosa, M. P.; Veneziani, P.

    1982-01-01

    The efficiency of some criteria developed for the utilization of small scale and low resolution remote sensing products to map geological and structural features was demonstrated. Those criteria were adapted from the Logical Method of Photointerpretation which consists of textural qualitative analysis of landforms and drainage net patterns. LANDSAT images of channel 5 and 7, 4 LANDSAT-RBV scenes, and 1 radar mosiac were utilized. The region of study is characterized by supracrustal metassediments (quartzites and micaschist) folded according to a "zig-zag" pattern and gnaissic basement. Lithological-structural definition was considered outstanding when compared to data acquired during field work, bibliographic data and geologic maps acquired in larger scales.

  5. Lipid nanotechnologies for structural studies of membrane-associated proteins.

    PubMed

    Stoilova-McPhie, Svetla; Grushin, Kirill; Dalm, Daniela; Miller, Jaimy

    2014-11-01

    We present a methodology of lipid nanotubes (LNT) and nanodisks technologies optimized in our laboratory for structural studies of membrane-associated proteins at close to physiological conditions. The application of these lipid nanotechnologies for structure determination by cryo-electron microscopy (cryo-EM) is fundamental for understanding and modulating their function. The LNTs in our studies are single bilayer galactosylceramide based nanotubes of ∼20 nm inner diameter and a few microns in length, that self-assemble in aqueous solutions. The lipid nanodisks (NDs) are self-assembled discoid lipid bilayers of ∼10 nm diameter, which are stabilized in aqueous solutions by a belt of amphipathic helical scaffold proteins. By combining LNT and ND technologies, we can examine structurally how the membrane curvature and lipid composition modulates the function of the membrane-associated proteins. As proof of principle, we have engineered these lipid nanotechnologies to mimic the activated platelet's phosphtaidylserine rich membrane and have successfully assembled functional membrane-bound coagulation factor VIII in vitro for structure determination by cryo-EM. The macromolecular organization of the proteins bound to ND and LNT are further defined by fitting the known atomic structures within the calculated three-dimensional maps. The combination of LNT and ND technologies offers a means to control the design and assembly of a wide range of functional membrane-associated proteins and complexes for structural studies by cryo-EM. The presented results confirm the suitability of the developed methodology for studying the functional structure of membrane-associated proteins, such as the coagulation factors, at a close to physiological environment.

  6. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

    PubMed

    Guo, Qi; Gakhar, Lokesh; Wickersham, Kyle; Francis, Kevin; Vardi-Kilshtain, Alexandra; Major, Dan T; Cheatum, Christopher M; Kohen, Amnon

    2016-05-17

    The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented. PMID:27100912

  7. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

    PubMed

    Guo, Qi; Gakhar, Lokesh; Wickersham, Kyle; Francis, Kevin; Vardi-Kilshtain, Alexandra; Major, Dan T; Cheatum, Christopher M; Kohen, Amnon

    2016-05-17

    The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented.

  8. Density Functional Study of the structural properties in Tamoxifen

    NASA Astrophysics Data System (ADS)

    de Coss-Martinez, Romeo; Tapia, Jorge A.; Quijano-Quiñones, Ramiro F.; Canto, Gabriel I.

    2013-03-01

    Using the density functional theory, we have studied the structural properties of Tamoxifen. The calculations were performed with two methodological approaches, which were implemented in SIESTA and Spartan codes. For SIESTA, we considerate a linear combination of atomic orbitals method, using pseudopotentials and the van der Waals approximation for the exchange-correlation potential. Here we analyzed and compared the atomic structure between our results and other theoretical study. We found differences in the bond lengths between the results, that could be attributed to code approaches in each one. This work was supported under Grant FOMIX 2011-09 N: 170297 of Ph.D. A. Tapia.

  9. Polarization-correlation study of biotissue multifractal structure

    NASA Astrophysics Data System (ADS)

    Olar, O. I.; Ushenko, A. G.

    2003-09-01

    This paper presents the results of polarization-correlation study of multifractal collagen structure of physiologically normal and pathologically changed tissues of women"s reproductive sphere and skin. The technique of polarization selection of coherent images of biotissues with further determination of their autocorrelation functions and spectral densities is suggested. The correlation-optical criteria of early diagnostics of appearance of pathological changes in the cases of myometry (forming the germ of fibromyoma) and skin (psoriasis) are determined. This study is directed to investigate the possibilities of recognition of pathological changes of biotissue morphological structure by determining the polarization-dependent autocorrelation functions (ACF) and corresponding spectral densities of tissue coherent images.

  10. NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

    PubMed Central

    Konrat, Robert

    2014-01-01

    Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

  11. A study of structural concepts for ultralightweight spacecraft

    NASA Technical Reports Server (NTRS)

    Miller, R. K.; Knapp, K.; Hedgepeth, J. M.

    1984-01-01

    Structural concepts for ultralightweight spacecraft were studied. Concepts for ultralightweight space structures were identified and the validity of heir potential application in advanced spacecraft was assessed. The following topics were investigated: (1) membrane wrinkling under pretensioning; (2) load-carrying capability of pressurized tubes; (3) equilibrium of a precompressed rim; (4) design of an inflated reflector spacecraft; (5) general instability of a rim; and (6) structural analysis of a pressurized isotensoid column. The design approaches for a paraboloidal reflector spacecraft included a spin-stiffened design, both inflated and truss central columns, and to include both deep truss and rim-stiffened geodesic designs. The spinning spacecraft analysis is included, and the two truss designs are covered. The performances of four different approaches to the structural design of a paraboloidal reflector spacecraft are compared. The spinning and inflated configurations result in very low total masses and some concerns about their performance due to unresolved questions about dynamic stability and lifetimes, respectively.

  12. Study of nanoscale structural biology using advanced particle beam microscopy

    NASA Astrophysics Data System (ADS)

    Boseman, Adam J.

    This work investigates developmental and structural biology at the nanoscale using current advancements in particle beam microscopy. Typically the examination of micro- and nanoscale features is performed using scanning electron microscopy (SEM), but in order to decrease surface charging, and increase resolution, an obscuring conductive layer is applied to the sample surface. As magnification increases, this layer begins to limit the ability to identify nanoscale surface structures. A new technology, Helium Ion Microscopy (HIM), is used to examine uncoated surface structures on the cuticle of wild type and mutant fruit flies. Corneal nanostructures observed with HIM are further investigated by FIB/SEM to provide detailed three dimensional information about internal events occurring during early structural development. These techniques are also used to reconstruct a mosquito germarium in order to characterize unknown events in early oogenesis. Findings from these studies, and many more like them, will soon unravel many of the mysteries surrounding the world of developmental biology.

  13. Structural modeling of proteins by integrating small-angle x-ray scattering data

    NASA Astrophysics Data System (ADS)

    Zhang, Yong-Hui; Peng, Jun-Hui; Zhang, Zhi-Yong

    2015-12-01

    Elucidating the structure of large biomolecules such as multi-domain proteins or protein complexes is challenging due to their high flexibility in solution. Recently, an “integrative structural biology” approach has been proposed, which aims to determine the protein structure and characterize protein flexibility by combining complementary high- and low-resolution experimental data using computer simulations. Small-angle x-ray scattering (SAXS) is an efficient technique that can yield low-resolution structural information, including protein size and shape. Here, we review computational methods that integrate SAXS with other experimental datasets for structural modeling. Finally, we provide a case study of determination of the structure of a protein complex formed between the tandem SH3 domains in c-Cb1-associated protein and the proline-rich loop in human vinculin. Project supported by the National Key Basic Research Program of China (Grant Nos. 2013CB910203 and 2011CB911104), the National Natural Science Foundation of China (Grant No. 31270760), the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDB08030102), and the Specialized Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20113402120013).

  14. Structuralism.

    ERIC Educational Resources Information Center

    Piaget, Jean

    Provided is an overview of the analytical method known as structuralism. The first chapter discusses the three key components of the concept of a structure: the view of a system as a whole instead of so many parts; the study of the transformations in the system; and the fact that these transformations never lead beyond the system but always…

  15. Neutron scattering studies on chromatin higher-order structure

    SciTech Connect

    Graziano, V.; Gerchman, S.E.; Schneider, D.K.; Ramakrishnan, V.

    1994-12-31

    We have been engaged in studies of the structure and condensation of chromatin into the 30nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist.

  16. Fluid-thermal-structural study of aerodynamically heated leading edges

    NASA Technical Reports Server (NTRS)

    Deuchamphai, Pramote; Thornton, Earl A.; Wieting, Allan R.

    1988-01-01

    A finite element approach for integrated fluid-thermal-structural analysis of aerodynamically heated leading edges is presented. The Navier-Stokes equations for high speed compressible flow, the energy equation, and the quasi-static equilibrium equations for the leading edge are solved using a single finite element approach in one integrated, vectorized computer program called LIFTS. The fluid-thermal-structural coupling is studied for Mach 6.47 flow over a 3-in diam cylinder for which the flow behavior and the aerothermal loads are calibrated by experimental data. Issues of the thermal-structural response are studied for hydrogen-cooled, super thermal conducting leading edges subjected to intense aerodynamic heating.

  17. Impacts on foam stabilised composite structures: Experimental and numerical study

    NASA Astrophysics Data System (ADS)

    Rivallant, S.; Ferrero, J. F.; Barrau, J. J.

    2003-09-01

    A dropweight tester is used to make low velocity tests on specific sandwich type structures. Sandwich are made of glass-epoxy skin and polyurethane foam core. The skins can be straight or little curved, and impact direction is the global skin direction. The aim of these tests is to study the initiation of rupture in such structures: local buckling of skin and foam core rupture. Experimental results are given. They show the evolution of buckling critical stress in the skin when impact velocity increases. The rupture mode in curved skin specimen is also studied: rupture is no more provoked by buckling. A numerical analysis is proposed to model the behaviour of the structure and the rupture initiation. Finally, a method is developed, in order to predict the propagation of skin debonding during impact: an element layer under the skin is damaged with a specific law to simulate debonding.

  18. Thermal-structural combined loads design criteria study

    NASA Technical Reports Server (NTRS)

    Deriugin, V.; Brogren, E. W.; Jaeck, C. L.; Brown, A. L.; Clingan, B. E.

    1972-01-01

    A study was conducted to determine methodology for combining thermal structural loads and assessing the effects of the combined loads on the design of a thermal protection system and a hot structure of a high cross range delta wing space shuttle orbiter vehicle. The study presents guidelines for establishing a basis for predicting thermal and pressure environments and for determining limit and ultimate design loads on the vehicle during reentry. Limit trajectories were determined by using dispersions on a representative nominal mission and system parameters expected during the life of the vehicle. Nine chosen locations on the vehicle surface having TPS or hot structures were examined, and weight sensitivity analyses were performed for each location.

  19. Isotope labeling for NMR studies of macromolecular structure and interactions

    SciTech Connect

    Wright, P.E.

    1994-12-01

    Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

  20. Structural Studies of GABAA Receptor Binding Sites: Which Experimental Structure Tells us What?

    PubMed Central

    Puthenkalam, Roshan; Hieckel, Marcel; Simeone, Xenia; Suwattanasophon, Chonticha; Feldbauer, Roman V.; Ecker, Gerhard F.; Ernst, Margot

    2016-01-01

    Atomic resolution structures of cys-loop receptors, including one of a γ-aminobutyric acid type A receptor (GABAA receptor) subtype, allow amazing insights into the structural features and conformational changes that these pentameric ligand-gated ion channels (pLGICs) display. Here we present a comprehensive analysis of more than 30 cys-loop receptor structures of homologous proteins that revealed several allosteric binding sites not previously described in GABAA receptors. These novel binding sites were examined in GABAA receptor homology models and assessed as putative candidate sites for allosteric ligands. Four so far undescribed putative ligand binding sites were proposed for follow up studies based on their presence in the GABAA receptor homology models. A comprehensive analysis of conserved structural features in GABAA and glycine receptors (GlyRs), the glutamate gated ion channel, the bacterial homologs Erwinia chrysanthemi (ELIC) and Gloeobacter violaceus GLIC, and the serotonin type 3 (5-HT3) receptor was performed. The conserved features were integrated into a master alignment that led to improved homology models. The large fragment of the intracellular domain that is present in the structure of the 5-HT3 receptor was utilized to generate GABAA receptor models with a corresponding intracellular domain fragment. Results of mutational and photoaffinity ligand studies in GABAA receptors were analyzed in the light of the model structures. This led to an assignment of candidate ligands to two proposed novel pockets, candidate binding sites for furosemide and neurosteroids in the trans-membrane domain were identified. The homology models can serve as hypotheses generators, and some previously controversial structural interpretations of biochemical data can be resolved in the light of the presented multi-template approach to comparative modeling. Crystal and cryo-EM microscopic structures of the closest homologs that were solved in different conformational

  1. Overexpression of membrane proteins in mammalian cells for structural studies

    PubMed Central

    Andréll, Juni

    2013-01-01

    The number of structures of integral membrane proteins from higher eukaryotes is steadily increasing due to a number of innovative protein engineering and crystallization strategies devised over the last few years. However, it is sobering to reflect that these structures represent only a tiny proportion of the total number of membrane proteins encoded by a mammalian genome. In addition, the structures determined to date are of the most tractable membrane proteins, i.e., those that are expressed functionally and to high levels in yeast or in insect cells using the baculovirus expression system. However, some membrane proteins that are expressed inefficiently in these systems can be produced at sufficiently high levels in mammalian cells to allow structure determination. Mammalian expression systems are an under-used resource in structural biology and represent an effective way to produce fully functional membrane proteins for structural studies. This review will discuss examples of vertebrate membrane protein overexpression in mammalian cells using a variety of viral, constitutive or inducible expression systems. PMID:22963530

  2. Structure study of a microemulsion system with an ionic liquid.

    PubMed

    Kang, Tae Hui; Jeon, Yoonnam; Kim, Mahn Won

    2015-11-01

    We found that an ionic liquid (IL) with a long alkyl chain moiety, 1-tetradecyl-3-methylimidazolium chloride (C14MIM·Cl), forms a single crystal after the addition of octanol in an alkane solvent. But the solution exhibits a structural change after adding a small amount of water. An optically clear solution is found within limits, and it is stable for several months. Since the IL molecule has an amphiphilic property, it behaves as a surfactant in the microemulsion system. But the IL formed a single crystal rather than a lyotropic liquid crystalline structure, unlike a typical surfactant. Therefore, it is important to understand the structure of the microemulsion system. We used the small angle neutron scattering (SANS) technique to investigate the structure. The scattering intensity was analyzed using a spherical core-shell model with the Schultz size distribution, and a contrast matching method was used to study the internal structure. The structure of the solution is confirmed to be a water-in-oil microemulsion system, and the swelling law is obeyed in the microemulsion system. PMID:26439624

  3. Structural and functional studies of mycobacterial IspD enzymes.

    PubMed

    Björkelid, Christofer; Bergfors, Terese; Henriksson, Lena M; Stern, Ana Laura; Unge, Torsten; Mowbray, Sherry L; Jones, T Alwyn

    2011-05-01

    A number of pathogens, including the causative agents of tuberculosis and malaria, synthesize isopentenyl diphosphate via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway rather than the classical mevalonate pathway found in humans. As part of a structure-based drug-discovery program against tuberculosis, IspD, the enzyme that carries out the third step in the MEP pathway, was targeted. Constructs of both the Mycobacterium smegmatis and the Mycobacterium tuberculosis enzymes that were suitable for structural and inhibitor-screening studies were engineered. Two crystal structures of the M. smegmatis enzyme were produced, one in complex with CTP and the other in complex with CMP. In addition, the M. tuberculosis enzyme was crystallized in complex with CTP. Here, the structure determination and crystallographic refinement of these crystal forms and the enzymatic characterization of the M. tuberculosis enzyme construct are reported. A comparison with known IspD structures allowed the definition of the structurally conserved core of the enzyme. It indicates potential flexibility in the enzyme and in particular in areas close to the active site. These well behaved constructs provide tools for future target-based screening of potential inhibitors. The conserved nature of the extended active site suggests that any new inhibitor will potentially exhibit broad-spectrum activity. PMID:21543842

  4. Structure-property study of keto-ether polyimides

    NASA Technical Reports Server (NTRS)

    Dezern, James F.; Croall, Catharine I.

    1991-01-01

    As part of an on-going effort to develop an understanding of how changes in the chemical structure affect polymer properties, an empirical study was performed on polyimides containing only ether and/or carbonyl connecting groups in the polymer backbone. During the past two decades the structure-property relationships in linear aromatic polyimides have been extensively investigated. More recently, work has been performed to study the effect of isomeric attachment of keto-ether polyimides on properties such as glass transition temperature and solubility. However, little work has been reported on the relation of polyimide structure to mechanical properties. The purpose of this study was to determine the effect of structural changes in the backbone of keto-ether polyimides on their mechanical properties, specifically, unoriented thin film tensile properties. This study was conducted in two stages. The purpose of the initial stage was to examine the physical and mechanical properties of a representative group (four) of polyimide systems to determine the optimum solvent and cure cycle requirements. These optimum conditions were then utilized in the second stage to prepare films of keto-ether polyimides which were evaluated for mechanical and physical properties. All of the polyimides were prepared using isomers of oxydianiline (ODA) and diaminobenzophenone (DABP) in combination with 3,3',4,4'-benzophenonetetracarboxylic dianhydride (BTDA) and 4,4'-oxydiphthalic anhydride (ODPA).

  5. Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies

    ERIC Educational Resources Information Center

    Smith, John A.

    2013-01-01

    This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…

  6. School Reform in Chicago: A Study of Structures and Symbols.

    ERIC Educational Resources Information Center

    Stefkovich, Jacqueline A.; Guba, Gloria J.

    1995-01-01

    The structures and symbols of the Chicago (Illinois) school reform movement were explored through a case study in one Chicago elementary school. Changes were built on a framework of organizational symbols and metaphors of the building as a home, the school as a family, and the principal as leader. (SLD)

  7. Studies in the Structure of the Urban Economy.

    ERIC Educational Resources Information Center

    Mills, Edwin S.

    Consisting of a set of closely related studies of urban spatial structure, this monograph focuses on the decentralization of metropolitan areas. Foremost is the belief that decentralization, or suburbanization, lies at the root of most of the social problems that plague urban areas. Therefore, an understanding of the process is basic to policies…

  8. Neutron scatter studies of chromatin structures related to functions

    SciTech Connect

    Bradbury, E.M.

    1991-01-01

    We have completed a study on the structure of trypsin trimmed histone octamers using small angle neutron and X-ray scattering studies and nuclear magnetic resonance. We have also completed studies on the structure of TFIIIA induced DNA bending by a circular permutation gel electrophoresis assay. Individual acetylated species of core histones from butyrate treated HeLa cells were isolated and reconstituted into nucleosomes using a 5S rDNA nucleosome positioning DNA sequence from sea urchin. These nucleosomes were characterized by sulfhydryl group probing, nucleoprotein particle gel electrophoresis and DNase I footprinting. Fully acetylated species of histones H3 and H4 were also reconstituted in closed circular minichromosomes and the effect of DNA topology changes caused by acetylation was studied. Finally, protamines isolated from human sperm were characterized and a full set of core histones were isolated and characterized. 7 refs.

  9. Structural studies on an internal loop from a hairpin ribozyme

    SciTech Connect

    Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr.

    1994-12-01

    Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.

  10. High-pressure structural study of MnF2

    DOE PAGESBeta

    Stavrou, Elissaios; Yao, Yansun; Goncharov, Alexander F.; Konopkova, Zuzana; Raptis, Constantine

    2015-02-01

    In this study, manganese fluoride (MnF2) with the tetragonal rutile-type structure has been studied using a synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy in a diamond anvil cell up to 60 GPa at room temperature combined with first-principles density functional calculations. The experimental data reveal two pressure-induced structural phase transitions with the following sequence: rutile → SrI2 type (3 GPa)→ α–PbCl2 type (13 GPa). Complete structural information, including interatomic distances, has been determined in the case of MnF2 including the exact structure of the debated first high-pressure phase. First-principles density functional calculations confirm this phase transition sequence, and themore » two calculated transition pressures are in excellent agreement with the experiment. Lattice dynamics calculations also reproduce the experimental Raman spectra measured for the ambient and high-pressure phases. The results are discussed in line with the possible practical use of rutile-type fluorides in general and specifically MnF2 as a model compound to reveal the HP structural behavior of rutile-type SiO2 (Stishovite).« less

  11. Structure and thermochemical kinetic studies of coal pyrolysis

    SciTech Connect

    Dodoo, J.N.D.

    1991-01-01

    The overall objectives of this project is an intensive effort on the application of laser to the microscopic structure and thermochemical kinetic studies of coal particles pyrolysis, char combustion and ash transformation at combustion level heat fluxes in a laser beam. Research emphasis in FY91 is placed on setup and calibration of the laser pyrolysis system, preparation and mass loss studies of Beulah lignite and subbituminous coals. The task is therefore divided into three subtasks.

  12. Physicochemical and structural studies of clathrate hydrates of tetrabutylammonium polyacrylates.

    PubMed

    Terekhova, Irina S; Manakov, Andrey Yu; Komarov, Vladislav Yu; Villevald, Galina V; Burdin, Alexander A; Karpova, Tamara D; Aladko, Eugeny Ya

    2013-03-01

    In this work, physicochemical and structural studies have been carried out for semiclathrate hydrates of linear (un-cross-linked) and cross-linked tetrabutylammonium polyacrylates with different degrees of cross-linking of the polymeric guest molecules (n = 0.5, 1, 2, 3%) and different degrees of substitution of proton ions of carboxylic groups in poly(acrylic acid) for TBA cations (x = 1, 0.8, 0.6). The changes in the hydrates' stability and composition depending on the outlined parameters were examined in the course of phase diagram studies of the binary systems water-tetrabutylammonium polyacrylates using differential thermal analysis method and calorimetric measurements of fusion enthalpies of the hydrates. Phase diagram studies of the binary system water-linear tetrabutylammonium polyacrylate revealed the formation of four hydrates. Based on the data of chemical analysis of hydrate crystals the compositions of all hydrates have been determined. Single-crystal X-ray diffraction studies revealed a tetragonal structure, space group 4/m, and unit cell parameters are close for different hydrates and lie in the ranges a = 23.4289-23.4713 Å and c = 12.3280-12.3651 Å (150 K). The structure can be related to tetragonal structure I typical for the clathrate hydrates of tetraalkylammonium salts with monomeric anions. Powder X-ray diffraction analyses confirmed the identity of the above crystal structure to that of the hydrates with cross-linked tetrabutylammonium polyacrylates. The behavior of TBA polyacrylate hydrates under the pressure of methane was studied and quantitative assessment of the gas content in the hydrates was made using volumetric analysis method.

  13. Physicochemical and structural studies of clathrate hydrates of tetrabutylammonium polyacrylates.

    PubMed

    Terekhova, Irina S; Manakov, Andrey Yu; Komarov, Vladislav Yu; Villevald, Galina V; Burdin, Alexander A; Karpova, Tamara D; Aladko, Eugeny Ya

    2013-03-01

    In this work, physicochemical and structural studies have been carried out for semiclathrate hydrates of linear (un-cross-linked) and cross-linked tetrabutylammonium polyacrylates with different degrees of cross-linking of the polymeric guest molecules (n = 0.5, 1, 2, 3%) and different degrees of substitution of proton ions of carboxylic groups in poly(acrylic acid) for TBA cations (x = 1, 0.8, 0.6). The changes in the hydrates' stability and composition depending on the outlined parameters were examined in the course of phase diagram studies of the binary systems water-tetrabutylammonium polyacrylates using differential thermal analysis method and calorimetric measurements of fusion enthalpies of the hydrates. Phase diagram studies of the binary system water-linear tetrabutylammonium polyacrylate revealed the formation of four hydrates. Based on the data of chemical analysis of hydrate crystals the compositions of all hydrates have been determined. Single-crystal X-ray diffraction studies revealed a tetragonal structure, space group 4/m, and unit cell parameters are close for different hydrates and lie in the ranges a = 23.4289-23.4713 Å and c = 12.3280-12.3651 Å (150 K). The structure can be related to tetragonal structure I typical for the clathrate hydrates of tetraalkylammonium salts with monomeric anions. Powder X-ray diffraction analyses confirmed the identity of the above crystal structure to that of the hydrates with cross-linked tetrabutylammonium polyacrylates. The behavior of TBA polyacrylate hydrates under the pressure of methane was studied and quantitative assessment of the gas content in the hydrates was made using volumetric analysis method. PMID:23383955

  14. Immunoelectronmicroscopic study of the nucleoid structure of hydrogen bacteria.

    PubMed

    Mogilnaya, O A; Kiselyova, E V; Medvedeva, S E; Puzir, A P; Guseynov, O A; Kulyba, N N; Kozlov, A V

    1992-01-01

    Electron microscopical studies of the nucleoid structure of hydrogen bacteria using ultrahin sections and spread DNA from bacterial cell lysates revealed a different DNA packaging in the cell. A compact state of the major part of DNA at all growth stages and stability of nucleosome-like structures were shown. The use of antibodies to HU protein of E. coli labelled by protein A-colloidal gold demonstrated the immunological relationship between HU protein of E. coli and histone-like proteins of Alcaligenes eutrophus and their possible role in the nucleosome-like DNA packaging in procariotic genome.

  15. Rf breakdown studies in copper electron linac structures

    SciTech Connect

    Wang, J.W.; Loew, G.A.

    1989-03-01

    This paper presents a summary of rf breakdown-limited electric fields observed in experimental linac structures at SLAC and a discussion of how these experiments can be interpreted against the background of existing, yet incomplete, theories. The motivation of these studies, begun in 1984, is to determine the maximum accelerating field gradients that might be used safely in future e/sup /+-// colliders, to contribute to the basic understanding of the rf breakdown mechanism, and to discover if a special surface treatment might make it possible to supersede the field limits presently reachable in room temperature copper structures. 6 refs., 4 figs., 1 tab.

  16. Studies of N* Structure from the CLAS Meson Electroproduction Data

    SciTech Connect

    Mokeev, Viktor I.; Aznauryan, Inna G.

    2014-01-01

    The transition {gamma}{sub v}pN amplitudes (electrocouplings) for prominent excited nucleon states obtained in a wide area of photon virtualities offer valuable information for the exploration of the N structure at different distances and allow us to access the complex dynamics of non-perturbative strong interaction. The current status in the studies of {gamma}{sub v}pN electrocouplings from the data on exclusive meson electroproduction off protons measured with the CLAS detector at Jefferson Lab is presented. The impact of these results on exploration of the N structure is discussed.

  17. [Microscopic studies of the structures of different dental floss types].

    PubMed

    Dörfer, C; Böök, M; Staehle, H J

    1993-01-01

    26 different dental flosses, made from silk, polyamide (Nylon) or Teflon, were analyzed with respect to their surface structure and their cross-section. Principally, two different types of manufacturing could be distinguished. The dental flosses either consisted of a large number of individual fibers, or a single, falted membrane. Even flosses that were manufactured in the same manner revealed considerable differences. Apart from the chemical composition, the structure of dental flosses is decisive for their use and this is why an exact classification would be desirable. In this study the requirements for classifying dental flosses are provided.

  18. ADVANCED SOLIDS NMR STUDIES OF COAL STRUCTURE AND CHEMISTRY

    SciTech Connect

    1997-09-01

    This report covers the progress made on the title project for the project period. The study of coal chemical structure is a vital component of research efforts to develop better chemical utilization of coals, and for furthering our basic understanding of coal geochemistry. In this grant we are addressing several structural questions pertaining to coals with advances in state of the art solids NMR methods. The main activity during this granting period was a completion of a detailed comparative analysis of the suite of spectral editing techniques developed in our laboratory for this purpose. The appended report is a manuscript being submitted to the Journal of Magnetic Resonance on this subject.

  19. ADVANCED SOLIDS NMR STUDIES OF COAL STRUCTURE AND CHEMISTRY

    SciTech Connect

    1998-03-01

    This report covers the progress made on the title project for the project period. The study of coal chemical structure is a vital component of research efforts to develop better chemical utilization of coals, and for furthering our basic understanding of coal geochemistry. In this grant we are addressing several structural questions pertaining to coals with advances in state of the art solids NMR methods. The main activity during this granting period was a detailed comparative analysis of the suite of spectral editing results obtained on the Argonne coals. We have extended our fitting procedure to include carbons of all types in the analysis.

  20. Lunar Lander Structural Design Studies at NASA Langley

    NASA Technical Reports Server (NTRS)

    Wu, K. Chauncey; Antol, Jeffrey; Watson, Judith J.; Flick, John J.; Saucillo, Rudolph J.; Mazanek, Daniel D.; North, David D.

    2007-01-01

    The National Aeronautics and Space Administration is currently developing mission architectures, vehicle concepts and flight hardware to support the planned human return to the Moon. During Phase II of the 2006 Lunar Lander Preparatory Study, a team from the Langley Research Center was tasked with developing and refining two proposed Lander concepts. The Descent-Assisted, Split Habitat Lander concept uses a disposable braking stage to perform the lunar orbit insertion maneuver and most of the descent from lunar orbit to the surface. The second concept, the Cargo Star Horizontal Lander, carries ascent loads along its longitudinal axis, and is then rotated in flight so that its main engines (mounted perpendicular to the vehicle longitudinal axis) are correctly oriented for lunar orbit insertion and a horizontal landing. Both Landers have separate crew transport volumes and habitats for surface operations, and allow placement of large cargo elements very close to the lunar surface. As part of this study, lightweight, efficient structural configurations for these spacecraft were proposed and evaluated. Vehicle structural configurations were first developed, and preliminary structural sizing was then performed using finite element-based methods. Results of selected structural design and trade studies performed during this activity are presented and discussed.

  1. Electronic structure studies of nanocrystalline diamond grain boundaries

    SciTech Connect

    Zapol, P.; Sternberg, M.; Frauenheim, T.; Gruen, D. M.; Curtiss, L. A.

    1999-11-29

    Diamond growth from hydrogen-poor plasmas results in diamond structures that are profoundly different from conventionally CVD-grown diamond. High concentration of carbon dimers in the microwave plasma results in a high rate of heterogeneous renucleation leading to formation of nanocrystalline diamond with a typical grain size of 3--10 nm. Therefore, up to 10% of carbon atoms are located in the grain boundaries. In this paper the authors report on density-functional based tight-binding molecular dynamics calculations of the structure of a {Sigma}13 twist (100) grain boundary in diamond. Beginning with a coincidence site lattice model, simulated annealing of the initial structure was performed at 1,500 K followed by relaxation toward lower temperatures. About one-half of the carbons in the grain boundary are found to be three-coordinated. Coordination numbers, bond length and bond angle distributions are analyzed and compared to those obtained in previous studies.

  2. Analytical studies of spectrum broadcast structures in quantum Brownian motion

    NASA Astrophysics Data System (ADS)

    Tuziemski, J.; Korbicz, J. K.

    2016-11-01

    Spectrum broadcast structures are a new and fresh concept in the quantum-to-classical transition, introduced recently in the context of decoherence and the appearance of objective features in quantum mechanics. These are specific quantum state structures, responsible for the objectivization of the decohered state of a system. Recently, they have been demonstrated by means of the well-known quantum Brownian motion model of the recoilless limit (infinitely massive central system), as the principal interest lies in information transfer from the system to the environment. However, a final analysis relied on numerics. Here, after a presentation of the main concepts, we perform analytical studies of the model, showing the timescales and the efficiency of the spectrum broadcast structure formation. We consider a somewhat simplified environment, being random with a uniform distribution of frequencies.

  3. A structural study of the bovine vaginal fluid at estrus.

    PubMed

    Rutllant, J; López-Gatius, F; Camón, J; López-Béjar, M; López-Plana, C

    1999-01-01

    The present study describes the structural components of the bovine vaginal fluid at estrus by scanning electron microscopy (SEM) following critical point- and freeze-drying preparation procedures. Confocal scanning laser microscopy (CLSM) was also used to evaluate the structural integrity of samples, and a control sample was assessed by adding sperm to the vaginal fluid. Samples were collected from 10 cows at the time of artificial insemination, prepared for SEM by using critical point- and freeze-drying procedures, gold coated, and observed by SEM. Mesh size and filament thickness were measured with an image analyzer. Of the 10 samples processed, 4 were considered altered following critical point drying. Compaction and lack of filaments were observed in these samples. A small area of one sample showed a honey comb-like structure when freeze drying was used. Nonoriented filaments with different thicknesses and with a network-like structure were observed throughout the remainder of the samples. Filaments throughout all samples were also observed by CSLM. After critical point drying, the mesh area ranged from 0.8 to 101.4 microns 2; the minor axis from 0.7 to 10.8 microns; and filament thickness from 40 to 442 nm. Using freeze drying, the mesh area ranged from 0.9 to 493.8 microns 2; the minor axis from 0.7 to 27.5 microns; and filament thickness from 40 to 800 nm. When samples were freeze dried, mesh values were similar to the interstrand channels observed by CSLM. In sperm-vaginal fluid samples, following critical point- or freeze-drying procedures, spermatozoa were oriented randomly in the vaginal fluid and did not seem to alter filamentous structure. Our data suggest that the freeze-drying procedure better preserves the true structural dimensions of the vaginal fluid. Furthermore, the filamentous structure of the vaginal fluid does not appear to impede sperm transport. PMID:10390865

  4. High-pressure structural study of MnF2

    NASA Astrophysics Data System (ADS)

    Stavrou, Elissaios; Yao, Yansun; Goncharov, Alexander F.; Konôpková, Zuzana; Raptis, Constantine

    2016-02-01

    Manganese fluoride (MnF2) with the tetragonal rutile-type structure has been studied using a synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy in a diamond anvil cell up to 60 GPa at room temperature combined with first-principles density functional calculations. The experimental data reveal two pressure-induced structural phase transitions with the following sequence: rutile → SrI2 type (3 GPa)→ α -PbCl2 type (13 GPa). Complete structural information, including interatomic distances, has been determined in the case of MnF2 including the exact structure of the debated first high-pressure phase. First-principles density functional calculations confirm this phase transition sequence, and the two calculated transition pressures are in excellent agreement with the experiment. Lattice dynamics calculations also reproduce the experimental Raman spectra measured for the ambient and high-pressure phases. The results are discussed in line with the possible practical use of rutile-type fluorides in general and specifically MnF2 as a model compound to reveal the HP structural behavior of rutile-type SiO2 (Stishovite).

  5. COMPOSITION AND STRUCTURAL STUDIES OF STRONG GLOW DISCHARGE POLYMER COATINGS

    SciTech Connect

    CZECHOWICZ, DG; CASTILLO, ER; NIKROO, A

    2002-04-01

    OAK A271 COMPOSITION AND STRUCTURAL STUDIES OF STRONG GLOW DISCHARGE POLYMER COATINGS. An investigation of the chemical composition and structure of strong glow discharge (GDP) polymer shells made for cryogenic experiments at OMEGA is described. The investigation was carried out using combustion and Fourier Transform Infrared Spectroscopy (FTIR) analysis. The strongest coatings were observed to have the lowest hydrogen content or hydrogen/carbon H/C ratio, whereas the weakest coatings had the highest hydrogen content or H/C ratio. Chemical composition results from combustion were used to complement FTIR analysis to determine the relative hydrogen content of as-fabricated coatings. Good agreement was observed between composition results obtained from combustion and FTIR analysis. FTIR analysis of coating structures showed the strongest coatings to have less terminal methyl groups and a more double bond or olefinic structure. Strong GDP coatings that were aged in air react more with oxygen and moisture than standard GDP coatings. In addition to a more olefinic structure, there may also be more free-radial sites present in strong GDP coatings, which leads to greater oxygen uptake.

  6. Structural design feasibility study of Space Station long spacer truss

    NASA Technical Reports Server (NTRS)

    Armand, Sasan C.; Funk, Gregory P.; Dohogne, Caroline A.

    1994-01-01

    The structural design and configuration feasibility of the long spacer truss assembly that will be used as part of the Space Station Freedom is the focus of this study. The structural analysis discussed herein is derived from the transient loading events presented in the Space Transportation System Interface Control Document (STS ICD). The transient loading events are liftoff, landing, and emergency landing loads. Quasi-static loading events were neglected in this study since the magnitude of the quasi-static acceleration factors is lower than that of the transient acceleration factors. Structural analysis of the proposed configuration of the long spacer truss with four longerons indicated that negative safety margins are possible. As a result, configuration changes were proposed. The primary configuration change suggested was to increase the number of truss longerons to six. The six-longeron truss appears to be a more promising structure than the four-longeron truss because it offers a positive margin of safety and more volume in its second bay (BAY2). This additional volume can be used for resupply of some of the orbital replacement units (such as a battery box). Note that the design effort on the long spacer truss has not fully begun and that calculations and reports of the negative safety margins are, to date, based on concept only.

  7. Numerical studies of multipactor in dielectric-loaded accelerator structures

    NASA Astrophysics Data System (ADS)

    Sinitsyn, Oleksandr; Nusinovich, Gregory; Antonsen, Thomas

    2009-11-01

    Multipactor (MP) is known as the avalanche growth of the number of secondary electrons emitted from a solid surface exposed to an rf electric field under vacuum conditions. MP may occur in various microwave and rf systems such as microwave tubes, rf windows and launchers, accelerating structures, and rf satellite payloads. In this work we present results of MP analysis in dielectric-loaded accelerator (DLA) structures. The starting point of our work was experimental and theoretical studies of DLA structures jointly done by Argonne National Laboratory and Naval Research Laboratory (J. G. Power et al., Phys. Rev. Lett. 92, 164801 (2004); J. G. Power et al., AIP Conf. Proc. 877, 362 (2006)). In the theoretical model developed during those studies the space-charge field due to the total number of particles is taken into account as a parameter. We perform our studies using a self-consistent approach with the help of time-dependent two-dimensional code developed at the University of Maryland (O. V. Sinitsyn et al., Phys. Plasmas 16, 073102 (2009)). Results include analysis of MP evolution at an early stage, detailed studies of individual electron trajectories, analysis of MP onset time under various conditions and comparison of some results with the experimental data.

  8. Retrospective study on structural neuroimaging in first-episode psychosis

    PubMed Central

    Silva-dos-Santos, Amilcar; Talina, Miguel Cotrim

    2016-01-01

    Background. No consensus between guidelines exists regarding neuroimaging in first-episode psychosis. The purpose of this study is to assess anomalies found in structural neuroimaging exams (brain computed tomography (CT) and magnetic resonance imaging (MRI)) in the initial medical work-up of patients presenting first-episode psychosis. Methods. The study subjects were 32 patients aged 18–48 years (mean age: 29.6 years), consecutively admitted with first-episode psychosis diagnosis. Socio-demographic and clinical data and neuroimaging exams (CT and MRI) were retrospectively studied. Diagnostic assessments were made using the Operational Criteria Checklist +. Neuroimaging images (CT and MRI) and respective reports were analysed by an experienced consultant psychiatrist. Results. None of the patients had abnormalities in neuroimaging exams responsible for psychotic symptoms. Thirty-seven percent of patients had incidental brain findings not causally related to the psychosis (brain atrophy, arachnoid cyst, asymmetric lateral ventricles, dilated lateral ventricles, plagiocephaly and falx cerebri calcification). No further medical referral was needed for any of these patients. No significant differences regarding gender, age, diagnosis, duration of untreated psychosis, in-stay and cannabis use were found between patients who had neuroimaging abnormalities versus those without. Discussion. This study suggests that structural neuroimaging exams reveal scarce abnormalities in young patients with first-episode psychosis. Structural neuroimaging is especially useful in first-episode psychosis patients with neurological symptoms, atypical clinical picture and old age. PMID:27257547

  9. Study of Daedalus Interstellar Spacecraft Reaction Chamber and Thrust Structure

    NASA Astrophysics Data System (ADS)

    Reddy, S. K.; Benaroya, H.

    Project Daedalus was the 1978 trade study that proved the feasibility of space travel utilizing fusion-based propulsion (Inertial Confinement Fusion). This paper analyzes some of the key structural aspects of the Daedalus spacecraft, in particular, the reaction chamber and thrust structure that is integral to the Daedalus spacecraft, which supports the loads resulting from the fusion reactions. First, the reaction chamber is studied computationally in terms of static loading and vibrational characteristics utilizing the finite element method. Next, a proposed bracing system is integrated into the reaction chamber and the effects are studied. Lastly, the field coils with their supporting truss structure are added to the assembly. Concepts are introduced for actuators and course-correction mechanisms that ensure the spacecraft maintains the required trajectory to rendezvous with the target system. Present-day materials and manufacturing considerations are explored based on the assumptions made in the Daedalus study. Testing, qualification, and assembly of the spacecraft are also discussed. This paper is a summary of the first author's Master's Thesis at Rutgers University.

  10. Retrospective study on structural neuroimaging in first-episode psychosis.

    PubMed

    Coentre, Ricardo; Silva-Dos-Santos, Amilcar; Talina, Miguel Cotrim

    2016-01-01

    Background. No consensus between guidelines exists regarding neuroimaging in first-episode psychosis. The purpose of this study is to assess anomalies found in structural neuroimaging exams (brain computed tomography (CT) and magnetic resonance imaging (MRI)) in the initial medical work-up of patients presenting first-episode psychosis. Methods. The study subjects were 32 patients aged 18-48 years (mean age: 29.6 years), consecutively admitted with first-episode psychosis diagnosis. Socio-demographic and clinical data and neuroimaging exams (CT and MRI) were retrospectively studied. Diagnostic assessments were made using the Operational Criteria Checklist +. Neuroimaging images (CT and MRI) and respective reports were analysed by an experienced consultant psychiatrist. Results. None of the patients had abnormalities in neuroimaging exams responsible for psychotic symptoms. Thirty-seven percent of patients had incidental brain findings not causally related to the psychosis (brain atrophy, arachnoid cyst, asymmetric lateral ventricles, dilated lateral ventricles, plagiocephaly and falx cerebri calcification). No further medical referral was needed for any of these patients. No significant differences regarding gender, age, diagnosis, duration of untreated psychosis, in-stay and cannabis use were found between patients who had neuroimaging abnormalities versus those without. Discussion. This study suggests that structural neuroimaging exams reveal scarce abnormalities in young patients with first-episode psychosis. Structural neuroimaging is especially useful in first-episode psychosis patients with neurological symptoms, atypical clinical picture and old age. PMID:27257547

  11. The study of virus structure and function: a personal history

    NASA Astrophysics Data System (ADS)

    Rossmann, Michael G.

    2014-09-01

    I describe my gradually evolving role as a scientist from my birth in Frankfurt (Germany) to my education in the UK, my post-doc years and my experiences as an independent investigator at Purdue University1. I discuss the significance of my post-doctoral work in Minnesota where I had my first encounter with an electronic computer and subsequently in Cambridge where I participated in the first structure determination of proteins. After six years back in England my family moved to Indiana (USA) where my home remains to this day. At Purdue University I first studied the structure of enzymes and in the process I discovered the organization and slow evolution of protein domains, each with a specific function. With this success I started what had been on my mind already for a long time, namely the structural analysis of viruses. Initially we studied plant viruses but then switched to small RNA animal viruses, discovering that some plant and animal RNA viruses have closely similar structures and therefore presumably had a common evolutionary origin. Next I became interested in somewhat larger viruses that had lipid membrane envelopes. In turn that has led to the study of very large dsDNA viruses as big as small bacteria as well as studies of bacterial viruses that require complex molecular motors for different parts of their life cycle. While developing crystallographic techniques for the study of viruses it has become progressively more apparent that electron microscopy is an important new tool that is likely to eclipse x-ray crystallography in the next decade.

  12. Semi Active Control of Civil Structures, Analytical and Numerical Studies

    NASA Astrophysics Data System (ADS)

    Kerboua, M.; Benguediab, M.; Megnounif, A.; Benrahou, K. H.; Kaoulala, F.

    numerical example of the parallel R-L piezoelectric vibration shunt control simulated with MATLAB® is presented. An analytical study of the resistor-inductor (R-L) passive piezoelectric vibration shunt control of a cantilever beam was undertaken. The modal and strain analyses were performed by varying the material properties and geometric configurations of the piezoelectric transducer in relation to the structure in order to maximize the mechanical strain produced in the piezoelectric transducer.

  13. Conceptural Study of Gyroscopic Damping Systems for Structural Indentification

    NASA Astrophysics Data System (ADS)

    Furuya, H.; Senba, A.

    2002-01-01

    System identification of the adaptive gyroscopic damper system (AGDS) is treated in this paper. The adaptive gyroscopic damper system was proposed as the extension of the conventional gyroscopic damper under the concept of intelligent adaptive structure systems [1]. The conventional gyroscopic damper has passive characteristics similar to a tuned mass damper (TMD). Because the conventional gyroscopic damper has one natural frequency, several applications to the ground structures have been studied to suppress the fundamental vibration mode (e.g. [2]). On the other hand, as the AGDS has a property of adjusting the natural frequency of the gimbal to that of the structural system by controlling the moment of inertia around its gimbal axis, the performance for suppressing the vibration of one-DOF system was improved. In addition, by extending this property, suppression of multiple modes vibration by quasi-static control for the AGDS was demonstrated [3]. To realize the high performance for suppressing the structural vibration, the identification of characteristics of the structural system with AGDS is significant, because the adaptability of the AGDS to the natural frequency of the system reflects to the performance. By using a capability of AGDS as changing its moment of inertia around its gimbals axis by controlling appendage mass, the system identification is also possible. A sensitivity analysis for the change of the response amplitude and the natural frequency with modal parameters is applied to the method. The errors included in the identification results of modal parameters for cantilevered beam model is examined. The numerical demonstrations were performed to investigate the identification errors of system parameters by the response amplitude and the natural frequency with modal parameters, respectively. The results show that the technique used in the study can identify the structural system and the identification errors occur for near the natural frequency of

  14. Structure-Property Study of Piezoelectricity in Polyimides

    NASA Technical Reports Server (NTRS)

    Ounaies, Zoubeida; Park, Cheol; Harrison, Joycelyn S.; Smith, Joseph G.; Hinkley, Jeffrey

    1999-01-01

    High performance piezoelectric polymers are of interest to NASA as they may be useful for a variety of sensor applications. Over the past few years research on piezoelectric polymers has led to the development of promising high temperature piezoelectric responses in some novel polyimides. In this study, a series of polyimides have been studied with systematic variations in the diamine monomers that comprise the polyimide while holding the dianhydride constant. The effect of structural changes, including variations in the nature and concentration of dipolar groups, on the remanent polarization and piezoelectric coefficient is examined. Fundamental structure-piezoelectric property insight will enable the molecular design of polymers possessing distinct improvements over state-of-the-art piezoelectric polymers including enhanced polarization, polarization stability at elevated temperatures, and improved processability.

  15. Structural study of Fe (II) adsorption on hematite (1102)

    SciTech Connect

    Tanwar, K.S.; Petitto, S.C.; Ghose, S.K.; Eng, P.J.; Trainor, T.P.

    2008-07-15

    The structure of {alpha}-Fe{sub 2}O{sub 3}(1{bar 1}02) reacted with Fe(II) under anoxic conditions was studied using crystal truncation rod (CTR) diffraction. The CTR results show the crystalline termination of {alpha}-Fe{sub 2}O{sub 3}(1{bar 1}02) is modified due to adsorption of Fe(II) at crystallographic lattice sites. In addition, the binding sites for adsorbed Fe are similar for all studied conditions: reaction for 2 h at pH 5.0, for 34 d at pH 5.0, and for 5.5 h at pH 7.0. The occupancy of adsorbed Fe increases with both reaction time and pH, which is consistent with typical cation adsorption behavior on iron (hydr)oxide surfaces. The metal-oxygen bond lengths of the (ordered) surface Fe atoms are characteristic of Fe(III), which provides indirect evidence for oxidation of adsorbed Fe(II) and is consistent with recent studies indicating that Fe(III)-hydroxides are effective oxidants for dissolved ferrous iron. Grazing-incidence X-ray diffraction measurements indicate that no crystalline surface reaction products formed during the course of Fe(II) reaction. Overall, the structural characterization of the Fe(II) adsorption reaction results in an enhanced understanding of how reduced iron affects the structure, stability and reactivity of hematite.

  16. Effects of colchicine on parotid gland: structural and biochemical studies.

    PubMed

    Malberti, A I; González de Crosa, M

    1998-01-01

    The present study involves the analysis of structural, ultrastructural and biochemical modifications induced by colchicine (Col) in Guinea Pig parotid gland. The biochemical studies showed that the highest concentration of soluble proteins occurred 4 hs after colchicine injection. The curve of a-amylase activity in the gland showed an increase in enzyme activity over control at approximately 4 hs post-injection. At 8 hours the rise was even greater. The structural and ultrastructural analyses of the gland revealed that 4 hs post-injection colchicine exerts its maximum inhibitory effect on secretion. At this treatment time, the cytoplasm contained granules of various sizes and sharp outlines. Large areas of the cytoplasm exhibited material which resembled the granular content and seemed to result from the fusion of granules. No secretion was found in the lumen of the ducts. The inhibitory effect on secretion would be due to the disassembly of microtubules which would in turn impair transport of the granules to the apical surface of the membrane and eventual exocytosis. We herein propose that the effects of colchicine in the experimental conditions of this study would be largely reversible at 24 hours. At this time, structural, ultrastructural and biochemical features were similar to those of controls. PMID:11885456

  17. X-ray scattering data and structural genomics

    NASA Astrophysics Data System (ADS)

    Doniach, Sebastian

    2003-03-01

    High throughput structural genomics has the ambitious goal of determining the structure of all, or a very large number of protein folds using the high-resolution techniques of protein crystallography and NMR. However, the program is facing significant bottlenecks in reaching this goal, which include problems of protein expression and crystallization. In this talk, some preliminary results on how the low-resolution technique of small-angle X-ray solution scattering (SAXS) can help ameliorate some of these bottlenecks will be presented. One of the most significant bottlenecks arises from the difficulty of crystallizing integral membrane proteins, where only a handful of structures are available compared to thousands of structures for soluble proteins. By 3-dimensional reconstruction from SAXS data, the size and shape of detergent-solubilized integral membrane proteins can be characterized. This information can then be used to classify membrane proteins which constitute some 25% of all genomes. SAXS may also be used to study the dependence of interparticle interference scattering on solvent conditions so that regions of the protein solution phase diagram which favor crystallization can be elucidated. As a further application, SAXS may be used to provide physical constraints on computational methods for protein structure prediction based on primary sequence information. This in turn can help in identifying structural homologs of a given protein, which can then give clues to its function. D. Walther, F. Cohen and S. Doniach. "Reconstruction of low resolution three-dimensional density maps from one-dimensional small angle x-ray scattering data for biomolecules." J. Appl. Cryst. 33(2):350-363 (2000). Protein structure prediction constrained by solution X-ray scattering data and structural homology identification Zheng WJ, Doniach S JOURNAL OF MOLECULAR BIOLOGY , v. 316(#1) pp. 173-187 FEB 8, 2002

  18. High-resolution crystal structure reveals a HEPN domain at the C-terminal region of S. cerevisiae RNA endonuclease Swt1

    SciTech Connect

    Peng, Shuxia Zhou, Ke; Wang, Wenjia; Gao, Zengqiang; Dong, Yuhui; Liu, Quansheng

    2014-10-31

    Highlights: • Crystal structure of the C-terminal (CT) domain of Swt1 was determined at 2.3 Å. • Structure of the CT domain was identified as HEPN domain superfamily member. • Low-resolution envelope of Swt1 full-length in solution was analyzed by SAXS. • The middle and CT domains gave good fit to SAXS structural model. - Abstract: Swt1 is an RNA endonuclease that plays an important role in quality control of nuclear messenger ribonucleoprotein particles (mRNPs) in eukaryotes; however, its structural details remain to be elucidated. Here, we report the crystal structure of the C-terminal (CT) domain of Swt1 from Saccharomyces cerevisiae, which shares common characteristics of higher eukaryotes and prokaryotes nucleotide binding (HEPN) domain superfamily. To study in detail the full-length protein structure, we analyzed the low-resolution architecture of Swt1 in solution using small angle X-ray scattering (SAXS) method. Both the CT domain and middle domain exhibited a good fit upon superimposing onto the molecular envelope of Swt1. Our study provides the necessary structural information for detailed analysis of the functional role of Swt1, and its importance in the process of nuclear mRNP surveillance.

  19. Structural magnetism: Experimental studies of the relations between structures and magnetic properties

    NASA Astrophysics Data System (ADS)

    Lin, Tao

    The magnetic properties of transition metals are known to depend strongly upon their crystal structure. One way to artificially control the structure is through the preparation of superlattices, where a metastable phase of one element may be stabilized through epitaxial growth. Many metastable systems achieved exhibit unusual properties. Some newly developed technologies make this study possible. Epitaxial sputtering was established within this decade and it is our primary growth method. X-ray diffraction is still the most important technique in determining crystal structure. Magnetic optical Kerr effect (MOKE) can give lots of important information on magnetic properties such as the coercivity and the saturation Kerr effect. The theory of the X-ray magnetic circular dichroism (XMCD) is quite similar to MOKE except that it uses X-rays instead of visible light. This feature enables XMCD to detect the element specific magnetic properties which play a central role in this study. The studies on Fe/Ni and Fe/Ru multilayers discovered many extraordinary behaviors of Ni and Ru. in their metastable phase. For example, as an important ferromagnetic metal, Ni is found enhanced magnetic moment in bct structure for the first time. The study on the Slater-Pauling curve for the 4d elements is to continue a 70-year construction of Slater-Pauling curve. Benefited from those new techniques, the construction of the Slater- Pauling curve for the 4d elements was accomplished. Metastable phase fct-Fe is of particular interesting because it displays a large variety of structural magnetic properties. It was found in this project that Fe magnetic moment in the [4d alloy/Fe/4d alloy] structure has a strong dependence on the electron interaction between Fe and 4d element. Although there is no solid evidence indicating that the resistance of tunneling junctions with GdN barrier have dependence on external magnetic field, lots of interesting results were still found, such as the relation

  20. Studies on structures of lipid A-monophosphate clusters

    NASA Astrophysics Data System (ADS)

    Faunce, Chester A.; Reichelt, Hendrik; Paradies, Henrich H.

    2011-03-01

    Single crystalline clusters of lipid A-monophosphate were grown from organic dispersions containing 5-15% (v/v) water at various volume fractions, ϕ, and temperatures. The morphology of the single lipid A-monophosphate crystals was either rhombohedral or hexagonal. The hexagonal crystals were needlelike or cylindrical in shape, with the long dimension parallel to the c axis of the unit cell. The crystalline clusters were studied using electron microscopy and x-ray powder diffraction. Employing molecular location methods following a Rietveld refinement and whole-pattern refinement revealed two monoclinic crystal structures in the space groups P21 and C2, both converged with RF = 0.179. The two monoclinic crystal structures were packing (hydrocarbon chains) and conformational (sugar) polymorphs. Neither of these two structures had been encountered previously. Only intramolecular hydrogen bonding was observed for the polymorphs, which were located between the amide and the carboxyl groups. Another crystalline structure was found in the volume-fraction range 2.00 × 10-3 ≤ ϕ ≤ 2.50 × 10-3, which displayed hexagonal symmetry. The hexagonal symmetry of the self-assembled lipid A-monophosphate crystalline phase might be reconciled with the monoclinic symmetry found at low-volume-fractions. Therefore, lowering the symmetry from cubic, i.e., Ia overline 3d, to rhombohedral R overline 3 m, and finally to the monoclinic space group C2 was acceptable if the lipid A-monophosphate anion was completely orientationally ordered.

  1. Crystal structure studies on sulfur oxygenase reductase from Acidianus tengchongensis

    SciTech Connect

    Li Mei; Chen Zhiwei; Zhang Pingfeng; Pan Xiaowei; Jiang Chengying; An Xiaomin; Liu Shuangjiang; Chang Wenrui

    2008-05-09

    Sulfur oxygenase reductase (SOR) simultaneously catalyzes oxidation and reduction of elemental sulfur to produce sulfite, thiosulfate, and sulfide in the presence of molecular oxygen. In this study, crystal structures of wild type and mutants of SOR from Acidianus tengchongensis (SOR-AT) in two different crystal forms were determined and it was observed that 24 identical SOR monomers form a hollow sphere. Within the icosatetramer sphere, the tetramer and trimer channels were proposed as the paths for the substrate and products, respectively. Moreover, a comparison of SOR-AT with SOR-AA (SOR from Acidianus ambivalens) structures showed that significant differences existed at the active site. Firstly, Cys31 is not persulfurated in SOR-AT structures. Secondly, the iron atom is five-coordinated rather than six-coordinated, since one of the water molecules ligated to the iron atom in the SOR-AA structure is lost. Consequently, the binding sites of substrates and a hypothetical catalytic process of SOR were proposed.

  2. Analysis of time-series of total and plant water stress levels using a dual-source energy balance model over agricultural crops and medium to low resolution thermal infra red remote sensing data

    NASA Astrophysics Data System (ADS)

    Boulet, Gilles; Mougenot, Bernard; Bahir, Malik; Fanise, Pascal; Saadi, Sameh; Simonneaux, Vincent; Chebbi, Wafa; Kassouk, Zeineb; Oualid, Toufik; Olioso, Albert; Lagouarde, Jean-Pierre; Le Dantec, Valérie; Rivalland, Vincent; Zribi, Mehrez; Lili-Chabaane, Zohra

    2015-04-01

    Detecting, monitoring and mapping plant water stress with remote sensing data is a crucial component of modern agricultural water management, especially in areas with scarce water resources such as the south and the eastern parts of the Mediterranean region. Developing efficient operational methods dedicated to those three actions is thus necessary to design observing systems for areas with a mixture of irrigated, rainfed and deficit irrigation agriculture. Those systems can assist managers in tasks such as early warning of drought, real time irrigated area mapping etc. A way to quantify plant and total water stress levels is to exploit the available surface temperature data from remote sensing as a signature of the surface energy balance, including the latent heat flux. Remotely sensed energy balance models enable to estimate evapotranspiration and the water status of continental surfaces. Two-source models, such as TSEB (Norman et al., 1995) allow deriving a rough estimate of the water stress of the vegetation instead of that of a soil-vegetation composite. For the latter, a realistic underlying assumption enables to invert two unknowns (evaporation and transpiration) from a single piece of information. This assumption states that, in most cases, vegetation is unstressed, and that if vegetation is stressed, evaporation is negligible. In the latter case, if vegetation stress is not properly accounted for, the resulting evaporation will decrease to unrealistic levels (negative fluxes) in order to maintain the same total surface temperature. Actual and potential transpiration rates are combined to derive an index of plant water stress applicable to low resolution data. Here, we evaluate time series of plant water stress indices in the Kairouan area in Central Tunisia in the last few years by comparing them with 1- maps of the irrigation sectors as well as rainfall data and 2- turbulent heat flux measurements obtained at low resolution (scintillometer, eddy

  3. Antimicrobial profile of some novel keto esters: Synthesis, crystal structures and structure-activity relationship studies.

    PubMed

    Khan, Imtiaz; Saeed, Aamer; Arshad, Mohammad Ifzan; White, Jonathan Michael

    2016-01-01

    Rapid increase in bacterial resistance has become a major public concern by escalating alongside a lack of development of new anti-infective drugs. Novel remedies in the battle against multidrug-resistant bacterial strains are urgently needed. So, in this context, the present work is towards the investigation of antimicrobial efficacy of some novel keto ester derivatives, which are prepared by the condensation of substituted benzoic acids with various substituted phenacyl bromides in dimethylformamide at room temperature using triethylamine as a catalyst. The structural build-up of the target compounds was accomplished by spectroscopic techniques including FTIR, (1)H and (13)C NMR spectroscopy and mass spectrometry. The purity of the synthesized compounds was ascertained by elemental analysis. The molecular structures of compounds (4b) and (4l) were established by X-ray crystallographic analysis. The prepared analogues were evaluated for their antimicrobial activity against Gram-positive (Staphylococcus aureus, Micrococcus leuteus) and Gram-negative (Pseudomonas picketti, Salmonella setuball) bacteria and two fungal pathogenic strains (Aspergillus niger, Aspergillus flavus), respectively. Among the screened derivatives, several compounds were found to possess significant activity but (4b) and (4l) turned out to be lead molecules with remarkable antimicrobial efficacy. The structure-activity relationship analysis of this study also revealed that structural modifications on the basic skeleton affected the antimicrobial activity of the synthesized compounds. PMID:26826838

  4. Two-dimensional low resolution Raman spectroscopy applied to fast discrimination of microorganisms that cause pharyngitis: A whole-organism fingerprinting approach

    NASA Astrophysics Data System (ADS)

    Mello, Cesar; Severi, Eza; Coelho, Lucinda; Marangoni, Antônio; Dezuane, Christiane; Ricci, Emiliane; Ribeiro, Diórginis; Poppi, Ronei Jesus

    2008-07-01

    The discrimination of the bacteria that cause pharyngitis through classical-microbiological methods is very efficient in the great majority of the cases. However, the high cost of chemicals and the time spent for such identifications, about four days, could generate serious consequences for the patients. Thus, the search for low cost spectroscopic methods which would allow a fast and reagentless discrimination of these microorganisms is extremely relevant. In this work, the main microorganisms that cause pharyngitis: S. aureus, S. pyogenes and Neisseria gonorrhoeae were studied. For each of the microorganisms 60 different dispersions were prepared using physiological solution as solvent and its Raman spectra were recorded. The 1D spectra obtained were similar, making it very difficult to differentiate the microorganisms. However, applying the 2D correlation method, it was possible to identify the microorganisms evaluated using the synchronous spectrum as "whole-organism fingerprinting" in a reduced time interval (˜10 h).

  5. Study of Exotic Nuclear Structures via Total Reaction Cross Sections

    NASA Astrophysics Data System (ADS)

    Takechi, Maya

    2009-10-01

    Nuclear radius is one of the most basic physical quantities to study unknown exotic nuclei. A number of radii for unstable nuclei were studied through measurements of interaction cross sections (σI) at high energies, using the Glauber-type calculation (Optical-Limit approximation (OLA) of Glauber theory) to investigate halo and skin structures of exotic nuclei. On the other hand, it was indicated that reaction cross sections (σR) at intermediate energies (from several tens to hundreds of MeV/nucleon) were more sensitive to dilute nucleon density distribution owing to large nucleon-nucleon total cross sections (σNN) compared to high-energy region. Recently, we developed a new method to deduce nucleon density distributions from the energy dependences of σ R, through the precise measurements of σ R for various nuclei and some modifications of Glauber-type calculation. Using this method, we studied nucleon density distributions of light nuclei by measuring σ R for those nuclei at HIMAC (Heavy ion Medical Accelerator in CHIBA), NIRS (National Institute of Radiological Sciences). And very recently, we deduced nuclear radii of neutron-rich Ne isotopes (^28-32Ne) which are in the island-of-inversion region by measuring σI using BigRIPS at RIBF (RI Beam Factory) to study nuclear structures of those isotopes using our method. In this workshop, results of nucleon density distributions obtained at HIMAC and results of the studies of Ne isotopes at RIBF will be introduced and discussed.

  6. Structural Design Feasibility Study for the Global Climate Experiment

    SciTech Connect

    Lewin,K.F.; Nagy, J.

    2008-12-01

    Neon, Inc. is proposing to establish a Global Change Experiment (GCE) Facility to increase our understanding of how ecological systems differ in their vulnerability to changes in climate and other relevant global change drivers, as well as provide the mechanistic basis for forecasting ecological change in the future. The experimental design was initially envisioned to consist of two complementary components; (A) a multi-factor experiment manipulating CO{sub 2}, temperature and water availability and (B) a water balance experiment. As the design analysis and cost estimates progressed, it became clear that (1) the technical difficulties of obtaining tight temperature control and maintaining elevated atmospheric carbon dioxide levels within an enclosure were greater than had been expected and (2) the envisioned study would not fit into the expected budget envelope if this was done in a partially or completely enclosed structure. After discussions between NEON management, the GCE science team, and Keith Lewin, NEON, Inc. requested Keith Lewin to expand the scope of this design study to include open-field exposure systems. In order to develop the GCE design to the point where it can be presented within a proposal for funding, a feasibility study of climate manipulation structures must be conducted to determine design approaches and rough cost estimates, and to identify advantages and disadvantages of these approaches including the associated experimental artifacts. NEON, Inc requested this design study in order to develop concepts for the climate manipulation structures to support the NEON Global Climate Experiment. This study summarizes the design concepts considered for constructing and operating the GCE Facility and their associated construction, maintenance and operations costs. Comparisons and comments about experimental artifacts, construction challenges and operational uncertainties are provided to assist in selecting the final facility design. The overall goal

  7. Compositional Density Structure of the Upper Mantle from Constrained 3-D Inversion of Gravity Anomaly: A Case Study of Southeast Asia

    NASA Astrophysics Data System (ADS)

    Liang, Q.; Chen, C.; Kaban, M. K.; Thomas, M.

    2014-12-01

    Mantle density structure is a key for tectonics. The density variations in the upper mantle are affected by temperature and composition. Seismic tomography method has been widely applied to obtain the P- and S-wave velocity structure in the mantle, which is then used to calculate the density perturbation. However, the velocity model is mainly due to the thermal effects but not the compositional effects. A method of 3-D inversion of gravity anomaly developed in spherical coordinates is used to image the large-scale density structure of upper mantle in Southeast Asia. The mantle gravity anomalies used in inversion are calculated by removing the crustal effects from the observed gravity. With constraints of thermal density model from seismic tomography, the integrative density structure is estimated from gravity inversion. Consequently, we obtain the compositional density by subtracting the thermal density from the integrative structure. The result of inversion shows the anisotropic composition of subduction zones, Cratons and plates boundary in Southeast Asia. In the shallow depth, the compositional density anomalies of large scales present uniform features in oceanic and continental mantle. In depth of 75-175 km, there are differences between the thermal and the compositional variations. The density anomalies at these depths are both affected by temperature and composition of the upper mantle. Below 175-km depth, the density anomalies are dominated by the compositional variations. Furthermore, comparing with high seismicity occurred at moderate-depth (50-300 km), we found that the compositional density variations is one of the factor that inducing earthquakes. The constrained inversion of mantle gravity anomaly has possibility to reveal the subduction which is not clearly seen from low-resolution tomography data, and may reveal the relation of seismicity and composition in the upper mantle. This study is supported by the Program of International Science and

  8. Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument

    PubMed Central

    Shen, Shichen; Sheng, Quanhu; Shyr, Yu; Qu, Jun

    2016-01-01

    The recently-introduced Orbitrap Fusion mass spectrometry permits various types of MS2 acquisition methods. To date, these different MS2 strategies and the optimal data interpretation approach for each have not been adequately evaluated. This study comprehensively investigated the four MS2 strategies: HCD-OT (higher-energy-collisional-dissociation with Orbitrap detection), HCD-IT (HCD with ion trap, IT), CID-IT (collision-induced-dissociation with IT) and CID-OT on Orbitrap Fusion. To achieve extensive comparison and identify the optimal data interpretation method for each technique, several search engines (SEQUEST and Mascot) and post-processing methods (score-based, PeptideProphet, and Percolator) were assessed for all techniques for the analysis of a human cell proteome. It was found that divergent conclusions could be made from the same dataset when different data interpretation approaches were used and therefore requiring a relatively fair comparison among techniques. Percolator was chosen for comparison of techniques because it performs the best among all search engines and MS2 strategies. For the analysis of human cell proteome using individual MS2 strategies, the highest number of identifications was achieved by HCD-OT, followed by HCD-IT and CID-IT. Based on these results, we concluded that a relatively fair platform for data interpretation is necessary to avoid divergent conclusions from the same dataset, and HCD-OT and HCD-IT may be preferable for protein/peptide identification using Orbitrap Fusion. PMID:27472422

  9. Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument.

    PubMed

    Tu, Chengjian; Li, Jun; Shen, Shichen; Sheng, Quanhu; Shyr, Yu; Qu, Jun

    2016-01-01

    The recently-introduced Orbitrap Fusion mass spectrometry permits various types of MS2 acquisition methods. To date, these different MS2 strategies and the optimal data interpretation approach for each have not been adequately evaluated. This study comprehensively investigated the four MS2 strategies: HCD-OT (higher-energy-collisional-dissociation with Orbitrap detection), HCD-IT (HCD with ion trap, IT), CID-IT (collision-induced-dissociation with IT) and CID-OT on Orbitrap Fusion. To achieve extensive comparison and identify the optimal data interpretation method for each technique, several search engines (SEQUEST and Mascot) and post-processing methods (score-based, PeptideProphet, and Percolator) were assessed for all techniques for the analysis of a human cell proteome. It was found that divergent conclusions could be made from the same dataset when different data interpretation approaches were used and therefore requiring a relatively fair comparison among techniques. Percolator was chosen for comparison of techniques because it performs the best among all search engines and MS2 strategies. For the analysis of human cell proteome using individual MS2 strategies, the highest number of identifications was achieved by HCD-OT, followed by HCD-IT and CID-IT. Based on these results, we concluded that a relatively fair platform for data interpretation is necessary to avoid divergent conclusions from the same dataset, and HCD-OT and HCD-IT may be preferable for protein/peptide identification using Orbitrap Fusion. PMID:27472422

  10. Protein Structure Refinement of CASP Target Proteins Using GNEIMO Torsional Dynamics Method

    PubMed Central

    2015-01-01

    A longstanding challenge in using computational methods for protein structure prediction is the refinement of low-resolution structural models derived from comparative modeling methods into highly accurate atomistic models useful for detailed structural studies. Previously, we have developed and demonstrated the utility of the internal coordinate molecular dynamics (MD) technique, generalized Newton–Euler inverse mass operator (GNEIMO), for refinement of small proteins. Using GNEIMO, the high-frequency degrees of freedom are frozen and the protein is modeled as a collection of rigid clusters connected by torsional hinges. This physical model allows larger integration time steps and focuses the conformational search in the low frequency torsional degrees of freedom. Here, we have applied GNEIMO with temperature replica exchange to refine low-resolution protein models of 30 proteins taken from the continuous assessment of structure prediction (CASP) competition. We have shown that GNEIMO torsional MD method leads to refinement of up to 1.3 Å in the root-mean-square deviation in coordinates for 30 CASP target proteins without using any experimental data as restraints in performing the GNEIMO simulations. This is in contrast with the unconstrained all-atom Cartesian MD method performed under the same conditions, where refinement requires the use of restraints during the simulations. PMID:24397429

  11. Algorithmic study on systolic array structures. Master's thesis

    SciTech Connect

    Souza, L.J.

    1985-06-01

    Computation bound problems impose a severe burden on the CPU. In order to speed up computation, specific problems that are identified as the main burden can be done using parallel processing. In this way, the time consuming tasks can be executed on specially tailored hardware. This hardware is designed to implement an algorithm-oriented parallel-processing structure that works more efficiently than the CPU for these specific tasks. This thesis is a study of the mapping of the algorithms onto a kind of structure called systolic array. The development and utilization of a software tool designed to assist on such analysis is presented here. This tool, named Systolic Array Graphics Simulator (SYSGRAS), has the capability to represent any type of systolic array, no matter how complex the cells and structure are. Because of the capability of SYSGRAS, an interactive computer program simulator, the study of systolic arrays is simplified. The complexity of the time-space relationships is analyzed with the help of some color-graphics techniques. The visualization of the data interaction is thus enhanced and the user is alleviated from the burden of keeping track of partial results and can dedicate attention to the processing algorithm.

  12. Integrated reservoir study - M/T structure offshore Abu Dhabi

    SciTech Connect

    Cartier, G.; Combes, J.T. des; Hassan, T.H.

    1995-08-01

    A multidisciplinary approach involving geology, geophysics, petrophysics and reservoir engineering is used to assess the oil-bearing Thamama reservoirs in the Offshore Abu Dhabi M/T Structure. The structural definition is hampered by subtle variations of the seismic velocities created by shallow high velocity channel fills. Improved time to depth conversion was achieved through detailed velocity studies and layer caking. As currently defined at the Thamama level, the M/T structure is a gentle low relief feature with closure of about 125 feet. The Lower Cretaceous Thamama Group comprises the producing zones and consists of a succession which was deposited over an extensive carbonate ramp platform. Seven depositional environments and fifteen associated lithofacies range from slope or basin edge, gradually passing to fore shoal, algal shoal, and rudistid backshoal of the inner ramp. Three third order sequences, their associated systems tracts, sequence boundaries and shallowing upwards parasequences are recognised. Based on geological and petrophysical data, a rock type scheme was developed as a basis for detailed reservoir layering and simulation studies. The main diagenetic processes which adversely affect porosity are circumgranular, ferroan and non-ferroan calcite and saddle dolomite cementation, while leaching is the primary porosity-enhancing process. Conventional and special core analyses indicate that specific poroperm, petrophysical and engineering parameters can be assigned to various rock types. The integration of all disciplines will optimise future appraisal drilling and lead to a more efficient development strategy of this field.

  13. Health monitoring studies on composite structures for aerospace applications

    SciTech Connect

    James, G.; Roach, D.; Hansche, B.; Meza, R.; Robinson, N.

    1996-02-01

    This paper discusses ongoing work to develop structural health monitoring techniques for composite aerospace structures such as aircraft control surfaces, fuselage sections or repairs, and reusable launch vehicle fuel tanks. The overall project is divided into four tasks: Operational evaluation, diagnostic measurements, information condensation, and damage detection. Five composite plates were constructed to study delaminations, disbonds, and fluid retention issues as the initial step in creating an operational system. These four square feet plates were graphite-epoxy with nomex honeycomb cores. The diagnostic measurements are composed of modal tests with a scanning laser vibrometer at over 500 scan points per plate covering the frequency range up to 2000 Hz. This data has been reduced into experimental dynamics matrices using a generic, software package developed at the University of Colorado at Boulder. The continuing effort will entail performing a series of damage identification studies to detect, localize, and determine the extent of the damage. This work is providing understanding and algorithm development for a global NDE technique for composite aerospace structures.

  14. Studies of Fe-Cu microwires with nanogranular structure

    NASA Astrophysics Data System (ADS)

    Zhukov, A.; García, C.; DelVal, J. J.; Gonzalez, J.; Knobel, M.; Serantes, D.; Baldomir, D.; Zhukova, V.

    2009-01-01

    We report on the fabrication, and structural and magnetic characterization of Cu63Fe37 microwires with granular structure produced by rapid quenching, using the Tailor-Ulitovsky method, from the immiscible alloys. X-ray diffraction study demonstrated that the structure consists of small (6-45 nm) crystallites of Cu and body centred cubic α-Fe. Magnetic properties have been measured in the range of 5-300 K using a SQUID (superconducting quantum interference device) magnetometer. The temperature dependences of the magnetization measured in a cooling regime when no external magnetic field is applied (zero-field cooling) and in the presence of the field (field cooling) show considerable difference below 20 K. This difference could be related to the presence of small α-Fe grains embedded in the Cu matrix. Those α-Fe grains appear to be blocked at temperatures below that at which the maximum of the magnetization is observed in the low temperature range. Significant magnetoresistance (about 7%) has been found in the samples studied. The shape of the observed dependences is typical of a giant magnetoresistance effect.

  15. Supersonic cruise research aircraft structural studies: Methods and results

    NASA Technical Reports Server (NTRS)

    Sobieszczanski-Sobieski, J.; Gross, D.; Kurtze, W.; Newsom, J.; Wrenn, G.; Greene, W.

    1981-01-01

    NASA Langley Research Center SCAR in-house structural studies are reviewed. In methods development, advances include a new system of integrated computer programs called ISSYS, progress in determining aerodynamic loads and aerodynamically induced structural loads (including those due to gusts), flutter optimization for composite and metal airframe configurations using refined and simplified mathematical models, and synthesis of active controls. Results given address several aspects of various SCR configurations. These results include flutter penalties on composite wing, flutter suppression using active controls, roll control effectiveness, wing tip ground clearance, tail size effect on flutter, engine weight and mass distribution influence on flutter, and strength and flutter optimization of new configurations. The ISSYS system of integrated programs performed well in all the applications illustrated by the results, the diversity of which attests to ISSYS' versatility.

  16. Dual keel space station control/structures interaction study

    NASA Technical Reports Server (NTRS)

    Young, John W.; Lallman, Frederick J.; Cooper, Paul A.

    1987-01-01

    A study was made to determine the influence of truss bay size on the performance of the space station control system. The objective was to determine if any control problems existed during reboost and to assess the level of potential control/structures interaction during operation of the control moment gyros used for vertical stabilization. The models analyzed were detailed finite-element representations of the 5 meter and 9 foot growth versions of the 300 kW dual keel station. Results are presented comparing the performance of the reboost control system for both versions of the space station. Standards for comparison include flexible effects at the attitude control sensor locations and flexible contributions to pointing error at the solar collectors. Bode analysis results are presented for the attitude control system and control, structural, and damping sensitivities are examined.

  17. Synthesis and Structural Activity Relationship Study of Antitubercular Carboxamides

    PubMed Central

    Ugwu, D. I.; Ezema, B. E.; Eze, F. U.; Ugwuja, D. I.

    2014-01-01

    The unusual structure and chemical composition of the mycobacterial cell wall, the tedious duration of therapy, and resistance developed by the microorganism have made the recurrence of the disease multidrug resistance and extensive or extreme drug resistance. The prevalence of tuberculosis in synergy with HIV/AIDS epidemic augments the risk of developing the disease by 100-fold. The need to synthesize new drugs that will shorten the total duration of effective treatment and/or significantly reduce the dosage taken under DOTS supervision, improve on the treatment of multidrug-resistant tuberculosis which defies the treatment with isoniazid and rifampicin, and provide effective treatment for latent TB infections which is essential for eliminating tuberculosis prompted this review. In this review, we considered the synthesis and structure activity relationship study of carboxamide derivatives with antitubercular potential. PMID:25610646

  18. Structure of human chromosomes studied by atomic force microscopy.

    PubMed

    Tamayo, Javier

    2003-03-01

    In this work human chromosomes have been treated with RNase and pepsin to remove the layer of cellular material that covers the standard preparations on glass slides. This allows characterization of the topography of chromosomes at nanometer scale in air and in physiological solution by atomic force microscopy. Imaging of the dehydrated structure in air indicates radial arrangement of chromatin loops as the last level of DNA packing. However, imaging in liquid reveals a last level of organization consisting of a hierarchy of bands and coils. Additionally force curves between the tip and the chromosome in liquid are consistent with radial chromatin loops. These results and previous electron microscopy studies are analyzed, and a model is proposed for the chromosome structure in which radial loops and helical coils coexist.

  19. Electronic structure study of strongly correlated Mott-insulators

    NASA Astrophysics Data System (ADS)

    Yin, Quan

    Strongly correlated electronic systems have presented the most challenging problems to condensed matter theorists for many years and this continues to be the case. They are complicated materials with active d or f orbitals, whose valence electrons are in the intermediate region between itinerant (band-like) and highly localized (atomic-like) limits, which demand genuine many-body treatment. Although dealing with strongly correlated systems is a notorious problem, they have drawn broad interests of both theoretical and experimental condensed matter physicists, with intensive studies carried out in the past and present. This is due to the most exotic properties associated with strongly correlated materials, such as high-temperature superconductivity, metal-insulator transition, volume collapse, Kondo effect, colossal magnetoresistance, and many others. Although density functional theory (DFT) within local density approximation (LDA) is very successful in describing a wide range of materials, it encounters difficulty in predicting strongly correlated systems. Traditionally, they have been studied by model Hamiltonians with empirical parameters. The development of dynamical mean field theory (DMFT) and its marriage to DFT have brought new hope for first-principle study of strongly correlated systems. In this work, electronic structures of select strongly correlated systems are studied using LDA+DMFT. As theoretical backgrounds, reviews of DFT and DMFT are given in the first few chapters, where we also introduce the philosophy and workflow of LDA+DMFT. In the following chapters, applications to transition metal oxides, undoped high-temperature superconductors and actinide oxides are presented, where electronic structures of these materials and other properties derived from electronic structures are calculated and compared with experiments where available. Generally good agreements have been found between theory and experiments.

  20. Using proteinase K to study the structure of prions.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background/Introduction. The secondary structure of prions is composed almost entirely of '-sheet secondary structure. Structural constraints suggest that the '-sheet secondary structure is arranged in a '-solenoid. The '-sheet secondary structure is thought to be responsible for the remarkable ...

  1. Neutron scatter studies of chromatin structures related to functions

    SciTech Connect

    Bradbury, E.M.

    1992-01-01

    We have made considerable progress in chromatin reconstitution with very lysine rich histone H1/H5 and in understanding the dynamics of nucleosomes. A ferromagnetic fluid was developed to align biological molecules for structural studies using small-angle-neutron-scattering. We have also identified and characterized in intrinsically bent DNA region flaking the RNA polymerase I binding site of the ribosomal RNA gene in Physarum Polycephalum. Finally projects in progress are in the areas of studying the interactions of histone H4 amino-terminus peptide 1-23 and acetylated 1-23 peptide with DNA using thermal denaturation; study of GGAAT repeats found in human centromeres using high resolution Nuclear Magnetic Resonance and nuclease sentivity assay; and the role of histones and other sperm specific proteins with sperm chromatin.

  2. Neutron scatter studies of chromatin structures related to functions

    SciTech Connect

    Bradbury, E.M.

    1992-01-01

    Despite of setbacks in the lack of neutrons for the proposed We have made considerable progress in chromatin reconstitution with the VLR histone H1/H5 and in understanding the dynamics of nucleosomes. A ferromagnetic fluid was developed to align biological molecules for structural studies using small-angle-neutron-scattering. We have also identified and characterized an intrinsically bent DNA region flanking the RNA polymerase I binding site of the ribosomal RNA gene in Physarum Polycephalum. Finally projects in progress are in the areas of studying the interatctions of histone H4 amino-terminus peptide 1-23 and acetylated 1-23 peptide with DNA using thermal denaturation; study of GGAAT repeats found in human centromeres using high resolution Nuclear magnetic Resonance and nuclease sentivity assay; and the role of histones and other sperm specific proteins with sperm chromatin.

  3. Geologic structure in California: Three studies with ERTS-1 imagery

    NASA Technical Reports Server (NTRS)

    Lowman, P. D., Jr.

    1974-01-01

    Results are presented of three early applications of imagery from the NASA Earth Resources Technology Satellite to geologic studies in California. In the Coast Ranges near Monterey Bay, numerous linear drainage features possibly indicating unmapped fracture zones were mapped within one week after launch of the satellite. A similar study of the Sierra Nevada near Lake Tahoe revealed many drainage features probably formed along unmapped joint or faults in granitic rocks. The third study, in the Peninsular Ranges, confirmed existence of several major faults not shown on published maps. One of these, in the Sawtooth Range, crosses in Elsinore fault without lateral offset; associated Mid-Cretaceous structures have also been traced continuously across the fault without offset. It therefore appears that displacement along the Elsinore fault has been primarily of a dip-slip nature, at least in this area, despite evidence for lateral displacement elsewhere.

  4. Nuclear structure studies with medium energy probes. [Northwestern Univ

    SciTech Connect

    Seth, Kamal K.

    1980-01-01

    Progress in the continuing program of experimental research in nuclear structure with medium-energy probes during the year 1979-1980 is reviewed, and the research activities planned for the year 1980-1981 are discussed. In the study of pion-induced reactions emphasis is placed on investigation of isovector characteristics of nuclear excitations and on double charge exchange reactions. Pion production studies form the major part of the program of experiments with proton beams of 400 to 800 MeV at LAMPF. Current emphasis is on the bearing of these investigations on di-baryon existence. The study of high-spin states and magnetic scattering constitute the main goals of the electron scattering program at Bates. Representative results are presented; completed work is reported in the usual publications. (RWR)

  5. Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

    PubMed Central

    Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; Markvardsen, Anders J.; Gutmann, Matthias J.; Barends, Thomas R. M.; Mattle, Daniel; Shoeman, Robert L.; Doak, R. Bruce; Boutet, Sébastien; Messerschmidt, Marc; Seibert, Marvin M.; Williams, Garth J.; Foucar, Lutz; Reinhard, Linda; Sitsel, Oleg; Gregersen, Jonas L.; Clausen, Johannes D.; Boesen, Thomas; Gotfryd, Kamil; Wang, Kai-Tuo; Olesen, Claus; Møller, Jesper V.; Nissen, Poul; Schlichting, Ilme

    2015-01-01

    Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins. PMID:26175901

  6. Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

    SciTech Connect

    Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; Markvardsen, Anders J.; Gutmann, Matthias J.; Barends, Thomas R. M.; Mattle, Daniel; Shoeman, Robert L.; Doak, R. Bruce; Boutet, Sébastien; Messerschmidt, Marc; Seibert, Marvin M.; Williams, Garth J.; Foucar, Lutz; Reinhard, Linda; Sitsel, Oleg; Gregersen, Jonas L.; Clausen, Johannes D.; Boesen, Thomas; Gotfryd, Kamil; Wang, Kai-Tuo; Olesen, Claus; Møller, Jesper V.; Nissen, Poul; Schlichting, Ilme

    2015-06-11

    Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

  7. Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

    DOE PAGESBeta

    Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; Markvardsen, Anders J.; Gutmann, Matthias J.; Barends, Thomas R. M.; Mattle, Daniel; Shoeman, Robert L.; Doak, R. Bruce; Boutet, Sébastien; et al

    2015-06-11

    Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data revealmore » the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.« less

  8. Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

    SciTech Connect

    Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; Markvardsen, Anders J.; Gutmann, Matthias J.; Barends, Thomas R. M.; Mattle, Daniel; Shoeman, Robert L.; Doak, R. Bruce; Boutet, Sébastien; Messerschmidt, Marc; Seibert, Marvin M.; Williams, Garth J.; Foucar, Lutz; Reinhard, Linda; Sitsel, Oleg; Gregersen, Jonas L.; Clausen, Johannes D.; Boesen, Thomas; Gotfryd, Kamil; Wang, Kai -Tuo; Olesen, Claus; Møller, Jesper V.; Nissen, Poul; Schlichting, Ilme

    2015-06-11

    Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

  9. Structural and optical studies on selected web spinning spider silks.

    PubMed

    Karthikeyani, R; Divya, A; Mathavan, T; Asath, R Mohamed; Benial, A Milton Franklin; Muthuchelian, K

    2017-01-01

    This study investigates the structural and optical properties in the cribellate silk of the sheet web spider Stegodyphus sarasinorum Karsch (Eresidae) and the combined dragline, viscid silk of the orb-web spiders Argiope pulchella Thorell (Araneidae) and Nephila pilipes Fabricius (Nephilidae). X-ray diffraction (XRD), Fourier transform infra-red (FTIR), Ultraviolet-visible (UV-Vis) and fluorescence spectroscopic techniques were used to study these three spider silk species. X-ray diffraction data are consistent with the amorphous polymer network which is arising from the interaction of larger side chain amino acid contributions due to the poly-glycine rich sequences known to be present in the proteins of cribellate silk. The same amorphous polymer networks have been determined from the combined dragline and viscid silk of orb-web spiders. From FTIR spectra the results demonstrate that, cribellate silk of Stegodyphus sarasinorum, combined dragline viscid silk of Argiope pulchella and Nephila pilipes spider silks are showing protein peaks in the amide I, II and III regions. Further they proved that the functional groups present in the protein moieties are attributed to α-helical and side chain amino acid contributions. The optical properties of the obtained spider silks such as extinction coefficients, refractive index, real and imaginary dielectric constants and optical conductance were studied extensively from UV-Vis analysis. The important fluorescent amino acid tyrosine is present in the protein folding was investigated by using fluorescence spectroscopy. This research would explore the protein moieties present in the spider silks which were found to be associated with α-helix and side chain amino acid contributions than with β-sheet secondary structure and also the optical relationship between the three different spider silks are investigated. Successful spectroscopic knowledge of the internal protein structure and optical properties of the spider silks could

  10. Structural and optical studies on selected web spinning spider silks.

    PubMed

    Karthikeyani, R; Divya, A; Mathavan, T; Asath, R Mohamed; Benial, A Milton Franklin; Muthuchelian, K

    2017-01-01

    This study investigates the structural and optical properties in the cribellate silk of the sheet web spider Stegodyphus sarasinorum Karsch (Eresidae) and the combined dragline, viscid silk of the orb-web spiders Argiope pulchella Thorell (Araneidae) and Nephila pilipes Fabricius (Nephilidae). X-ray diffraction (XRD), Fourier transform infra-red (FTIR), Ultraviolet-visible (UV-Vis) and fluorescence spectroscopic techniques were used to study these three spider silk species. X-ray diffraction data are consistent with the amorphous polymer network which is arising from the interaction of larger side chain amino acid contributions due to the poly-glycine rich sequences known to be present in the proteins of cribellate silk. The same amorphous polymer networks have been determined from the combined dragline and viscid silk of orb-web spiders. From FTIR spectra the results demonstrate that, cribellate silk of Stegodyphus sarasinorum, combined dragline viscid silk of Argiope pulchella and Nephila pilipes spider silks are showing protein peaks in the amide I, II and III regions. Further they proved that the functional groups present in the protein moieties are attributed to α-helical and side chain amino acid contributions. The optical properties of the obtained spider silks such as extinction coefficients, refractive index, real and imaginary dielectric constants and optical conductance were studied extensively from UV-Vis analysis. The important fluorescent amino acid tyrosine is present in the protein folding was investigated by using fluorescence spectroscopy. This research would explore the protein moieties present in the spider silks which were found to be associated with α-helix and side chain amino acid contributions than with β-sheet secondary structure and also the optical relationship between the three different spider silks are investigated. Successful spectroscopic knowledge of the internal protein structure and optical properties of the spider silks could

  11. Tridimensional Photomicroscopical Study And Automatic Drawing Of Cytological Structures

    NASA Astrophysics Data System (ADS)

    Couderc, H.; Raynal, J.

    1980-07-01

    The method here described allows a quantitative study by photonic microscopy of thick material without injuring its structure. A tridimensional photographic model is built through superposing in parallel planes a set of microphotographic transparencies of successive optical cross-optical through the material. This stereomodel exactly features the spatial structure of the object and allows, either directly or by means of a stereogram, to measure its tridimensional coordinates. These data are computerized to obtain linear and angular measurements, and also to produce sets of automacic successive perspective drawings of the object, obtained by rotating the reference axes. The microscope must be fitted up with objectives with a wide numerical aperture and a plane field. An interferential device controls the focusing. The method has been initially worked out to study metaphasic chromosomes in situ within the cell without using any of the customary techniques : squash, hypotonic shock, cross-sections, etc..., which result in a definite loss of information. Basically it is applicable to most of the biological materials, and has produced, as it seems for the fist time in 1968, a tridimensional quantitative study of cellular components by photonic microscopy.

  12. Studies of the magnetic structure at the ferromagnet - antiferromagnet interface

    SciTech Connect

    Scholl, A.; Nolting, F.; Stohr, J.; Luning, J.; Seo, J.W.; Locquet, J.-P.; Anders, S.; Ohldag, H.; Padmore, H.A.

    2001-01-02

    Antiferromagnetic layers are a scientifically challenging component in magneto-electronic devices such as magnetic sensors in hard disk heads, or magnetic RAM elements. In this paper we show that photo-electron emission microscopy (PEEM) is capable of determining the magnetic structure at the interface of ferromagnets and antiferromagnets with high spatial resolution (down to 20 nm). Dichroism effects at the L edges of the magnetic 3d transition metals, using circularly or linearly polarized soft x-rays from a synchrotron source, give rise to a magnetic image contrast. Images, acquired with the PEEM2 experiment at the Advanced Light Source, show magnetic contrast for antiferromagnetic LaFeO{sub 3}, microscopically resolving the magnetic domain structure in an antiferromagnetically ordered thin film for the first time. Magnetic coupling between LaFeO{sub 3} and an adjacent Co layer results in a complete correlation of their magnetic domain structures. From field dependent measurements a unidirectional anisotropy resulting in a local exchange bias of up to 30 Oe in single domains could be deduced. The elemental specificity and the quantitative magnetic sensitivity render PEEM a perfect tool to study magnetic coupling effects in multi-layered thin film samples.

  13. Micromechanical-biochemical studies of mitotic chromosome elasticity and structure

    NASA Astrophysics Data System (ADS)

    Poirier, Michael Guy

    The structure of mitotic chromosomes was studied by combining micromechanical force measurements with microfluidic biochemical exposures. Our method is to use glass micropipettes attached to either end of a single chromosome to do mechanical experiments in the extracellular buffer. A third pipette can be used to locally 'spray' reactants so as to carry out dynamical mechanical-chemical experiments. The following elastic properties of mitotic chromosomes are found: Young's modulus, Y = 300 Pa; Poisson ratio, sigma = 0.1; Bending rigidity, B = 1 x 10 -22 J·m; Internal viscosity, eta' = 100 kg/m·sec; Volume fraction, ϕ = 0.7; Extensions of less than 3 times the relaxed length are linear and reversible; Extensions beyond 30 fold exhibit a force plateau at 15 nN and convert the chromosome to a disperse ghost-like state with little change in chromatin structure; Mitotic chromosomes are relatively isotropic; dsDNA cuts of at least every 3 kb cause the a mitotic chromosomes to fall apart; dsDNA cuts less frequently than every 50 kb do not affect mitotic chromosome structure. These results lead to the conclusion that mitotic chromosomes are a network crosslinked every 50 kb between which chromatin is fold by chromatin folding proteins, which are likely to be condensins.

  14. Structural characterization studies on the natural mineral pyrophyllite

    NASA Astrophysics Data System (ADS)

    Reddy, T. Ravindra; Lakshmi Reddy, S.; Endo, Tamio

    2016-03-01

    A light-yellow-colored pyrophyllite (Al2O3.SiO2) mineral obtained from Vempalli, Cuddapah district, Andhra Pradesh, India, is investigated in the present work. Chemical analysis carried out using energy-dispersive spectroscopy (EDX) shows that Fe2O3 is present by about 1.56 wt%. Structural characterization was performed using X-ray diffraction (XRD). XRD results suggest that the unit cell is monoclinic with a = 5.16, b = 8.798, c = 9.347 Å and β = 100.46°. The ligands around the metal ion present in the structure are investigated using FTIR spectroscopy. EDX analysis indicates that iron and titanium are only two transition metals present in it. Morphology studied using scanning electron microscopy suggests that the unit cell consists of a dioctahedral layered structure. Fe3+ is present in the location of Al3+ in the unit cell of pyrophyllite. Electron paramagnetic resonance results indicate that the unit cell of the crystal contains Fe(III), and its g values are found to be 4.10 and 2.0. Infrared properties are due to the presence of silicate and hydroxyl anions as ligands. Nonlinear optical measurements carried out using Z-scan reveal the occurrence of strong nonlinear optical limiting in the material, indicating potential applications in laser safety devices.

  15. Multiple sclerosis, cannabis, and cognition: A structural MRI study

    PubMed Central

    Romero, Kristoffer; Pavisian, Bennis; Staines, William R.; Feinstein, Anthony

    2015-01-01

    Objective A subset of patients with multiple sclerosis (MS) smoke cannabis to relieve symptoms including spasticity and pain. Recent evidence suggests that smoking cannabis further impairs cognition in people with MS and is linked to impaired functional brain changes. No such association, however, has been reported between cannabis use and structural brain changes, hence the focus of the present study. Methods Twenty patients with MS who smoke cannabis for symptom relief, and 19 matched non-cannabis-smoking MS patients were given the Brief Repeatable Neuropsychological Battery and structural MRI scans. Images were segmented into gray matter and white matter, and subsequently analysed with Partial Least Squares, a data-driven multivariate technique that explores brain–behaviour associations. Results In both groups, the Partial Least Squares analysis yielded significant correlations between cognitive scores and both gray matter (33% variance, p < .0001) and white matter (17% variance, p < .05) volume. Gray matter volume in the thalamus, basal ganglia, medial temporal, and medial prefrontal regions, and white matter volume in the fornix correlated with cognitive deficits. Crucially, the analysis indicated that brain volume reductions were associated with more extensive cognitive impairment in the cannabis versus the non-cannabis MS group. Interpretation These results suggest that cannabis use in MS results in more widespread cognitive deficits, which correlate with tissue volume in subcortical, medial temporal, and prefrontal regions. These are the first findings demonstrating an association between cannabis use, cognitive impairment and structural brain changes in MS patients. PMID:26106538

  16. Structural Studies of Complex Carbohydrates of Plant Cell Walls

    SciTech Connect

    Darvill, Alan; Hahn, Michael G.; O'Neill, Malcolm A.; York, William S.

    2015-02-17

    Most of the solar energy captured by land plants is converted into the polysaccharides (cellulose, hemicellulose, and pectin) that are the predominant components of the cell wall. These walls, which account for the bulk of plant biomass, have numerous roles in the growth and development of plants. Moreover, these walls have a major impact on human life as they are a renewable source of biomass, a source of diverse commercially useful polymers, a major component of wood, and a source of nutrition for humans and livestock. Thus, understanding the molecular mechanisms that lead to wall assembly and how cell walls and their component polysaccharides contribute to plant growth and development is essential to improve and extend the productivity and value of plant materials. The proposed research will develop and apply advanced analytical and immunological techniques to study specific changes in the structures and interactions of the hemicellulosic and pectic polysaccharides that occur during differentiation and in response to genetic modification and chemical treatments that affect wall biosynthesis. These new techniques will make it possible to accurately characterize minute amounts of cell wall polysaccharides so that subtle changes in structure that occur in individual cell types can be identified and correlated to the physiological or developmental state of the plant. Successful implementation of this research will reveal fundamental relationships between polysaccharide structure, cell wall architecture, and cell wall functions.

  17. Hyperfine structure and isotope shift study in singly ionized lead

    NASA Astrophysics Data System (ADS)

    Wąsowicz, T. J.; Drozdowski, R.; Kwela, J.

    2005-12-01

    Hyperfine structure and isotope shifts in five optical transitions: 424.5 nm (6s^25f ^2textrm{F}_{7/2} 6s^26d^2 textrm{D}_{5/2}), 537.2 nm (6s^25f ^2textrm{F}_{7/2} 6s6p^2 ^4textrm{P}_{5/2}), 554.5 nm (6s^27d ^2textrm{D}_{5/2} 6s^27p ^2textrm{P}_{3/2}), 560.9 nm (6s^27p^2 textrm{P}_{3/2} 6s^27s ^2textrm{S}_{1/2}) and 666.0 nm (6s^27p ^2textrm{P}_{1/2} 6s^27s ^2textrm{S}_{1/2}) of Pb II have been measured. As a light source the discharge tube was used. The hyperfine structure measurements were performed using metallic isotope 207Pb. For isotope shifts measurements natural lead was used. The high resolution spectral apparatus consisted of a silver coated Fabry-Perot etalon and a grating spectrograph combined with a CCD camera used as a detector. In the analysis of the spectra a computer simulation technique was used. The hyperfine structure observations yielded the splitting constants A for seven levels of Pb II. The isotope shift studies enabled to separate the mass and the field shifts and to determine values of changes of the mean square nuclear charge radii.

  18. Structural study of coacervation in protein-polyelectrolyte complexes

    NASA Astrophysics Data System (ADS)

    Chodankar, S.; Aswal, V. K.; Kohlbrecher, J.; Vavrin, R.; Wagh, A. G.

    2008-09-01

    Coacervation is a dense liquid-liquid phase separation and herein we report coacervation of protein bovine serum albumin (BSA) in the presence of polyelectrolyte sodium polystyrene sulfonate (NaPSS) under varying solution conditions. Small-angle neutron scattering (SANS) measurements have been performed on above protein-polyelectrolyte complexes to study the structural evolution of the process that leads to coacervation and the phase separated coacervate as a function of solution pH , protein-polyelectrolyte ratio and ionic strength. SANS study prior to phase separation on the BSA-NaPSS complex shows a fractal structure representing a necklace model of protein macromolecules randomly distributed along the polystyrene sulfonate chain. The fractal dimension of the complex decreases as pH is shifted away from the isoelectric point (˜4.7) of BSA protein, which indicates the decrease in the compactness of the complex structure due to increase in the charge repulsion between the protein macromolecules bound to the polyelectrolyte. Concentration-dependence studies of the polyelectrolyte in the complex suggest coexistence of two populations of polyelectrolytes, first one fully saturated with proteins and another one free from proteins. Coacervation phase has been obtained through the turbidity measurement by varying pH of the aqueous solution containing protein and polyelectrolyte from neutral to acidic regime to get them to where the two components are oppositely charged. The spontaneous formation of coacervates is observed for pH values less than 4. SANS study on coacervates shows two length scales related to complex aggregations (mesh size and overall extent of the complex) hierarchically branched to form a larger network. The mesh size represents the distance between cross-linked points in the primary complex, which decreases with increase in ionic strength and remains the same on varying the protein-polyelectrolyte ratio. On the other hand, the overall extent of the

  19. Study of the crystal structure of silicon nanoislands on sapphire

    SciTech Connect

    Krivulin, N. O. Pirogov, A. V.; Pavlov, D. A.; Bobrov, A. I.

    2015-02-15

    The results of studies of the crystal structure of silicon nanoislands on sapphire are reported. It is shown that the principal defects in silicon nanoislands on sapphire are twinning defects. As a result of the formation of such defects, different crystallographic orientations are formed in silicon nanoislands on sapphire. In the initial stages of the molecular-beam epitaxy of silicon on sapphire, there are two basic orientations: the (001) orientation parallel to the surface and the (001) orientation at an angle of 70° to the surface.

  20. Structural and mechanical studies of cadmium manganese thiocyanate crystal

    NASA Astrophysics Data System (ADS)

    Manikandan, M. R.; Vijayaprasath, G.; babu, G. Anandha; Bhagavannarayan, G.; Vijayan, N.; Ravi, G.

    2012-06-01

    Single crystals of cadmium manganese thiocyanate (CMTC) have been synthesized successfully and grown by slow evaporation method. The structural perfection of the grown crystals has been analyzed by High resolution X-ray diffraction (HRXRD), which shows the crystalline perfection of the grown crystal is quite good. Optical behavior was assessed by UV-Vis analysis and found that no absorption in the UV visible region and it may be useful for second harmonic applications. The mechanical hardness of the grown crystals was studied and Vicker's microhardness, Stiffness constant was calculated.

  1. Static High Pressure Structural studies on Dy to 119 GPa

    SciTech Connect

    Patterson, J R; Saw, C K; Akella, J

    2003-11-12

    Structural phase transitions in the rare-earth metal Dysprosium have been studied in a Diamond Anvil Cell (DAC) to 119 GPa by x-ray diffraction. Four transformations following the sequence hcp {yields} Sm-type {yields} dhcp {yields} hR24 (hexagonal) {yields} bcm (monoclinic) are observed at 6, 15, 43, and 73 GPa respectively. The hexagonal to monoclinic transformation is accompanied by a 6% reduction in volume, which is attributed to delocalization of the 4f electrons, similar to that seen in Ce, Pr, and Gd.

  2. Arbutin: Isolation, X-ray structure and computional studies

    NASA Astrophysics Data System (ADS)

    Nycz, Jacek E.; Malecki, Grzegorz; Morag, Monika; Nowak, Gerard; Ponikiewski, Lukasz; Kusz, Joachim; Switlicka, Anna

    2010-09-01

    Arbutin, an active component originated from Serratula quinquefolia for skin-whitening use and treating skin related allergic inflammation, was characterized by microanalysis, FTIR, UV-Vis, multinuclear NMR spectroscopy, and single crystal X-ray diffraction method. The geometries of the studied compound were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. Electronic spectra were calculated by TDDFT method. In general, the predicted bond lengths and angles are in a good agreement with the values based on the X-ray crystal structure data.

  3. Theoretical studies of the electronic structure of small metal clusters

    NASA Technical Reports Server (NTRS)

    Jordan, K. D.

    1982-01-01

    Theoretical studies of the electronic structure of metal clusters, in particular clusters of Group IIA and IIB atoms were conducted. Early in the project it became clear that electron correlation involving d orbitals plays a more important role in the binding of these clusters than had been previously anticipated. This necessitated that computer codes for calculating two electron integrals and for constructing the resulting CI Hamiltonions be replaced with newer, more efficient procedures. Program modification, interfacing and testing were performed. Results of both plans are reported.

  4. Neutron scatter studies of chromatin structure related to functions

    SciTech Connect

    Bradbury, E.M.

    1989-01-01

    Neutron scatter studies have been performed at LANSCE, LANL and at the Institute Laue Langevin, Grenoble, France. In the previous progress report (April 1, 1988--July 1, 1988) the following objectives were listed: shape of the histone octamer; location of the N-terminal domains of histone in the nucleosome core particle (specific aim 1 of original grant proposal); effect of acetylation on nucleosome structure (specific aim 2); location of the globular domain of histone H1 (specific aim 6); and complexes of the transcription factor 3A with its DNA binding site. Progress is briefly discussed.

  5. Artificial membranes for membrane protein purification, functionality and structure studies.

    PubMed

    Parmar, Mayuriben J; Lousa, Carine De Marcos; Muench, Stephen P; Goldman, Adrian; Postis, Vincent L G

    2016-06-15

    Membrane proteins represent one of the most important targets for pharmaceutical companies. Unfortunately, technical limitations have long been a major hindrance in our understanding of the function and structure of such proteins. Recent years have seen the refinement of classical approaches and the emergence of new technologies that have resulted in a significant step forward in the field of membrane protein research. This review summarizes some of the current techniques used for studying membrane proteins, with overall advantages and drawbacks for each method. PMID:27284055

  6. Nuclear structure studies with gamma-ray beams

    DOE PAGESBeta

    Tonchev, Anton; Bhatia, Chitra; Kelley, John; Raut, Rajarshi; Rusev, Gencho; Tornow, Werner; Tsoneva, Nadia

    2015-05-28

    In stable and weakly bound neutron-rich nuclei, a resonance-like concentration of dipole states has been observed for excitation energies below the neutron-separation energy. This clustering of strong dipole states has been named the Pygmy Dipole Resonance (PDR) in contrast to the Giant Dipole Resonance (GDR) that dominates the E1 response. Understanding the PDR is presently of great interest in nuclear structure and nuclear astrophysics. High-sensitivity studies of E1 and M1 transitions in closed-shell nuclei using monoenergetic and 100% linearly-polarized photon beams are presented.

  7. Study of structures and dynamical decay mechanisms for multiquark systems

    NASA Astrophysics Data System (ADS)

    Liu, Xuewen; Ke, Hong-Wei; Liu, Xiang; Li, Xue-Qian

    2016-04-01

    The inner structures of the multiquark states are an interesting subject in hadron physics, generally they may be in tetraquark states which are composed of colored constituents, or in molecular states which are composed of two color singlets, or their mixtures. Therefore, the mechanisms which bind the constituents in a unique system and induce the multiquark states to decay would be different in those cases. In this work, using the quantum mechanics we analyze the dynamical mechanisms inducing decays of the tetraquarks where Y (4630 ) stands as an example for the study, we also comment on the molecular states without making numerical computations.

  8. Raman study of phase transformation from diamond structure to wurtzite structure in the silicon nanowires

    NASA Astrophysics Data System (ADS)

    Shukla, A. K.; Dixit, Saurabh

    2016-07-01

    Hexagonal silicon has emerged as an exciting material due to its novel vibrational and electronic properties. Synthesis of the wurtzite silicon nanowires (w-SiNWs) is studied here using metal assisted chemical etching (MACE) technique. Stress induced in the SiNWs during wet chemical etching is attributed to formation of the w-SiNWs. Presence of the w-SiNWs is revealed by first-order and second-order Raman spectra. The effect of variation of deposition time of silver (catalyst) is explicitly studied for growth of w-SiNWs. The deposition time enhances the density of SiNWs in an island of vertically aligned SiNWs. Absorption coefficient studies of the w-SiNWs are also conducted using UV-vis spectroscopy as a function of deposition time. Increase in the absorption coefficient in SiNWs is noticed with increasing deposition time. The prominent quantum confinement along with stress and porosity is shown to be mainly responsible for the transformation from diamond structure to wurtzite structure in the silicon nanowires.

  9. Structural basis of AMPK regulation by adenine nucleotides and glycogen

    SciTech Connect

    Li, Xiaodan; Wang, Lili; Zhou, X. Edward; Ke, Jiyuan; de Waal, Parker W.; Gu, Xin; Tan, M. H. Eileen; Wang, Dongye; Wu, Donghai; Xu, H. Eric; Melcher, Karsten

    2014-11-21

    AMP-activated protein kinase (AMPK) is a central cellular energy sensor and regulator of energy homeostasis, and a promising drug target for the treatment of diabetes, obesity, and cancer. Here we present low-resolution crystal structures of the human α1β2γ1 holo-AMPK complex bound to its allosteric modulators AMP and the glycogen-mimic cyclodextrin, both in the phosphorylated (4.05 Å) and non-phosphorylated (4.60 Å) state. In addition, we have solved a 2.95 Å structure of the human kinase domain (KD) bound to the adjacent autoinhibitory domain (AID) and have performed extensive biochemical and mutational studies. Altogether, these studies illustrate an underlying mechanism of allosteric AMPK modulation by AMP and glycogen, whose binding changes the equilibria between alternate AID (AMP) and carbohydrate-binding module (glycogen) interactions.

  10. Structural basis of AMPK regulation by adenine nucleotides and glycogen

    DOE PAGESBeta

    Li, Xiaodan; Wang, Lili; Zhou, X. Edward; Ke, Jiyuan; de Waal, Parker W.; Gu, Xin; Tan, M. H. Eileen; Wang, Dongye; Wu, Donghai; Xu, H. Eric; et al

    2014-11-21

    AMP-activated protein kinase (AMPK) is a central cellular energy sensor and regulator of energy homeostasis, and a promising drug target for the treatment of diabetes, obesity, and cancer. Here we present low-resolution crystal structures of the human α1β2γ1 holo-AMPK complex bound to its allosteric modulators AMP and the glycogen-mimic cyclodextrin, both in the phosphorylated (4.05 Å) and non-phosphorylated (4.60 Å) state. In addition, we have solved a 2.95 Å structure of the human kinase domain (KD) bound to the adjacent autoinhibitory domain (AID) and have performed extensive biochemical and mutational studies. Altogether, these studies illustrate an underlying mechanism of allostericmore » AMPK modulation by AMP and glycogen, whose binding changes the equilibria between alternate AID (AMP) and carbohydrate-binding module (glycogen) interactions.« less

  11. A fuselage/tank structure study for actively cooled hypersonic cruise vehicles: Structural analysis

    NASA Technical Reports Server (NTRS)

    Baker, A. H.

    1975-01-01

    The effects of fuselage cross-section (circular and elliptical) and structural arrangement (integral and nonintegral tanks) on the performance of actively cooled hypersonic cruise vehicles was evaluated. It was found that integrally machined stiffening of the tank walls, while providing the most weight-efficient use of materials, results in higher production costs. Fatigue and fracture mechanics appeared to have little effect on the weight of the three study aircraft. The need for thermal strain relief through insulation is discussed. Aircraft size and magnitude of the internal pressure are seen to be significant factors in tank design.

  12. Emulation to simulate low resolution atmospheric data

    SciTech Connect

    Hebbur Venkata Subba Rao, Vishwas; Archibald, Richard K; Evans, Katherine J

    2012-08-01

    Climate simulations require significant compute power, they are complex and therefore it is time consuming to simulate them. We have developed an emulator to simulate unknown climate datasets. The emulator uses stochastic collocation and multi-dimensional in- terpolation to simulate the datasets. We have used the emulator to determine various physical quantities such as temperature, short and long wave cloud forcing, zonal winds etc. The emulation gives results which are very close to those obtained by simulations. The emulator was tested on 2 degree atmospheric datasets. The work evaluates the pros and cons of evaluating the mean first and inter- polating and vice versa. To determine the physical quantities, we have assumed them to be a function of time, longitude, latitude and a random parameter. We have looked at parameters that govern high stable clouds, low stable clouds, timescale for convection etc. The emulator is especially useful as it requires negligible compute times when compared to the simulation itself.

  13. Analysis of low resolution mass spectra

    NASA Technical Reports Server (NTRS)

    Babst, R. W.; Shapiro, H.

    1971-01-01

    Computer program determines gas constituents from measurements of mass/peak-height spectrum from residual gas analyzer. Applications of program include residual gas analysis for work in space environmental simulators, space environment contamination, and air pollution monitoring.

  14. Structural Studies on a Glucosamine/Glucosaminide N-Acetyltransferase.

    PubMed

    Dopkins, Brandon J; Tipton, Peter A; Thoden, James B; Holden, Hazel M

    2016-08-16

    Glucosamine/glucosaminide N-acetyltransferase or GlmA catalyzes the transfer of an acetyl group from acetyl CoA to the primary amino group of glucosamine. The enzyme from Clostridium acetobutylicum is thought to be involved in cell wall rescue. In addition to glucosamine, GlmA has been shown to function on di- and trisaccharides of glucosamine as well. Here we present a structural and kinetic analysis of the enzyme. For this investigation, eight structures were determined to resolutions of 2.0 Å or better. The overall three-dimensional fold of GlmA places it into the tandem GNAT superfamily. Each subunit of the dimer folds into two distinct domains which exhibit high three-dimensional structural similarity. Whereas both domains bind acetyl CoA, it is the C-terminal domain that is catalytically competent. On the basis of the various structures determined in this investigation, two amino acid residues were targeted for further study: Asp 287 and Tyr 297. Although their positions in the active site suggested that they may play key roles in catalysis by functioning as active site bases and acids, respectively, this was not borne out by characterization of the D287N and Y297F variants. The kinetic properties revealed that both residues were important for substrate binding but had no critical roles as acid/base catalysts. Kinetic analyses also indicated that GlmA follows an ordered mechanism with acetyl CoA binding first followed by glucosamine. The product N-acetylglucosamine is then released prior to CoA. The investigation described herein provides significantly new information on enzymes belonging to the tandem GNAT superfamily.

  15. Structural Studies on a Glucosamine/Glucosaminide N-Acetyltransferase.

    PubMed

    Dopkins, Brandon J; Tipton, Peter A; Thoden, James B; Holden, Hazel M

    2016-08-16

    Glucosamine/glucosaminide N-acetyltransferase or GlmA catalyzes the transfer of an acetyl group from acetyl CoA to the primary amino group of glucosamine. The enzyme from Clostridium acetobutylicum is thought to be involved in cell wall rescue. In addition to glucosamine, GlmA has been shown to function on di- and trisaccharides of glucosamine as well. Here we present a structural and kinetic analysis of the enzyme. For this investigation, eight structures were determined to resolutions of 2.0 Å or better. The overall three-dimensional fold of GlmA places it into the tandem GNAT superfamily. Each subunit of the dimer folds into two distinct domains which exhibit high three-dimensional structural similarity. Whereas both domains bind acetyl CoA, it is the C-terminal domain that is catalytically competent. On the basis of the various structures determined in this investigation, two amino acid residues were targeted for further study: Asp 287 and Tyr 297. Although their positions in the active site suggested that they may play key roles in catalysis by functioning as active site bases and acids, respectively, this was not borne out by characterization of the D287N and Y297F variants. The kinetic properties revealed that both residues were important for substrate binding but had no critical roles as acid/base catalysts. Kinetic analyses also indicated that GlmA follows an ordered mechanism with acetyl CoA binding first followed by glucosamine. The product N-acetylglucosamine is then released prior to CoA. The investigation described herein provides significantly new information on enzymes belonging to the tandem GNAT superfamily. PMID:27348258

  16. A DFT study on structural, vibrational properties, and quasiparticle band structure of solid nitromethane.

    PubMed

    Appalakondaiah, S; Vaitheeswaran, G; Lebègue, S

    2013-05-14

    We report a detailed theoretical study of the structural and vibrational properties of solid nitromethane using first principles density functional calculations. The ground state properties were calculated using a plane wave pseudopotential code with either the local density approximation, the generalized gradient approximation, or with a correction to include van der Waals interactions. Our calculated equilibrium lattice parameters and volume using a dispersion correction are found to be in reasonable agreement with the experimental results. Also, our calculations reproduce the experimental trends in the structural properties at high pressure. We found a discontinuity in the bond length, bond angles, and also a weakening of hydrogen bond strength in the pressure range from 10 to 12 GPa, picturing the structural transition from phase I to phase II. Moreover, we predict the elastic constants of solid nitromethane and find that the corresponding bulk modulus is in good agreement with experiments. The calculated elastic constants show an order of C11> C22 > C33, indicating that the material is more compressible along the c-axis. We also calculated the zone center vibrational frequencies and discuss the internal and external modes of this material under pressure. From this, we found the softening of lattice modes around 8-11 GPa. We have also attempted the quasiparticle band structure of solid nitromethane with the G0W0 approximation and found that nitromethane is an indirect band gap insulator with a value of the band gap of about 7.8 eV with G0W0 approximation. Finally, the optical properties of this material, namely the absorptive and dispersive part of the dielectric function, and the refractive index and absorption spectra are calculated and the contribution of different transition peaks of the absorption spectra are analyzed. The static dielectric constant and refractive indices along the three inequivalent crystallographic directions indicate that this material

  17. Hydrothermal chemistry, structures, and luminescence studies of alkali hafnium fluorides.

    PubMed

    Underwood, Christopher C; McMillen, Colin D; Chen, Hongyu; Anker, Jeffery N; Kolis, Joseph W

    2013-01-01

    This paper describes the hydrothermal chemistry of alkali hafnium fluorides, including the synthesis and structural characterization of five new alkali hafnium fluorides. Two ternary alkali hafnium fluorides are described: Li(2)HfF(6) in space group P31m with a = 4.9748(7) Å and c = 4.6449(9) Å and Na(5)Hf(2)F(13) in space group C2/m with a = 11.627(2) Å, b = 5.5159(11) Å, and c = 8.4317(17) Å. Three new alkali hafnium oxyfluorides are also described: two fluoroelpasolites, K(3)HfOF(5) and (NH(4))(3)HfOF(5), in space group Fm3m with a = 8.9766(10) and 9.4144(11) Å, respectively, and K(2)Hf(3)OF(12) in space group R3m with a = 7.6486(11) Å and c = 28.802(6) Å. Infrared (IR) spectra were obtained for the title solids to confirm the structure solutions. Comparison of these materials was made based on their structures and synthesis conditions. The formation of these species in hydrothermal fluids appears to be dependent upon both the concentration of the alkali fluoride mineralizer solution and the reaction temperature. Both X-ray and visible fluorescence studies were conducted on compounds synthesized in this study and showed that fluorescence was affected by a variety of factors, such as alkali metal size, the presence/absence of oxygen in the compound, and the coordination environment of Hf(4+).

  18. Magnetization reversal studies in structurally tailored cobalt nanowires

    NASA Astrophysics Data System (ADS)

    Kaur, Daljit; Chaudhary, Sujeet; Pandya, Dinesh K.; Gupta, Rekha; Kotnala, R. K.

    2013-10-01

    Cobalt nanowires (NWs) having hcp crystal structure are structurally tailored for different preferred orientations (PO) of (0002), (101¯0), (112¯0) and (101¯1) by varying bath temperature and bath concentration in commercially available 50 nm pore diameter polycarbonate (PCT) and 20 nm pore diameter anodic alumina (AAO) membranes. The magnetization studies show orientation dependent competition of magneto-crystalline anisotropy with shape anisotropy. The large effective anisotropy, Keff (along longitudinal direction) of 1.42×106 erg/cc is observed in (0002) PO NWs, which changes sign (-1.50×106 erg/cc) in (101¯0) PO NWs. The angular dependence of coercivity [HC(θ)] in (0002) oriented Co NWs exhibits a non-monotonic behavior in both the 50 nm and 20 nm samples. The fitting of HC(θ) data reveals that the magnetization reversal mechanism initially takes place by curling and subsequently changes to coherent rotation mode after a certain transition angle, which is higher in case of denser NW array. This increase in transition angle can be attributed to the increased magneto-static interactions in the AAO membrane array having 103 times higher NW areal-density than that in PCT membrane array. Role of dipolar/ magnetostatic anisotropy studied by varying NW areal-density and NW diameter.

  19. Nucleon Resonance Structure Studies via Exclusive KY Electroproduction

    NASA Astrophysics Data System (ADS)

    Carman, Daniel S.

    2016-10-01

    Studying the structure of excited nucleon states employing the electroproduction of exclusive reactions is an important avenue for exploring the nature of the non-perturbative strong interaction. The electrocouplings of N^* states in the mass range below 1.8 GeV have been determined from analyses of CLAS π N, η N, and π π N data. This work has made it clear that consistent results from independent analyses of several exclusive channels with different couplings and non-resonant backgrounds but the same N^* electro-excitation amplitudes, is essential to have confidence in the extracted results. In terms of hadronic coupling, many high-lying N^* states preferentially decay through the π π N channel instead of π N. Data from the KY channels will therefore be critical to provide an independent analysis to compare the extracted electrocouplings for the high-lying N^* states against those determined from the π N and π π {N} channels. A program to study excited N^* state structure in both non-strange and strange exclusive electroproduction channels using CLAS12 will measure differential cross sections and polarization observables to be used as input to extract the γ _v{it{NN}}^* electrocoupling amplitudes for the most prominent N^* states in the range of invariant energy W up 3 GeV in the virtually unexplored domain of momentum transfers Q^2 up to 12 GeV^2.

  20. Computational study of hydroxyapatite structures, properties and defects

    NASA Astrophysics Data System (ADS)

    Bystrov, V. S.; Coutinho, J.; Bystrova, A. V.; Dekhtyar, Yu D.; Pullar, R. C.; Poronin, A.; Palcevskis, E.; Dindune, A.; Alkan, B.; Durucan, C.; Paramonova, E. V.

    2015-03-01

    Hydroxyapatite (HAp) was studied from a first principle approach using the local density approximation (LDA) method in AIMPRO code, in combination with various quantum mechanical (QM) and molecular mechanical (MM) methods from HypemChem 7.5/8.0. The data obtained were used for studies of HAp structures, the physical properties of HAp (density of electronic states—DOS, bulk modulus etc) and defects in HAp. Computed data confirmed that HAp can co-exist in different phases—hexagonal and monoclinic. Ordered monoclinic structures, which could reveal piezoelectric properties, are of special interest. The data obtained allow us to characterize the properties of the following defects in HAp: O, H and OH vacancies; H and OH interstitials; substitutions of Ca by Mg, Sr, Mn or Se, and P by Si. These properties reveal the appearance of additional energy levels inside the forbidden zone, shifts of the top of the valence band or the bottom of the conduction band, and subsequent changes in the width of the forbidden zone. The data computed are compared with other known data, both calculated and experimental, such as alteration of the electron work functions under different influences of various defects and treatments, obtained by photoelectron emission. The obtained data are very useful, and there is an urgent need for such analysis of modified HAp interactions with living cells and tissues, improvement of implant techniques and development of new nanomedical applications.

  1. Nucleon resonance structure studies via exclusive KY electroproduction

    DOE PAGESBeta

    Carman, Daniel S.

    2016-06-16

    Studying the structure of excited nucleon states employing the electroproduction of exclusive reactions is an important avenue for exploring the nature of the non-perturbative strong interaction. The electrocouplings ofmore » $N^*$ states in the mass range below 1.8~GeV have been determined from analyses of CLAS $$\\pi N$$, $$\\eta N$$, and $$\\pi \\pi N$$ data. This work has made it clear that consistent results from independent analyses of several exclusive channels with different couplings and non-resonant backgrounds but the same $N^*$ electro excitation amplitudes, is essential to have confidence in the extracted results. In terms of hadronic coupling, many high-lying $N^*$ states preferentially decay through the $$\\pi \\pi N$$ channel instead of $$\\pi N$$. Data from the $KY$ channels will therefore be critical to provide an independent analysis to compare the extracted electrocouplings for the high-lying $N^*$ states against those determined from the $$\\pi N$$ and $$\\pi \\pi N$$ channels. Lastly, a program to study excited $N^*$ state structure in both non-strange and strange exclusive electroproduction channels using CLAS12 will measure differential cross sections and polarization observables to be used as input to extract the $$\\gamma_vNN^*$$ electrocoupling amplitudes for the most prominent $N^*$ states in the range of invariant energy $W$ up 3~GeV in the virtually unexplored domain of momentum transfers $Q^2$ up to 12~GeV$^2$.« less

  2. Deployable-erectable trade study for space station truss structures

    NASA Technical Reports Server (NTRS)

    Mikulas, M. M., Jr.; Wright, A. S., Jr.; Bush, H. G.; Watson, J. J.; Dean, E. B.; Twigg, L. T.; Rhodes, M. D.; Cooper, P. A.; Dorsey, J. T.; Lake, M. S.

    1985-01-01

    The results of a trade study on truss structures for constructing the space station are presented. Although this study was conducted for the reference gravity gradient space station, the results are generally applicable to other configurations. The four truss approaches for constructing the space station considered in this paper were the 9 foot single fold deployable, the 15 foot erectable, the 10 foot double fold tetrahedral, and the 15 foot PACTRUSS. The primary rational for considering a 9 foot single-fold deployable truss (9 foot is the largest uncollapsed cross-section that will fit in the Shuttle cargo bay) is that of ease of initial on-orbit construction and preintegration of utility lines and subsystems. The primary rational for considering the 15 foot erectable truss is that the truss bay size will accommodate Shuttle size payloads and growth of the initial station in any dimension is a simple extension of the initial construction process. The primary rational for considering the double-fold 10 foot tetrahedral truss is that a relatively large amount of truss structure can be deployed from a single Shuttle flight to provide a large number of nodal attachments which present a pegboard for attaching a wide variety of payloads. The 15 foot double-fold PACTRUSS was developed to incorporate the best features of the erectable truss and the tetrahedral truss.

  3. Nucleon Resonance Structure Studies via Exclusive KY Electroproduction

    NASA Astrophysics Data System (ADS)

    Carman, Daniel S.

    2016-06-01

    Studying the structure of excited nucleon states employing the electroproduction of exclusive reactions is an important avenue for exploring the nature of the non-perturbative strong interaction. The electrocouplings of N^* states in the mass range below 1.8 GeV have been determined from analyses of CLAS π N , η N , and π π N data. This work has made it clear that consistent results from independent analyses of several exclusive channels with different couplings and non-resonant backgrounds but the same N^* electro-excitation amplitudes, is essential to have confidence in the extracted results. In terms of hadronic coupling, many high-lying N^* states preferentially decay through the π π N channel instead of π N . Data from the KY channels will therefore be critical to provide an independent analysis to compare the extracted electrocouplings for the high-lying N^* states against those determined from the π N and π π {N} channels. A program to study excited N^* state structure in both non-strange and strange exclusive electroproduction channels using CLAS12 will measure differential cross sections and polarization observables to be used as input to extract the γ _v{{NN}}^* electrocoupling amplitudes for the most prominent N^* states in the range of invariant energy W up 3 GeV in the virtually unexplored domain of momentum transfers Q^2 up to 12 GeV^2.

  4. Electronic Structure Study of Singlet Fission in Tetracene Derivatives.

    PubMed

    Casanova, David

    2014-01-14

    A detailed theoretical study of the singlet fission process in tetracene and two of its derivatives, that is 5,12-diphenyltetracene (DPT) and rubrene, is presented. This work aims to unravel the intricacies and the differences of their singlet fission mechanism by means of electronic structure calculations using molecular and cluster models and a variety of computational tools. Although the electronic structure at the molecular level is very similar for the three compounds, their different crystal packing has important consequences in their ability to produce two triplet states from a single exciton. The results obtained indicate that the lowest singlet is found to delocalize at least over seven molecules. Computed relative energies rule out the presence of charge transfer (CT) states as intermediates in a two-step mechanism in all cases. On the other hand, CT states do play a role as mediators, specially in tetracene. They decisively participate in the coupling between single and multiexcitonic states through second-order contributions. Finally, the present study pinpoints that the transition from the optically allowed exciton to the dark multiexciton state might be facilitated by intramolecular motion toward the lowest excited singlet geometry. PMID:26579913

  5. Studying Atomic Structures by Aberration-Corrected Transmission Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Urban, Knut W.

    2008-07-01

    Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations.

  6. Studying atomic structures by aberration-corrected transmission electron microscopy.

    PubMed

    Urban, Knut W

    2008-07-25

    Seventy-five years after its invention, transmission electron microscopy has taken a great step forward with the introduction of aberration-corrected electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at atomic-scale resolution. These new possibilities are meeting the growing demand of nanosciences and nanotechnology for the atomic-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy-loss spectrometers, the new instruments allow studies not only of structure but also of elemental composition and chemical bonding. The energy resolution is about 100 milli-electron volts, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mechanical computer calculations. PMID:18653874

  7. Control Of Flexible Structures-2 (COFS-2) flight control, structure and gimbal system interaction study

    NASA Technical Reports Server (NTRS)

    Fay, Stanley; Gates, Stephen; Henderson, Timothy; Sackett, Lester; Kirchwey, Kim; Stoddard, Isaac; Storch, Joel

    1988-01-01

    The second Control Of Flexible Structures Flight Experiment (COFS-2) includes a long mast as in the first flight experiment, but with the Langley 15-m hoop column antenna attached via a gimbal system to the top of the mast. The mast is to be mounted in the Space Shuttle cargo bay. The servo-driven gimbal system could be used to point the antenna relative to the mast. The dynamic interaction of the Shuttle Orbiter/COFS-2 system with the Orbiter on-orbit Flight Control System (FCS) and the gimbal pointing control system has been studied using analysis and simulation. The Orbiter pointing requirements have been assessed for their impact on allowable free drift time for COFS experiments. Three fixed antenna configurations were investigated. Also simulated was Orbiter attitude control behavior with active vernier jets during antenna slewing. The effect of experiment mast dampers was included. Control system stability and performance and loads on various portions of the COFS-2 structure were investigated. The study indicates possible undesirable interaction between the Orbiter FCS and the flexible, articulated COFS-2 mast/antenna system, even when restricted to vernier reaction jets.

  8. Characterization of adhesive from oysters: A structural and compositional study

    NASA Astrophysics Data System (ADS)

    Alberts, Erik

    The inability for man-made adhesives to set in wet or humid environments is an ongoing challenging the design of biomedical and marine adhesive materials. However, we see that nature has already overcome this challenge. Mussels, barnacles, oysters and sandcastle worms all have unique mechanisms by which they attach themselves to surfaces. By understanding what evolution has already spent millions of years perfecting, we can design novel adhesive materials inspired by nature's elegant designs. The well-studied mussel is currently the standard for design of marine inspired biomimetic polymers. In the work presented here, we aim to provide new insights into the adhesive produced by the eastern oyster, Crassostrea virginica. Unlike the mussel, which produces thread-like plaques comprised of DOPA containing-protein, the oyster secretes an organic-inorganic hybrid adhesive as it settles and grows onto a surface. This form of adhesion renders the oyster to be permanently fixed in place. Over time, hundreds of thousands of oyster grow and agglomerate to form extensive reef structures. These reefs are not only essential to survival of the oyster, but are also vital to intertidal ecosystems. While the shell of the oyster has been extensively studied, curiously, only a few conflicting insights have been made into the nature of the adhesive and contact zone between shell and substrate, and even lesfs information has been ascertained on organic and inorganic composition. In this work, we provide microscopy and histochemical studies to characterize the structure and composition of the adhesive, using oyster in the adult and juvenile stages of life. Preliminary work on extracting and characterizing organic components through collaborative help with solid-state NMR (SSNMR) and proteomics are also detailed here. We aim to provide a full, comprehensive characterization of oyster adhesive so that in the future, we may apply what we learn to the design of new materials.

  9. Angiogenesis of buffalo choroid plexuses: structural and immunocytochemical study.

    PubMed

    Scala, Gaetano; Maruccio, Lucianna

    2012-08-01

    Mammalian choroid plexuses (CPs) are vascularized structures involved in numerous exchange processes that supply nutrients and hormones to the brain, and that remove deleterious compounds and metabolites from the brain. Studies in the adult Mediterranean buffalo have investigated the morphology of CPs using histochemical and immunohistochemical techniques. To date, however, there have been no studies conducted on ruminants regarding this removal process which serves to repair functional vascular damage in the CPs. Each of these vascular repair processes is a very complex and none of these has not yet been completely understood. Then, the aim of the present study is to investigate the morphological processes during angiogenesis in the CPs of healthy adult buffaloes, utilizing transmission electron microscopy (TEM), scanning electron microscopy (SEM), and immunogold-labeling SEM analysis (biomarkers: angiopoietin-2 [Ang-2], vascular endothelial growth factor receptor-3 [VEGFR-3], and CD133). At TEM, the inner surface of the blood capillaries sometimes showed pillar-like cells, which in contact with endothelial cells formed prominences, which in turn formed neo-blood capillaries. With immunogold-labeling SEM analysis, the CP blood capillaries showed Ang-2 and VEGF-3, respectively, in positive particles and spheroid formations. In addition, the external surface of the blood capillaries showed spheroid formations that originated from the neo-vascular capillaries whose terminals formed a capillary network, positive to CD133. On the basis of these results, the following hypothesis can be made, namely, that these CPs are vascular structures which play a fundamental role in maintaining brain homeostasis and self-repairing of functional vascular damage, independently of the presence of rete mirabile in this species. PMID:22434550

  10. Molecular and Supramolecular Structural Studies on Human Tropoelastin Sequences

    PubMed Central

    Ostuni, Angela; Bochicchio, Brigida; Armentano, Maria F.; Bisaccia, Faustino; Tamburro, Antonio M.

    2007-01-01

    One of the unusual properties of elastin is its ability to coacervate, which has been proposed to play an important role in the alignment of monomeric elastin for cross-linking into the polymeric elastin matrix. The temperature at which this transition takes place depends on several factors including protein concentration, ionic strength, and pH. Previously, polypeptide sequences encoded by different exons of the human tropoelastin gene have been analyzed for their ability to coacervate and to self-assemble. Few of them were indeed able to coacervate and only one, that encoded by exon 30 (EX30), gave amyloid fibers. In this article, we report on two chemically synthesized peptides—a decapeptide and an octadecapeptide—whose sequences are contained in the longer EX30 peptide and on a polypeptide (EX1–7) of 125 amino-acid residues corresponding to the sequence coded by the exons 1–7 and on a polypeptide (EX2–7) of 99 amino-acid residues encoded by exons 2–7 of human tropoelastin obtained by recombinant DNA techniques. Molecular and supramolecular structural characterization of these peptides showed that a minimum sequence of ∼20 amino acids is needed to form amyloid fibers in the exon 30-derived peptides. The N-terminal region of mature tropoelastin (EX2–7) gives rise to a coacervate and forms elastinlike fibers, whereas the polypeptide sequence containing the signal peptide (EX1–7) forms mainly amyloid fibers. Circular dichroism spectra show that β-structure is ubiquitous in all the sequences studied, suggesting that the presence of a β-structure is a necessary, although not sufficient, requirement for the appearance of amyloid fibers. PMID:17693470

  11. Theoretical studies in nuclear reactions and nuclear structure

    SciTech Connect

    Not Available

    1992-05-01

    Research in the Maryland Nuclear Theory Group focusses on problems in four basic areas of current relevance. Hadrons in nuclear matter; the structure of hadrons; relativistic nuclear physics and heavy ion dynamics and related processes. The section on hadrons in nuclear matter groups together research items which are aimed at exploring ways in which the properties of nucleons and the mesons which play a role in the nuclear force are modified in the nuclear medium. A very interesting result has been the finding that QCD sum rules supply a new insight into the decrease of the nucleon's mass in the nuclear medium. The quark condensate, which characterizes spontaneous chiral symmetry breaking of the late QCD vacuum, decreases in nuclear matter and this is responsible for the decrease of the nucleon's mass. The section on the structure of hadrons contains progress reports on our research aimed at understanding the structure of the nucleon. Widely different approaches are being studied, e.g., lattice gauge calculations, QCD sum rules, quark-meson models with confinement and other hedgehog models. A major goal of this type of research is to develop appropriate links between nuclear physics and QCD. The section on relativistic nuclear physics represents our continuing interest in developing an appropriate relativistic framework for nuclear dynamics. A Lorentz-invariant description of the nuclear force suggests a similar decrease of the nucleon's mass in the nuclear medium as has been found from QCD sum rules. Work in progress extends previous successes in elastic scattering to inelastic scattering of protons by nuclei. The section on heavy ion dynamics and related processes reports on research into the e{sup +}e{sup {minus}} problem and heavy ion dynamics.

  12. Theoretical studies in nuclear reactions and nuclear structure. Progress report

    SciTech Connect

    Not Available

    1992-05-01

    Research in the Maryland Nuclear Theory Group focusses on problems in four basic areas of current relevance. Hadrons in nuclear matter; the structure of hadrons; relativistic nuclear physics and heavy ion dynamics and related processes. The section on hadrons in nuclear matter groups together research items which are aimed at exploring ways in which the properties of nucleons and the mesons which play a role in the nuclear force are modified in the nuclear medium. A very interesting result has been the finding that QCD sum rules supply a new insight into the decrease of the nucleon`s mass in the nuclear medium. The quark condensate, which characterizes spontaneous chiral symmetry breaking of the late QCD vacuum, decreases in nuclear matter and this is responsible for the decrease of the nucleon`s mass. The section on the structure of hadrons contains progress reports on our research aimed at understanding the structure of the nucleon. Widely different approaches are being studied, e.g., lattice gauge calculations, QCD sum rules, quark-meson models with confinement and other hedgehog models. A major goal of this type of research is to develop appropriate links between nuclear physics and QCD. The section on relativistic nuclear physics represents our continuing interest in developing an appropriate relativistic framework for nuclear dynamics. A Lorentz-invariant description of the nuclear force suggests a similar decrease of the nucleon`s mass in the nuclear medium as has been found from QCD sum rules. Work in progress extends previous successes in elastic scattering to inelastic scattering of protons by nuclei. The section on heavy ion dynamics and related processes reports on research into the e{sup +}e{sup {minus}} problem and heavy ion dynamics.

  13. A statistical study of magnetopause structures: Tangential versus rotational discontinuities

    NASA Astrophysics Data System (ADS)

    Chou, Y.-C.; Hau, L.-N.

    2012-08-01

    A statistical study of the structure of Earth's magnetopause is carried out by analyzing two-year AMPTE/IRM plasma and magnetic field data. The analyses are based on the minimum variance analysis (MVA), the deHoffmann-Teller (HT) frame analysis and the Walén relation. A total of 328 magnetopause crossings are identified and error estimates associated with MVA and HT frame analyses are performed for each case. In 142 out of 328 events both MVA and HT frame analyses yield high quality results which are classified as either tangential-discontinuity (TD) or rotational-discontinuity (RD) structures based only on the Walén relation: Events withSWA ≤ 0.4 (SWA ≥ 0.5) are classified as TD (RD), and rest (with 0.4 < SWA < 0.5) is classified as "uncertain," where SWA refers to the Walén slope. With this criterion, 84% of 142 events are TDs, 12% are RDs, and 4% are uncertain events. There are a large portion of TD events which exhibit a finite normal magnetic field component Bnbut have insignificant flow as compared to the Alfvén velocity in the HT frame. Two-dimensional Grad-Shafranov reconstruction of forty selected TD and RD events show that single or multiple X-line accompanied with magnetic islands are common feature of magnetopause current. A survey plot of the HT velocity associated with TD structures projected onto the magnetopause shows that the flow is diverted at the subsolar point and accelerated toward the dawn and dusk flanks.

  14. Structural and binding studies of SAP-1 protein with heparin.

    PubMed

    Yadav, Vikash K; Mandal, Rahul S; Puniya, Bhanwar L; Kumar, Rahul; Dey, Sharmistha; Singh, Sarman; Yadav, Savita

    2015-03-01

    SAP-1 is a low molecular weight cysteine protease inhibitor (CPI) which belongs to type-2 cystatins family. SAP-1 protein purified from human seminal plasma (HuSP) has been shown to inhibit cysteine and serine proteases and exhibit interesting biological properties, including high temperature and pH stability. Heparin is a naturally occurring glycosaminoglycan (with varied chain length) which interacts with a number of proteins and regulates multiple steps in different biological processes. As an anticoagulant, heparin enhances inhibition of thrombin by the serpin antithrombin III. Therefore, we have employed surface plasmon resonance (SPR) to improve our understanding of the binding interaction between heparin and SAP-1 (protease inhibitor). SPR data suggest that SAP-1 binds to heparin with a significant affinity (KD = 158 nm). SPR solution competition studies using heparin oligosaccharides showed that the binding of SAP-1 to heparin is dependent on chain length. Large oligosaccharides show strong binding affinity for SAP-1. Further to get insight into the structural aspect of interactions between SAP-1 and heparin, we used modelled structure of the SAP-1 and docked with heparin and heparin-derived polysaccharides. The results suggest that a positively charged residue lysine plays important role in these interactions. Such information should improve our understanding of how heparin, present in the reproductive tract, regulates cystatins activity.

  15. X-ray structures and computational studies of several cathinones

    NASA Astrophysics Data System (ADS)

    Nycz, Jacek E.; Malecki, Grzegorz; Zawiazalec, Marcin; Pazdziorek, Tadeusz

    2011-09-01

    2-(Ethylamino)-1-(4-methylphenyl)propan-1-one (shortly named 4-MEC) ( 1a), 1-(1,3-benzodioxol-5-yl)-2-(methylamino)propan-1-one (shortly named methylone or 3,4-methylenedioxymethcathinone) ( 1b), 1-(3,4-dimethylphenyl)-2-(methylamino)propan-1-one ( 1c), 2-methylamino-1-(4-methylphenyl)propan-1-one (shortly named mephedrone; 4-MMC or 4-methylmethcathinone) ( 1d) and 2-(methylamino)-1-phenylbutan-1-one (shortly named buphedrone) ( 1e) and their aminium salts ( 2a-e), are examples of cathinones which were characterized by FTIR, UV-Vis, multinuclear NMR spectroscopy. By single crystal X-ray diffraction method structures of 2a, 2b, 2c and 2d were determined. NMR solution spectra showed readily diagnostic H-1 and C-13 signals from methyl, ethyl, N-methyl or N-ethyl groups. The diastereotopic methylene protons of 1a appear as an ABX 3, and 1e and 2e appear as an ABMX 3 system. The geometries of the studied compounds were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. Electronic spectra were calculated by TDDFT method. In general, the predicted bond lengths and angles are in good agreement with the values based on the X-ray crystal structure data.

  16. Structure-Activity Relationship Study of Hydroxycoumarins and Mushroom Tyrosinase.

    PubMed

    Asthana, Shailendra; Zucca, Paolo; Vargiu, Attilio V; Sanjust, Enrico; Ruggerone, Paolo; Rescigno, Antonio

    2015-08-19

    The structure-activity relationships of four hydroxycoumarins, two with the hydroxyl group on the aromatic ring of the molecule and two with the hydroxyl group replacing hydrogen of the pyrone ring, and their interactions with mushroom tyrosinase were studied. These compounds displayed different behaviors upon action of the enzyme. The two compounds, ar-hydroxylated 6-hydroxycoumarin and 7-hydroxycoumarin, were both weak substrates of the enzyme. Interestingly, in both cases, the product of the catalysis was the 6,7-hydroxycoumarin, although 5,6- and 7,8-isomers could also theoretically be formed. Additionally, both were able to reduce the formation of dopachrome when tyrosinase acted on its typical substrate, L-tyrosine. Although none of the compounds that contained a hydroxyl group on the pyrone ring were substrates of tyrosinase, the 3-hydroxycoumarin was a potent inhibitor of the enzyme, and the 4-hydroxycoumarin was not an inhibitor. These results were compared with those obtained by in silico molecular docking predictions to obtain potentially useful information for the synthesis of new coumarin-based inhibitors that resemble the structure of the 3-hydroxycoumarin.

  17. The study of precision measurement of pelvis spatial structure

    NASA Astrophysics Data System (ADS)

    Ma, Xiang; Ouyang, Jianfei; Qu, Xinghua

    2010-03-01

    Osteometry is fundamental for anthropometry. It provides the key technology and value to the study of palaeoanthropology, medicine, and criminal investigation. The traditional osteometry that has been widely accepted and used since 18th century has no longer met the information demand for modern research and application. It is significant and necessary to create an advanced 3-dimensional osteometry technique for anthropometry. This paper presents a new quick and accurate method to measure human pelvis through mathematical modeling. The pelvis is a complex combination of bones, which consists of three connected parts: hipbones, sacrum, and coccyx. There are over 40 items to be measured for the 1-dimension characteristics. In this paper, a combined measuring technology is developed for pelvis measurement. It uses machine vision systems and a portable measuring arm to obtain key geometry parameters of the pelvis. The mathematics models of the pelvis spatial structure and its parts are created through the process of data collecting, digging, assembling, and modeling. The experiment shows that the proposed technology can meet traditional osteometry and obtain entire 1D geometric parameters of the pelvis, such as maximum breadth and height, diameter of obstetric conjugata, inclination angle, and sakralneigungswinkel, etc. at the same time after modeling. Besides making the measurements above, the proposed technology can measure the geometry characteristics of pelvis and its parts, such as volume, surface area, curvature, and spatial structure, which are almost impossible for traditional technology. The overall measuring error is less than 0.1mm.

  18. Nuclear Structure Studies at the Future FAIR facility

    SciTech Connect

    Rubio, Berta

    2010-04-26

    This article is intended to be an introduction to studies of nuclear structure at the future FAIR facility. It addresses interested readers not necessarily expert in the field. It outlines the physics aims and experiments to be carried out at FAIR in the field of nuclear structure and astrophysics. Starting with a brief description of what can be achieved in experiments with intense, high quality stable beams the article leads the reader to how beams of unstable radioactive nuclei will be produced and exploited at FAIR. The characteristics of the beams from the main separation device, the Super-FRS, are outlined and the limitations they impose on experiment are discussed. The various setups at the three experimental branches associated with the Super-FRS are described. The aims of the various experimental setups, how they complement each other and the physics they will address are all explained. The concept of the r-process of nucleosynthesis is outlined at the beginning and used as a running example of how useful it will be to be able to carry out experiments with beams of short-lived, exotic ions.

  19. A Study of Flexible Composites for Expandable Space Structures

    NASA Technical Reports Server (NTRS)

    Scotti, Stephen J.

    2016-01-01

    Payload volume for launch vehicles is a critical constraint that impacts spacecraft design. Deployment mechanisms, such as those used for solar arrays and antennas, are approaches that have successfully accommodated this constraint, however, providing pressurized volumes that can be packaged compactly at launch and expanded in space is still a challenge. One approach that has been under development for many years is to utilize softgoods - woven fabric for straps, cloth, and with appropriate coatings, bladders - to provide this expandable pressure vessel capability. The mechanics of woven structure is complicated by a response that is nonlinear and often nonrepeatable due to the discrete nature of the woven fiber architecture. This complexity reduces engineering confidence to reliably design and certify these structures, which increases costs due to increased requirements for system testing. The present study explores flexible composite materials systems as an alternative to the heritage softgoods approach. Materials were obtained from vendors who utilize flexible composites for non-aerospace products to determine some initial physical and mechanical properties of the materials. Uniaxial mechanical testing was performed to obtain the stress-strain response of the flexible composites and the failure behavior. A failure criterion was developed from the data, and a space habitat application was used to provide an estimate of the relative performance of flexible composites compared to the heritage softgoods approach. Initial results are promising with a 25% mass savings estimated for the flexible composite solution.

  20. Tooth structure studied using the atomic force microscope

    NASA Astrophysics Data System (ADS)

    Kasas, Sandor; Berdal, Ariane; Celio, Marco R.

    1993-06-01

    We used the atomic force microscope (AFM) to observe structure of the tooth, both rat and human. The rigidity and the surface flatness of thin sections of this mineralized tissue, allow us to attain good resolution with the AFM. As enamel contains uniquely large crystals of hydroxyapatite it can be investigated at high resolution. Tooth enamel and thin slices of undecalcified developing tooth germs from 2 - 12 day old rats were observed, embedded in acrylic resin (Lowicryl K4M). In addition, as orthophosphoric acid is widely used clinically to etch tooth enamel before restoring with composites, we studied its action at pH2 on the tooth surface during 1 hour of exposition. Hydroxyapatite crystals and collagen fibers were seen in the tooth slices observed in air, and the classical structure of the enamel was visible. The etched enamel surface under liquid, showed dramatic differences to that imaged in air. Modifications to the surface were also seen during exposure to the acid.

  1. Kinetic and Structural Studies of Interactions between Glycosaminoglycans and Langerin.

    PubMed

    Zhao, Jing; Liu, Xinyue; Kao, Chelsea; Zhang, Emily; Li, Quanhong; Zhang, Fuming; Linhardt, Robert J

    2016-08-16

    Langerin, a C-type lectin, is expressed in Langerhans cells. It was reported that langerin binds sulfated glycans, which is an important initial step for its role in blocking human immunodeficiency virus (HIV) transmission by capturing HIV pathogens and mediating their internalization into Birbeck granules for their elimination. It is fundamentally important to understand these interactions at the molecular level for the design of new highly specific therapeutic agents for HIV. Surface plasmon resonance (SPR), which allows for the real-time, direct, quantitative analysis of the label-free molecular interactions, has been used successfully for biophysical characterization of glycosaminoglycan (GAG)-protein interactions. In this study, we report kinetics, structural analysis, and the effects of physiological conditions (e.g., pH, salt concentration, and Ca(2+) and Zn(2+)concentrations) on the interactions between GAGs and langerin using SPR. SPR results revealed that langerin binds to heparin with high affinity (KD ∼ 2.4 nM) and the oligosaccharide length required for the interactions is larger than a tetrasaccharide. This heparin/heparan sulfate-binding protein also interacts with other GAGs, including dermatan sulfate, chondroitin sulfates C-E and KS. In addition, liquid chromatography-mass spectrometry analysis was used to characterize the structure of sulfated glycans that bound to langerin. PMID:27447199

  2. The study of precision measurement of pelvis spatial structure

    NASA Astrophysics Data System (ADS)

    Ma, Xiang; Ouyang, Jianfei; Qu, Xinghua

    2009-12-01

    Osteometry is fundamental for anthropometry. It provides the key technology and value to the study of palaeoanthropology, medicine, and criminal investigation. The traditional osteometry that has been widely accepted and used since 18th century has no longer met the information demand for modern research and application. It is significant and necessary to create an advanced 3-dimensional osteometry technique for anthropometry. This paper presents a new quick and accurate method to measure human pelvis through mathematical modeling. The pelvis is a complex combination of bones, which consists of three connected parts: hipbones, sacrum, and coccyx. There are over 40 items to be measured for the 1-dimension characteristics. In this paper, a combined measuring technology is developed for pelvis measurement. It uses machine vision systems and a portable measuring arm to obtain key geometry parameters of the pelvis. The mathematics models of the pelvis spatial structure and its parts are created through the process of data collecting, digging, assembling, and modeling. The experiment shows that the proposed technology can meet traditional osteometry and obtain entire 1D geometric parameters of the pelvis, such as maximum breadth and height, diameter of obstetric conjugata, inclination angle, and sakralneigungswinkel, etc. at the same time after modeling. Besides making the measurements above, the proposed technology can measure the geometry characteristics of pelvis and its parts, such as volume, surface area, curvature, and spatial structure, which are almost impossible for traditional technology. The overall measuring error is less than 0.1mm.

  3. Human LDL Structural Diversity Studied by IR Spectroscopy

    PubMed Central

    Fernández-Higuero, José A.; Salvador, Ana M.; Martín, Cesar; Milicua, José Carlos G.; Arrondo, José L. R.

    2014-01-01

    Lipoproteins are responsible for cholesterol traffic in humans. Low density lipoprotein (LDL) delivers cholesterol from liver to peripheral tissues. A misleading delivery can lead to the formation of atherosclerotic plaques. LDL has a single protein, apoB-100, that binds to a specific receptor. It is known that the failure associated with a deficient protein-receptor binding leads to plaque formation. ApoB-100 is a large single lipid-associated polypeptide difficulting the study of its structure. IR spectroscopy is a technique suitable to follow the different conformational changes produced in apoB-100 because it is not affected by the size of the protein or the turbidity of the sample. We have analyzed LDL spectra of different individuals and shown that, even if there are not big structural changes, a different pattern in the intensity of the band located around 1617 cm−1 related with strands embedded in the lipid monolayer, can be associated with a different conformational rearrangement that could affect to a protein interacting region with the receptor. PMID:24642788

  4. Molecular structure-adsorption study on current textile dyes.

    PubMed

    Örücü, E; Tugcu, G; Saçan, M T

    2014-01-01

    This study was performed to investigate the adsorption of a diverse set of textile dyes onto granulated activated carbon (GAC). The adsorption experiments were carried out in a batch system. The Langmuir and Freundlich isotherm models were applied to experimental data and the isotherm constants were calculated for 33 anthraquinone and azo dyes. The adsorption equilibrium data fitted more adequately to the Langmuir isotherm model than the Freundlich isotherm model. Added to a qualitative analysis of experimental results, multiple linear regression (MLR), support vector regression (SVR) and back propagation neural network (BPNN) methods were used to develop quantitative structure-property relationship (QSPR) models with the novel adsorption data. The data were divided randomly into training and test sets. The predictive ability of all models was evaluated using the test set. Descriptors were selected with a genetic algorithm (GA) using QSARINS software. Results related to QSPR models on the adsorption capacity of GAC showed that molecular structure of dyes was represented by ionization potential based on two-dimensional topological distances, chromophoric features and a property filter index. Comparison of the performance of the models demonstrated the superiority of the BPNN over GA-MLR and SVR models. PMID:25529487

  5. Oxidation of rubrene thin films: an electronic structure study.

    PubMed

    Sinha, Sumona; Wang, C-H; Mukherjee, M; Mukherjee, T; Yang, Y-W

    2014-12-30

    The performances of organic semiconductor devices are crucially linked with their stability at the ambient atmosphere. The evolution of electronic structures of 20 nm thick rubrene films exposed to ambient environment with time has been studied by UV and X-ray photoemission spectroscopy (UPS and XPS), near edge X-ray absorption fine structure (NEXAFS) spectroscopy, and density functional theory (DFT). XPS, NEXAFS data, and DFT calculated values suggest the formation of rubrene-epoxide and rubrene-endoperoxide through reaction of tetracene backbone with oxygen of ambient environment. Angle dependent XPS measurement indicates that the entire probed depth of the films reacts with oxygen by spending only about 120 min in ambient environment. The HOMO peak of pristine rubrene films almost disappears by exposure of 120 min to ambient environment. The evolution of the valence band (occupied states) and NEXAFS (unoccupied states) spectra indicates that the films become more insulating with exposure as the HOMO-LUMO gap increases on oxidation. Oxygen induced chemical reaction completely destroys the delocalized nature of the electron distribution in the tetracene backbone of rubrene. The results are relevant to the performance and reliability of rubrene based devices in the environment. PMID:25383646

  6. Combining skin texture and facial structure for face identification

    NASA Astrophysics Data System (ADS)

    Manoni, R. E.; Canosa, R. L.

    2012-03-01

    Current face identification systems are not robust enough to accurately identify the same individual in different images with changes in head pose, facial expression, occlusion, length of hair, illumination, aging, etc. This is especially a problem for facial images that are captured using low resolution video cameras or webcams. This paper introduces a new technique for facial identification in low resolution images that combines facial structure with skin texture to accommodate changes in lighting and head pose. Experiments using this new technique show that combining facial structure features with skin texture features results in a facial identification system for low resolution images that is more robust to pose and illumination conditions than either technique used alone.

  7. Structure-Activity Relationship Study of Novel Peptoids That Mimic the Structure of Antimicrobial Peptides

    PubMed Central

    Mojsoska, Biljana; Zuckermann, Ronald N.

    2015-01-01

    The constant emergence of new bacterial strains that resist the effectiveness of marketed antimicrobials has led to an urgent demand for and intensive research on new classes of compounds to combat bacterial infections. Antimicrobial peptoids comprise one group of potential candidates for antimicrobial drug development. The present study highlights a library of 22 cationic amphipathic peptoids designed to target bacteria. All the peptoids share an overall net charge of +4 and are 8 to 9 residues long; however, the hydrophobicity and charge distribution along the abiotic backbone varied, thus allowing an examination of the structure-activity relationship within the library. In addition, the toxicity profiles of all peptoids were assessed in human red blood cells (hRBCs) and HeLa cells, revealing the low toxicity exerted by the majority of the peptoids. The structural optimization also identified two peptoid candidates, 3 and 4, with high selectivity ratios of 4 to 32 and 8 to 64, respectively, and a concentration-dependent bactericidal mode of action against Gram-negative Escherichia coli. PMID:25941221

  8. Structural considerations on acridine/acridinium derivatives: Synthesis, crystal structure, Hirshfeld surface analysis and computational studies

    NASA Astrophysics Data System (ADS)

    Wera, Michał; Storoniak, Piotr; Serdiuk, Illia E.; Zadykowicz, Beata

    2016-02-01

    This article describes a detailed study of the molecular packing and intermolecular interactions in crystals of four derivatives of acridine, i.e. 9-methyl-, 9-ethyl, 9-bromomethyl- and 9-piperidineacridine (1, 2, 3 and 4, respectively) and three 10-methylacridinium salts containing the trifluoromethanesulphonate anion and 9-vinyl-, 9-bromomethyl, and 9-phenyl-10-methylacridinium cations (5, 6 and 7, respectively). The crystal structures of all of the compounds are stabilized by long-range electrostatic interactions, as well as by a network of short-range C-HṡṡṡO (in hydrates and salts 3 and 5-7, respectively), C-Hṡṡṡπ, π-π, C-Fṡṡṡπ and S-Oṡṡṡπ (in salts 5-7) interactions. Hirshfeld surface analysis shows that various intermolecular contacts play an important role in the crystal packing, graphically exhibiting the differences in spatial arrangements of the acridine/acridinium derivatives under scrutiny here. Additionally, computational methods have been used to compare the intermolecular interactions in the crystal structures of the investigated compounds. Computations have confirmed the great contribution of dispersive interactions for crystal lattice stability in the case of 9-substituted acridine and electrostatic interactions for the crystal lattice stability in the case of 9-substituted 10-methylacridinium trifluoromethanesulphonates. The value of crystal lattice energy and the electrostatic contribution in the crystal lattice energy of monohydrated acridine derivatives have confirmed that these compounds have behave as acridinium derivatives.

  9. Studies on structural properties of clay magnesium ferrite nano composite

    SciTech Connect

    Kaur, Manpreet Singh, Mandeep; Jeet, Kiran Kaur, Rajdeep

    2015-08-28

    Magnesium ferrite-bentonite clay composite was prepared by sol-gel combustion method employing citric acid as complexing agent and fuel. The effect of clay on the structural properties was studied with X-ray diffraction (XRD), Fourier transform infrared (FT-IR) Spectroscopy, Scanning electron microscopy (SEM), SEM- Energy dispersive Spectroscope (EDS) and BET surface area analyzer. Decrease in particle size and density was observed on addition of bentonite clay. The BET surface area of nano composite containing just 5 percent clay was 74.86 m{sup 2}/g. Whereas porosity increased from 40.5 per cent for the pure magnesium ferrite to 81.0 percent in the composite showing that nano-composite has potential application as an adsorbent.

  10. Structural and optical studies of CuO nanostructures

    SciTech Connect

    Chand, Prakash Gaur, Anurag Kumar, Ashavani

    2014-04-24

    In the present study, copper oxide (CuO) nanostructures have been synthesized at 140 °C for different aging periods, 1, 24, 48 and 96 hrs by hydrothermal method to investigate their effects on structural and optical properties. The X-ray diffractometer (XRD) pattern indicates the pure phase formation of CuO and the particle size, calculated from XRD data, has been found to be increasing from 21 to 36 nm for the samples synthesized at different aging periods. Field emission scanning electron microscope (FESEM) analysis also shows that the average diameter and length of these rectangular nano flakes increases with increasing the aging periods. Moreover Raman spectrums also confirm the phase formation of CuO. The optical band gaps calculated through UV-visible spectroscopy are found to be decreasing from 2.92 to 2.69 eV with increase in aging periods, 1 to 96 hrs, respectively.

  11. Studies of the correlation of electrode kinetics with molecular structure

    NASA Astrophysics Data System (ADS)

    Weaver, M. J.

    1983-06-01

    The overall objective is to develop our understanding of the connections between the kinetics and mechanisms of heterogeneous electron-transfer reactions at metal-electrolyte interfaces and the molecular structure of the reactant and the interfacial region. We have chiefly focussed attention on transition-metal redox couples, especially Co(III)/(II), Cr(III)/(II), and Ru(III)/(II) containing adsorbing inorganic and organic ligands at a number of electrocatalytic solid surfaces, especially silver, platinum, and gold, as well as at mercury electrodes. By combining electrochemical kinetic and reactant adsorption thermodynamic measurements, along with in situ vibrational spectroscopic studies using Surface-Enhanced Raman Scattering (SERS), the various catalytic influences exerted by the metal interface upon the energetics of electrode reactions have been probed in detail.

  12. Material and structural studies of metal and polymer matrix composites

    NASA Technical Reports Server (NTRS)

    Signorelli, R. A.; Serafini, T. T.; Johns, R. H.

    1972-01-01

    The application of fiber composites to aeronautical and space vehicle systems indicates the following: It appears quite probable that resin/fiber composites can be developed for service at 315 C for several thousand hours and at 370 C for a few hundred hours. The retention of resin/fiber strength at these high temperatures can be achieved by modifying the polymer molecular structure or by developing new processing techniques, or both. Carbon monofilament with attractive strength values has been produced and fabrication studies to reinforce aluminum with such monofilaments have been initiated. Refractory wire-superalloy composites have demonstrated sufficiently high strength and impact values to suggest that they have potential for application to turbine blades at temperatures to 1200 C and above.

  13. Structural studies in columnar basalts from crystallographic and magnetic fabrics

    NASA Astrophysics Data System (ADS)

    Tiphaine, Boiron; Jérôme, Bascou; Pierre, Camps; Eric, Ferre; Claire, Maurice; Bernard, Guy; Marie-Christine, Gerbe

    2010-05-01

    The purpose of this study is to better characterize the columnar and the associated microstructure development in basalt flows. The thermal contraction (O'Reilly, 1879) is the main hypothesis to explain the columnar formation. However, neither the structures which appear in basalt flow constituted of three levels (Tomkeieff, 1940) nor circular and radial structures within the prisms (for which weathering nor fracturing can account for) can be explained by the thermal contraction theory alone. An early structuring process during solidification (Guy and Le Coze, 1990) could play for a part that must be discussed (Guy, 2010). We studied two recent basalt flows (75 000 years) from the French Massif Central, in which the three flow levels are clearly observed. In the first basalt flow (La Palisse, Ardèche), the emission centre and the flow direction are known. In the second one (Saint Arcons d'Allier, Haute Loire), the prismatic columns are particularly well developed. In order to characterize the flow structure at different scales, from the flow to the grain scale, anisotropy of magnetic susceptibility (AMS) measurements were performed. The AMS data were coupled with crystallographic preferred orientation measurements of magnetite, plagioclase and clinopyroxene using Electron Backscattered Diffraction (EBSD) and image analyses from perpendicular thin sections. Magnetic mineralogy studies of the La Palisse basalts, in particular the thermomagnetic curves, indicate that the main carrier of AMS is high-Ti titanomagnetite (Tc≈130°C). AMS measurements of about a hundred samples show a higher degree of AMS (P parameter) in the middle level in comparison to the base. Inversely, the bulk magnetic susceptibility (Km) is higher at the flow base. Distinctive parameters for the different levels of the basaltic flows could be then provided by AMS measurements.. Moreover, the comparison between AMS and EBSD data indicate that the magnetic susceptibility carried by the magnetic

  14. Structure-activity relationship studies of pyrrolone antimalarial agents.

    PubMed

    Murugesan, Dinakaran; Kaiser, Marcel; White, Karen L; Norval, Suzanne; Riley, Jennifer; Wyatt, Paul G; Charman, Susan A; Read, Kevin D; Yeates, Clive; Gilbert, Ian H

    2013-09-01

    Previously reported pyrrolones, such as TDR32570, exhibited potential as antimalarial agents; however, while these compounds have potent antimalarial activity, they suffer from poor aqueous solubility and metabolic instability. Here, further structure-activity relationship studies are described that aimed to solve the developability issues associated with this series of compounds. In particular, further modifications to the lead pyrrolone, involving replacement of a phenyl ring with a piperidine and removal of a potentially metabolically labile ester by a scaffold hop, gave rise to derivatives with improved in vitro antimalarial activities against Plasmodium falciparum K1, a chloroquine- and pyrimethamine-resistant parasite strain, with some derivatives exhibiting good selectivity for parasite over mammalian (L6) cells. Three representative compounds were selected for evaluation in a rodent model of malaria infection, and the best compound showed improved ability to decrease parasitaemia and a slight increase in survival.

  15. Capsaicin and its analogues: structure-activity relationship study.

    PubMed

    Huang, X-F; Xue, J-Y; Jiang, A-Q; Zhu, H-L

    2013-01-01

    Capsaicin, the main ingredient responsible for the hot pungent taste of chilli peppers, is an alkaloid found in the Capsicum family. Capsaicin was traditionally used for muscular pain, headaches, to improve circulation and for its gastrointestinal protective effects. It was also commonly added to herbal formulations because it acts as a catalyst for other herbs and aids in their absorption. In addition, capsaicin and other capsaicinoid compounds showed strong evidence of having promising potential in the fight against many types of cancer. The mechanism of action of capsaicin has been extensively studied over the past decade. It has been established that capsaicin binds to the transient receptor potential vanilloid 1 receptor which was expressed predominantly by sensory neurons. And many analogues of capsaicin have been synthesized and evaluated for diverse bioactivities. In this review, we will attempt to summarize the biology and structure-activity relationship of capsaicinoids.

  16. Structural, morphological and electroluminescence studies of Zno:Co nanophosphor

    NASA Astrophysics Data System (ADS)

    Singh, Anju; Vishwakarma, H. L.

    2016-09-01

    The nanoparticles of zinc oxide (ZnO) doped with various concentrations of cobalt (Co) were synthesized by chemical precipitation method in the presence of capping agent polyvinylpyrrolidone (PVP). The effect of doping concentration on structural and morphological properties has been studied by X-ray diffraction (XRD) and scanning electron microscope (SEM). Cell volume, bond length, texture coefficient, lattice constants and dislocation density are also studied. Here, we also compared the interplaner spacing and relative peak intensities from their standard values with different angles. Crystallite sizes have been calculated by Debye-Scherrer's formula whose values are decreasing with increase in cobalt content up to 3 %. It has been seen that the growth orientation of the prepared ZnO nanorods was (101). The XRD analysis also ensures that ZnO has a hexagonal (wurtzite) crystal structure. The electroluminescence (EL) cells were prepared by placing pure and cobalt-doped ZnO nanoparticles between ITO-coated conducting glass plate and aluminium foil. Alternating voltage of various frequencies was applied, and EL brightness at different voltages was measured and corresponding current was also recorded. The voltage dependence of electroluminescence (EL) brightness of the ZnO:Co shows exponential increase. The linear voltage-current characteristic indicates ohmic nature. The EL brightness at a particular voltage is found to increase by increasing Co doping, but for higher percentage of Co the EL brightness is reduced. It is also seen that Co does not influence the threshold voltage. The brightness is also affected by increasing the frequency of AC signal.

  17. Cystathionine γ-lyase: clinical, metabolic, genetic, and structural studies

    PubMed Central

    Kraus, Jan P.; Hašek, Jindrich; Kožich, Viktor; Collard, Renata; Venezia, Sarah; Janošíková, Bohumila; Wang, Jian; Stabler, Sally P.; Allen, Robert H.; Jakobs, Cornelis; Finn, Christine T.; Chien, Yin-Hsiu; Hwu, Wuh-Liang; Hegele, Robert A.; Mudd, S. Harvey

    2009-01-01

    We report studies of six individuals with marked elevations of cystathionine in plasma and/or urine. Studies of CTH, the gene that encodes cystathionine γ-lyase, revealed the presence among these individuals of either homozygous or compound heterozygous forms of a novel large deletion, p.Gly57_Gln196del, two novel missense mutations, c.589C>T (p.Arg197Cys) and c.932C>T (p.Thr311Ile), and one previously reported alteration, c.200C>T (p.Thr67Ile). Another novel missense mutation, c.185G>T (p.Arg62His), was found in heterozygous form in three mildly hypercystathioninemic members of a Taiwanese family. In one severely hypercystathioninemic individual no CTH mutation was found. Brief clinical histories of the cystathioninemic/cystathioninuric patients are presented. Most of the novel mutations were expressed and the CTH activities of the mutant proteins determined. The crystal structure of the human enzyme, hCTH, and the evidence available as to the effects of the mutations in question, as well as those of the previously reported p.Gln240Glu, on protein structure, enzymatic activity, and responsiveness to vitamin B6 administration are discussed. Among healthy Czech controls, 9.3% were homozygous for CTH c.1208G>T (p.Ser403Ile), previously found homozygously in 7.5% of Canadians for whom plasma total homocysteine (tHcy) had been measured. Compared to wild-type homozygotes, among the 55 Czech c.1208G>T (p.Ser403Ile) homozygotes a greater level of plasma cystathionine was found only after methionine loading. Three of the four individuals homozygous or compound heterozygous for inactivating CTH mutations had mild plasma tHcy elevations, perhaps indicating a cause-and-effect relationship. The experience with the present patients provides no evidence that severe loss of CTH activity is accompanied by adverse clinical effects. PMID:19428278

  18. Structural and morphological studies on wet-etched InAlGaN barrier HEMT structures

    NASA Astrophysics Data System (ADS)

    Brazzini, T.; Tadjer, M. J.; Gačević, Ž.; Pandey, S.; Cavallini, A.; Calle, F.

    2013-05-01

    Developer-based wet chemical etch of nearly lattice-matched InAlGaN/GaN heterostructures (HEMT-like) has been studied in detail by means of Rutherford backscattering spectroscopy, x-ray diffraction, atomic force microscopy and reciprocal space mapping (RSM). Etch isotropy depended on the rms surface roughness of the as-grown material. The profiles of etched samples varied in crack density, giving rise to island-like structures. We found that a possible reason for the preferential etching can be ascribed to the dislocations present in the quaternary layers originating in the underlying GaN. Moreover, the etched material suffers crystal relaxation as confirmed by RSM.

  19. Implementation of a Matrix Organizational Structure: A Case Study.

    ERIC Educational Resources Information Center

    Whorton, David M.

    The implementation of a matrix structure as an alternative to the traditional collegial/bureaucratic form at a college of education in a medium-size state university is described. Matrix organizational structures are differentiated from hierarchical bureaucratic structures by dividing the organization's tasks into functional units across which an…

  20. Source localization of intermittent rhythmic delta activity in a patient with acute confusional migraine: cross-spectral analysis using standardized low-resolution brain electromagnetic tomography (sLORETA).

    PubMed

    Kim, Dae-Eun; Shin, Jung-Hyun; Kim, Young-Hoon; Eom, Tae-Hoon; Kim, Sung-Hun; Kim, Jung-Min

    2016-01-01

    Acute confusional migraine (ACM) shows typical electroencephalography (EEG) patterns of diffuse delta slowing and frontal intermittent rhythmic delta activity (FIRDA). The pathophysiology of ACM is still unclear but these patterns suggest neuronal dysfunction in specific brain areas. We performed source localization analysis of IRDA (in the frequency band of 1-3.5 Hz) to better understand the ACM mechanism. Typical IRDA EEG patterns were recorded in a patient with ACM during the acute stage. A second EEG was obtained after recovery from ACM. To identify source localization of IRDA, statistical non-parametric mapping using standardized low-resolution brain electromagnetic tomography was performed for the delta frequency band comparisons between ACM attack and non-attack periods. A difference in the current density maximum was found in the dorsal anterior cingulated cortex (ACC). The significant differences were widely distributed over the frontal, parietal, temporal and limbic lobe, paracentral lobule and insula and were predominant in the left hemisphere. Dorsal ACC dysfunction was demonstrated for the first time in a patient with ACM in this source localization analysis of IRDA. The ACC plays an important role in the frontal attentional control system and acute confusion. This dysfunction of the dorsal ACC might represent an important ACM pathophysiology.

  1. Novel aldehyde and thiosemicarbazone derivatives: Synthesis, spectroscopic characterization, structural studies and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Karakurt, Tuncay; Tahtaci, Hakan; Subasi, Nuriye Tuna; Er, Mustafa; Ağar, Erbil

    2016-12-01

    In this study our purpose is that, synthesis and characterization of compounds containing the aldehyde and thiosemicarbazone groups and comparison of the theoretical results with the experimental results. The structures of all synthesized compounds were elucidated by IR, 1H NMR, 13C NMR, elemental analyses techniques. The structure of compound (4) (C9H8N4O2S) was also elucidated by X-ray diffraction analysis. In addition, the theoretical IR spectrum, 1H NMR and 13C NMR chemical shift values, frontier molecular orbital values (FMO) of these molecules were analyzed by using Becke-3- Lee-Yang-Parr (B3LYP) method with LanL2DZ basis set. Finally, molecular docking studies were performed on synthesized compounds using the 4DKI beta-lactam protein structure to determine the potential binding mode of inhibitors.

  2. WAXS studies of the structural diversity of hemoglobin in solution.

    SciTech Connect

    Makowski, L.; Bardhan, J.; Gore, D.; Lal, J.; Mandava, S.; Park, S.; Rodi, D. J.; Ho, N. T.; Ho, C.; Fischetti, R. F.

    2011-01-01

    Specific ligation states of hemoglobin are, when crystallized, capable of taking on multiple quaternary structures. The relationship between these structures, captured in crystal lattices, and hemoglobin structure in solution remains uncertain. Wide-angle X-ray solution scattering (WAXS) is a sensitive probe of protein structure in solution that can distinguish among similar structures and has the potential to contribute to these issues. We used WAXS to assess the relationships among the structures of human and bovine hemoglobins in different liganded forms in solution. WAXS data readily distinguished among the various forms of hemoglobins. WAXS patterns confirm some of the relationships among hemoglobin structures that have been defined through crystallography and NMR and extend others. For instance, methemoglobin A in solution is, as expected, nearly indistinguishable from HbCO A. Interestingly, for bovine hemoglobin, the differences between deoxy-Hb, methemoglobin and HbCO are smaller than the corresponding differences in human hemoglobin. WAXS data were also used to assess the spatial extent of structural fluctuations of various hemoglobins in solution. Dynamics has been implicated in allosteric control of hemoglobin, and increased dynamics has been associated with lowered oxygen affinity. Consistent with that notion, WAXS patterns indicate that deoxy-Hb A exhibits substantially larger structural fluctuations than HbCO A. Comparisons between the observed WAXS patterns and those predicted on the basis of atomic coordinate sets suggest that the structures of Hb in different liganded forms exhibit clear differences from known crystal structure.

  3. Structural design studies of a supersonic cruise arrow wing configuration

    NASA Technical Reports Server (NTRS)

    Sobieszczanski, J.; Mccullers, L. A.; Ricketts, R. H.; Santoro, N. J.; Beskenis, S. D.; Kurtze, W. L.

    1976-01-01

    Structural member cross sections were sized with a system of integrated computer programs to satisfy strength and flutter design requirements for several variants of the arrow wing supersonic cruise vehicle. The resulting structural weights provide a measure of the structural efficiency of the planform geometry, structural layout, type of construction, and type of material including composites. The material distribution was determined for a baseline metallic structure and the results indicate that an approximate fatigue constraint has an important effect on the structural weight required for strength but, in all cases, additional material had to be added to satisfy flutter requirements with lighter mass engines with minimum fuel onboard. The use of composite materials on the baseline configuration was explored and indicated increased structural efficiency. In the strength sizing, the all-composite construction provided a lower weight design than the hybrid construction which contained composites only in the wing cover skins. Subsequent flutter analyses indicated a corresponding lower flutter speed.

  4. Approximation method to compute domain related integrals in structural studies

    NASA Astrophysics Data System (ADS)

    Oanta, E.; Panait, C.; Raicu, A.; Barhalescu, M.; Axinte, T.

    2015-11-01

    Various engineering calculi use integral calculus in theoretical models, i.e. analytical and numerical models. For usual problems, integrals have mathematical exact solutions. If the domain of integration is complicated, there may be used several methods to calculate the integral. The first idea is to divide the domain in smaller sub-domains for which there are direct calculus relations, i.e. in strength of materials the bending moment may be computed in some discrete points using the graphical integration of the shear force diagram, which usually has a simple shape. Another example is in mathematics, where the surface of a subgraph may be approximated by a set of rectangles or trapezoids used to calculate the definite integral. The goal of the work is to introduce our studies about the calculus of the integrals in the transverse section domains, computer aided solutions and a generalizing method. The aim of our research is to create general computer based methods to execute the calculi in structural studies. Thus, we define a Boolean algebra which operates with ‘simple’ shape domains. This algebraic standpoint uses addition and subtraction, conditioned by the sign of every ‘simple’ shape (-1 for the shapes to be subtracted). By ‘simple’ shape or ‘basic’ shape we define either shapes for which there are direct calculus relations, or domains for which their frontiers are approximated by known functions and the according calculus is carried out using an algorithm. The ‘basic’ shapes are linked to the calculus of the most significant stresses in the section, refined aspect which needs special attention. Starting from this idea, in the libraries of ‘basic’ shapes, there were included rectangles, ellipses and domains whose frontiers are approximated by spline functions. The domain triangularization methods suggested that another ‘basic’ shape to be considered is the triangle. The subsequent phase was to deduce the exact relations for the

  5. Electrical and Optical Studies of Double Barrier Structures

    NASA Astrophysics Data System (ADS)

    White, Christopher Richard Hardy

    energy. Hence, the quantum well photoluminescence is transmitted through this layer unattenuated. This leads to a strong difference between the optical properties of this device and those of a more conventional structure. The Fractional Quantum Hall Effect is investigated in a single, narrow (100A), quantum well structure. The development of the 2/3, 4/3 and 5/3 fractional filling states is studied as a function of the sheet carrier concentration and electron mobility in the quantum well. The sheet carrier concentration and mobility are changed by a series of short illumination pulses, the energy of which is less than the band gap energy of the material.

  6. Preparation, structural and morphological studies of Ni doped titania nanoparticles.

    PubMed

    Rajamannan, B; Mugundan, S; Viruthagiri, G; Shanmugam, N; Gobi, R; Praveen, P

    2014-07-15

    TiO2 nanoparticles doped with different weight percentages (4%, 8%, 12% and 16%) of nickel contents were prepared by a modified sol-gel method using Titanium tetra iso propoxide and nickel nitrate as precursors and 2-propanol as a solvent. X-ray diffraction studies show that the as prepared and annealed products show anatase structure with average particle sizes running between of 8 and 16 nm. FTIR results demonstrate the presence of strong chemical bonding at the interface of TiO2 nanoparticles. The optical properties of bare and doped samples were carried out using UV-DRS and photoluminescence measurements. The surface morphology and the element constitution of the nickel doped TiO2 nanoparticles were studied by scanning electron microscope attached with energy dispersive X-ray spectrometer arrangement. The non linear optical properties of the products were confirmed by Kurtz second harmonic generation (SHG) test and the output power generated by the nanoparticle was compared with that of potassium di hydrogen phosphate (KDP).

  7. STM study on the structures of SnSe surfaces

    NASA Astrophysics Data System (ADS)

    Kim, Tae Hoon; Kim, Sang-Ui; Thi Ly, Trinh; Duong, Anh Tuan; Cho, Sunglae; Rhim, S. H.; Kim, Jungdae

    SnSe is a 2 dimensional layered material, and each layer is coupled by van deer Waals forces allowing very easy cleaving though the layer surfaces. SnSe has been studied for various potential applications because of its high stability and elemental abundance in earth. Recently, it was also reported that bulk SnSe has an excellent thermoelectric property of ZT =2.6 at 923 K along the b axis (Zhao et al., Nature 508 373 (2014)). The surface of a single crystal SnSe was studied via a home-built low temperature scanning tunneling microscopy (STM). Clear atomic images of SnSe surfaces were observed at the filled and empty state measurements, and detail atomic structures were analyzed by comparing with DFT simulations. We found that the atomic image of SnSe surfaces measured by STM is not trivial to understand. Only Sn atoms were visible on STM topographic images for the both of filled and empty state probing. This work was supported by the National Research Foundation of Korea(NRF) [Nos. NRF-2013R1A1A1008724, NRF-2009-0093818, and NRF-2014R1A4A1071686].

  8. Studies of Nuclear Structure and Decay Properties of Actinide Nuclei

    SciTech Connect

    Kondev, F. G.; Ahmad, I.; Carpenter, M. P.; Chiara, C. J.; Greene, J. P.; Janssens, R. V. F.; Khoo, T. L.; Lauritsen, T.; Lister, C. J.; Moore, E. F.; Seweryniak, D.; Zhu, S.; Kellett, M. A.; Nichols, A. L.

    2009-01-28

    The identification of single-particle states in heavy actinide nuclei by means of studying their decay schemes plays a seminal role in understanding the structure of the heaviest elements and testing the predictive power of modern theoretical models. The heaviest odd-mass nuclides available in sufficient quantity for detailed decay spectroscopic studies are 20-h {sup 255} Fm(for neutrons) and 20-d {sup 253}Es(for protons). Decay spectra of these isotopes, together with those for the odd-odd 276-d {sup 254}Es nuclide, were measured using a variety of {alpha}-particle and {gamma}-ray spectroscopy techniques. Well-defined decay data are also essential pre-requisites for the detection and accurate characterization of fissile radionuclides. The parameters of greatest relevance include actinide half-lives, branching fractions, and {alpha}-particle and {gamma}-ray energies and emission probabilities. Their quantification to good accuracy provides the means of monitoring their presence, behavior and transport in nuclear facilities as well as any clandestine movement and usage. As a consequence of recommendations made at recent IAEA research coordination meetings on 'Updated Decay Data Library for Actinides,' measurements were undertaken to determine specific decay data of the more inadequately defined radionuclides.

  9. Synthesis, structural and fungicidal studies of hydrazone based coordination compounds

    NASA Astrophysics Data System (ADS)

    Sharma, Amit Kumar; Chandra, Sulekh

    2013-02-01

    The coordination compounds of the Co(II), Ni(II) and Cu(II) metal ions derived from imine based ligand, benzil bis(carbohydarzone) were structurally and pharmaceutically studied. The compounds have the general stoichiometry [M(L)]X2 and [Co(L)X2], where M = Ni(II) and Cu(II), and X=NO3- and Cl- ions. The analytical techniques like elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, UV/Visible, NMR, ESI mass and EPR were used to study the compounds. The key IR bands, i.e., amide I, amide II and amide III stretching vibrations accounts for the tetradentate metal binding nature of the ligand. The electronic and EPR spectral results suggest the square planar Ni(II) and Cu(II) complexes (giso = 2.11-2.22) and tetragonal geometry Co(II) complexes (giso = 2.10-2.17). To explore the compounds in the biological field, they were examined against the opportunistic pathogens, i.e., Alternaria brassicae, Aspergillus niger and Fusarium oxysporum. The partial covalent character of metal-ligand bond is supported by the orbital reduction factor k (0.62-0.92) and nephalauxetic parameter β (0.55-0.57).

  10. Bicuspid aortic valve hemodynamics: a fluid-structure interaction study

    NASA Astrophysics Data System (ADS)

    Chandra, Santanu; Seaman, Clara; Sucosky, Philippe

    2011-11-01

    The bicuspid aortic valve (BAV) is a congenital defect in which the aortic valve forms with two leaflets instead of three. While calcific aortic valve disease (CAVD) also develops in the normal tricuspid aortic valve (TAV), its progression in the BAV is more rapid. Although studies have suggested a mechano-potential root for the disease, the native BAV hemodynamics remains largely unknown. This study aimed at characterizing BAV hemodynamics and quantifying the degree of wall-shear stress (WSS) abnormality on BAV leaflets. Fluid-structure interaction models validated with particle-image velocimetry were designed to predict the flow and leaflet dynamics in idealized TAV and BAV anatomies. Valvular function was quantified in terms of the effective orifice area. The regional leaflet WSS was characterized in terms of oscillatory shear index, temporal shear magnitude and temporal shear gradient. The predictions indicate the intrinsic degree of stenosis of the BAV anatomy, reveal drastic differences in shear stress magnitude and pulsatility on BAV and TAV leaflets and confirm the side- and site-specificity of the leaflet WSS. Given the ability of abnormal fluid shear stress to trigger valvular inflammation, these results support the existence of a mechano-etiology of CAVD in the BAV.

  11. Photodegradation products of propranolol: the structures and pharmacological studies.

    PubMed

    Uwai, Koji; Tani, Marie; Ohtake, Yosuke; Abe, Shinya; Maruko, Akiko; Chiba, Takashi; Hamaya, Yoshiro; Ohkubo, Yasuhito; Takeshita, Mitsuhiro

    2005-12-12

    Recently, single-dose drug packaging systems, allowing the administration of multiple drugs in a single pill, have become popular for the convenience of the patient. The quality of drugs and an accurate measurement of their photostabilities within this system, however, have not been carefully addressed. Drugs that are unstable in light should be carefully handled to protect their potency and ensure their safety. Propranolol (1), a beta-adrenergic receptor antagonist, is widely used for angina pectoris, arrhythmia, and hypertension. Due to its naphthalene skeleton, this drug may be both light unstable and a photosensitizing agent. In this study, we isolated three photodegraded products of propranolol (1): 1-naphthol (2), N-acetylpropranolol (3), and N-formylpropranolol (4). The structures of these compounds were determined by spectroscopic methods and chemical syntheses. We also examined the acute toxicities of these substances in mice and their binding to beta-adrenergic receptors using rat cerebellum cortex membranes. Although the photoproducts isolated in this study did not exhibit any acute toxicity or significant binding to beta-adrenergic receptors, these results serve as a warning to single-dose packaging systems, as propranolol (1) must be handled carefully to protect the compound from light-induced degradation.

  12. Nuclear structure and reaction studies at medium energies

    SciTech Connect

    Hoffmann, G.W.; Ray, R.L.

    1990-10-01

    This document constitutes the (1988--1991) technical progress report for the ongoing medium energy physics research program supported by the US Department of Energy through special Research Grant FG05-88ER40444. The experiments discussed are conducted at the Los Alamos National Laboratory's (LANL) Clinton P. Anderson Meson Physics Facility (LAMPF), the Alternating Gradient Synchrotron (AGS) facility of the Brookhaven National Laboratory (BNL), and at the Fermi National Accelerator Laboratory (FNAL). The overall motivation for the work discussed in this document is driven by three main objectives: (1) provide hadron-nucleon and hadron-nucleus scattering data which serve to facilitate the study of effective two-body interactions, test (and possibly determine) nuclear structure, and help study reaction mechanisms and dynamics;(2) provide unique, first-of-a-kind exploratory'' hadron-nucleus scattering data in the hope that such data will lead to discovery of new phenomena and new physics; and (3) perform precision tests of fundamental interactions, such as rare decay searches, whose observation would imply fundamental new physics.

  13. Preparation, structural and morphological studies of Ni doped titania nanoparticles

    NASA Astrophysics Data System (ADS)

    Rajamannan, B.; Mugundan, S.; Viruthagiri, G.; Shanmugam, N.; Gobi, R.; Praveen, P.

    2014-07-01

    TiO2 nanoparticles doped with different weight percentages (4%, 8%, 12% and 16%) of nickel contents were prepared by a modified sol-gel method using Titanium tetra iso propoxide and nickel nitrate as precursors and 2-propanol as a solvent. X-ray diffraction studies show that the as prepared and annealed products show anatase structure with average particle sizes running between of 8 and 16 nm. FTIR results demonstrate the presence of strong chemical bonding at the interface of TiO2 nanoparticles. The optical properties of bare and doped samples were carried out using UV-DRS and photoluminescence measurements. The surface morphology and the element constitution of the nickel doped TiO2 nanoparticles were studied by scanning electron microscope attached with energy dispersive X-ray spectrometer arrangement. The non linear optical properties of the products were confirmed by Kurtz second harmonic generation (SHG) test and the output power generated by the nanoparticle was compared with that of potassium di hydrogen phosphate (KDP).

  14. Synthesis, structural and fungicidal studies of hydrazone based coordination compounds.

    PubMed

    Sharma, Amit Kumar; Chandra, Sulekh

    2013-02-15

    The coordination compounds of the Co(II), Ni(II) and Cu(II) metal ions derived from imine based ligand, benzil bis(carbohydarzone) were structurally and pharmaceutically studied. The compounds have the general stoichiometry [M(L)]X(2) and [Co(L)X(2)], where M=Ni(II) and Cu(II), and X=NO(3)(-) and Cl(-) ions. The analytical techniques like elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, UV/Visible, NMR, ESI mass and EPR were used to study the compounds. The key IR bands, i.e., amide I, amide II and amide III stretching vibrations accounts for the tetradentate metal binding nature of the ligand. The electronic and EPR spectral results suggest the square planar Ni(II) and Cu(II) complexes (g(iso)=2.11-2.22) and tetragonal geometry Co(II) complexes (g(iso)=2.10-2.17). To explore the compounds in the biological field, they were examined against the opportunistic pathogens, i.e., Alternaria brassicae, Aspergillus niger and Fusarium oxysporum. The partial covalent character of metal-ligand bond is supported by the orbital reduction factor k (0.62-0.92) and nephalauxetic parameter β (0.55-0.57).

  15. Biochemical and Structural Studies of Yeast Vps4 Oligomerization

    PubMed Central

    Gonciarz, Malgorzata D.; Whitby, Frank G.; Eckert, Debra M.; Kieffer, Collin; Heroux, Annie; Sundquist, Wesley I.; Hill, Christopher P.

    2008-01-01

    The ESCRT pathway functions in vesicle formation at the multivesicular body, the budding of enveloped RNA viruses such as HIV-1, and the final abscission stage of cytokinesis. As the only known enzyme in the ESCRT pathway, the AAA ATPase Vps4 provides the energy required for multiple rounds of vesicle formation. Like other Vps4 proteins, yeast Vps4 cycles through two states: a catalytically inactive disassembled state that we show here is a dimer, and a catalytically active higher order assembly that we have modeled as a dodecamer composed of two stacked hexameric rings. We also report crystal structures of yeast Vps4 proteins in the apo- and ATPγS-bound states. In both cases, Vps4 subunits assembled into continuous helices with six-fold screw axes that are analogous to helices seen previously in other Vps4 crystal forms. The helices are stabilized by extensive interactions between the large and small AAA ATPase domains of adjacent Vps4 subunits, suggesting that these contact surfaces may be used to build both the catalytically active dodecamer and catalytically inactive dimer. Consistent with this model, we have identified interface mutants that specifically inhibit Vps4 dimerization, dodecamerization, or both. Thus, the Vps4 dimer and dodecamer likely form distinct but overlapping interfaces. Finally, our structural studies have allowed us to model the conformation of a conserved loop (Pore Loop 2) that is predicted to form an arginine-rich pore at the center of one of the Vps4 hexameric rings. Our mutational analyses demonstrate that Pore Loop 2 residues Arg241 and Arg251 are required for efficient HIV-1 budding, thereby supporting a role for this “arginine collar” in Vps4 function. PMID:18929572

  16. Biochemical and Structural Studies of YEast Vps4 Oligomerization

    SciTech Connect

    Gonciarz, M.; Whitby, F; Eckert, D; Kieffer, C; Heroux, A; Sundquist, W; Hill, C

    2008-01-01

    The ESCRT (endosomal sorting complexes required for transport) pathway functions in vesicle formation at the multivesicular body, the budding of enveloped RNA viruses such as HIV-1, and the final abscission stage of cytokinesis. As the only known enzyme in the ESCRT pathway, the AAA ATPase (ATPase associated with diverse cellular activities) Vps4 provides the energy required for multiple rounds of vesicle formation. Like other Vps4 proteins, yeast Vps4 cycles through two states: a catalytically inactive disassembled state that we show here is a dimer and a catalytically active higher-order assembly that we have modeled as a dodecamer composed of two stacked hexameric rings. We also report crystal structures of yeast Vps4 proteins in the apo- and ATPS (adenosine 5'-O-(3-thiotriphosphate))-bound states. In both cases, Vps4 subunits assembled into continuous helices with 6-fold screw axes that are analogous to helices seen previously in other Vps4 crystal forms. The helices are stabilized by extensive interactions between the large and small AAA ATPase domains of adjacent Vps4 subunits, suggesting that these contact surfaces may be used to build both the catalytically active dodecamer and catalytically inactive dimer. Consistent with this model, we have identified interface mutants that specifically inhibit Vps4 dimerization, dodecamerization, or both. Thus, the Vps4 dimer and dodecamer likely form distinct but overlapping interfaces. Finally, our structural studies have allowed us to model the conformation of a conserved loop (pore loop 2) that is predicted to form an arginine-rich pore at the center of one of the Vps4 hexameric rings. Our mutational analyses demonstrate that pore loop 2 residues Arg241 and Arg251 are required for efficient HIV-1 budding, thereby supporting a role for this 'arginine collar' in Vps4 function.

  17. Transport and structural studies of metallic multilayer films

    SciTech Connect

    Florczak, J.M.

    1992-01-01

    A comprehensive study has been made of the structural and transport properties of Fe/Ag and Fe/V multilayer films. The films used in this investigation were prepared by sequential deposition in a UHV compatible sputtering system. High-angle X-ray diffraction experiments reveal modulation satellites in the Fe/V multilayers but none in the Fe/Ag. This observation indicates the existence of a long coherence length in the Fe/V multilayers and a short coherence length in the Fe/Ag films. For bilayer thicknesses greater than 40[angstrom] both series have numerous satellite peaks in the low-angle diffraction data. X-ray diffraction measurements indicate structural degradation in the Fe/Ag multilayers with bilayer thicknesses less than 40[angstrom]. This effect is not present in the Fe/V films. The transport properties of these films were characterized by resistivity, anisotropic magnetoresistance, extraordinary Hall effect, and ordinary Hall effect measurements. For the Fe/Ag samples, a reduction in the bilayer thickness results in increases of the resistivity, anisotropic magnetoresistance, and extra ordinary Hall coefficients. The ordinary Hall coefficient is nearly the same for all the Fe/Ag multilayers. In the Fe/V samples, at 295K there are increases in all transport parameters except the anisotropic magnetoresistance, which decreases. On the other hand, at 4.2K, all of these quantities increase including the anisotropic magnetoresistance. These trends in the transport measurements are discussed using both a simple circuit analogy and a sophisticated statistical analysis of the conduction in multilayer films. The models suggest the electronic mean free paths of the nonmagnetic metals are responsible for the detailed behavior of the AMR ratio in the Fe/V and Fe/Ag multilayers.

  18. Cross-Linking and Mass Spectrometry Methodologies to Facilitate Structural Biology: Finding a Path through the Maze

    SciTech Connect

    Merkley, Eric D.; Cort, John R.; Adkins, Joshua N.

    2013-09-01

    Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature. These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.

  19. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  20. Neutron multiplicities in spontaneous fission and nuclear structure studies

    SciTech Connect

    Hamilton, J.H.; Kormicki, J.; Lu, Q.

    1993-12-31

    New insights into the fission process can be gained by better quantitative knowledge of how the energy released in fission is distributed between the kinetic energy of the two fragments, the excitation energy of the two fragments and the number of neutrons emitted. Studies of prompt gamma-rays emitted in spontaneous fission (SF) with large arrays of Compton suppressed Ge detector arrays are providing new quantitative answers to longstanding questions concerning fission as well as new insights into the structure of neutron-rich nuclei. For the first time the triple gamma coincidence technique was employed in spontaneous fission studies. Studies of SF of {sup 252}Cf and {sup 242}Pu have been carried out. These {gamma}-{gamma}-{gamma} data provide powerful ways to identify uniquely gamma rays from a particular nucleus in the very complex gamma-ray spectra given off by the over 100 different nuclei produced. The emphasis of this paper is on the first quantitative measurements of the multiplicities of the neutrons emitted in SF and the energy levels populated in the fragments. Indeed, in the break up into Mo-Ba pairs, we have identified for the first time fragments associated with from zero up to ten neutrons emitted and observed the excited energy states populated in these nuclei. The zero neutron emission pairs like {sup 104}Mo- {sup 148}Ba, {sup 106}Mo- {sup 146}Ba and {sup 104}Zr- {sup 148}Ce observed in this work are particularly interesting because they represent a type of cold fission or a new mode of cluster radioactivity as proposed by Greiner, Sandulescu and co-workers. These data provide new insights into the processes of cluster radioactivity and cold fission.

  1. A structural study of Hypocrea jecorina Cel5A.

    PubMed

    Lee, Toni M; Farrow, Mary F; Arnold, Frances H; Mayo, Stephen L

    2011-11-01

    Interest in generating lignocellulosic biofuels through enzymatic hydrolysis continues to rise as nonrenewable fossil fuels are depleted. The high cost of producing cellulases, hydrolytic enzymes that cleave cellulose into fermentable sugars, currently hinders economically viable biofuel production. Here, we report the crystal structure of a prevalent endoglucanase in the biofuels industry, Cel5A from the filamentous fungus Hypocrea jecorina. The structure reveals a general fold resembling that of the closest homolog with a high-resolution structure, Cel5A from Thermoascus aurantiacus. Consistent with previously described endoglucanase structures, the H. jecorina Cel5A active site contains a primarily hydrophobic substrate binding groove and a series of hydrogen bond networks surrounding two catalytic glutamates. The reported structure, however, demonstrates stark differences between side-chain identity, loop regions, and the number of disulfides. Such structural information may aid efforts to improve the stability of this protein for industrial use while maintaining enzymatic activity through revealing nonessential and immutable regions.

  2. A structural study of Hypocrea jecorina Cel5A

    PubMed Central

    Lee, Toni M; Farrow, Mary F; Arnold, Frances H; Mayo, Stephen L

    2011-01-01

    Interest in generating lignocellulosic biofuels through enzymatic hydrolysis continues to rise as nonrenewable fossil fuels are depleted. The high cost of producing cellulases, hydrolytic enzymes that cleave cellulose into fermentable sugars, currently hinders economically viable biofuel production. Here, we report the crystal structure of a prevalent endoglucanase in the biofuels industry, Cel5A from the filamentous fungus Hypocrea jecorina. The structure reveals a general fold resembling that of the closest homolog with a high-resolution structure, Cel5A from Thermoascus aurantiacus. Consistent with previously described endoglucanase structures, the H. jecorina Cel5A active site contains a primarily hydrophobic substrate binding groove and a series of hydrogen bond networks surrounding two catalytic glutamates. The reported structure, however, demonstrates stark differences between side-chain identity, loop regions, and the number of disulfides. Such structural information may aid efforts to improve the stability of this protein for industrial use while maintaining enzymatic activity through revealing nonessential and immutable regions. PMID:21898652

  3. A structural study of Hypocrea jecorina Cel5A.

    PubMed

    Lee, Toni M; Farrow, Mary F; Arnold, Frances H; Mayo, Stephen L

    2011-11-01

    Interest in generating lignocellulosic biofuels through enzymatic hydrolysis continues to rise as nonrenewable fossil fuels are depleted. The high cost of producing cellulases, hydrolytic enzymes that cleave cellulose into fermentable sugars, currently hinders economically viable biofuel production. Here, we report the crystal structure of a prevalent endoglucanase in the biofuels industry, Cel5A from the filamentous fungus Hypocrea jecorina. The structure reveals a general fold resembling that of the closest homolog with a high-resolution structure, Cel5A from Thermoascus aurantiacus. Consistent with previously described endoglucanase structures, the H. jecorina Cel5A active site contains a primarily hydrophobic substrate binding groove and a series of hydrogen bond networks surrounding two catalytic glutamates. The reported structure, however, demonstrates stark differences between side-chain identity, loop regions, and the number of disulfides. Such structural information may aid efforts to improve the stability of this protein for industrial use while maintaining enzymatic activity through revealing nonessential and immutable regions. PMID:21898652

  4. High pressure dielectric studies on the structural and orientational glass.

    PubMed

    Kaminska, E; Tarnacka, M; Jurkiewicz, K; Kaminski, K; Paluch, M

    2016-02-01

    High pressure dielectric studies on the H-bonded liquid D-glucose and Orientationally Disordered Crystal (ODIC) 1,6-anhydro-D-glucose (levoglucosan) were carried out. It was shown that in both compounds, the structural relaxation is weakly sensitive to compression. It is well reflected in the low pressure coefficient of the glass transition and orientational glass transition temperatures which is equal to 60 K/GPa for both D-glucose and 1,6-anhydro-D-glucose. Although it should be noted that ∂Tg(0)/∂p evaluated for the latter compound seems to be enormously high with respect to other systems forming ODIC phase. We also found that the shape of the α-loss peak stays constant for the given relaxation time independently on the thermodynamic condition. Consequently, the Time Temperature Pressure (TTP) rule is satisfied. This experimental finding seems to be quite intriguing since the TTP rule was shown to work well in the van der Waals liquids, while in the strongly associating compounds, it is very often violated. We have also demonstrated that the sensitivity of the structural relaxation process to the temperature change measured by the steepness index (mp) drops with pressure. Interestingly, this change is much more significant in the case of D-glucose with respect to levoglucosan, where the fragility changes only slightly with compression. Finally, kinetics of ODIC-crystal phase transition was studied at high compression. It is worth mentioning that in the recent paper, Tombari and Johari [J. Chem. Phys. 142, 104501 (2015)] have shown that ODIC phase in 1,6-anhydro-D-glucose is stable in the wide range of temperatures and there is no tendency to form more ordered phase at ambient pressure. On the other hand, our isochronal measurements performed at varying thermodynamic conditions indicated unquestionably that the application of pressure favors solid (ODIC)-solid (crystal) transition in 1,6-anhydro-D-glucose. This result mimics the impact of pressure on the

  5. High pressure dielectric studies on the structural and orientational glass.

    PubMed

    Kaminska, E; Tarnacka, M; Jurkiewicz, K; Kaminski, K; Paluch, M

    2016-02-01

    High pressure dielectric studies on the H-bonded liquid D-glucose and Orientationally Disordered Crystal (ODIC) 1,6-anhydro-D-glucose (levoglucosan) were carried out. It was shown that in both compounds, the structural relaxation is weakly sensitive to compression. It is well reflected in the low pressure coefficient of the glass transition and orientational glass transition temperatures which is equal to 60 K/GPa for both D-glucose and 1,6-anhydro-D-glucose. Although it should be noted that ∂Tg(0)/∂p evaluated for the latter compound seems to be enormously high with respect to other systems forming ODIC phase. We also found that the shape of the α-loss peak stays constant for the given relaxation time independently on the thermodynamic condition. Consequently, the Time Temperature Pressure (TTP) rule is satisfied. This experimental finding seems to be quite intriguing since the TTP rule was shown to work well in the van der Waals liquids, while in the strongly associating compounds, it is very often violated. We have also demonstrated that the sensitivity of the structural relaxation process to the temperature change measured by the steepness index (mp) drops with pressure. Interestingly, this change is much more significant in the case of D-glucose with respect to levoglucosan, where the fragility changes only slightly with compression. Finally, kinetics of ODIC-crystal phase transition was studied at high compression. It is worth mentioning that in the recent paper, Tombari and Johari [J. Chem. Phys. 142, 104501 (2015)] have shown that ODIC phase in 1,6-anhydro-D-glucose is stable in the wide range of temperatures and there is no tendency to form more ordered phase at ambient pressure. On the other hand, our isochronal measurements performed at varying thermodynamic conditions indicated unquestionably that the application of pressure favors solid (ODIC)-solid (crystal) transition in 1,6-anhydro-D-glucose. This result mimics the impact of pressure on the

  6. High pressure dielectric studies on the structural and orientational glass

    NASA Astrophysics Data System (ADS)

    Kaminska, E.; Tarnacka, M.; Jurkiewicz, K.; Kaminski, K.; Paluch, M.

    2016-02-01

    High pressure dielectric studies on the H-bonded liquid d-glucose and Orientationally Disordered Crystal (ODIC) 1,6-anhydro-d-glucose (levoglucosan) were carried out. It was shown that in both compounds, the structural relaxation is weakly sensitive to compression. It is well reflected in the low pressure coefficient of the glass transition and orientational glass transition temperatures which is equal to 60 K/GPa for both d-glucose and 1,6-anhydro-d-glucose. Although it should be noted that ∂ Tg 0 / ∂ p evaluated for the latter compound seems to be enormously high with respect to other systems forming ODIC phase. We also found that the shape of the α-loss peak stays constant for the given relaxation time independently on the thermodynamic condition. Consequently, the Time Temperature Pressure (TTP) rule is satisfied. This experimental finding seems to be quite intriguing since the TTP rule was shown to work well in the van der Waals liquids, while in the strongly associating compounds, it is very often violated. We have also demonstrated that the sensitivity of the structural relaxation process to the temperature change measured by the steepness index (mp) drops with pressure. Interestingly, this change is much more significant in the case of d-glucose with respect to levoglucosan, where the fragility changes only slightly with compression. Finally, kinetics of ODIC-crystal phase transition was studied at high compression. It is worth mentioning that in the recent paper, Tombari and Johari [J. Chem. Phys. 142, 104501 (2015)] have shown that ODIC phase in 1,6-anhydro-d-glucose is stable in the wide range of temperatures and there is no tendency to form more ordered phase at ambient pressure. On the other hand, our isochronal measurements performed at varying thermodynamic conditions indicated unquestionably that the application of pressure favors solid (ODIC)-solid (crystal) transition in 1,6-anhydro-d-glucose. This result mimics the impact of pressure on the

  7. Structural study and geochronology in the Hook Batholith, Central Zambia

    NASA Astrophysics Data System (ADS)

    Naydenov, K.; Lehmann, J.; Saalmann, K.; Milani, L.; Kinnaird, J.; Charlesworth, G.; Frei, D.

    2013-12-01

    The Pan-African Hook batholith is emplaced N of the Mwembeshi dislocation, a regional scale structure at the contact between Zambezi Belt and Lufilian Arc in Central Zambia. Exposed over 12000 km2 the batholith is composed mainly of fine-grained and coarse-grained porphyritic granites and leucogranites affected by solid-state deformation along high-strain zones. Two main zones of deformation were investigated - the Itezhi-Tezhi Zone (ITZ) in the SW part of the batholith and the Nalusanga Zone (NZ) to the NE. The 2.5 km wide, N-S trending, subvertical ITZ is a medium-grade, pure shear dominated structure, reflecting probably regional scale E-W shortening. In the central part of the zone, augen-gneiss textures developed. Mineral lineations plunging ~40° S are recorded occasionally. The deformed feldspar porphyroclasts show symmetrical tails and rarely sinistral stair-stepping. In the SE part of the Hook batholith the continuation of the ITZ trends E-W. This orientation can be explained by rotation of the original ITZ trend by N-S shortening that also has been recorded in the siliciclastic metasediments S of the contact. S dipping, up to 15 cm wide thrust zones observed in the ITZ area were probably formed during this tectonic event. The 3 km wide NZ is a subvertical to steeply SSW dipping structure, parallel to the NE contact of the batholith, with well-developed foliation and mineral stretching lineations. Field and microstructural analyses defined the NZ as a medium-grade, non-coaxial, sinistral strike-slip shear zone. The transition from weak foliated granite to S-C mylonites and ultramylonites was observed. The sinistral shearing is consistent with E-W shortening in agreement with the tectonic framework of the ITZ. The low grade metasediments to the E of the granite are folded in N to NNW trending structures also implying E-W shortening. Temperature conditions during the deformation in ITZ and NZ inferred from microstructural analyses are about 500°-550°C. The

  8. A Structural Study of Neptunium-Bearing Uranium Oxides

    NASA Astrophysics Data System (ADS)

    Finch, R. J.

    2002-05-01

    Neptunium is an element of significant concern at several contaminated DOE sites, as well as being potentially the largest long-term contributor of radiation dose to people living near the high-level nuclear-waste repository recently recommended by the President for construction at Yucca Mountain, Nevada. In order to understand potential structural effects of Np substitution into uranium minerals, we have synthesized a series of Np-doped U oxides and present here results of a structural study of Np-doped U3O8 (NpxU3-xO8). Although not a mineral, U3O8 bears significant structural similarities to numerous uranyl minerals with both known and potential importance as radionuclide hosts in the environment (Burns et al., Can. Mineral. 34, 845, 1997). Qualitative chemical analyses of U3O8 powders by energy-dispersive x-ray emission spectroscopy (EDS) in a scanning electron microscope indicate that sample powders are homogeneous at the micrometer scale. Further examinations by electron energy-loss spectroscopy (EELS) and EDS in a transmission electron microscope do not reveal compositional inhomogeneities or discernable variability in the Np:U ratios within samples having Np:U ratios of 1:80 and 1:8. Bulk samples of Np-doped U3O8 powders having Np:U ratios of 1:160, 1:80, 1:25, and 1:8, were also analyzed by X-ray absorption near-edge spectroscopy (XANES), which indicates that Np occupies distorted U sites and is predominantly tetravalent. X-ray powder diffraction (XRD) analyses of pure U3O8 and Np-doped U3O8 show that incorporation of Np into U3O8 affects positions and intensities of diffraction peaks, but that all samples are isostructural with alpha-U3O8. No spurious diffraction peaks are observed in any powder patterns of U3O8 with Np:U from 1:160 to 1:8. Lattice parameters vary smoothly as a function of Np concentration. The c cell parameter (perpendicular to the plane of the structural sheets in U3O8) shows little or no dependence on Np concentration, whereas the a

  9. Structural studies of molecular and metallic overlayers using angle- resolved photoemission extended fine structure

    SciTech Connect

    Huang, Z.

    1992-10-01

    Angle-resolved photoemission extended fine structure (ARPEFS) was used to study molecular and metallic overlayers on metal surfaces through analysis of p2mg(2[times]1)CO/Ni(110) and the p(2[times]2)K/Ni(111) adsorption. For the dense p2mg(2[times]1)CO/Ni(110) surface layer, photoemission intensities from C 1s level were measured in three directions at photoelectron kinetic energies 60-400 eV. Using multiple-scattering spherical-wave (MSSW) modeling, it was found that CO molecules are adsorbed on short-bridge sites, with adjacent CO along the [110] direction displaced alternatively in opposite directions towards the [001] azimuths to form a zigzag chain geometry. The tilt angle is 16[plus minus]2[degree] from the surface normal for the direction linking the C atom and the center of the Ni bridge. The carbon C-Ni interatomic distance was determined to be 1.94[plus minus]0.02[Angstrom]. The first- to second-layer spacing of Ni is 1.27[plus minus]0.04[Angstrom], up from 1.10[Angstrom] for the clean Ni(110) surface, but close to the 1.25[Angstrom] Ni interlayer spacing in the bulk. The C-O bond length and tilt angle were varied within small ranges (1.10--1.20[Angstrom] and 15--23[degrees]) in our MSSW simulations. Best agreement between experiment and simulations was achieved at 1.16[Angstrom] and 19[degrees]. This yields an O-O distance of 2.95[Angstrom] for the two nearest CO molecules, (van der Waals' radius [approximately] 1.5 [Angstrom] for oxygen). Two different partial-wave phase-shifts were used in MSSW, and structural results from both are in very good agreement. For the p(2[times]2)K/Ni(111) overlayer, ARPEFS [chi](k) curves from K 1s level measured along [111] and [771] at 130K showed that the K atoms are preferentially adsorbed on the atop sites, in agreement with a LEED study of the same system.

  10. Structural studies of molecular and metallic overlayers using angle- resolved photoemission extended fine structure

    SciTech Connect

    Huang, Z.

    1992-10-01

    Angle-resolved photoemission extended fine structure (ARPEFS) was used to study molecular and metallic overlayers on metal surfaces through analysis of p2mg(2{times}1)CO/Ni(110) and the p(2{times}2)K/Ni(111) adsorption. For the dense p2mg(2{times}1)CO/Ni(110) surface layer, photoemission intensities from C 1s level were measured in three directions at photoelectron kinetic energies 60-400 eV. Using multiple-scattering spherical-wave (MSSW) modeling, it was found that CO molecules are adsorbed on short-bridge sites, with adjacent CO along the [110] direction displaced alternatively in opposite directions towards the [001] azimuths to form a zigzag chain geometry. The tilt angle is 16{plus_minus}2{degree} from the surface normal for the direction linking the C atom and the center of the Ni bridge. The carbon C-Ni interatomic distance was determined to be 1.94{plus_minus}0.02{Angstrom}. The first- to second-layer spacing of Ni is 1.27{plus_minus}0.04{Angstrom}, up from 1.10{Angstrom} for the clean Ni(110) surface, but close to the 1.25{Angstrom} Ni interlayer spacing in the bulk. The C-O bond length and tilt angle were varied within small ranges (1.10--1.20{Angstrom} and 15--23{degrees}) in our MSSW simulations. Best agreement between experiment and simulations was achieved at 1.16{Angstrom} and 19{degrees}. This yields an O-O distance of 2.95{Angstrom} for the two nearest CO molecules, (van der Waals` radius {approximately} 1.5 {Angstrom} for oxygen). Two different partial-wave phase-shifts were used in MSSW, and structural results from both are in very good agreement. For the p(2{times}2)K/Ni(111) overlayer, ARPEFS {chi}(k) curves from K 1s level measured along [111] and [771] at 130K showed that the K atoms are preferentially adsorbed on the atop sites, in agreement with a LEED study of the same system.

  11. Integrated controls/structures study of advanced space systems

    NASA Technical Reports Server (NTRS)

    Greene, C. S.; Cunningham, T. B.

    1982-01-01

    A cost tradeoff is postulated for a stiff structure utilizing minimal controls (and control expense) to point and stabilize the vehicle. Extra costs for a stiff structure are caused by weight, packaging size, etc. Likewise, a more flexible vehicle should result in reduced structural costs but increased costs associated with additional control hardware and data processing required for vibration control of the structure. This tradeoff occurs as the ratio of the control bandwidth required for the mission to the lowest (significant) bending mode of the vehicle. The cost of controlling a spacecraft for a specific mission and the same basic configuration but varying the flexibility is established.

  12. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  13. Studying the Thermal and Structural Evolution of Planetary Bodies

    NASA Astrophysics Data System (ADS)

    Karimi, Mohammadali

    The focus of this research is to study the thermal and structural evolution of three planetary bodies, Mars, Venus and the asteroid Vesta. The almost uniform spatial distribution of craters on the surfaces of planets makes them excellent candidates to examine the evolution of planets as a whole. By modeling the viscoelastic deformation of craters at the surface and subsurface with the Finite Element Method (FEM), this study investigated the role of lower crustal flow in crater relaxation, and since lower crustal flow is sensitive to the thermal state, it serves as a probe into the thermal evolution of planets. The thermal history of Mars was explored by modeling the evolution of large craters and Quasi-Circular Depressions (QCDs) in the Southern Highlands and Northern Lowlands, respectively. Because of the spatial distribution of craters, this study yielded a thermal map for Mars that is more complete and less biased regionally relative to other studies. The results revealed a higher background heat flux for the Northern Lowlands relative to the Southern Highlands during the most ancient Noachian epoch, which suggests a thermal fingerprint to whatever process that formed the hemispherical crustal dichotomy, the oldest and most prominent geomorphic feature on Mars. Next, the largest crater on the surface of Venus, Mead, also appears to have undergone significant lower crustal flow. Modeling the viscoelastic deformation of Mead puts constraints on the thermal state of our sister planet in the vicinity of the basin. The background heat flux of Venus estimated here is higher than globally average values predicted by previous thermal models. Moreover, this study showed that Venus's crust and mantle seem to be dry relative to those of the Earth. Last, modeling the evolution of two large craters in the south polar region of Vesta (Rheasilvia and Veneneia) showed that the shallow topography and large central peak of these craters are likely the products of a planetary

  14. Structural, optical and electronic structure studies of Al doped ZnO thin films

    NASA Astrophysics Data System (ADS)

    Devi, Vanita; Kumar, Manish; Shukla, D. K.; Choudhary, R. J.; Phase, D. M.; Kumar, Ravindra; Joshi, B. C.

    2015-07-01

    Structural, optical and electronic structure of Al doped ZnO thin films grown using pulsed laser deposition on glass substrate are investigated. X-ray diffraction measurements reveal that all the films are textured along the c-axis and have wurtzite structure. Al doping in ZnO films leads to increase in grain size due to relaxation in compressive stress. Enhancement in band gap of ZnO films with the Al doping is also noticed which can be ascribed to the Brustein-Moss shift. The changes in the electronic structure caused by Al in the doped thin film samples are understood through X-ray absorption measurements.

  15. Study on the Response Coefficient of Setback Structures Compared to Regular Moment Frame Structures

    SciTech Connect

    Mirghaderi, S. Rasoul; Khafaf, Bardia; Epackachi, Siamak

    2008-07-08

    In design practice of many countries, seismic analysis and proportioning of structures are usually based upon linear elastic analysis due to reduced seismic forces by response coefficient; R. Setback structures are one of the most popular shapes of the constructed buildings. In setback structures, the shape and proportions of the building have a major effect on distribution of earthquake forces as they work their way through the building. On the other hand, geometric configuration has a profound effect on the structural-dynamic response of a building. Therefore, when a building has irregular features, such as asymmetric in height or vertical discontinuity, the traditional assumptions used in development of seismic criteria for regular buildings may not be applicable. Inelastic seismic behavior of these types of structures seems to be quite different from the regular steel moment resisting structures in which the overall ductility is localized at beam-ends.In order to investigate the seismic behavior and estimate the Response Coefficient of those structures, nonlinear static analysis (pushover) are used for three categories of setback structures namely low rise, medium rise and high rise buildings with different setbacks in their height. The Response Coefficient are calculated and compared with those taken from regular type of moment frame structures.

  16. Study of Magnetic Structure in the Solar Photosphere and Chromosphere

    NASA Technical Reports Server (NTRS)

    Noyes, Robert W.; Avrett, Eugene; Nisenson, Peter; Uitenbroek, Han; vanBallegooijen, Adriaan

    1998-01-01

    This grant funded an observational and theoretical program to study the structure and dynamics of the solar photosphere and low chromosphere, and the spectral signatures that result. The overall goal is to learn about mechanisms that cause heating of the overlying atmosphere, and produce variability of solar emission in spectral regions important for astrophysics and space physics. The program exploited two new ground-based observational capabilities: one using the Swedish Solar Telescope on La Palma for very high angular resolution observations of the photospheric intensity field (granulation) and proxies of the magnetic field (G-band images); and the other using the Near Infrared Magnetograph at the McMath-Pierce Solar Facility to map the spatial variation and dynamic behavior of the solar temperature minimum region using infrared CO lines. We have interpreted these data using a variety of theoretical and modelling approaches, some developed especially for this project. Previous annual reports cover the work done up to 31 May 1997. This final report summarizes our work for the entire period, including the period of no-cost extension from 1 June 1997 through September 30 1997. In Section 2 we discuss observations and modelling of the photospheric flowfields and their consequences for heating of the overlying atmosphere, and in Section 3 we discuss imaging spectroscopy of the CO lines at 4.67 mu.

  17. Three pharmaceuticals cocrystals of adefovir: Syntheses, structures and dissolution study

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoming; Sun, Fuxing; Zhang, Tingting; Jia, Jiangtao; Su, Hongmin; Wang, Chenhui; Zhu, Guangshan

    2015-11-01

    We report here three novel cocrystals, which are composed of adefovir as the API (Active Pharmaceutical Ingredient) with p-aminobenzoic acid (1, 2C8H12N5O4P·C7H6NO2·3H2O), 3,5-dihydroxybenzoic acid (2, C8H12N5O4P·C7H6O4·H2O) and 2,6-pyridinedicarboxlic acid (3, C8H12N5O4P·C7H5NO4) as CCFs (cocrystal formers) respectively by crystal engineering strategy. Their structures were characterized by single crystal X-ray diffraction, powder X-ray diffraction (PXRD) analysis, thermogravimetric analyses (TGA), elemental analysis (EA) and infrared spectral analysis (IR). The analysis of single crystal X-ray diffraction demonstrate that cocrystal 1 and 2 form a strong hydrogen-bonded assembly through the phosphoric acids of API with water in the lattice and carboxylic acids of CCF respectively. Cocrystal 3 is formed in which the phosphoric acid groups of API are also held by the carboxylic acid groups of CCF. The PXRD results indicate their high purity of as-synthesized samples. The TGA, EA, IR and dissolution study of API and the cocrystals were also measured and discussed.

  18. X-ray microscopic studies of labeled nuclear cell structures

    NASA Astrophysics Data System (ADS)

    Vogt, S.; Schneider, G.; Steuernagel, A.; Lucchesi, J.; Schulze, E.; Rudolph, D.; Schmahl, G.

    2000-05-01

    In X-ray microscopy different proteins are not readily distinguishable. However, in cell biology it is often desirable to localize single proteins, e.g., inside the cell nucleus. This can be achieved by immunogold labeling. Colloidal gold conjugated antibodies are used to mark the protein specifically. With silver solution these are enlarged so as to heighten their contrast. The strong absorption of silver allows easy visualization of the label in the nuclei. In this study male specific lethal 1 protein in male Drosophila melanogaster cells was labeled. This protein forms, together with four other proteins, a complex that is associated with the male X chromosome. It regulates dosage compensation by enhancing X-linked gene transcription in males. Room temperature and cyro transmission X-ray microscopic images (taken with the Göttingen TXM at BESSY) of these labeled cells are shown. Confocal laser scan microscopy ascertains the correct identification of the label in the X-ray micrographs, and allows comparison of the structural information available from both instruments.

  19. Receptor Recognition Mechanisms of Coronaviruses: a Decade of Structural Studies

    PubMed Central

    2014-01-01

    Receptor recognition by viruses is the first and essential step of viral infections of host cells. It is an important determinant of viral host range and cross-species infection and a primary target for antiviral intervention. Coronaviruses recognize a variety of host receptors, infect many hosts, and are health threats to humans and animals. The receptor-binding S1 subunit of coronavirus spike proteins contains two distinctive domains, the N-terminal domain (S1-NTD) and the C-terminal domain (S1-CTD), both of which can function as receptor-binding domains (RBDs). S1-NTDs and S1-CTDs from three major coronavirus genera recognize at least four protein receptors and three sugar receptors and demonstrate a complex receptor recognition pattern. For example, highly similar coronavirus S1-CTDs within the same genus can recognize different receptors, whereas very different coronavirus S1-CTDs from different genera can recognize the same receptor. Moreover, coronavirus S1-NTDs can recognize either protein or sugar receptors. Structural studies in the past decade have elucidated many of the puzzles associated with coronavirus-receptor interactions. This article reviews the latest knowledge on the receptor recognition mechanisms of coronaviruses and discusses how coronaviruses have evolved their complex receptor recognition pattern. It also summarizes important principles that govern receptor recognition by viruses in general. PMID:25428871

  20. Structure, IR and Raman spectra of phosphotrihydrazide studied by DFT

    NASA Astrophysics Data System (ADS)

    Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

    2016-09-01

    The FTIR and FT Raman measurements of the phosphotrihydrazide (S)P[N(Me)-NH2]3 have been performed. This compound is a zero generation dendrimer G0 with terminal amine groups. Structural optimization and normal mode analysis were obtained for G0 by the density functional theory (DFT). Optimized geometric bond length and angles obtained by DFT show good agreement with experiment. The amine terminal groups are characterized by the well-defined bands at 3321, 3238, 1614 cm- 1 in the experimental IR spectrum and by bands at 3327, 3241 cm- 1 in the Raman spectrum of G0. The experimental frequencies of asymmetric and symmetric NH2 stretching vibrations of amine group are lower than theoretical values due to intramolecular Nsbnd H ⋯ S hydrogen bond. This hydrogen bond is also responsible for higher experimental infrared intensity of these bands as compared with theoretical values. Relying on DFT calculations a complete vibrational assignment is proposed for the studied dendrimer.