Science.gov

Sample records for accurate structure determination

  1. Accurate SHAPE-directed RNA structure determination

    PubMed Central

    Deigan, Katherine E.; Li, Tian W.; Mathews, David H.; Weeks, Kevin M.

    2009-01-01

    Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis. PMID:19109441

  2. Accurate determination of atomic structure of multiwalled carbon nanotubes by nondestructive nanobeam electron diffraction

    SciTech Connect

    Liu Zejian; Zhang Qi; Qin Luchang

    2005-05-09

    We report a method that allows direct, systematic, and accurate determination of the atomic structure of multiwalled carbon nanotubes by analyzing the scattering intensities on the nonequatorial layer lines in the electron diffraction pattern. Complete structure determination of a quadruple-walled carbon nanotube is described as an example, and it was found that the intertubular distance varied from 0.36 nm to 0.5 nm with a mean value of 0.42 nm.

  3. Fuzzy Reasoning to More Accurately Determine Void Areas on Optical Micrographs of Composite Structures

    NASA Technical Reports Server (NTRS)

    Dominquez, Jesus A.; Tate, Lanetra C.; Wright, M. Clara; Caraccio, Anne

    2013-01-01

    Accomplishing the best-performing composite matrix (resin) requires that not only the processing method but also the cure cycle generate low-void-content structures. If voids are present, the performance of the composite matrix will be significantly reduced. This is usually noticed by significant reductions in matrix-dominated properties, such as compression and shear strength. Voids in composite materials are areas that are absent of the composite components: matrix and fibers. The characteristics of the voids and their accurate estimation are critical to determine for high performance composite structures. One widely used method of performing void analysis on a composite structure sample is acquiring optical micrographs or Scanning Electron Microscope (SEM) images of lateral sides of the sample and retrieving the void areas within the micrographs/images using an image analysis technique. Segmentation for the retrieval and subsequent computation of void areas within the micrographs/images is challenging as the gray-scaled values of the void areas are close to the gray-scaled values of the matrix leading to the need of manually performing the segmentation based on the histogram of the micrographs/images to retrieve the void areas. The use of an algorithm developed by NASA and based on Fuzzy Reasoning (FR) proved to overcome the difficulty of suitably differentiate void and matrix image areas with similar gray-scaled values leading not only to a more accurate estimation of void areas on composite matrix micrographs but also to a faster void analysis process as the algorithm is fully autonomous.

  4. Fuzzy Reasoning to More Accurately Determine Void Areas on Optical Micrographs of Composite Structures

    NASA Astrophysics Data System (ADS)

    Dominguez, Jesus A.; Tate, Lanetra C.; Wright, M. Clara; Caraccio, Anne

    2013-12-01

    Accomplishing the best-performing composite matrix (resin) requires that not only the processing method but also the cure cycle generate low-void-content structures. If voids are present, the performance of the composite matrix will be significantly reduced. This is usually noticed by significant reductions in matrix-dominated properties, such as compression and shear strength. Voids in composite materials are areas that are absent of the composite components: matrix and fibers. The characteristics of the voids and their accurate estimation are critical to determine for high performance composite structures. One widely used method of performing void analysis on a composite structure sample is acquiring optical micrographs or Scanning Electron Microscope (SEM) images of lateral sides of the sample and retrieving the void areas within the micrographs/images using an image analysis technique. Segmentation for the retrieval and subsequent computation of void areas within the micrographs/images is challenging as the gray-scaled values of the void areas are close to the gray-scaled values of the matrix leading to the need of manually performing the segmentation based on the histogram of the micrographs/images to retrieve the void areas. The use of an algorithm developed by NASA and based on Fuzzy Reasoning (FR) proved to overcome the difficulty of suitably differentiate void and matrix image areas with similar gray-scaled values leading not only to a more accurate estimation of void areas on composite matrix micrographs but also to a faster void analysis process as the algorithm is fully autonomous.

  5. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: determination of accurate ionization energy and cationic structure.

    PubMed

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae; Kwon, Chan Ho

    2014-11-01

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73,570 ± 6 cm(-1) (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state ((2)A2), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C(2v) symmetry through the C-N axis.

  6. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: Determination of accurate ionization energy and cationic structure

    SciTech Connect

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae E-mail: hlkim@kangwon.ac.kr; Kwon, Chan Ho E-mail: hlkim@kangwon.ac.kr

    2014-11-07

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73 570 ± 6 cm{sup −1} (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state ({sup 2}A{sub 2}), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C{sub 2v} symmetry through the C-N axis.

  7. Accurate determination of the fine-structure intervals in the 3P ground states of C-13 and C-12 by far-infrared laser magnetic resonance

    NASA Technical Reports Server (NTRS)

    Cooksy, A. L.; Saykally, R. J.; Brown, J. M.; Evenson, K. M.

    1986-01-01

    Accurate values are presented for the fine-structure intervals in the 3P ground state of neutral atomic C-12 and C-13 as obtained from laser magnetic resonance spectroscopy. The rigorous analysis of C-13 hyperfine structure, the measurement of resonant fields for C-12 transitions at several additional far-infrared laser frequencies, and the increased precision of the C-12 measurements, permit significant improvement in the evaluation of these energies relative to earlier work. These results will expedite the direct and precise measurement of these transitions in interstellar sources and should assist in the determination of the interstellar C-12/C-13 abundance ratio.

  8. Accurate determination of characteristic relative permeability curves

    NASA Astrophysics Data System (ADS)

    Krause, Michael H.; Benson, Sally M.

    2015-09-01

    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  9. Under proper control, oxidation of proteins with known chemical structure provides an accurate and absolute method for the determination of their molar concentration.

    PubMed

    Guermant, C; Azarkan, M; Smolders, N; Baeyens-Volant, D; Nijs, M; Paul, C; Brygier, J; Vincentelli, J; Looze, Y

    2000-01-01

    Oxidation at 120 degrees C of inorganic and organic (including amino acids, di- and tripeptides) model compounds by K(2)Cr(2)O(7) in the presence of H(2)SO(4) (mass fraction: 0.572), Ag(2)SO(4) (catalyst), and HgSO(4) results in the quantitative conversion of their C-atoms into CO(2) within 24 h or less. Under these stressed, well-defined conditions, the S-atoms present in cysteine and cystine residues are oxidized into SO(3) while, interestingly, the oxidation states of all the other (including the N-) atoms normally present in a protein do remain quite unchanged. When the chemical structure of a given protein is available, the total number of electrons the protein is able to transfer to K(2)Cr(2)O(7) and thereof, the total number of moles of Cr(3+) ions which the protein is able to generate upon oxidation can be accurately calculated. In such cases, unknown protein molar concentrations can thus be determined through straightforward spectrophotometric measurements of Cr(3+) concentrations. The values of molar absorption coefficients for several well-characterized proteins have been redetermined on this basis and observed to be in excellent agreement with the most precise values reported in the literature, which fully assesses the validity of the method. When applied to highly purified proteins of known chemical structure (more generally of known atomic composition), this method is absolute and accurate (+/-1%). Furthermore, it is well adapted to series measurements since available commercial kits for chemical oxygen demand (COD) measurements can readily be adapted to work under the experimental conditions recommended here for the protein assay. PMID:10610688

  10. Accurate Method for Determining Adhesion of Cantilever Beams

    SciTech Connect

    Michalske, T.A.; de Boer, M.P.

    1999-01-08

    Using surface micromachined samples, we demonstrate the accurate measurement of cantilever beam adhesion by using test structures which are adhered over long attachment lengths. We show that this configuration has a deep energy well, such that a fracture equilibrium is easily reached. When compared to the commonly used method of determining the shortest attached beam, the present method is much less sensitive to variations in surface topography or to details of capillary drying.

  11. The importance of suppressing spin diffusion effects in the accurate determination of the spatial structure of a flexible molecule by nuclear Overhauser effect spectroscopy

    NASA Astrophysics Data System (ADS)

    Khodov, I. A.; Efimov, S. V.; Klochkov, V. V.; Batista de Carvalho, L. A. E.; Kiselev, M. G.

    2016-02-01

    Two-dimensional nuclear Overhauser effect spectroscopy is applied to the elucidation of conformation distribution of small molecules in solution. An essential influence of the nonlinear multistep magnetization transfer (spin diffusion) on the NMR-based analysis of conformers distribution for small druglike molecules in solution was revealed. Therefore, the spin diffusion should be eliminated from the obtained NMR data in order to obtain accurate results. Efficiency of QUIET-NOESY spectroscopy in solving the problem of accurate determination of inter-proton distances in a small molecule was shown in a study of ibuprofen. Although it requires much experimental time, this technique was found to be helpful to solve the spin diffusion problem.

  12. Accurate determination of the amino acid content of selected feedstuffs.

    PubMed

    Rutherfurd, Shane M

    2009-01-01

    The accurate determination of the amino acid content is important. In the present study, a least-squares non-linear regression model of the amino acid content determined over multiple hydrolysis times was used to accurately determine the content of amino acids in five different feedstuffs. These values were compared with 24-h hydrolysis values determined for the same feedstuffs. Overall, approximately two-thirds of the amino acids determined in this study (aspartic acid, threonine, glutamic acid, proline, glycine, alanine, leucine, tyrosine, phenylalanine and arginine) using 24-h hydrolysis were in good agreement (<3% difference). When examined across feedstuffs, the concentration of serine was underestimated by the 24-h hydrolysis method by 4.8%, while the concentrations of histidine and lysine were overestimated by 3.9% and 3.1%, respectively.

  13. Precise and Accurate Density Determination of Explosives Using Hydrostatic Weighing

    SciTech Connect

    B. Olinger

    2005-07-01

    Precise and accurate density determination requires weight measurements in air and water using sufficiently precise analytical balances, knowledge of the densities of air and water, knowledge of thermal expansions, availability of a density standard, and a method to estimate the time to achieve thermal equilibrium with water. Density distributions in pressed explosives are inferred from the densities of elements from a central slice.

  14. Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.

    PubMed

    Puzzarini, Cristina

    2015-11-25

    The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed.

  15. Accurate Determination of Conformational Transitions in Oligomeric Membrane Proteins

    PubMed Central

    Sanz-Hernández, Máximo; Vostrikov, Vitaly V.; Veglia, Gianluigi; De Simone, Alfonso

    2016-01-01

    The structural dynamics governing collective motions in oligomeric membrane proteins play key roles in vital biomolecular processes at cellular membranes. In this study, we present a structural refinement approach that combines solid-state NMR experiments and molecular simulations to accurately describe concerted conformational transitions identifying the overall structural, dynamical, and topological states of oligomeric membrane proteins. The accuracy of the structural ensembles generated with this method is shown to reach the statistical error limit, and is further demonstrated by correctly reproducing orthogonal NMR data. We demonstrate the accuracy of this approach by characterising the pentameric state of phospholamban, a key player in the regulation of calcium uptake in the sarcoplasmic reticulum, and by probing its dynamical activation upon phosphorylation. Our results underline the importance of using an ensemble approach to characterise the conformational transitions that are often responsible for the biological function of oligomeric membrane protein states. PMID:26975211

  16. Accurate fluorescence quantum yield determination by fluorescence correlation spectroscopy.

    PubMed

    Kempe, Daryan; Schöne, Antonie; Fitter, Jörg; Gabba, Matteo

    2015-04-01

    Here, we present a comparative method for the accurate determination of fluorescence quantum yields (QYs) by fluorescence correlation spectroscopy. By exploiting the high sensitivity of single-molecule spectroscopy, we obtain the QYs of samples in the microliter range and at (sub)nanomolar concentrations. Additionally, in combination with fluorescence lifetime measurements, our method allows the quantification of both static and collisional quenching constants. Thus, besides being simple and fast, our method opens up the possibility to photophysically characterize labeled biomolecules under application-relevant conditions and with low sample consumption, which is often important in single-molecule studies.

  17. Accurate and reproducible determination of lignin molar mass by acetobromination.

    PubMed

    Asikkala, Janne; Tamminen, Tarja; Argyropoulos, Dimitris S

    2012-09-12

    The accurate and reproducible determination of lignin molar mass by using size exclusion chromatography (SEC) is challenging. The lignin association effects, known to dominate underivatized lignins, have been thoroughly addressed by reaction with acetyl bromide in an excess of glacial acetic acid. The combination of a concerted acetylation with the introduction of bromine within the lignin alkyl side chains is thought to be responsible for the observed excellent solubilization characteristics acetobromination imparts to a variety of lignin samples. The proposed methodology was compared and contrasted to traditional lignin derivatization methods. In addition, side reactions that could possibly be induced under the acetobromination conditions were explored with native softwood (milled wood lignin, MWL) and technical (kraft) lignin. These efforts lend support toward the use of room temperature acetobromination being a facile, effective, and universal lignin derivatization medium proposed to be employed prior to SEC measurements. PMID:22870925

  18. Accurate determination of segmented X-ray detector geometry

    PubMed Central

    Yefanov, Oleksandr; Mariani, Valerio; Gati, Cornelius; White, Thomas A.; Chapman, Henry N.; Barty, Anton

    2015-01-01

    Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical for many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. We show that the refined detector geometry greatly improves the results of experiments. PMID:26561117

  19. Accurate determination of segmented X-ray detector geometry.

    PubMed

    Yefanov, Oleksandr; Mariani, Valerio; Gati, Cornelius; White, Thomas A; Chapman, Henry N; Barty, Anton

    2015-11-01

    Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical for many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. We show that the refined detector geometry greatly improves the results of experiments.

  20. Accurate determination of segmented X-ray detector geometry.

    PubMed

    Yefanov, Oleksandr; Mariani, Valerio; Gati, Cornelius; White, Thomas A; Chapman, Henry N; Barty, Anton

    2015-11-01

    Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical for many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. We show that the refined detector geometry greatly improves the results of experiments. PMID:26561117

  1. A versatile phenomenological model for the S-shaped temperature dependence of photoluminescence energy for an accurate determination of the exciton localization energy in bulk and quantum well structures

    NASA Astrophysics Data System (ADS)

    Dixit, V. K.; Porwal, S.; Singh, S. D.; Sharma, T. K.; Ghosh, Sandip; Oak, S. M.

    2014-02-01

    Temperature dependence of the photoluminescence (PL) peak energy of bulk and quantum well (QW) structures is studied by using a new phenomenological model for including the effect of localized states. In general an anomalous S-shaped temperature dependence of the PL peak energy is observed for many materials which is usually associated with the localization of excitons in band-tail states that are formed due to potential fluctuations. Under such conditions, the conventional models of Varshni, Viña and Passler fail to replicate the S-shaped temperature dependence of the PL peak energy and provide inconsistent and unrealistic values of the fitting parameters. The proposed formalism persuasively reproduces the S-shaped temperature dependence of the PL peak energy and provides an accurate determination of the exciton localization energy in bulk and QW structures along with the appropriate values of material parameters. An example of a strained InAs0.38P0.62/InP QW is presented by performing detailed temperature and excitation intensity dependent PL measurements and subsequent in-depth analysis using the proposed model. Versatility of the new formalism is tested on a few other semiconductor materials, e.g. GaN, nanotextured GaN, AlGaN and InGaN, which are known to have a significant contribution from the localized states. A quantitative evaluation of the fractional contribution of the localized states is essential for understanding the temperature dependence of the PL peak energy of bulk and QW well structures having a large contribution of the band-tail states.

  2. Nanoparticle counting: towards accurate determination of the molar concentration.

    PubMed

    Shang, Jing; Gao, Xiaohu

    2014-11-01

    Innovations in nanotechnology have brought tremendous opportunities for the advancement of many research frontiers, ranging from electronics, photonics, energy, to medicine. To maximize the benefits of nano-scaled materials in different devices and systems, precise control of their concentration is a prerequisite. While concentrations of nanoparticles have been provided in other forms (e.g., mass), accurate determination of molar concentration, arguably the most useful one for chemical reactions and applications, has been a major challenge (especially for nanoparticles smaller than 30 nm). Towards this significant yet chronic problem, a variety of strategies are currently under development. Most of these strategies are applicable to a specialized group of nanoparticles due to their restrictions on the composition and size range of nanoparticles. As research and uses of nanomaterials are being explored in an unprecedented speed, it is necessary to develop universal strategies that are easy to use and are compatible with nanoparticles of different sizes, compositions, and shapes. This review outlines the theories and applications of current strategies to measure nanoparticle molar concentration, discusses the advantages and limitations of these methods, and provides insights into future directions.

  3. Accurate Classification of RNA Structures Using Topological Fingerprints

    PubMed Central

    Li, Kejie; Gribskov, Michael

    2016-01-01

    While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC > 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at https://github.rcac.purdue.edu/mgribsko/XIOS_RNA_fingerprint. PMID:27755571

  4. Fast and accurate determination of modularity and its effect size

    NASA Astrophysics Data System (ADS)

    Treviño, Santiago, III; Nyberg, Amy; Del Genio, Charo I.; Bassler, Kevin E.

    2015-02-01

    We present a fast spectral algorithm for community detection in complex networks. Our method searches for the partition with the maximum value of the modularity via the interplay of several refinement steps that include both agglomeration and division. We validate the accuracy of the algorithm by applying it to several real-world benchmark networks. On all these, our algorithm performs as well or better than any other known polynomial scheme. This allows us to extensively study the modularity distribution in ensembles of Erdős-Rényi networks, producing theoretical predictions for means and variances inclusive of finite-size corrections. Our work provides a way to accurately estimate the effect size of modularity, providing a z-score measure of it and enabling a more informative comparison of networks with different numbers of nodes and links.

  5. Apparatus enables accurate determination of alkali oxides in alkali metals

    NASA Technical Reports Server (NTRS)

    Dupraw, W. A.; Gahn, R. F.; Graab, J. W.; Maple, W. E.; Rosenblum, L.

    1966-01-01

    Evacuated apparatus determines the alkali oxide content of an alkali metal by separating the metal from the oxide by amalgamation with mercury. The apparatus prevents oxygen and moisture from inadvertently entering the system during the sampling and analytical procedure.

  6. Accurate Determination of the Volume of an Irregular Helium Balloon

    NASA Astrophysics Data System (ADS)

    Blumenthal, Jack; Bradvica, Rafaela; Karl, Katherine

    2013-02-01

    In a recent paper, Zable described an experiment with a near-spherical balloon filled with impure helium. Measuring the temperature and the pressure inside and outside the balloon, the lift of the balloon, and the mass of the balloon materials, he described how to use the ideal gas laws and Archimedes' principal to compute the average molecular mass and density of the impure helium. This experiment required that the volume of the near-spherical balloon be determined by some approach, such as measuring the girth. The accuracy of the experiment was largely determined by the balloon volume, which had a reported uncertainty of about 4%.

  7. Accurate Optical Target Pose Determination for Applications in Aerial Photogrammetry

    NASA Astrophysics Data System (ADS)

    Cucci, D. A.

    2016-06-01

    We propose a new design for an optical coded target based on concentric circles and a position and orientation determination algorithm optimized for high distances compared to the target size. If two ellipses are fitted on the edge pixels corresponding to the outer and inner circles, quasi-analytical methods are known to obtain the coordinates of the projection of the circles center. We show the limits of these methods for quasi-frontal target orientations and in presence of noise and we propose an iterative refinement algorithm based on a geometric invariant. Next, we introduce a closed form, computationally inexpensive, solution to obtain the target position and orientation given the projected circle center and the parameters of the outer circle projection. The viability of the approach is demonstrated based on aerial pictures taken by an UAV from elevations between 10 to 100 m. We obtain a distance RMS below 0.25 % under 50 m and below 1 % under 100 m with a target size of 90 cm, part of which is a deterministic bias introduced by image exposure.

  8. Structural Determination of Circulation.

    ERIC Educational Resources Information Center

    Blankenburg, William B.

    1981-01-01

    Analyzes the effects of both structural factors (demographics, economic conditions, and competition) and discretionary factors (content, design, and marketing techniques) and concludes that it is the former that determine a newspaper's circulation. (FL)

  9. Accurate Determination of Torsion and Pure Bending Moment for Viscoelastic Measurements

    NASA Astrophysics Data System (ADS)

    Wang, Yun-Che; Ko, Chih-Chin; Shiau, Li-Ming

    Measurements of time-dependent material properties in the context of linear viscoelasticity, at a given frequency and temperature, require accurate determination of both loading and deformation that are subjected to the testing materials. A pendulum-type viscoelastic spectroscopy is developed to experimentally measure loss tangent and the magnitude of dynamic modulus of solid materials. The mechanical system of the device is based on the behavior of the cantilever beam, and torsion and pure bending moment are generated from the interaction between a permanent magnet and the Helmholtz coils. The strength of the magnetic interactions may be determined with a material with known mechanical properties, such as aluminum 6061T4 alloy. The sensitivity of the torque measurement is on the order of one micro N-m level. With the high accurate torque measurement and deformation detection from a laser-based displacement measurement system, viscoelastic properties of materials can be experimentally measured in different frequency regimes. Sinusoidal driving signals are adopted for measuring complex modulus in the sub-resonant regime, and dc bias driving for creep tests in the low frequency limit. At structural resonant frequencies, the full-width-at-half-maximum (FWHM) method or Lorentzian curve fitting method is adopted to extract material properties. The completion of determining material properties in the wide frequency spectrum may help to identify the deformation mechanisms of the material and to create better models for simulation work.

  10. Fast and accurate determination of sites along the FUT2 in vitro transcript that are accessible to antisense oligonucleotides by application of secondary structure predictions and RNase H in combination with MALDI-TOF mass spectrometry

    PubMed Central

    Gabler, Angelika; Krebs, Stefan; Seichter, Doris; Förster, Martin

    2003-01-01

    Alteration of gene expression by use of antisense oligonucleotides has considerable potential for therapeutic purposes and scientific studies. Although applied for almost 25 years, this technique is still associated with difficulties in finding antisense-effective regions along the target mRNA. This is mainly due to strong secondary structures preventing binding of antisense oligonucleotides and RNase H, playing a major role in antisense-mediated degradation of the mRNA. These difficulties make empirical testing of a large number of sequences complementary to various sites in the target mRNA a very lengthy and troublesome procedure. To overcome this problem, more recent strategies to find efficient antisense sites are based on secondary structure prediction and RNase H-dependent mechanisms. We were the first who directly combined these two strategies; antisense oligonucleotides complementary to predicted unpaired target mRNA regions were designed and hybridized to the corresponding RNAs. Incubation with RNase H led to cleavage of the RNA at the respective hybridization sites. Analysis of the RNA fragments by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, which has not been used in this context before, allowed exact determination of the cleavage site. Thus the technique described here is very promising when searching for effective antisense sites. PMID:12888531

  11. Accurate determination of the vapor pressure of potassium using optical absorption

    NASA Technical Reports Server (NTRS)

    Shirinzadeh, B.; Wang, C. C.

    1983-01-01

    The vapor pressure of potassium has been measured in absorption using a CW tunable laser and calibrated against the accurate radiative lifetime of the 4s-4p doublet of potassium. An accurate value of 20,850 + or - 30 cal/mol for the heat of vaporization (from the liquid phase) at the melting point was determined.

  12. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    PubMed Central

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  13. Fluorescence polarization immunoassays for rapid, accurate, and sensitive determination of mycotoxins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analytical methods for the determination of mycotoxins in foods are commonly based on chromatographic techniques (GC, HPLC or LC-MS). Although these methods permit a sensitive and accurate determination of the analyte, they require skilled personnel and are time-consuming, expensive, and unsuitable ...

  14. Corrigendum to "The importance of suppressing spin diffusion effects in the accurate determination of the spatial structure of a flexible molecule by nuclear Overhauser effect spectroscopy" [J. Mol. Struct. 1106 (2016) 373-381

    NASA Astrophysics Data System (ADS)

    Khodov, I. A.; Efimov, S. V.; Kiselev, M. G.; Batista de Carvalho, L. A. E.; Klochkov, V. V.

    2016-06-01

    The original article to which this erratum refers was published in Journal of Molecular Structure, vol. 1106 (2016) [1]. In the original version of this article, Table 1 contained an error in column 10 (interatom distance averaging following the (r6)-algorithm, proton pairs H9-H5 and H7-H9). Analogous mistype was also present in Table 2 in Ref. [2] for distances H7-H9. Values present in Refs. [1,2] were far too small, but they were presented only for the sake of comparison of different averaging methods and did not influence the final conformer distribution. The Table 1 is reproduced below with the error corrected.

  15. Optical coherence tomography enables accurate measurement of equine cartilage thickness for determination of speed of sound.

    PubMed

    Puhakka, Pia H; Te Moller, Nikae C R; Tanska, Petri; Saarakkala, Simo; Tiitu, Virpi; Korhonen, Rami K; Brommer, Harold; Virén, Tuomas; Jurvelin, Jukka S; Töyräs, Juha

    2016-08-01

    Background and purpose - Arthroscopic estimation of articular cartilage thickness is important for scoring of lesion severity, and measurement of cartilage speed of sound (SOS)-a sensitive index of changes in cartilage composition. We investigated the accuracy of optical coherence tomography (OCT) in measurements of cartilage thickness and determined SOS by combining OCT thickness and ultrasound (US) time-of-flight (TOF) measurements. Material and methods - Cartilage thickness measurements from OCT and microscopy images of 94 equine osteochondral samples were compared. Then, SOS in cartilage was determined using simultaneous OCT thickness and US TOF measurements. SOS was then compared with the compositional, structural, and mechanical properties of cartilage. Results - Measurements of non-calcified cartilage thickness using OCT and microscopy were significantly correlated (ρ = 0.92; p < 0.001). With calcified cartilage included, the correlation was ρ = 0.85 (p < 0.001). The mean cartilage SOS (1,636 m/s) was in agreement with the literature. However, SOS and the other properties of cartilage lacked any statistically significant correlation. Interpretation - OCT can give an accurate measurement of articular cartilage thickness. Although SOS measurements lacked accuracy in thin equine cartilage, the concept of SOS measurement using OCT appears promising.

  16. Factors affecting the accurate determination of cerebrovascular blood flow using high-speed droplet imaging

    NASA Astrophysics Data System (ADS)

    Rudin, Stephen; Divani, Afshin; Wakhloo, Ajay K.; Lieber, Baruch B.; Granger, William; Bednarek, Daniel R.; Yang, Chang-Ying J.

    1998-07-01

    Detailed cerebrovascular blood flow can be more accurately determined radiographically from the new droplet tracking method previously introduced by the authors than from standard soluble contrast techniques. For example, arteriovenous malformation (AVM) transit times which are crucial for proper glue embolization treatments, were shown to be about half when using droplets compared to those measured using soluble contrast techniques. In this work, factors such as x-ray pulse duration, frame rate, system spatial resolution (focal spot size), droplet size, droplet and system contrast parameters, and system noise are considered in relation to their affect on the accurate determination of droplet location and velocity.

  17. Aperture taper determination for the half-scale accurate antenna reflector

    NASA Technical Reports Server (NTRS)

    Lambert, Kevin M.

    1990-01-01

    A simulation is described of a proposed microwave reflectance measurement in which the half scale reflector is used in a compact range type of application. The simulation is used to determine an acceptable aperture taper for the reflector which will allow for accurate measurements. Information on the taper is used in the design of a feed for the reflector.

  18. On canonical cylinder sections for accurate determination of contact angle in microgravity

    SciTech Connect

    Concus, P.; Zabihi, F. California Univ., Berkeley, CA . Dept. of Mathematics); Finn, R. . Dept. of Mathematics)

    1992-07-01

    Large shifts of liquid arising from small changes in certain container shapes in zero gravity can be used as a basis for accurately determining contact angle. Canonical'' geometries for this purpose, recently developed mathematically, are investigated here computationally. It is found that the desired nearly- discontinuous'' behavior can be obtained and that the shifts of liquid have sufficient volume to be readily observed.

  19. On canonical cylinder sections for accurate determination of contact angle in microgravity

    SciTech Connect

    Concus, P.; Zabihi, F. |; Finn, R.

    1992-07-01

    Large shifts of liquid arising from small changes in certain container shapes in zero gravity can be used as a basis for accurately determining contact angle. ``Canonical`` geometries for this purpose, recently developed mathematically, are investigated here computationally. It is found that the desired ``nearly- discontinuous`` behavior can be obtained and that the shifts of liquid have sufficient volume to be readily observed.

  20. The determination of accurate dipole polarizabilities alpha and gamma for the noble gases

    NASA Technical Reports Server (NTRS)

    Rice, Julia E.; Taylor, Peter R.; Lee, Timothy J.; Almlof, Jan

    1991-01-01

    Accurate static dipole polarizabilities alpha and gamma of the noble gases He through Xe were determined using wave functions of similar quality for each system. Good agreement with experimental data for the static polarizability gamma was obtained for Ne and Xe, but not for Ar and Kr. Calculations suggest that the experimental values for these latter ions are too low.

  1. How accurately can the peak skin dose in fluoroscopy be determined using indirect dose metrics?

    SciTech Connect

    Jones, A. Kyle; Ensor, Joe E.; Pasciak, Alexander S.

    2014-07-15

    Purpose: Skin dosimetry is important for fluoroscopically-guided interventions, as peak skin doses (PSD) that result in skin reactions can be reached during these procedures. There is no consensus as to whether or not indirect skin dosimetry is sufficiently accurate for fluoroscopically-guided interventions. However, measuring PSD with film is difficult and the decision to do so must be madea priori. The purpose of this study was to assess the accuracy of different types of indirect dose estimates and to determine if PSD can be calculated within ±50% using indirect dose metrics for embolization procedures. Methods: PSD were measured directly using radiochromic film for 41 consecutive embolization procedures at two sites. Indirect dose metrics from the procedures were collected, including reference air kerma. Four different estimates of PSD were calculated from the indirect dose metrics and compared along with reference air kerma to the measured PSD for each case. The four indirect estimates included a standard calculation method, the use of detailed information from the radiation dose structured report, and two simplified calculation methods based on the standard method. Indirect dosimetry results were compared with direct measurements, including an analysis of uncertainty associated with film dosimetry. Factors affecting the accuracy of the different indirect estimates were examined. Results: When using the standard calculation method, calculated PSD were within ±35% for all 41 procedures studied. Calculated PSD were within ±50% for a simplified method using a single source-to-patient distance for all calculations. Reference air kerma was within ±50% for all but one procedure. Cases for which reference air kerma or calculated PSD exhibited large (±35%) differences from the measured PSD were analyzed, and two main causative factors were identified: unusually small or large source-to-patient distances and large contributions to reference air kerma from cone

  2. Accurate and precise determination of isotopic ratios by MC-ICP-MS: a review.

    PubMed

    Yang, Lu

    2009-01-01

    For many decades the accurate and precise determination of isotope ratios has remained a very strong interest to many researchers due to its important applications in earth, environmental, biological, archeological, and medical sciences. Traditionally, thermal ionization mass spectrometry (TIMS) has been the technique of choice for achieving the highest accuracy and precision. However, recent developments in multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) have brought a new dimension to this field. In addition to its simple and robust sample introduction, high sample throughput, and high mass resolution, the flat-topped peaks generated by this technique provide for accurate and precise determination of isotope ratios with precision reaching 0.001%, comparable to that achieved with TIMS. These features, in combination with the ability of the ICP source to ionize nearly all elements in the periodic table, have resulted in an increased use of MC-ICP-MS for such measurements in various sample matrices. To determine accurate and precise isotope ratios with MC-ICP-MS, utmost care must be exercised during sample preparation, optimization of the instrument, and mass bias corrections. Unfortunately, there are inconsistencies and errors evident in many MC-ICP-MS publications, including errors in mass bias correction models. This review examines "state-of-the-art" methodologies presented in the literature for achievement of precise and accurate determinations of isotope ratios by MC-ICP-MS. Some general rules for such accurate and precise measurements are suggested, and calculations of combined uncertainty of the data using a few common mass bias correction models are outlined.

  3. Accurate determination of absolute carrier-envelope phase dependence using photo-ionization.

    PubMed

    Sayler, A M; Arbeiter, M; Fasold, S; Adolph, D; Möller, M; Hoff, D; Rathje, T; Fetić, B; Milošević, D B; Fennel, T; Paulus, G G

    2015-07-01

    The carrier-envelope phase (CEP) dependence of few-cycle above-threshold ionization (ATI) of Xe is calibrated for use as a reference measurement for determining and controlling the absolute CEP in other interactions. This is achieved by referencing the CEP-dependent ATI measurements of Xe to measurements of atomic H, which are in turn referenced to ab initio calculations for atomic H. This allows for the accurate determination of the absolute CEP dependence of Xe ATI, which enables relatively easy determination of the offset between the relative CEP measured and/or controlled by typical devices and the absolute CEP in the interaction. PMID:26125386

  4. Ultrasound Dilution: An Accurate Means of Determining Cardiac Output in Children

    PubMed Central

    Crittendon, Ivory; Dreyer, William J.; Decker, Jamie A; Kim, Jeffrey J.

    2011-01-01

    Background Cardiac output (CO) is a useful measure of myocardial performance. CO monitoring is frequently performed in critically ill adults in order to guide physicians’ treatment strategies. However, standard methods of determining CO in children are not without risk and can be problematic secondary to their invasive nature and other technical problems. COstatus® system (Transonic Systems Inc, NY, USA), which is based on ultrasound dilution technology, works off in situ catheters and uses an innocuous indicator to allow for routine measurements of cardiac output and blood volumes in pediatric patients. The purpose of this study was to validate CO measured by COstatus® with those obtained by the clinical standard technique of pulmonary artery (PAC) thermodilution. Methods This was a prospective evaluation performed at a single institution. Any child with a structurally normal heart undergoing hemodynamic evaluation in the cardiac catheterization laboratory was included. A prograde right heart catheterization was performed, and CO was first determined by using the PAC thermodilution technique. Thermodilution results were then compared with CO measurements obtained using the COstatus system. The results were analyzed by standard correlation, Bland-Altman, and Crichtley and Critchley analyses. Results Twenty-eight patients were evaluated with a median age of 8 yrs and a median weight of 31 kg. The mean thermodilution cardiac index = 3.18 L/min (+/− 1.35 L/min), and the mean COstatus® cardiac index = 3.17 L/min (+/− 1.31 L/min). Standard Pearson correlation tests revealed an excellent correlation coefficient of 0.95 (p<0.0001). Bland-Altman analysis revealed good clinical agreement with a mean difference of −0.004 L/min with a precision of 0.8 L/min/ at 2 SD. A percentage error of 25.4% was noticed in this study which is less than the clinically acceptable limit. Conclusion The ultrasound dilution technique of determining CO using the COstatus® system

  5. Rapid and accurate determination of the lignin content of lignocellulosic biomass by solid-state NMR.

    PubMed

    Fu, Li; McCallum, Scott A; Miao, Jianjun; Hart, Courtney; Tudryn, Gregory J; Zhang, Fuming; Linhardt, Robert J

    2015-02-01

    Biofuels and biomaterials, produced from lignocellulosic feedstock, require facile access to cellulose and hemicellulose to be competitive with petroleum processing and sugar-based fermentation. Physical-chemical barriers resulting from lignin complicates the hydrolysis biomass into fermentable sugars. Thus, the amount of lignin within a substrate is critical in determining biomass processing. The application of (13)C cross-polarization, magic-angle spinning, and solid-state nuclear magnetic resonance for the direct quantification of lignin content in biomass is examined. Using a standard curve constructed from pristine lignin and cellulose, the lignin content of a biomass sample is accurately determined through direct measurement without chemical or enzymatic pre-treatment.

  6. Determining structural performance

    NASA Technical Reports Server (NTRS)

    Ernst, Michael A.; Kiraly, Louis J.

    1987-01-01

    An overview is given of the methods and concepts developed to enhance and predict structural dynamic characteristics of advanced aeropropulsion systems. Aeroelasticity, Vibration Control, Dynamic Systems, and Computational Structural Methods are four disciplines that make up the research program at NASA/Lewis Research Center. The Aeroelasticity program develops analytical and experimental methods to minimize flutter and forced vibration of aerospace propulsion systems. Both frequency domain and time domain methods have been developed for applications on the turbofan, turbopump, and advanced turboprop. To improve life and performance, the Vibration Control program conceives, analyzes, develops, and demonstrates new methods to control vibrations in aerospace systems. Active and passive vibration control is accomplished with electromagnetic dampers, magnetic bearings, and piezoelectric crystals to control rotor vibrations. The Dynamic Systems program analyzes and verifies the dynamics of interacting systems, as well as develops concepts and methods for high-temperature dynamic seals. The Computational Structural Methods program uses computer science to improve solutions of structural problems.

  7. Accurate determination of aldehydes in amine catalysts or amines by 2,4-dinitrophenylhydrazine derivatization.

    PubMed

    Barman, Bhajendra N

    2014-01-31

    Carbonyl compounds, specifically aldehydes, present in amine catalysts or amines are determined by reversed-phase liquid chromatography using ultraviolet detection of their corresponding 2,4-dinitrophenylhydrazones. The primary focus has been to establish optimum conditions for determining aldehydes accurately because these add exposure concerns when the amine catalysts are used to manufacture polyurethane products. Concentrations of aldehydes determined by this method are found to vary with the pH of the aqueous amine solution and the derivatization time, the latter being problematic when the derivatization reaction proceeds slowly and not to completion in neutral and basic media. Accurate determination of aldehydes in amines through derivatization can be carried out at an effective solution pH of about 2 and with derivatization time of 20min. Hydrochloric acid has been used for neutralization of an amine. For complete derivatization, it is essential to protonate all nitrogen atoms in the amine. An approach for the determination of an adequate amount of acid needed for complete derivatization has been described. Several 0.2M buffer solutions varying in pH from 4 to 8 have also been used to make amine solutions for carrying out derivatization of aldehydes. These solutions have effective pHs of 10 or higher and provide much lower aldehyde concentrations compared to their true values. Mechanisms for the formation of 2,4-dinitrophenylhydrazones in both acidic and basic media are discussed. PMID:24411140

  8. A highly accurate method for determination of dissolved oxygen: gravimetric Winkler method.

    PubMed

    Helm, Irja; Jalukse, Lauri; Leito, Ivo

    2012-09-01

    A high-accuracy Winkler titration method has been developed for determination of dissolved oxygen concentration. Careful analysis of uncertainty sources relevant to the Winkler method was carried out and the method was optimized for minimizing all uncertainty sources as far as practical. The most important improvements were: gravimetric measurement of all solutions, pre-titration to minimize the effect of iodine volatilization, accurate amperometric end point detection and careful accounting for dissolved oxygen in the reagents. As a result, the developed method is possibly the most accurate method of determination of dissolved oxygen available. Depending on measurement conditions and on the dissolved oxygen concentration the combined standard uncertainties of the method are in the range of 0.012-0.018 mg dm(-3) corresponding to the k=2 expanded uncertainty in the range of 0.023-0.035 mg dm(-3) (0.27-0.38%, relative). This development enables more accurate calibration of electrochemical and optical dissolved oxygen sensors for routine analysis than has been possible before.

  9. Determining structural performance

    NASA Technical Reports Server (NTRS)

    Ernst, Michael A. (Editor); Brown, Gerald; Dirusso, Eliseo; Fleming, David; Janetzke, David; Kascak, Albert; Kaza, Krishna; Kielb, Robert; Kiraly, Louis J.; Lawrence, Charles

    1990-01-01

    An overview of the methods and concepts developed to enhance and predict structural dynamic characteristics of advanced aeropropulsion systems is presented. Aeroelasticity, vibration control, dynamic systems, and computational structural methods are four disciplines that make up the structural dynamic effort at LeRC. The aeroelasticity program develops analytical and experimental methods for minimizing flutter and forced vibration of aerospace propulsion systems. Both frequency domain and time domain methods were developed for applications on the turbofan, turbopump, and advanced turboprop. In order to improve life and performance, the vibration control program conceives, analyzes, develops, and demonstrates new methods for controlling vibrations in aerospace systems. Active and passive vibration control is accomplished with electromagnetic dampers, magnetic bearings, and piezoelectric crystals to control rotor vibrations. The dynamic systems program analyzes and verifies the dynamics of interacting systems, as well as develops concepts and methods for high-temperature dynamic seals. Work in this field involves the analysis and parametric identification of large, nonlinear, damped, stochastic systems. The computational structural methods program exploits modern computer science as an aid to the solutions of structural problems.

  10. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

  11. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations

    PubMed Central

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-01-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-‘one-click’ experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  12. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  13. Accurate determination of protein methionine oxidation by stable isotope labeling and LC-MS analysis.

    PubMed

    Liu, Hongcheng; Ponniah, Gomathinayagam; Neill, Alyssa; Patel, Rekha; Andrien, Bruce

    2013-12-17

    Methionine (Met) oxidation is a major modification of proteins, which converts Met to Met sulfoxide as the common product. It is challenging to determine the level of Met sulfoxide, because it can be generated during sample preparation and analysis as an artifact. To determine the level of Met sulfoxide in proteins accurately, an isotope labeling and LC-MS peptide mapping method was developed. Met residues in proteins were fully oxidized using hydrogen peroxide enriched with (18)O atoms before sample preparation. Therefore, it was impossible to generate Met sulfoxide as an artifact during sample preparation. The molecular weight difference of 2 Da between Met sulfoxide with the (16)O atom and Met sulfoxide with the (18)O atom was used to differentiate and calculate the level of Met sulfoxide in the sample originally. Using a recombinant monoclonal antibody as a model protein, much lower levels of Met sulfoxide were detected for the two susceptible Met residues with this new method compared to a typical peptide mapping procedure. The results demonstrated efficient elimination of the analytical artifact during LC-MS peptide mapping for the measurement of Met sulfoxide. This method can thus be used when accurate determination of the level of Met sulfoxide is critical.

  14. The Development of a Digital Processing System for Accurate Range Determinations. [for Teleoperator Maneuvering Systems

    NASA Technical Reports Server (NTRS)

    Pujol, A., Jr.

    1983-01-01

    The development of an accurate close range (from 0.0 meters to 30.0 meters) radar system for Teleoperator Maneuvering Systems (TMS) is discussed. The system under investigation is a digital processor that converts incoming signals from the radar system into their related frequency spectra. Identification will be attempted by correlating spectral characteristics with accurate range determinataions. The system will utilize an analog to digital converter for sampling and converting the signal from the radar system into 16-bit digital words (two bytes) for RAM storage, data manipulations, and computations. To remove unwanted frequency components the data will be retrieved from RAM and digitally filtered using large scale integration (LSI) circuits. Filtering will be performed by a biquadratic routine within the chip which carries out the required filter algorithm. For conversion to a frequency spectrum the filtered data will be processed by a Fast Fourier Transform chip. Analysis and identification of spectral characteristics for accurate range determinations will be made by microcomputer computations.

  15. A powerful test of independent assortment that determines genome-wide significance quickly and accurately

    PubMed Central

    Stewart, W C L; Hager, V R

    2016-01-01

    In the analysis of DNA sequences on related individuals, most methods strive to incorporate as much information as possible, with little or no attention paid to the issue of statistical significance. For example, a modern workstation can easily handle the computations needed to perform a large-scale genome-wide inheritance-by-descent (IBD) scan, but accurate assessment of the significance of that scan is often hindered by inaccurate approximations and computationally intensive simulation. To address these issues, we developed gLOD—a test of co-segregation that, for large samples, models chromosome-specific IBD statistics as a collection of stationary Gaussian processes. With this simple model, the parametric bootstrap yields an accurate and rapid assessment of significance—the genome-wide corrected P-value. Furthermore, we show that (i) under the null hypothesis, the limiting distribution of the gLOD is the standard Gumbel distribution; (ii) our parametric bootstrap simulator is approximately 40 000 times faster than gene-dropping methods, and it is more powerful than methods that approximate the adjusted P-value; and, (iii) the gLOD has the same statistical power as the widely used maximum Kong and Cox LOD. Thus, our approach gives researchers the ability to determine quickly and accurately the significance of most large-scale IBD scans, which may contain multiple traits, thousands of families and tens of thousands of DNA sequences. PMID:27245422

  16. A powerful test of independent assortment that determines genome-wide significance quickly and accurately.

    PubMed

    Stewart, W C L; Hager, V R

    2016-08-01

    In the analysis of DNA sequences on related individuals, most methods strive to incorporate as much information as possible, with little or no attention paid to the issue of statistical significance. For example, a modern workstation can easily handle the computations needed to perform a large-scale genome-wide inheritance-by-descent (IBD) scan, but accurate assessment of the significance of that scan is often hindered by inaccurate approximations and computationally intensive simulation. To address these issues, we developed gLOD-a test of co-segregation that, for large samples, models chromosome-specific IBD statistics as a collection of stationary Gaussian processes. With this simple model, the parametric bootstrap yields an accurate and rapid assessment of significance-the genome-wide corrected P-value. Furthermore, we show that (i) under the null hypothesis, the limiting distribution of the gLOD is the standard Gumbel distribution; (ii) our parametric bootstrap simulator is approximately 40 000 times faster than gene-dropping methods, and it is more powerful than methods that approximate the adjusted P-value; and, (iii) the gLOD has the same statistical power as the widely used maximum Kong and Cox LOD. Thus, our approach gives researchers the ability to determine quickly and accurately the significance of most large-scale IBD scans, which may contain multiple traits, thousands of families and tens of thousands of DNA sequences.

  17. Accurate bulk density determination of irregularly shaped translucent and opaque aerogels

    NASA Astrophysics Data System (ADS)

    Petkov, M. P.; Jones, S. M.

    2016-05-01

    We present a volumetric method for accurate determination of bulk density of aerogels, calculated from extrapolated weight of the dry pure solid and volume estimates based on the Archimedes' principle of volume displacement, using packed 100 μm-sized monodispersed glass spheres as a "quasi-fluid" media. Hard particle packing theory is invoked to demonstrate the reproducibility of the apparent density of the quasi-fluid. Accuracy rivaling that of the refractive index method is demonstrated for both translucent and opaque aerogels with different absorptive properties, as well as for aerogels with regular and irregular shapes.

  18. Accurate orbit determination strategies for the tracking and data relay satellites

    NASA Technical Reports Server (NTRS)

    Oza, D. H.; Bolvin, D. T.; Lorah, J. M.; Lee, T.; Doll, C. E.

    1995-01-01

    The National Aeronautics and Space Administration (NASA) has developed the Tracking and Data Relay Satellite (TDRS) System (TDRSS) for tracking and communications support of low Earth-orbiting satellites. TDRSS has the operational capability of providing 85% coverage for TDRSS-user spacecraft. TDRSS currently consists of five geosynchronous spacecraft and the White Sands Complex (WSC) at White Sands, New Mexico. The Bilateration Ranging Transponder System (BRTS) provides range and Doppler measurements for each TDRS. The ground-based BRTS transponders are tracked as if they were TDRSS-user spacecraft. Since the positions of the BRTS transponders are known, their radiometric tracking measurements can be used to provide a well-determined ephemeris for the TDRS spacecraft. For high-accuracy orbit determination of a TDRSS user, such as the Ocean Topography Experiment (TOPEX)/Poseidon spacecraft, high-accuracy TDRS orbits are required. This paper reports on successive refinements in improved techniques and procedures leading to more accurate TDRS orbit determination strategies using the Goddard Trajectory Determination System (GTDS). These strategies range from the standard operational solution using only the BRTS tracking measurements to a sophisticated iterative process involving several successive simultaneous solutions for multiple TDRSs and a TDRSS-user spacecraft. Results are presented for GTDS-generated TDRS ephemerides produced in simultaneous solutions with the TOPEX/Poseidon spacecraft. Strategies with different user spacecraft, as well as schemes for recovering accurate TDRS orbits following a TDRS maneuver, are also presented. In addition, a comprehensive assessment and evaluation of alternative strategies for TDRS orbit determination, excluding BRTS tracking measurements, are presented.

  19. Accurate determination of the temperature dependent thermalization coefficient (Q) in InAs/AlAsSb quantum wells

    NASA Astrophysics Data System (ADS)

    Esmaielpour, Hamidreza; Tang, Jinfeng; Whiteside, Vincent R.; Vijeyaragunathan, Sangeetha; Mishima, Tetsuya D.; Santos, Michael B.; Sellers, Ian R.

    2015-03-01

    We present an investigation of hot carriers in InAs/AlAsSb quantum wells as a practical candidate for a hot carrier solar cell absorber. The thermalization coefficient (Q) of the sample is investigated using continuous wave photoluminescence (PL). The Q is accurately determined through transfer matrix calculations of the absorption, analysis of the power density, penetration depth, diffusion, and recombination rates using a combination of simulation and empirical methods. A precise measurement of laser spot size is important in order to determine the absorbed power density. Simulations were performed based on our PL geometry in order to calculate the excitation spot size, which was compared with experiment by measurements using variable diameter pinholes to determine beam radius. Here, these techniques are described, in addition to, the temperature dependent hot carrier dynamics and phonon mediated thermalization coefficient for the InAs/AlAsSb quantum well structure.

  20. Accurate determination of fiber water-retaining capability at process conditions by headspace gas chromatography.

    PubMed

    Zhang, Shu-Xin; Chai, Xin-Sheng; He, Liang

    2016-09-16

    This work reports on a method for the accurate determination of fiber water-retaining capability at process conditions by headspace gas chromatography (HS-GC) method. The method was based the HS-GC measurement of water vapor on a set closed vials containing in a given amount pulp with different amounts of water addition, from under-saturation to over-saturation. By plotting the equilibrated water vapor signal vs. the amount of water added in pulp, two different trend lines can be observed, in which the transition of the lines corresponds to fiber water-retaining capability. The results showed that the HS-GC method has good measurement precision (much better than the reference method) and good accuracy. The present method can be also used for determining pulp fiber water-retaining capability at the process temperatures in both laboratory research and mill applications. PMID:27554029

  1. Rapid and accurate determination of tissue optical properties using least-squares support vector machines

    PubMed Central

    Barman, Ishan; Dingari, Narahara Chari; Rajaram, Narasimhan; Tunnell, James W.; Dasari, Ramachandra R.; Feld, Michael S.

    2011-01-01

    Diffuse reflectance spectroscopy (DRS) has been extensively applied for the characterization of biological tissue, especially for dysplasia and cancer detection, by determination of the tissue optical properties. A major challenge in performing routine clinical diagnosis lies in the extraction of the relevant parameters, especially at high absorption levels typically observed in cancerous tissue. Here, we present a new least-squares support vector machine (LS-SVM) based regression algorithm for rapid and accurate determination of the absorption and scattering properties. Using physical tissue models, we demonstrate that the proposed method can be implemented more than two orders of magnitude faster than the state-of-the-art approaches while providing better prediction accuracy. Our results show that the proposed regression method has great potential for clinical applications including in tissue scanners for cancer margin assessment, where rapid quantification of optical properties is critical to the performance. PMID:21412464

  2. Rapid and accurate determination of tissue optical properties using least-squares support vector machines.

    PubMed

    Barman, Ishan; Dingari, Narahara Chari; Rajaram, Narasimhan; Tunnell, James W; Dasari, Ramachandra R; Feld, Michael S

    2011-01-01

    Diffuse reflectance spectroscopy (DRS) has been extensively applied for the characterization of biological tissue, especially for dysplasia and cancer detection, by determination of the tissue optical properties. A major challenge in performing routine clinical diagnosis lies in the extraction of the relevant parameters, especially at high absorption levels typically observed in cancerous tissue. Here, we present a new least-squares support vector machine (LS-SVM) based regression algorithm for rapid and accurate determination of the absorption and scattering properties. Using physical tissue models, we demonstrate that the proposed method can be implemented more than two orders of magnitude faster than the state-of-the-art approaches while providing better prediction accuracy. Our results show that the proposed regression method has great potential for clinical applications including in tissue scanners for cancer margin assessment, where rapid quantification of optical properties is critical to the performance. PMID:21412464

  3. Rapid and accurate determination of the lignin content of lignocellulosic biomass by solid-state NMR.

    PubMed

    Fu, Li; McCallum, Scott A; Miao, Jianjun; Hart, Courtney; Tudryn, Gregory J; Zhang, Fuming; Linhardt, Robert J

    2015-02-01

    Biofuels and biomaterials, produced from lignocellulosic feedstock, require facile access to cellulose and hemicellulose to be competitive with petroleum processing and sugar-based fermentation. Physical-chemical barriers resulting from lignin complicates the hydrolysis biomass into fermentable sugars. Thus, the amount of lignin within a substrate is critical in determining biomass processing. The application of (13)C cross-polarization, magic-angle spinning, and solid-state nuclear magnetic resonance for the direct quantification of lignin content in biomass is examined. Using a standard curve constructed from pristine lignin and cellulose, the lignin content of a biomass sample is accurately determined through direct measurement without chemical or enzymatic pre-treatment. PMID:25404762

  4. Rapid and accurate determination of the lignin content of lignocellulosic biomass by solid-state NMR

    PubMed Central

    Fu, Li; McCallum, Scott A.; Miao, Jianjun; Hart, Courtney; Tudryn, Gregory J.; Zhang, Fuming; Linhardt, Robert J.

    2014-01-01

    Biofuels and biomaterials, produced from lignocellulosic feedstock, require facile access to cellulose and hemicellulose to be competitive with petroleum processing and sugar-based fermentation. Physical-chemical barriers resulting from lignin complicates the hydrolysis biomass into fermentable sugars. Thus, the amount of lignin within a substrate is critical in determining biomass processing. The application of 13C cross-polarization, magic-angle spinning, and solid-state nuclear magnetic resonance for the direct quantification of lignin content in biomass is examined. Using a standard curve constructed from pristine lignin and cellulose, the lignin content of a biomass sample is accurately determined through direct measurement without chemical or enzymatic pre-treatment. PMID:25404762

  5. Accurate determination of renal function in patients with intestinal urinary diversions

    SciTech Connect

    McDougal, W.S.; Koch, M.O.

    1986-06-01

    The regular determination of renal function is a critical part of the management of patients who have had the urinary tract reconstructed with intestinal segments. These intestinal segments reabsorb urinary solutes and, thereby, complicate the determination of renal function by conventional methods. Urinary clearances of urea, creatinine and inulin were performed in patients with intestinal segments in the urinary tract and controls under varying diuretic conditions. Patients with intestinal diversions also underwent radioisotopic determination of renal function. The urinary clearances of urea, creatinine and inulin are highly dependent on the rate of urine flow in patients with intestinal segments in the urinary tract. Diuresis maximizes the urinary clearances of these solutes by minimizing intestinal reabsorption. Creatinine clearance prediction from the serum creatinine underestimates true glomerular filtration rate. Radioisotopic determination of renal function correlates poorly with true glomerular filtration rate. Only creatinine clearance measured under diuretic conditions correlates well with true renal function. Urine concentrating ability cannot be assessed accurately in patients with intestinal segments in the urinary tract, since osmolality rapidly equilibrates across the segments.

  6. An improved thin film approximation to accurately determine the optical conductivity of graphene from infrared transmittance

    SciTech Connect

    Weber, J. W.; Bol, A. A.; Sanden, M. C. M. van de

    2014-07-07

    This work presents an improved thin film approximation to extract the optical conductivity from infrared transmittance in a simple yet accurate way. This approximation takes into account the incoherent reflections from the backside of the substrate. These reflections are shown to have a significant effect on the extracted optical conductivity and hence on derived parameters as carrier mobility and density. By excluding the backside reflections, the error for these parameters for typical chemical vapor deposited (CVD) graphene on a silicon substrate can be as high as 17% and 45% for the carrier mobility and density, respectively. For the mid- and near-infrared, the approximation can be simplified such that the real part of the optical conductivity is extracted without the need for a parameterization of the optical conductivity. This direct extraction is shown for Fourier transform infrared (FTIR) transmittance measurements of CVD graphene on silicon in the photon energy range of 370–7000 cm{sup −1}. From the real part of the optical conductivity, the carrier density, mobility, and number of graphene layers are determined but also residue, originating from the graphene transfer, is detected. FTIR transmittance analyzed with the improved thin film approximation is shown to be a non-invasive, easy, and accurate measurement and analysis method for assessing the quality of graphene and can be used for other 2-D materials.

  7. Accurate determination of plasmid copy number of flow-sorted cells using droplet digital PCR.

    PubMed

    Jahn, Michael; Vorpahl, Carsten; Türkowsky, Dominique; Lindmeyer, Martin; Bühler, Bruno; Harms, Hauke; Müller, Susann

    2014-06-17

    Many biotechnological processes rely on the expression of a plasmid-based target gene. A constant and sufficient number of plasmids per cell is desired for efficient protein production. To date, only a few methods for the determination of plasmid copy number (PCN) are available, and most of them average the PCN of total populations disregarding heterogeneous distributions. Here, we utilize the highly precise quantification of DNA molecules by droplet digital PCR (ddPCR) and combine it with cell sorting using flow cytometry. A duplex PCR assay was set up requiring only 1000 sorted cells for precise determination of PCN. The robustness of this method was proven by thorough optimization of cell sorting, cell disruption, and PCR conditions. When non plasmid-harboring cells of Pseudomonas putida KT2440 were spiked with different dilutions of the expression plasmid pA-EGFP_B, a PCN from 1 to 64 could be accurately detected. As a proof of principle, induced cultures of P. putida KT2440 producing an EGFP-fused model protein by means of the plasmid pA-EGFP_B were investigated by flow cytometry and showed two distinct subpopulations, fluorescent and nonfluorescent cells. These two subpopulations were sorted for PCN determination with ddPCR. A remarkably diverging plasmid distribution was found within the population, with nonfluorescent cells showing a much lower PCN (≤1) than fluorescent cells (PCN of up to 5) under standard conditions.

  8. Efficient construction of robust artificial neural networks for accurate determination of superficial sample optical properties

    PubMed Central

    Chen, Yu-Wen; Tseng, Sheng-Hao

    2015-01-01

    In general, diffuse reflectance spectroscopy (DRS) systems work with photon diffusion models to determine the absorption coefficient μa and reduced scattering coefficient μs' of turbid samples. However, in some DRS measurement scenarios, such as using short source-detector separations to investigate superficial tissues with comparable μa and μs', photon diffusion models might be invalid or might not have analytical solutions. In this study, a systematic workflow of constructing a rapid, accurate photon transport model that is valid at short source-detector separations (SDSs) and at a wide range of sample albedo is revealed. To create such a model, we first employed a GPU (Graphic Processing Unit) based Monte Carlo model to calculate the reflectance at various sample optical property combinations and established a database at high speed. The database was then utilized to train an artificial neural network (ANN) for determining the sample absorption and reduced scattering coefficients from the reflectance measured at several SDSs without applying spectral constraints. The robustness of the produced ANN model was rigorously validated. We evaluated the performance of a successfully trained ANN using tissue simulating phantoms. We also determined the 500-1000 nm absorption and reduced scattering spectra of in-vivo skin using our ANN model and found that the values agree well with those reported in several independent studies. PMID:25798300

  9. Looking at the cooler hosts - accurate metallicity determination of M dwarfs with and without planets

    NASA Astrophysics Data System (ADS)

    Lindgren, Sara; Heiter, Ulrike

    2015-12-01

    M dwarfs constitute 70% of the stars in the local Galaxy and are becoming attractive targets in the search for Earth-sized planets and planets within the habitable zone. With our research we aim to extend the current understanding of planet formation theory and explore the planet - host metallicity correlation for these cooler hosts.Unlike their solar-type counterparts, the metallicity of M dwarfs is difficult to determine. Their low surface temperature results in plenty of diatomic and triatomic molecules in the photospheric layers. Especially in the optical wavelength region these molecules give rise to a forest of millions of weak lines, making accurate spectroscopy nearly impossible. Previous studies of M dwarfs have therefore established different metallicity calibrations using photometric colors or spectral indices. But these methods exclude the possibility of detailed chemical analysis. High-resolution spectrographs operating in the infrared have recently opened up a new window for investigating M dwarfs. In the infrared the number of molecular transitions is greatly reduced, allowing an accurate continuum placement, and a large number of unblended atomic lines are available. This enabled us to use similar methods as is standard for warmer solar-like stars, and determine the overall metallicity through synthetic spectral fitting.In the first part of our work we used high-resolution spectra taken in the J band (1100-1400nm) with the CRIRES spectrograph, VLT, to verify our method internally and externally by analyzing both components in several M+FGK binaries. In the second part of this study we are analyzing 20 single M dwarfs to achieve a good coverage of effective temperature and metallicity, where our sample covers subtypes M0-M6 and estimated metallicites ranging from +0.8 to -0.8 dex. With these data we aim to derive the to-date most accurate relationship between photometric colors and metallicity for M dwarfs. We will present the current status of our

  10. A method for accurate determination of terminal sequences of viral genomic RNA.

    PubMed

    Weng, Z; Xiong, Z

    1995-09-01

    A combination of ligation-anchored PCR and anchored cDNA cloning techniques were used to clone the termini of the saguaro cactus virus (SCV) RNA genome. The terminal sequences of the viral genome were subsequently determined from the clones. The 5' terminus was cloned by ligation-anchored PCR, whereas the 3' terminus was obtained by a technique we term anchored cDNA cloning. In anchored cDNA cloning, an anchor oligonucleotide was prepared by phosphorylation at the 5' end, followed by addition of a dideoxynucleotide at the 3' end to block the free hydroxyl group. The 5' end of the anchor was subsequently ligated to the 3' end of SCV RNA. The anchor-ligated, chimerical viral RNA was then reverse-transcribed into cDNA using a primer complementary to the anchor. The cDNA containing the complete 3'-terminal sequence was converted into ds-cDNA, cloned, and sequenced. Two restriction sites, one within the viral sequence and one within the primer sequence, were used to facilitate cloning. The combination of these techniques proved to be an easy and accurate way to determine the terminal sequences of SCV RNA genome and should be applicable to any other RNA molecules with unknown terminal sequences. PMID:9132274

  11. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions

    PubMed Central

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-01-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe− using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm−1 or 153.236(34) meV. The fine structures of Fe− were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm−1 accuracy. PMID:27138292

  12. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions

    NASA Astrophysics Data System (ADS)

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-05-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe‑ using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm‑1 or 153.236(34) meV. The fine structures of Fe‑ were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm‑1 accuracy.

  13. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions.

    PubMed

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-01-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe(-) using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm(-1) or 153.236(34) meV. The fine structures of Fe(-) were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm(-1) accuracy. PMID:27138292

  14. Accurate Determination of Comet and Asteroid Orbits Leading to Collision With Earth

    NASA Technical Reports Server (NTRS)

    Roithmayr, Carlos M.; Kay-Bunnell, Linda; Mazanek, Daniel D.; Kumar, Renjith R.; Seywald, Hans; Hausman, Matthew A.

    2005-01-01

    Movements of the celestial bodies in our solar system inspired Isaac Newton to work out his profound laws of gravitation and motion; with one or two notable exceptions, all of those objects move as Newton said they would. But normally harmonious orbital motion is accompanied by the risk of collision, which can be cataclysmic. The Earth s moon is thought to have been produced by such an event, and we recently witnessed magnificent bombardments of Jupiter by several pieces of what was once Comet Shoemaker-Levy 9. Other comets or asteroids may have met the Earth with such violence that dinosaurs and other forms of life became extinct; it is this possibility that causes us to ask how the human species might avoid a similar catastrophe, and the answer requires a thorough understanding of orbital motion. The two red square flags with black square centers displayed are internationally recognized as a warning of an impending hurricane. Mariners and coastal residents who know the meaning of this symbol and the signs evident in the sky and ocean can act in advance to try to protect lives and property; someone who is unfamiliar with the warning signs or chooses to ignore them is in much greater jeopardy. Although collisions between Earth and large comets or asteroids occur much less frequently than landfall of a hurricane, it is imperative that we learn to identify the harbingers of such collisions by careful examination of an object s path. An accurate determination of the orbit of a comet or asteroid is necessary in order to know if, when, and where on the Earth s surface a collision will occur. Generally speaking, the longer the warning time, the better the chance of being able to plan and execute action to prevent a collision. The more accurate the determination of an orbit, the less likely such action will be wasted effort or, what is worse, an effort that increases rather than decreases the probability of a collision. Conditions necessary for a collision to occur are

  15. Accurate and precise determination of critical properties from Gibbs ensemble Monte Carlo simulations

    SciTech Connect

    Dinpajooh, Mohammadhasan; Bai, Peng; Allan, Douglas A.; Siepmann, J. Ilja

    2015-09-21

    Since the seminal paper by Panagiotopoulos [Mol. Phys. 61, 813 (1997)], the Gibbs ensemble Monte Carlo (GEMC) method has been the most popular particle-based simulation approach for the computation of vapor–liquid phase equilibria. However, the validity of GEMC simulations in the near-critical region has been questioned because rigorous finite-size scaling approaches cannot be applied to simulations with fluctuating volume. Valleau [Mol. Simul. 29, 627 (2003)] has argued that GEMC simulations would lead to a spurious overestimation of the critical temperature. More recently, Patel et al. [J. Chem. Phys. 134, 024101 (2011)] opined that the use of analytical tail corrections would be problematic in the near-critical region. To address these issues, we perform extensive GEMC simulations for Lennard-Jones particles in the near-critical region varying the system size, the overall system density, and the cutoff distance. For a system with N = 5500 particles, potential truncation at 8σ and analytical tail corrections, an extrapolation of GEMC simulation data at temperatures in the range from 1.27 to 1.305 yields T{sub c} = 1.3128 ± 0.0016, ρ{sub c} = 0.316 ± 0.004, and p{sub c} = 0.1274 ± 0.0013 in excellent agreement with the thermodynamic limit determined by Potoff and Panagiotopoulos [J. Chem. Phys. 109, 10914 (1998)] using grand canonical Monte Carlo simulations and finite-size scaling. Critical properties estimated using GEMC simulations with different overall system densities (0.296 ≤ ρ{sub t} ≤ 0.336) agree to within the statistical uncertainties. For simulations with tail corrections, data obtained using r{sub cut} = 3.5σ yield T{sub c} and p{sub c} that are higher by 0.2% and 1.4% than simulations with r{sub cut} = 5 and 8σ but still with overlapping 95% confidence intervals. In contrast, GEMC simulations with a truncated and shifted potential show that r{sub cut} = 8σ is insufficient to obtain accurate results. Additional GEMC simulations for hard

  16. Accurate and precise determination of critical properties from Gibbs ensemble Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Bai, Peng; Allan, Douglas A.; Siepmann, J. Ilja

    2015-09-01

    Since the seminal paper by Panagiotopoulos [Mol. Phys. 61, 813 (1997)], the Gibbs ensemble Monte Carlo (GEMC) method has been the most popular particle-based simulation approach for the computation of vapor-liquid phase equilibria. However, the validity of GEMC simulations in the near-critical region has been questioned because rigorous finite-size scaling approaches cannot be applied to simulations with fluctuating volume. Valleau [Mol. Simul. 29, 627 (2003)] has argued that GEMC simulations would lead to a spurious overestimation of the critical temperature. More recently, Patel et al. [J. Chem. Phys. 134, 024101 (2011)] opined that the use of analytical tail corrections would be problematic in the near-critical region. To address these issues, we perform extensive GEMC simulations for Lennard-Jones particles in the near-critical region varying the system size, the overall system density, and the cutoff distance. For a system with N = 5500 particles, potential truncation at 8σ and analytical tail corrections, an extrapolation of GEMC simulation data at temperatures in the range from 1.27 to 1.305 yields Tc = 1.3128 ± 0.0016, ρc = 0.316 ± 0.004, and pc = 0.1274 ± 0.0013 in excellent agreement with the thermodynamic limit determined by Potoff and Panagiotopoulos [J. Chem. Phys. 109, 10914 (1998)] using grand canonical Monte Carlo simulations and finite-size scaling. Critical properties estimated using GEMC simulations with different overall system densities (0.296 ≤ ρt ≤ 0.336) agree to within the statistical uncertainties. For simulations with tail corrections, data obtained using rcut = 3.5σ yield Tc and pc that are higher by 0.2% and 1.4% than simulations with rcut = 5 and 8σ but still with overlapping 95% confidence intervals. In contrast, GEMC simulations with a truncated and shifted potential show that rcut = 8σ is insufficient to obtain accurate results. Additional GEMC simulations for hard-core square-well particles with various ranges of the

  17. An accurate, efficient algorithm for calculation of quantum transport in extended structures

    SciTech Connect

    Godin, T.J.; Haydock, R.

    1994-05-01

    In device structures with dimensions comparable to carrier inelastic scattering lengths, the quantum nature of carriers will cause interference effects that cannot be modeled by conventional techniques. The basic equations that govern these ``quantum`` circuit elements present significant numerical challenges. The authors describe the block recursion method, an accurate, efficient method for solving the quantum circuit problem. They demonstrate this method by modeling dirty inversion layers.

  18. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

    PubMed

    Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J; Brewster, Aaron S; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R; Miahnahri, Alan; White, William E; Schafer, Donald W; Seibert, M Marvin; Koglin, Jason E; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J; Glatzel, Pieter; Zwart, Petrus H; Grosse-Kunstleve, Ralf W; Bogan, Michael J; Messerschmidt, Marc; Williams, Garth J; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K; Adams, Paul D; Sauter, Nicholas K

    2014-05-01

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

  19. Accurate Determination of Interstrand Distances and Alignment in Amyloid Fibrils by Magic Angle Spinning NMR

    PubMed Central

    Caporini, Marc A.; Bajaj, Vikram S.; Veshtort, Mikhail; Fitzpatrick, Anthony; MacPhee, Cait E; Vendruscolo, Michele; Dobson, Christopher M.; Griffin, Robert G.

    2010-01-01

    Amyloid fibrils are structurally ordered aggregates of proteins whose formation is associated with many neurodegenerative and other diseases. For that reason, their high resolution structures are of considerable interest and have been studied using a wide range of techniques, notably electron microscopy, x-ray diffraction, and magic angle spinning (MAS) NMR. Because of the excellent resolution in the spectra, MAS NMR is uniquely capable of delivering site-specific, atomic resolution information about all levels of amyloid structure: (1) the monomer, which packs into several (2) protofilaments that in turn associate to form a (3) fibril. Building upon our high resolution structure of the monomer of an amyloid-forming peptide from transthyretin (TTR105-115), we introduce single 1-13C labeled amino acids at seven different sites in the peptide and measure intermolecular carbonyl-carbonyl distances with an accuracy of ~0.11 A. Our results conclusively establish a parallel, in register, topology for the packing of this peptide into a β-sheet and provide constraints essential for the determination of an atomic resolution structure of the fibril. Furthermore, the approach we employ, based on a combination of a double-quantum filtered variant of the DRAWS recoupling sequence and multispin numerical simulations in SPINEVOLUTION, is general and should be applicable to a wide range of systems. PMID:20925357

  20. A miniature shoe-mounted orientation determination system for accurate indoor heading and trajectory tracking.

    PubMed

    Zhang, Shengzhi; Yu, Shuai; Liu, Chaojun; Liu, Sheng

    2016-06-01

    Tracking the position of pedestrian is urgently demanded when the most commonly used GPS (Global Position System) is unavailable. Benefited from the small size, low-power consumption, and relatively high reliability, micro-electro-mechanical system sensors are well suited for GPS-denied indoor pedestrian heading estimation. In this paper, a real-time miniature orientation determination system (MODS) was developed for indoor heading and trajectory tracking based on a novel dual-linear Kalman filter. The proposed filter precludes the impact of geomagnetic distortions on pitch and roll that the heading is subjected to. A robust calibration approach was designed to improve the accuracy of sensors measurements based on a unified sensor model. Online tests were performed on the MODS with an improved turntable. The results demonstrate that the average RMSE (root-mean-square error) of heading estimation is less than 1°. Indoor heading experiments were carried out with the MODS mounted on the shoe of pedestrian. Besides, we integrated the existing MODS into an indoor pedestrian dead reckoning application as an example of its utility in realistic actions. A human attitude-based walking model was developed to calculate the walking distance. Test results indicate that mean percentage error of indoor trajectory tracking achieves 2% of the total walking distance. This paper provides a feasible alternative for accurate indoor heading and trajectory tracking. PMID:27370490

  1. Diagnostic methodology is critical for accurately determining the prevalence of ichthyophonus infections in wild fish populations

    USGS Publications Warehouse

    Kocan, R.; Dolan, H.; Hershberger, P.

    2011-01-01

    Several different techniques have been employed to detect and identify Ichthyophonus spp. in infected fish hosts; these include macroscopic observation, microscopic examination of tissue squashes, histological evaluation, in vitro culture, and molecular techniques. Examination of the peer-reviewed literature revealed that when more than 1 diagnostic method is used, they often result in significantly different results; for example, when in vitro culture was used to identify infected trout in an experimentally exposed population, 98.7% of infected trout were detected, but when standard histology was used to confirm known infected tissues from wild salmon, it detected ~50% of low-intensity infections and ~85% of high-intensity infections. Other studies on different species reported similar differences. When we examined a possible mechanism to explain the disparity between different diagnostic techniques, we observed non-random distribution of the parasite in 3-dimensionally visualized tissue sections from infected hosts, thus providing a possible explanation for the different sensitivities of commonly used diagnostic techniques. Based on experimental evidence and a review of the peer-reviewed literature, we have concluded that in vitro culture is currently the most accurate diagnostic technique for determining infection prevalence of Ichthyophonus, particularly when the exposure history of the population is not known.

  2. A highly accurate method for the determination of mass and center of mass of a spacecraft

    NASA Technical Reports Server (NTRS)

    Chow, E. Y.; Trubert, M. R.; Egwuatu, A.

    1978-01-01

    An extremely accurate method for the measurement of mass and the lateral center of mass of a spacecraft has been developed. The method was needed for the Voyager spacecraft mission requirement which limited the uncertainty in the knowledge of lateral center of mass of the spacecraft system weighing 750 kg to be less than 1.0 mm (0.04 in.). The method consists of using three load cells symmetrically located at 120 deg apart on a turntable with respect to the vertical axis of the spacecraft and making six measurements for each load cell. These six measurements are taken by cyclic rotations of the load cell turntable and of the spacecraft, about the vertical axis of the measurement fixture. This method eliminates all alignment, leveling, and load cell calibration errors for the lateral center of mass determination, and permits a statistical best fit of the measurement data. An associated data reduction computer program called MASCM has been written to implement this method and has been used for the Voyager spacecraft.

  3. The determination of accurate dipole polarizabilities alpha and gamma for the noble gases

    NASA Technical Reports Server (NTRS)

    Rice, Julia E.; Taylor, Peter R.; Lee, Timothy J.; Almloef, Jan

    1989-01-01

    The static dipole polarizabilities alpha and gamma for the noble gases helium through xenon were determined using large flexible one-particle basis sets in conjunction with high-level treatments of electron correlation. The electron correlation methods include single and double excitation coupled-cluster theory (CCSD), an extension of CCSD that includes a perturbational estimate of connected triple excitations, CCSD(T), and second order perturbation theory (MP2). The computed alpha and gamma values are estimated to be accurate to within a few percent. Agreement with experimental data for the static hyperpolarizability gamma is good for neon and xenon, but for argon and krypton the differences are larger than the combined theoretical and experimental uncertainties. Based on our calculations, we suggest that the experimental value of gamma for argon is too low; adjusting this value would bring the experimental value of gamma for krypton into better agreement with our computed result. The MP2 values for the polarizabilities of neon, argon, krypton and zenon are in reasonabe agreement with the CCSD and CCSD(T) values, suggesting that this less expensive method may be useful in studies of polarizabilities for larger systems.

  4. A miniature shoe-mounted orientation determination system for accurate indoor heading and trajectory tracking

    NASA Astrophysics Data System (ADS)

    Zhang, Shengzhi; Yu, Shuai; Liu, Chaojun; Liu, Sheng

    2016-06-01

    Tracking the position of pedestrian is urgently demanded when the most commonly used GPS (Global Position System) is unavailable. Benefited from the small size, low-power consumption, and relatively high reliability, micro-electro-mechanical system sensors are well suited for GPS-denied indoor pedestrian heading estimation. In this paper, a real-time miniature orientation determination system (MODS) was developed for indoor heading and trajectory tracking based on a novel dual-linear Kalman filter. The proposed filter precludes the impact of geomagnetic distortions on pitch and roll that the heading is subjected to. A robust calibration approach was designed to improve the accuracy of sensors measurements based on a unified sensor model. Online tests were performed on the MODS with an improved turntable. The results demonstrate that the average RMSE (root-mean-square error) of heading estimation is less than 1°. Indoor heading experiments were carried out with the MODS mounted on the shoe of pedestrian. Besides, we integrated the existing MODS into an indoor pedestrian dead reckoning application as an example of its utility in realistic actions. A human attitude-based walking model was developed to calculate the walking distance. Test results indicate that mean percentage error of indoor trajectory tracking achieves 2% of the total walking distance. This paper provides a feasible alternative for accurate indoor heading and trajectory tracking.

  5. Significance of accurate diffraction corrections for the second harmonic wave in determining the acoustic nonlinearity parameter

    SciTech Connect

    Jeong, Hyunjo; Zhang, Shuzeng; Li, Xiongbing; Barnard, Dan

    2015-09-15

    The accurate measurement of acoustic nonlinearity parameter β for fluids or solids generally requires making corrections for diffraction effects due to finite size geometry of transmitter and receiver. These effects are well known in linear acoustics, while those for second harmonic waves have not been well addressed and therefore not properly considered in previous studies. In this work, we explicitly define the attenuation and diffraction corrections using the multi-Gaussian beam (MGB) equations which were developed from the quasilinear solutions of the KZK equation. The effects of making these corrections are examined through the simulation of β determination in water. Diffraction corrections are found to have more significant effects than attenuation corrections, and the β values of water can be estimated experimentally with less than 5% errors when the exact second harmonic diffraction corrections are used together with the negligible attenuation correction effects on the basis of linear frequency dependence between attenuation coefficients, α{sub 2} ≃ 2α{sub 1}.

  6. Final Progress Report: Isotope Identification Algorithm for Rapid and Accurate Determination of Radioisotopes Feasibility Study

    SciTech Connect

    Rawool-Sullivan, Mohini; Bounds, John Alan; Brumby, Steven P.; Prasad, Lakshman; Sullivan, John P.

    2012-04-30

    This is the final report of the project titled, 'Isotope Identification Algorithm for Rapid and Accurate Determination of Radioisotopes,' PMIS project number LA10-HUMANID-PD03. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). It summarizes work performed over the FY10 time period. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). Human analysts begin analyzing a spectrum based on features in the spectrum - lines and shapes that are present in a given spectrum. The proposed work was to carry out a feasibility study that will pick out all gamma ray peaks and other features such as Compton edges, bremsstrahlung, presence/absence of shielding and presence of neutrons and escape peaks. Ultimately success of this feasibility study will allow us to collectively explain identified features and form a realistic scenario that produced a given spectrum in the future. We wanted to develop and demonstrate machine learning algorithms that will qualitatively enhance the automated identification capabilities of portable radiological sensors that are currently being used in the field.

  7. Can scintillation detectors with low spectral resolution accurately determine radionuclides content of building materials?

    PubMed

    Kovler, K; Prilutskiy, Z; Antropov, S; Antropova, N; Bozhko, V; Alfassi, Z B; Lavi, N

    2013-07-01

    The current paper makes an attempt to check whether the scintillation NaI(Tl) detectors, in spite of their poor energy resolution, can determine accurately the content of NORM in building materials. The activity concentrations of natural radionuclides were measured using two types of detectors: (a) NaI(Tl) spectrometer equipped with the special software based on the matrix method of least squares, and (b) high-purity germanium spectrometer. Synthetic compositions with activity concentrations varying in a wide range, from 1/5 to 5 times median activity concentrations of the natural radionuclides available in the earth crust and the samples of popular building materials, such as concrete, pumice and gypsum, were tested, while the density of the tested samples changed in a wide range (from 860 up to 2,410 kg/m(3)). The results obtained in the NaI(Tl) system were similar to those obtained with the HPGe spectrometer, mostly within the uncertainty range. This comparison shows that scintillation spectrometers equipped with a special software aimed to compensate for the lower spectral resolution of NaI(Tl) detectors can be successfully used for the radiation control of mass construction products. PMID:23542118

  8. Rapid, accurate, and direct determination of total lycopene content in tomato paste

    NASA Astrophysics Data System (ADS)

    Bicanic, D.; Anese, M.; Luterotti, S.; Dadarlat, D.; Gibkes, J.; Lubbers, M.

    2003-01-01

    Lycopene that imparts red color to the tomato fruit is the most potent antioxidant among carotenes, an important nutrient and also used as a color ingredient in many food formulations. Since cooked and processed foods derived from tomatoes were shown to provide optimal lycopene boost, products such as paste, puree, juice, etc. are nowadays gaining popularity as dietary sources. The analysis of lycopene in tomato paste (partially dehydrated product prepared by vacuum concentrating tomato juice) is carried out using either high pressure liquid chromatography (HPLC), spectrophotometry, or by evaluating the color. The instability of lycopene during processes of extraction, etc., handling, and disposal of organic solvents makes the preparation of a sample for the analysis a delicate task. Despite a recognized need for accurate and rapid assessment of lycopene in tomato products no such method is available at present. The study described here focuses on a direct determination of a total lycopene content in different tomato pastes by means of the laser optothermal window (LOW) method at 502 nm. The concentration of lycopene in tomato paste ranged between 25 and 150 mg per 100 g product; the results are in excellent agreement with those obtained by spectrophotometry. The time needed to complete LOW analysis is very short, so that decomposition of pigment and the formation of artifacts are minimized. Preliminary results indicate a good degree of reproducibility making the LOW method suitable for routine assays of lycopene content in tomato paste.

  9. Determining suitable image resolutions for accurate supervised crop classification using remote sensing data

    NASA Astrophysics Data System (ADS)

    Löw, Fabian; Duveiller, Grégory

    2013-10-01

    Mapping the spatial distribution of crops has become a fundamental input for agricultural production monitoring using remote sensing. However, the multi-temporality that is often necessary to accurately identify crops and to monitor crop growth generally comes at the expense of coarser observation supports, and can lead to increasingly erroneous class allocations caused by mixed pixels. For a given application like crop classification, the spatial resolution requirement (e.g. in terms of a maximum tolerable pixel size) differs considerably over different landscapes. To analyse the spatial resolution requirements for accurate crop identification via image classification, this study builds upon and extends a conceptual framework established in a previous work1. This framework allows defining quantitatively the spatial resolution requirements for crop monitoring based on simulating how agricultural landscapes, and more specifically the fields covered by a crop of interest, are seen by instruments with increasingly coarser resolving power. The concept of crop specific pixel purity, defined as the degree of homogeneity of the signal encoded in a pixel with respect to the target crop type, is used to analyse how mixed the pixels can be (as they become coarser), without undermining their capacity to describe the desired surface properties. In this case, this framework has been steered towards answering the question: "What is the spatial resolution requirement for crop identification via supervised image classification, in particular minimum and coarsest acceptable pixel sizes, and how do these requirements change over different landscapes?" The framework is applied over four contrasting agro-ecological landscapes in Middle Asia. Inputs to the experiment were eight multi-temporal images from the RapidEye sensor, the simulated pixel sizes range from 6.5 m to 396.5 m. Constraining parameters for crop identification were defined by setting thresholds for classification

  10. Crystal structure determination of Efavirenz

    NASA Astrophysics Data System (ADS)

    Popeneciu, Horea; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria; Dumitru, Ristoiu

    2015-12-01

    Needle-shaped single crystals of the title compound, C14H9ClF3NO2, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  11. Accurate molecular structure and spectroscopic properties of nucleobases: a combined computational-microwave investigation of 2-thiouracil as a case study.

    PubMed

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L

    2013-10-21

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.

  12. CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval

    PubMed Central

    Karim, Rezaul; Aziz, Mohd. Momin Al; Shatabda, Swakkhar; Rahman, M. Sohel; Mia, Md. Abul Kashem; Zaman, Farhana; Rakin, Salman

    2015-01-01

    The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226

  13. Determinants and Polynomial Root Structure

    ERIC Educational Resources Information Center

    De Pillis, L. G.

    2005-01-01

    A little known property of determinants is developed in a manner accessible to beginning undergraduates in linear algebra. Using the language of matrix theory, a classical result by Sylvester that describes when two polynomials have a common root is recaptured. Among results concerning the structure of polynomial roots, polynomials with pairs of…

  14. Accurate structure and dynamics of the metal-site of paramagnetic metalloproteins from NMR parameters using natural bond orbitals.

    PubMed

    Hansen, D Flemming; Westler, William M; Kunze, Micha B A; Markley, John L; Weinhold, Frank; Led, Jens J

    2012-03-14

    A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal-ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal-ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for (15)N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of (15)N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of (15)N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site.

  15. Accurate Structure and Dynamics of the Metal-Site of Paramagnetic Metalloproteins from NMR Parameters Using Natural Bond Orbitals

    PubMed Central

    2012-01-01

    A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal–ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal–ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for 15N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of 15N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of 15N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site. PMID:22329704

  16. Accurate calculation of control-augmented structural eigenvalue sensitivities using reduced-order models

    NASA Technical Reports Server (NTRS)

    Livne, Eli

    1989-01-01

    A method is presented for generating mode shapes for model order reduction in a way that leads to accurate calculation of eigenvalue derivatives and eigenvalues for a class of control augmented structures. The method is based on treating degrees of freedom where control forces act or masses are changed in a manner analogous to that used for boundary degrees of freedom in component mode synthesis. It is especially suited for structures controlled by a small number of actuators and/or tuned by a small number of concentrated masses whose positions are predetermined. A control augmented multispan beam with closely spaced natural frequencies is used for numerical experimentation. A comparison with reduced-order eigenvalue sensitivity calculations based on the normal modes of the structure shows that the method presented produces significant improvements in accuracy.

  17. Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

    PubMed

    Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

    2016-06-21

    We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results. PMID:27240749

  18. Accurate Damage Location in Complex Composite Structures and Industrial Environments using Acoustic Emission

    NASA Astrophysics Data System (ADS)

    Eaton, M.; Pearson, M.; Lee, W.; Pullin, R.

    2015-07-01

    The ability to accurately locate damage in any given structure is a highly desirable attribute for an effective structural health monitoring system and could help to reduce operating costs and improve safety. This becomes a far greater challenge in complex geometries and materials, such as modern composite airframes. The poor translation of promising laboratory based SHM demonstrators to industrial environments forms a barrier to commercial up take of technology. The acoustic emission (AE) technique is a passive NDT method that detects elastic stress waves released by the growth of damage. It offers very sensitive damage detection, using a sparse array of sensors to detect and globally locate damage within a structure. However its application to complex structures commonly yields poor accuracy due to anisotropic wave propagation and the interruption of wave propagation by structural features such as holes and thickness changes. This work adopts an empirical mapping technique for AE location, known as Delta T Mapping, which uses experimental training data to account for such structural complexities. The technique is applied to a complex geometry composite aerospace structure undergoing certification testing. The component consists of a carbon fibre composite tube with varying wall thickness and multiple holes, that was loaded under bending. The damage location was validated using X-ray CT scanning and the Delta T Mapping technique was shown to improve location accuracy when compared with commercial algorithms. The onset and progression of damage were monitored throughout the test and used to inform future design iterations.

  19. 5D model for accurate representation and visualization of dynamic cardiac structures

    NASA Astrophysics Data System (ADS)

    Lin, Wei-te; Robb, Richard A.

    2000-05-01

    Accurate cardiac modeling is challenging due to the intricate structure and complex contraction patterns of myocardial tissues. Fast imaging techniques can provide 4D structural information acquired as a sequence of 3D images throughout the cardiac cycle. To mode. The beating heart, we created a physics-based surface model that deforms between successive time point in the cardiac cycle. 3D images of canine hearts were acquired during one complete cardiac cycle using the DSR and the EBCT. The left ventricle of the first time point is reconstructed as a triangular mesh. A mass-spring physics-based deformable mode,, which can expand and shrink with local contraction and stretching forces distributed in an anatomically accurate simulation of cardiac motion, is applied to the initial mesh and allows the initial mesh to deform to fit the left ventricle in successive time increments of the sequence. The resulting 4D model can be interactively transformed and displayed with associated regional electrical activity mapped onto anatomic surfaces, producing a 5D model, which faithfully exhibits regional cardiac contraction and relaxation patterns over the entire heart. The model faithfully represents structural changes throughout the cardiac cycle. Such models provide the framework for minimizing the number of time points required to usefully depict regional motion of myocardium and allow quantitative assessment of regional myocardial motion. The electrical activation mapping provides spatial and temporal correlation within the cardiac cycle. In procedures which as intra-cardiac catheter ablation, visualization of the dynamic model can be used to accurately localize the foci of myocardial arrhythmias and guide positioning of catheters for optimal ablation.

  20. Accurate determination of the nuclear quadrupole moment of xenon from the molecular method

    NASA Astrophysics Data System (ADS)

    Canella, Guilherme A.; Santiago, Régis T.; Haiduke, Roberto L. A.

    2016-09-01

    This study provides a new determination of the nuclear electric quadrupole moment (NQM) for 131Xe, which is achieved by the molecular method. Dirac-Coulomb Coupled Cluster calculations with a Gaunt correction (DC+G-CC) of electric field gradients (EFGs) and experimental nuclear quadrupole coupling constants of six molecular systems (XeH+, XeCuF, XeCuCl, XeAgF, XeAgCl and XeAuF) were considered. The best NQM obtained by our DC+G-CCSD-T EFGs was -114.6(1.1) mbarn, which is recommended as the new reference value for this nuclide given the high level electron structure calculations done here.

  1. Modeling of Non-Gravitational Forces for Precise and Accurate Orbit Determination

    NASA Astrophysics Data System (ADS)

    Hackel, Stefan; Gisinger, Christoph; Steigenberger, Peter; Balss, Ulrich; Montenbruck, Oliver; Eineder, Michael

    2014-05-01

    Remote sensing satellites support a broad range of scientific and commercial applications. The two radar imaging satellites TerraSAR-X and TanDEM-X provide spaceborne Synthetic Aperture Radar (SAR) and interferometric SAR data with a very high accuracy. The precise reconstruction of the satellite's trajectory is based on the Global Positioning System (GPS) measurements from a geodetic-grade dual-frequency Integrated Geodetic and Occultation Receiver (IGOR) onboard the spacecraft. The increasing demand for precise radar products relies on validation methods, which require precise and accurate orbit products. An analysis of the orbit quality by means of internal and external validation methods on long and short timescales shows systematics, which reflect deficits in the employed force models. Following the proper analysis of this deficits, possible solution strategies are highlighted in the presentation. The employed Reduced Dynamic Orbit Determination (RDOD) approach utilizes models for gravitational and non-gravitational forces. A detailed satellite macro model is introduced to describe the geometry and the optical surface properties of the satellite. Two major non-gravitational forces are the direct and the indirect Solar Radiation Pressure (SRP). The satellite TerraSAR-X flies on a dusk-dawn orbit with an altitude of approximately 510 km above ground. Due to this constellation, the Sun almost constantly illuminates the satellite, which causes strong across-track accelerations on the plane rectangular to the solar rays. The indirect effect of the solar radiation is called Earth Radiation Pressure (ERP). This force depends on the sunlight, which is reflected by the illuminated Earth surface (visible spectra) and the emission of the Earth body in the infrared spectra. Both components of ERP require Earth models to describe the optical properties of the Earth surface. Therefore, the influence of different Earth models on the orbit quality is assessed. The scope of

  2. Crystal structure determination of Efavirenz

    SciTech Connect

    Popeneciu, Horea Dumitru, Ristoiu; Tripon, Carmen Borodi, Gheorghe Pop, Mihaela Maria

    2015-12-23

    Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 2}, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  3. Novel gene complex structure determination

    SciTech Connect

    Gatewood, J.M.

    1997-08-01

    This is the final report of a one-year, Laboratory-Directed Research and Development (LORD) project at the Los Alamos National Laboratory. `Operative` chromatin containing exclusively the minor hasten variants was successfully isolated. Linker hasten H1 is quantitatively missing from operative chromatin. One of the aims of this proposal was to determine the proteins responsible for stabilizing operative chromatin. This chromatin is stabilized by microtubule proteins tar and tubulin. Another goal of this project was the structural characterization of operate chromatin nucleosomes. Using solution scattering, nucleosomes containing the minor variants were shown to be structurally distinct from major variant containing nucleosomes. The unusual structure and stabilization of operative chromatin by microtubule proteins provides a possible mechanism for direct interaction of transcription machinery with specific chromatin domains.

  4. The crystallization of biological macromolecules under microgravity: a way to more accurate three-dimensional structures?

    PubMed

    Lorber, Bernard

    2002-09-23

    The crystallization of proteins and other biological particles (including nucleic acids, nucleo-protein complexes and large assemblies such as nucleosomes, ribosomal subunits or viruses) in a microgravity environment can produce crystals having lesser defects than crystals prepared under normal gravity on earth. Such microgravity-grown crystals can diffract X-rays to a higher resolution and have a lower mosaic spread. The inferred electron density maps can be richer in details owing to which more accurate three-dimensional structure models can be built. Major results reported in this field of research are reviewed. Novel ones obtained with the Advanced Protein Crystallization Facility are presented. For structural biology, practical applications and implications associated with crystallization and crystallography onboard the International Space Station are discussed.

  5. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

  6. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure. PMID:19950907

  7. DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.

    PubMed

    Irfanoglu, M Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B; Sadeghi, Neda; Thomas, Cibu P; Pierpaoli, Carlo

    2016-05-15

    In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM.

  8. Fast and accurate search for non-coding RNA pseudoknot structures in genomes

    PubMed Central

    Huang, Zhibin; Wu, Yong; Robertson, Joseph; Feng, Liang; Malmberg, Russell L.; Cai, Liming

    2008-01-01

    Motivation: Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective based on the covariance model and CYK-type dynamic programming. However, the computational difficulty in aligning an RNA sequence to a pseudoknot has prohibited fast and accurate search of arbitrary RNA structures. Our previous work introduced a graph model for RNA pseudoknots and proposed to solve the structure–sequence alignment by graph optimization. Given k candidate regions in the target sequence for each of the n stems in the structure, we could compute a best alignment in time O(ktn) based upon a tree width t decomposition of the structure graph. However, to implement this method to programs that can routinely perform fast yet accurate RNA pseudoknot searches, we need novel heuristics to ensure that, without degrading the accuracy, only a small number of stem candidates need to be examined and a tree decomposition of a small tree width can always be found for the structure graph. Results: The current work builds on the previous one with newly developed preprocessing algorithms to reduce the values for parameters k and t and to implement the search method into a practical program, called RNATOPS, for RNA pseudoknot search. In particular, we introduce techniques, based on probabilistic profiling and distance penalty functions, which can identify for every stem just a small number k (e.g. k ≤ 10) of plausible regions in the target sequence to which the stem needs to align. We also devised a specialized tree decomposition algorithm that can yield tree decomposition of small tree width t (e.g. t ≤ 4) for almost all RNA structure graphs. Our experiments show that with RNATOPS it is possible to routinely search prokaryotic and eukaryotic genomes for specific RNA structures of medium to large sizes, including pseudoknots, with high sensitivity and high

  9. Technique for determination of accurate heat capacities of volatile, powdered, or air-sensitive samples using relaxation calorimetry

    NASA Astrophysics Data System (ADS)

    Marriott, Robert A.; Stancescu, Maria; Kennedy, Catherine A.; White, Mary Anne

    2006-09-01

    We introduce a four-step technique for the accurate determination of the heat capacity of volatile or air-sensitive samples using relaxation calorimetry. The samples are encapsulated in a hermetically sealed differential scanning calorimetry pan, in which there is an internal layer of Apiezon N grease to assist thermal relaxation. Using the Quantum Design physical property measurement system to investigate benzoic acid and copper standards, we find that this method can lead to heat capacity determinations accurate to ±2% over the temperature range of 1-300K, even for very small samples (e.g., <10mg and contributing ca. 20% to the total heat capacity).

  10. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    SciTech Connect

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.

  11. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    NASA Astrophysics Data System (ADS)

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-01

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.

  12. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures

    PubMed Central

    Holton, James M; Classen, Scott; Frankel, Kenneth A; Tainer, John A

    2014-01-01

    In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree. These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill. Database Coordinates and structure factors for the real data have been submitted to the Protein Data Bank under accession 4tws. PMID:25040949

  13. Structure determination of enterovirus 71

    SciTech Connect

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G.

    2013-02-20

    Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

  14. Accurate determination of specific heat at high temperatures using the flash diffusivity method

    NASA Technical Reports Server (NTRS)

    Vandersande, J. W.; Zoltan, A.; Wood, C.

    1989-01-01

    The flash diffusivity method of Parker et al. (1961) was used to measure accurately the specific heat of test samples simultaneously with thermal diffusivity, thus obtaining the thermal conductivity of these materials directly. The accuracy of data obtained on two types of materials (n-type silicon-germanium alloys and niobium), was + or - 3 percent. It is shown that the method is applicable up to at least 1300 K.

  15. Structural determinants of GAD antigenicity.

    PubMed

    Arafat, Yasir; Fenalti, Gustavo; Whisstock, James C; Mackay, Ian R; Garcia de la Banda, Maria; Rowley, Merrill J; Buckle, Ashley M

    2009-12-01

    Our aim was to ascertain structural determinants of autoantigenicity based on the model of the diabetes autoantigen glutamic acid decarboxylase 65 kDa isoform (GAD65) in comparison with that of the non-autoantigenic isoform GAD67. This difference exists despite the two isoforms having the same fold and high sequence identity. Autoantibodies to GAD65 precede the development of type 1 diabetes and are clinical markers of this and certain neural autoimmune diseases. To date, epitope mapping has been based on particular amino acid differences between the two isoforms, and there is no explanation as to why autoantibodies that react with GAD65 only infrequently cross-react with GAD67. To characterize each isoform of the enzyme and gain insights into their contrasting autoantigenic properties, we have used the recently determined crystal structures of GAD65 and GAD67 to compare their structure, hydrophobicity, electrostatics, flexibility and physiochemical properties. The results revealed striking differences which appear almost exclusively at the C-terminal domain of the isoforms. Whereas GAD65 displayed a highly charged and flexible C-terminal domain containing numerous patches of high electrostatic and solvation energies, these characteristics were absent in the GAD67 molecule. Additionally, analysis indicated potential N-terminal and PLP domain binding sites surrounding the C-terminal domain of GAD65, a major region of autoantigenic activity, but not of GAD67. These features agree with good accuracy with published epitope-mapping data. Our analysis suggests that the high flexibility and charge of GAD65 in the C-terminal domain is coupled with the mobility of its catalytic loop, a property that is absolutely required for its enzymatic function. Thus, the structural features that distinguish GAD65 from GAD67 as a B cell autoantigen are related to functional requirements for its enzymatic mechanism. This could well apply to the various other enzyme autoantigens and, if

  16. Accurate determination of solid and liquid dispersions from spectra channeled with the Fabry-Perot interferometer.

    PubMed

    Khashan, M A; Nassif, A Y

    1997-09-20

    The band spacing of the fringes of equal chromatic order of a thin Fabry-Perot interferometer is compared when this interferometer contains air, a solid, or a liquid. This comparison enables the dispersion of the group velocity of light in these media to be known accurately to 2.4 parts in one thousand. The Sellmeier dispersion function is used to deduce the refractive indices with the same degree of accuracy. The order-transformation method is used to find the exact order values from the roughly known optical thickness. The exact order values for air and the sample are used to find the refractive index accurately to approximately 3 x 10(-5). A least-squares fitting of the accurate experimental data to the Sellmeier dispersion function enables the coefficients of the latter to be more precisely defined for solids such as glass and mica and for liquids such as glycerin and distilled water. The atomic parameters such as the density of states and the absorption wavelengths in the ultraviolet region of the spectrum for the given samples are deduced from the more precisely found Sellmeier coefficients. PMID:18259554

  17. Accurate airway segmentation based on intensity structure analysis and graph-cut

    NASA Astrophysics Data System (ADS)

    Meng, Qier; Kitsaka, Takayuki; Nimura, Yukitaka; Oda, Masahiro; Mori, Kensaku

    2016-03-01

    This paper presents a novel airway segmentation method based on intensity structure analysis and graph-cut. Airway segmentation is an important step in analyzing chest CT volumes for computerized lung cancer detection, emphysema diagnosis, asthma diagnosis, and pre- and intra-operative bronchoscope navigation. However, obtaining a complete 3-D airway tree structure from a CT volume is quite challenging. Several researchers have proposed automated algorithms basically based on region growing and machine learning techniques. However these methods failed to detect the peripheral bronchi branches. They caused a large amount of leakage. This paper presents a novel approach that permits more accurate extraction of complex bronchial airway region. Our method are composed of three steps. First, the Hessian analysis is utilized for enhancing the line-like structure in CT volumes, then a multiscale cavity-enhancement filter is employed to detect the cavity-like structure from the previous enhanced result. In the second step, we utilize the support vector machine (SVM) to construct a classifier for removing the FP regions generated. Finally, the graph-cut algorithm is utilized to connect all of the candidate voxels to form an integrated airway tree. We applied this method to sixteen cases of 3D chest CT volumes. The results showed that the branch detection rate of this method can reach about 77.7% without leaking into the lung parenchyma areas.

  18. Beyond Ellipse(s): Accurately Modelling the Isophotal Structure of Galaxies with ISOFIT and CMODEL

    NASA Astrophysics Data System (ADS)

    Ciambur, B. C.

    2015-09-01

    This work introduces a new fitting formalism for isophotes that enables more accurate modeling of galaxies with non-elliptical shapes, such as disk galaxies viewed edge-on or galaxies with X-shaped/peanut bulges. Within this scheme, the angular parameter that defines quasi-elliptical isophotes is transformed from the commonly used, but inappropriate, polar coordinate to the “eccentric anomaly.” This provides a superior description of deviations from ellipticity, better capturing the true isophotal shape. Furthermore, this makes it possible to accurately recover both the surface brightness profile, using the correct azimuthally averaged isophote, and the two-dimensional model of any galaxy: the hitherto ubiquitous, but artificial, cross-like features in residual images are completely removed. The formalism has been implemented into the Image Reduction and Analysis Facility tasks Ellipse and Bmodel to create the new tasks “Isofit,” and “Cmodel.” The new tools are demonstrated here with application to five galaxies, chosen to be representative case-studies for several areas where this technique makes it possible to gain new scientific insight. Specifically: properly quantifying boxy/disky isophotes via the fourth harmonic order in edge-on galaxies, quantifying X-shaped/peanut bulges, higher-order Fourier moments for modeling bars in disks, and complex isophote shapes. Higher order (n > 4) harmonics now become meaningful and may correlate with structural properties, as boxyness/diskyness is known to do. This work also illustrates how the accurate construction, and subtraction, of a model from a galaxy image facilitates the identification and recovery of over-lapping sources such as globular clusters and the optical counterparts of X-ray sources.

  19. Determining Sample Size for Accurate Estimation of the Squared Multiple Correlation Coefficient.

    ERIC Educational Resources Information Center

    Algina, James; Olejnik, Stephen

    2000-01-01

    Discusses determining sample size for estimation of the squared multiple correlation coefficient and presents regression equations that permit determination of the sample size for estimating this parameter for up to 20 predictor variables. (SLD)

  20. A Simple yet Accurate Method for Students to Determine Asteroid Rotation Periods from Fragmented Light Curve Data

    ERIC Educational Resources Information Center

    Beare, R. A.

    2008-01-01

    Professional astronomers use specialized software not normally available to students to determine the rotation periods of asteroids from fragmented light curve data. This paper describes a simple yet accurate method based on Microsoft Excel[R] that enables students to find periods in asteroid light curve and other discontinuous time series data of…

  1. New methods determine pour point more accurately than ASTM D-97

    SciTech Connect

    Khan, H.U.; Dilawar, S.V.K.; Nautiyal, S.P.; Srivastava, S.P. )

    1993-11-01

    A new, alternative method determines petroleum fluid pour points with [+-] 1 C. precision and better accuracy than the standard ASTM D-97 procedure. The new method measures the pour point of transparent fluids by determining wax appearance temperature (WAT). Also, pour points of waxy crude oils can be determined by measuring a flow characteristic called restart pressure.

  2. Accurate electronic-structure description of Mn complexes: a GGA+U approach

    NASA Astrophysics Data System (ADS)

    Li, Elise Y.; Kulik, Heather; Marzari, Nicola

    2008-03-01

    Conventional density-functional approach often fail in offering an accurate description of the spin-resolved energetics in transition metals complexes. We will focus here on Mn complexes, where many aspects of the molecular structure and the reaction mechanisms are still unresolved - most notably in the oxygen-evolving complex (OEC) of photosystem II and the manganese catalase (MC). We apply a self-consistent GGA + U approach [1], originally designed within the DFT framework for the treatment of strongly correlated materials, to describe the geometry, the electronic and the magnetic properties of various manganese oxide complexes, finding very good agreement with higher-order ab-initio calculations. In particular, the different oxidation states of dinuclear systems containing the [Mn2O2]^n+ (n= 2, 3, 4) core are investigated, in order to mimic the basic face unit of the OEC complex. [1]. H. J. Kulik, M. Cococcioni, D. A. Scherlis, N. Marzari, Phys. Rev. Lett., 2006, 97, 103001

  3. A survey of factors contributing to accurate theoretical predictions of atomization energies and molecular structures

    NASA Astrophysics Data System (ADS)

    Feller, David; Peterson, Kirk A.; Dixon, David A.

    2008-11-01

    High level electronic structure predictions of thermochemical properties and molecular structure are capable of accuracy rivaling the very best experimental measurements as a result of rapid advances in hardware, software, and methodology. Despite the progress, real world limitations require practical approaches designed for handling general chemical systems that rely on composite strategies in which a single, intractable calculation is replaced by a series of smaller calculations. As typically implemented, these approaches produce a final, or "best," estimate that is constructed from one major component, fine-tuned by multiple corrections that are assumed to be additive. Though individually much smaller than the original, unmanageable computational problem, these corrections are nonetheless extremely costly. This study presents a survey of the widely varying magnitude of the most important components contributing to the atomization energies and structures of 106 small molecules. It combines large Gaussian basis sets and coupled cluster theory up to quadruple excitations for all systems. In selected cases, the effects of quintuple excitations and/or full configuration interaction were also considered. The availability of reliable experimental data for most of the molecules permits an expanded statistical analysis of the accuracy of the approach. In cases where reliable experimental information is currently unavailable, the present results are expected to provide some of the most accurate benchmark values available.

  4. Low-energy structures of benzene clusters with a novel accurate potential surface.

    PubMed

    Bartolomei, M; Pirani, F; Marques, J M C

    2015-12-01

    The benzene-benzene (Bz-Bz) interaction is present in several chemical systems and it is known to be crucial in understanding the specificity of important biological phenomena. In this work, we propose a novel Bz-Bz analytical potential energy surface which is fine-tuned on accurate ab initio calculations in order to improve its reliability. Once the Bz-Bz interaction is modeled, an analytical function for the energy of the Bzn clusters may be obtained by summing up over all pair potentials. We apply an evolutionary algorithm (EA) to discover the lowest-energy structures of Bzn clusters (for n=2-25), and the results are compared with previous global optimization studies where different potential functions were employed. Besides the global minimum, the EA also gives the structures of other low-lying isomers ranked by the corresponding energy. Additional ab initio calculations are carried out for the low-lying isomers of Bz3 and Bz4 clusters, and the global minimum is confirmed as the most stable structure for both sizes. Finally, a detailed analysis of the low-energy isomers of the n = 13 and 19 magic-number clusters is performed. The two lowest-energy Bz13 isomers show S6 and C3 symmetry, respectively, which is compatible with the experimental results available in the literature. The Bz19 structures reported here are all non-symmetric, showing two central Bz molecules surrounded by 12 nearest-neighbor monomers in the case of the five lowest-energy structures.

  5. HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures.

    PubMed

    Li, Yunqi; Roy, Ambrish; Zhang, Yang

    2009-08-20

    Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD.

  6. Effect of sampling size on the determination of accurate pesticide residue levels in Japanese agricultural commodities.

    PubMed

    Fujita, Masahiro; Yajima, Tomonari; Iijima, Kazuaki; Sato, Kiyoshi

    2012-05-01

    The uncertainty in pesticide residue levels (UPRL) associated with sampling size was estimated using individual acetamiprid and cypermethrin residue data from preharvested apple, broccoli, cabbage, grape, and sweet pepper samples. The relative standard deviation from the mean of each sampling size (n = 2(x), where x = 1-6) of randomly selected samples was defined as the UPRL for each sampling size. The estimated UPRLs, which were calculated on the basis of the regulatory sampling size recommended by the OECD Guidelines on Crop Field Trials (weights from 1 to 5 kg, and commodity unit numbers from 12 to 24), ranged from 2.1% for cypermethrin in sweet peppers to 14.6% for cypermethrin in cabbage samples. The percentages of commodity exceeding the maximum residue limits (MRLs) specified by the Japanese Food Sanitation Law may be predicted from the equation derived from this study, which was based on samples of various size ranges with mean residue levels below the MRL. The estimated UPRLs have confirmed that sufficient sampling weight and numbers are required for analysis and/or re-examination of subsamples to provide accurate values of pesticide residue levels for the enforcement of MRLs. The equation derived from the present study would aid the estimation of more accurate residue levels even from small sampling sizes. PMID:22475588

  7. Accurate label-free reaction kinetics determination using initial rate heat measurements.

    PubMed

    Ebrahimi, Kourosh Honarmand; Hagedoorn, Peter-Leon; Jacobs, Denise; Hagen, Wilfred R

    2015-01-01

    Accurate label-free methods or assays to obtain the initial reaction rates have significant importance in fundamental studies of enzymes and in application-oriented high throughput screening of enzyme activity. Here we introduce a label-free approach for obtaining initial rates of enzyme activity from heat measurements, which we name initial rate calorimetry (IrCal). This approach is based on our new finding that the data recorded by isothermal titration calorimetry for the early stages of a reaction, which have been widely ignored, are correlated to the initial rates. Application of the IrCal approach to various enzymes led to accurate enzyme kinetics parameters as compared to spectroscopic methods and enabled enzyme kinetic studies with natural substrate, e.g. proteases with protein substrates. Because heat is a label-free property of almost all reactions, the IrCal approach holds promise in fundamental studies of various enzymes and in use of calorimetry for high throughput screening of enzyme activity.

  8. Accurate label-free reaction kinetics determination using initial rate heat measurements

    PubMed Central

    Ebrahimi, Kourosh Honarmand; Hagedoorn, Peter-Leon; Jacobs, Denise; Hagen, Wilfred R.

    2015-01-01

    Accurate label-free methods or assays to obtain the initial reaction rates have significant importance in fundamental studies of enzymes and in application-oriented high throughput screening of enzyme activity. Here we introduce a label-free approach for obtaining initial rates of enzyme activity from heat measurements, which we name initial rate calorimetry (IrCal). This approach is based on our new finding that the data recorded by isothermal titration calorimetry for the early stages of a reaction, which have been widely ignored, are correlated to the initial rates. Application of the IrCal approach to various enzymes led to accurate enzyme kinetics parameters as compared to spectroscopic methods and enabled enzyme kinetic studies with natural substrate, e.g. proteases with protein substrates. Because heat is a label-free property of almost all reactions, the IrCal approach holds promise in fundamental studies of various enzymes and in use of calorimetry for high throughput screening of enzyme activity. PMID:26574737

  9. Accurate response surface approximations for weight equations based on structural optimization

    NASA Astrophysics Data System (ADS)

    Papila, Melih

    Accurate weight prediction methods are vitally important for aircraft design optimization. Therefore, designers seek weight prediction techniques with low computational cost and high accuracy, and usually require a compromise between the two. The compromise can be achieved by combining stress analysis and response surface (RS) methodology. While stress analysis provides accurate weight information, RS techniques help to transmit effectively this information to the optimization procedure. The focus of this dissertation is structural weight equations in the form of RS approximations and their accuracy when fitted to results of structural optimizations that are based on finite element analyses. Use of RS methodology filters out the numerical noise in structural optimization results and provides a smooth weight function that can easily be used in gradient-based configuration optimization. In engineering applications RS approximations of low order polynomials are widely used, but the weight may not be modeled well by low-order polynomials, leading to bias errors. In addition, some structural optimization results may have high-amplitude errors (outliers) that may severely affect the accuracy of the weight equation. Statistical techniques associated with RS methodology are sought in order to deal with these two difficulties: (1) high-amplitude numerical noise (outliers) and (2) approximation model inadequacy. The investigation starts with reducing approximation error by identifying and repairing outliers. A potential reason for outliers in optimization results is premature convergence, and outliers of such nature may be corrected by employing different convergence settings. It is demonstrated that outlier repair can lead to accuracy improvements over the more standard approach of removing outliers. The adequacy of approximation is then studied by a modified lack-of-fit approach, and RS errors due to the approximation model are reduced by using higher order polynomials. In

  10. Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

    PubMed

    Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E

    2016-08-01

    Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system. PMID:27332140

  11. Communication: Accurate determination of side-chain torsion angle χ1 in proteins: Phenylalanine residues

    NASA Astrophysics Data System (ADS)

    Suardíaz, R.; Crespo-Otero, R.; Pérez, C.; Fabián, J. San; de la Vega, J. M. García

    2011-02-01

    Quantitative side-chain torsion angle χ1 determinations of phenylalanine residues in Desulfovibrio vulgaris flavodoxin are carried out using exclusively the correlation between the experimental vicinal coupling constants and theoretically determined Karplus equations. Karplus coefficients for nine vicinal coupling related with the torsion angle χ1 were calculated using the B3LYP functional and basis sets of different size. Optimized χ1 angles are in outstanding agreement with those previously reported by employing x ray and NMR measurements.

  12. Accurate determination of the binding energy of the formic acid dimer: the importance of geometry relaxation.

    PubMed

    Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2014-02-28

    The formic acid dimer in its C2h-symmetrical cyclic form is stabilized by two equivalent H-bonds. The currently accepted interaction energy is 18.75 kcal/mol whereas the experimental binding energy D0 value is only 14.22 ±0.12 kcal/mol [F. Kollipost, R. W. Larsen, A. V. Domanskaya, M. Nörenberg, and M. A. Suhm, J. Chem. Phys. 136, 151101 (2012)]. Calculation of the binding energies De and D0 at the CCSD(T) (Coupled Cluster with Single and Double excitations and perturbative Triple excitations)/CBS (Complete Basis Set) level of theory, utilizing CCSD(T)/CBS geometries and the frequencies of the dimer and monomer, reveals that there is a 3.2 kcal/mol difference between interaction energy and binding energy De, which results from (i) not relaxing the geometry of the monomers upon dissociation of the dimer and (ii) approximating CCSD(T) correlation effects with MP2. The most accurate CCSD(T)/CBS values obtained in this work are De = 15.55 and D0 = 14.32 kcal/mol where the latter binding energy differs from the experimental value by 0.1 kcal/mol. The necessity of employing augmented VQZ and VPZ calculations and relaxing monomer geometries of H-bonded complexes upon dissociation to obtain reliable binding energies is emphasized.

  13. Accurate determination of the binding energy of the formic acid dimer: The importance of geometry relaxation

    NASA Astrophysics Data System (ADS)

    Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2014-02-01

    The formic acid dimer in its C2h-symmetrical cyclic form is stabilized by two equivalent H-bonds. The currently accepted interaction energy is 18.75 kcal/mol whereas the experimental binding energy D0 value is only 14.22 ±0.12 kcal/mol [F. Kollipost, R. W. Larsen, A. V. Domanskaya, M. Nörenberg, and M. A. Suhm, J. Chem. Phys. 136, 151101 (2012)]. Calculation of the binding energies De and D0 at the CCSD(T) (Coupled Cluster with Single and Double excitations and perturbative Triple excitations)/CBS (Complete Basis Set) level of theory, utilizing CCSD(T)/CBS geometries and the frequencies of the dimer and monomer, reveals that there is a 3.2 kcal/mol difference between interaction energy and binding energy De, which results from (i) not relaxing the geometry of the monomers upon dissociation of the dimer and (ii) approximating CCSD(T) correlation effects with MP2. The most accurate CCSD(T)/CBS values obtained in this work are De = 15.55 and D0 = 14.32 kcal/mol where the latter binding energy differs from the experimental value by 0.1 kcal/mol. The necessity of employing augmented VQZ and VPZ calculations and relaxing monomer geometries of H-bonded complexes upon dissociation to obtain reliable binding energies is emphasized.

  14. A colorimetric-based accurate method for the determination of enterovirus 71 titer.

    PubMed

    Pourianfar, Hamid Reza; Javadi, Arman; Grollo, Lara

    2012-12-01

    The 50 % tissue culture infectious dose (TCID50) is still one of the most commonly used techniques for estimating virus titers. However, the traditional TCID50 assay is time consuming, susceptible to subjective errors and generates only quantal data. Here, we describe a colorimetric-based approach for the titration of Enterovirus 71 (EV71) using a modified method for making virus dilutions. In summary, the titration of EV71 using MTT or MTS staining with a modified virus dilution method decreased the time of the assay and eliminated the subjectivity of observational results, improving accuracy, reproducibility and reliability of virus titration, in comparison with the conventional TCID50 approach (p < 0.01). In addition, the results provided evidence that there was better correlation between a plaquing assay and our approach when compared to the traditional TCID50 approach. This increased accuracy also improved the ability to predict the number of virus plaque forming units present in a solution. These improvements could be of use for any virological experimentation, where a quick accurate titration of a virus capable of causing cell destruction is required or a sensible estimation of the number of viral plaques based on TCID50 of a virus is desired.

  15. Do Ecological Niche Models Accurately Identify Climatic Determinants of Species Ranges?

    PubMed

    Searcy, Christopher A; Shaffer, H Bradley

    2016-04-01

    Defining species' niches is central to understanding their distributions and is thus fundamental to basic ecology and climate change projections. Ecological niche models (ENMs) are a key component of making accurate projections and include descriptions of the niche in terms of both response curves and rankings of variable importance. In this study, we evaluate Maxent's ranking of environmental variables based on their importance in delimiting species' range boundaries by asking whether these same variables also govern annual recruitment based on long-term demographic studies. We found that Maxent-based assessments of variable importance in setting range boundaries in the California tiger salamander (Ambystoma californiense; CTS) correlate very well with how important those variables are in governing ongoing recruitment of CTS at the population level. This strong correlation suggests that Maxent's ranking of variable importance captures biologically realistic assessments of factors governing population persistence. However, this result holds only when Maxent models are built using best-practice procedures and variables are ranked based on permutation importance. Our study highlights the need for building high-quality niche models and provides encouraging evidence that when such models are built, they can reflect important aspects of a species' ecology. PMID:27028071

  16. Spreading of liquid droplets on cylindrical surfaces: Accurate determination of contact angle

    NASA Astrophysics Data System (ADS)

    Wagner, H. D.

    1990-02-01

    The characterization of the physicochemical nature of interfaces is a key problem in the field of advanced fibrous composites. The macroscopic regime contact angle, which reflects the energetics of wetting at the solid-liquid interface, is difficult to measure by usual methods in the case of very thin cylindrical fibers, but it may be calculated from the shape of a liquid droplet spread onto a cylindrical monofilament using a method developed by Yamaki and Katayama [J. Appl. Polym. Sci. 19, 2897 (1975)], and B. J. Carroll [J. Coll. Interf. Sci. 57, 488 (1976)]. Unfortunately, measurements of the contact angle based on this method are, so far, unable to provide an accuracy of better than about 5°. In the present article two simple extensions of the method of Yamaki and Katayama and Carroll, are presented, from which highly accurate values of the contact angle may be obtained. This is demonstrated experimentally from the spreading of glycerol droplets on carbon fibers and epoxy droplets on aramid fibers.

  17. Variant of more accurate determination of the locations of shortwave radio emission sources

    NASA Astrophysics Data System (ADS)

    Ivanov, V. F.; Myslivtsev, T. O.; Troitskii, B. V.

    2013-04-01

    The paper discusses how the trajectory calculation method can be used to solve the problem of locality determination of shortwave (SW) emission sources. The dependence of the electron concentration on the coordinates is specified using the SPIM model; it is corrected using the ionospheric solar activity index, which is specified with the help of maps of total electron content. We suggested a variant of how a regional map of the total electron content can be plotted according to measurements of signals from GLONASS/GPS navigation systems. It is shown that the trajectory calculation method, coupled with an adjustable ionospheric model, allows for a more exact locality determination of SW radio emission sources.

  18. Molecular Simulation of the Free Energy for the Accurate Determination of Phase Transition Properties of Molecular Solids

    NASA Astrophysics Data System (ADS)

    Sellers, Michael; Lisal, Martin; Brennan, John

    2015-06-01

    Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.

  19. Straightforward and accurate technique for post-coupler stabilization in drift tube linac structures

    NASA Astrophysics Data System (ADS)

    Khalvati, Mohammad Reza; Ramberger, Suitbert

    2016-04-01

    The axial electric field of Alvarez drift tube linacs (DTLs) is known to be susceptible to variations due to static and dynamic effects like manufacturing tolerances and beam loading. Post-couplers are used to stabilize the accelerating fields of DTLs against tuning errors. Tilt sensitivity and its slope have been introduced as measures for the stability right from the invention of post-couplers but since then the actual stabilization has mostly been done by tedious iteration. In the present article, the local tilt-sensitivity slope TSn' is established as the principal measure for stabilization instead of tilt sensitivity or some visual slope, and its significance is developed on the basis of an equivalent-circuit diagram of the DTL. Experimental and 3D simulation results are used to analyze its behavior and to define a technique for stabilization that allows finding the best post-coupler settings with just four tilt-sensitivity measurements. CERN's Linac4 DTL Tank 2 and Tank 3 have been stabilized successfully using this technique. The final tilt-sensitivity error has been reduced from ±100 %/MHz down to ±3 %/MHz for Tank 2 and down to ±1 %/MHz for Tank 3. Finally, an accurate procedure for tuning the structure using slug tuners is discussed.

  20. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.

    PubMed

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-06-20

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  1. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

    PubMed

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-05-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis.

  2. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

    PubMed Central

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-01-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

  3. Automated methods for accurate determination of the critical velocity of packed bed chromatography.

    PubMed

    Chang, Yu-Chih; Gerontas, Spyridon; Titchener-Hooker, Nigel J

    2012-01-01

    Knowing the critical velocity (ucrit) of a chromatography column is an important part of process development as it allows the optimization of chromatographic flow conditions. The conventional flow step method for determining ucrit is prone to error as it depends heavily on human judgment. In this study, two automated methods for determining ucrit have been developed: the automatic flow step (AFS) method and the automatic pressure step (APS) method. In the AFS method, the column pressure drop is monitored upon application of automated incremental increases in flow velocity, whereas in the APS method the flow velocity is monitored upon application of automated incremental increases in pressure drop. The APS method emerged as the one with the higher levels of accuracy, efficiency and ease of application having the greater potential to assist defining the best operational parameters of a chromatography column.

  4. Accurate determination of imaging modality using an ensemble of text- and image-based classifiers.

    PubMed

    Kahn, Charles E; Kalpathy-Cramer, Jayashree; Lam, Cesar A; Eldredge, Christina E

    2012-02-01

    Imaging modality can aid retrieval of medical images for clinical practice, research, and education. We evaluated whether an ensemble classifier could outperform its constituent individual classifiers in determining the modality of figures from radiology journals. Seventeen automated classifiers analyzed 77,495 images from two radiology journals. Each classifier assigned one of eight imaging modalities--computed tomography, graphic, magnetic resonance imaging, nuclear medicine, positron emission tomography, photograph, ultrasound, or radiograph-to each image based on visual and/or textual information. Three physicians determined the modality of 5,000 randomly selected images as a reference standard. A "Simple Vote" ensemble classifier assigned each image to the modality that received the greatest number of individual classifiers' votes. A "Weighted Vote" classifier weighted each individual classifier's vote based on performance over a training set. For each image, this classifier's output was the imaging modality that received the greatest weighted vote score. We measured precision, recall, and F score (the harmonic mean of precision and recall) for each classifier. Individual classifiers' F scores ranged from 0.184 to 0.892. The simple vote and weighted vote classifiers correctly assigned 4,565 images (F score, 0.913; 95% confidence interval, 0.905-0.921) and 4,672 images (F score, 0.934; 95% confidence interval, 0.927-0.941), respectively. The weighted vote classifier performed significantly better than all individual classifiers. An ensemble classifier correctly determined the imaging modality of 93% of figures in our sample. The imaging modality of figures published in radiology journals can be determined with high accuracy, which will improve systems for image retrieval.

  5. A rural hospital's use of software to determine accurate Medicare reimbursement levels.

    PubMed

    Weiszbrod, T

    1995-01-01

    This article details how a software program has helped a hospital collect more Medicare payments for which it was eligible than it previously had collected. The software simplifies the process of selecting complications by reminding the user when no complications have yet been entered, by determining whether each item entered qualifies as a complication, and by suggesting other possibilities. In many instances, these complications are possibilities that a person performing manual coding might not consider. PMID:10144983

  6. An accurate method for the determination of carboxyhemoglobin in postmortem blood using GC-TCD.

    PubMed

    Lewis, Russell J; Johnson, Robert D; Canfield, Dennis V

    2004-01-01

    During the investigation of aviation accidents, postmortem samples from accident victims are submitted to the FAA's Civil Aerospace Medical Institute for toxicological analysis. In order to determine if an accident victim was exposed to an in-flight/postcrash fire or faulty heating/exhaust system, the analysis of carbon monoxide (CO) is conducted. Although our laboratory predominantly uses a spectrophotometric method for the determination of carboxyhemoglobin (COHb), we consider it essential to confirm with a second technique based on a different analytical principle. Our laboratory encountered difficulties with many of our postmortem samples while employing a commonly used GC method. We believed these problems were due to elevated methemoglobin (MetHb) concentration in our specimens. MetHb does not bind CO; therefore, elevated MetHb levels will result in a loss of CO-binding capacity. Because most commonly employed GC methods determine %COHb from a ratio of unsaturated blood to CO-saturated blood, a loss of CO-binding capacity will result in an erroneously high %COHb value. Our laboratory has developed a new GC method for the determination of %COHb that incorporates sodium dithionite, which will reduce any MetHb present to Hb. Using blood controls ranging from 1% to 67% COHb, we found no statistically significant differences between %COHb results from our new GC method and our spectrophotometric method. To validate the new GC method, postmortem samples were analyzed with our existing spectrophotometric method, a GC method commonly used without reducing agent, and our new GC method with the addition of sodium dithionite. As expected, we saw errors up to and exceeding 50% when comparing the unreduced GC results with our spectrophotometric method. With our new GC procedure, the error was virtually eliminated. PMID:14987426

  7. Determination of the biotin content of select foods using accurate and sensitive HPLC/avidin binding

    PubMed Central

    Staggs, C.G.; Sealey, W.M.; McCabe, B.J.; Teague, A.M.; Mock, D.M.

    2006-01-01

    Assessing dietary biotin content, biotin bioavailability, and resulting biotin status are crucial in determining whether biotin deficiency is teratogenic in humans. Accuracy in estimating dietary biotin is limited both by data gaps in food composition tables and by inaccuracies in published data. The present study applied sensitive and specific analytical techniques to determine values for biotin content in a select group of foods. Total biotin content of 87 foods was determined using acid hydrolysis and the HPLC/avidin-binding assay. These values are consistent with published values in that meat, fish, poultry, egg, dairy, and some vegetables are relatively rich sources of biotin. However, these biotin values disagreed substantially with published values for many foods. Assay values varied between 247 times greater than published values for a given food to as much as 36% less than the published biotin value. Among 51 foods assayed for which published values were available, only seven agreed within analytical variability (720%). We conclude that published values for biotin content of foods are likely to be inaccurate. PMID:16648879

  8. Protein Structure Determination Using Protein Threading and Sparse NMR Data

    SciTech Connect

    Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.

    1999-11-14

    It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.

  9. Raman Spectroscopy Provides a Powerful Diagnostic Tool for Accurate Determination of Albumin Glycation

    PubMed Central

    Dingari, Narahara Chari; Horowitz, Gary L.; Kang, Jeon Woong; Dasari, Ramachandra R.; Barman, Ishan

    2012-01-01

    We present the first demonstration of glycated albumin detection and quantification using Raman spectroscopy without the addition of reagents. Glycated albumin is an important marker for monitoring the long-term glycemic history of diabetics, especially as its concentrations, in contrast to glycated hemoglobin levels, are unaffected by changes in erythrocyte life times. Clinically, glycated albumin concentrations show a strong correlation with the development of serious diabetes complications including nephropathy and retinopathy. In this article, we propose and evaluate the efficacy of Raman spectroscopy for determination of this important analyte. By utilizing the pre-concentration obtained through drop-coating deposition, we show that glycation of albumin leads to subtle, but consistent, changes in vibrational features, which with the help of multivariate classification techniques can be used to discriminate glycated albumin from the unglycated variant with 100% accuracy. Moreover, we demonstrate that the calibration model developed on the glycated albumin spectral dataset shows high predictive power, even at substantially lower concentrations than those typically encountered in clinical practice. In fact, the limit of detection for glycated albumin measurements is calculated to be approximately four times lower than its minimum physiological concentration. Importantly, in relation to the existing detection methods for glycated albumin, the proposed method is also completely reagent-free, requires barely any sample preparation and has the potential for simultaneous determination of glycated hemoglobin levels as well. Given these key advantages, we believe that the proposed approach can provide a uniquely powerful tool for quantification of glycation status of proteins in biopharmaceutical development as well as for glycemic marker determination in routine clinical diagnostics in the future. PMID:22393405

  10. Accurate mass determination of short-lived isotopes by a tandem Penning-trap mass spectrometer

    SciTech Connect

    Stolzenberg, H.; Becker, S.; Bollen, G.; Kern, F.; Kluge, H.; Otto, T.; Savard, G.; Schweikhard, L. ); Audi, G. ); Moore, R.B. ); The ISOLDE Collaboration

    1990-12-17

    A mass spectrometer consisting of two Penning traps has been set up for short-lived isotopes at the on-line mass separator ISOLDE at CERN. The ion beam is collected and cooled in the first trap. After delivery to the second trap, high-accuracy direct mass measurements are made by determining the cyclotron frequency of the stored ions. Measurements have been performed for {sup 118}Cs--{sup 137}Cs. A resolving power of over 10{sup 6} and an accuracy of 1.4{times}10{sup {minus}7} have been achieved, corresponding to about 20 keV.

  11. Photo-detachment signal analysis to accurately determine electronegativity, electron temperature, and charged species density

    NASA Astrophysics Data System (ADS)

    Oudini, N.; Sirse, N.; Taccogna, F.; Ellingboe, A. R.; Bendib, A.

    2016-09-01

    Laser pulse induced photo-detachment combined with Langmuir probing has been introduced to diagnose plasma electronegativity. This technique uses a laser pulse to convert negative ions into electron-atom pairs and tracks the change of electron saturation current by a Langmuir probe. The existing model determines plasma electronegativity as the ratio of electron saturation current before and after detachment. However, this model depends on various assumptions and neglects the formation of a potential barrier between the laser channel and surrounding electronegative plasma. In this letter, we present a new analytical model to analyze photo-detachment signals in order to improve the accuracy of electronegativity measurements and extend this technique for measuring electron temperature and charged species density. This analytical model is supported by Particle-In-Cell simulation of electronegative plasma dynamics following laser photo-detachment. The analysis of the signal, detected on a simulated probe, shows that the present analytical model determines electronegativity, electron temperature, and plasma density with a relative error of ˜20%, ˜20%, and ˜50%, respectively, whereas the electronegativity obtained from a previous model is underestimated by an order of magnitude.

  12. Optical aperture area determination for accurate illuminance and luminous efficacy measurements of LED lamps

    NASA Astrophysics Data System (ADS)

    Dönsberg, Timo; Mäntynen, Henrik; Ikonen, Erkki

    2016-06-01

    The measurement uncertainty of illuminance and, consequently, luminous flux and luminous efficacy of LED lamps can be reduced with a recently introduced method based on the predictable quantum efficient detector (PQED). One of the most critical factors affecting the measurement uncertainty with the PQED method is the determination of the aperture area. This paper describes an upgrade to an optical method for direct determination of aperture area where superposition of equally spaced Gaussian laser beams is used to form a uniform irradiance distribution. In practice, this is accomplished by scanning the aperture in front of an intensity-stabilized laser beam. In the upgraded method, the aperture is attached to the PQED and the whole package is transversely scanned relative to the laser beam. This has the benefit of having identical geometry in the laser scanning of the aperture area and in the actual photometric measurement. Further, the aperture and detector assembly does not have to be dismantled for the aperture calibration. However, due to small acceptance angle of the PQED, differences between the diffraction effects of an overfilling plane wave and of a combination of Gaussian laser beams at the circular aperture need to be taken into account. A numerical calculation method for studying these effects is discussed in this paper. The calculation utilizes the Rayleigh-Sommerfeld diffraction integral, which is applied to the geometry of the PQED and the aperture. Calculation results for various aperture diameters and two different aperture-to-detector distances are presented.

  13. A new sensor system for accurate and precise determination of sediment dynamics and position.

    NASA Astrophysics Data System (ADS)

    Maniatis, Georgios; Hoey, Trevor; Sventek, Joseph; Hodge, Rebecca

    2014-05-01

    Sediment transport processes control many significant geomorphological changes. Consequently, sediment transport dynamics are studied across a wide range of scales leading to application of a variety of conceptually different mathematical descriptions (models) and data acquisition techniques (sensing). For river sediment transport processes both Eulerian and Lagrangian formulations are used. Data are gathered using a very wide range of sensing techniques that are not always compatible with the conceptual formulation applied. We are concerned with small to medium sediment grain-scale motion in gravel-bed rivers, and other coarse-grained environments, and: a) are developing a customised environmental sensor capable of providing coherent data that reliably record the motion; and, b) provide a mathematical framework in which these data can be analysed and interpreted, this being compatible with current stochastic approaches to sediment transport theory. Here we present results from three different aspects of the above developmental process. Firstly, we present a requirement analysis for the sensor based on the state of the art of the existing technologies. We focus on the factors that enhance data coherence and representativeness, extending the common practice for optimization which is based exclusively on electronics/computing related criteria. This analysis leads to formalization of a method that permits accurate control on the physical properties of the sensor using contemporary rapid prototyping techniques [Maniatis et al. 2013]. Secondly the first results are presented from a series of entrainment experiments in a 5 x 0.8 m flume in which a prototype sensor was deployed to monitor entrainment dynamics under increasing flow conditions (0.037 m3.s-1). The sensor was enclosed in an idealized spherical case (111 mm diameter) and placed on a constructed bed of hemispheres of the same diameter. We measured 3-axial inertial acceleration (as a measure of flow stress

  14. Structure determination of transient transcription complexes.

    PubMed

    Cramer, Patrick

    2016-08-15

    The determination of detailed 3D structures of large and transient multicomponent complexes remains challenging. Here I describe the approaches that were used and developed by our laboratory to achieve structure solution of eukaryotic transcription complexes. I hope this collection serves as a resource for structural biologists seeking solutions for difficult structure determination projects. PMID:27528766

  15. An experimental correction proposed for an accurate determination of mass diffusivity of wood in steady regime

    NASA Astrophysics Data System (ADS)

    Zohoun, Sylvain; Agoua, Eusèbe; Degan, Gérard; Perre, Patrick

    2002-08-01

    This paper presents an experimental study of the mass diffusion in the hygroscopic region of four temperate species and three tropical ones. In order to simplify the interpretation of the phenomena, a dimensionless parameter called reduced diffusivity is defined. This parameter varies from 0 to 1. The method used is firstly based on the determination of that parameter from results of the measurement of the mass flux which takes into account the conditions of operating standard device (tightness, dimensional variations and easy installation of samples of wood, good stability of temperature and humidity). Secondly the reasons why that parameter has to be corrected are presented. An abacus for this correction of mass diffusivity of wood in steady regime has been plotted. This work constitutes an advanced deal nowadays for characterising forest species.

  16. Accurate determination of silver nanoparticles in animal tissues by inductively coupled plasma mass spectrometry

    NASA Astrophysics Data System (ADS)

    Veverková, Lenka; Hradilová, Šárka; Milde, David; Panáček, Aleš; Skopalová, Jana; Kvítek, Libor; Petrželová, Kamila; Zbořil, Radek

    2014-12-01

    This study examined recoveries of silver determination in animal tissues after wet digestion by inductively coupled plasma mass spectrometry. The composition of the mineralization mixture for microwave assisted digestion was optimized and the best recoveries were obtained for mineralization with HNO3 and addition of HCl promptly after digestion. The optimization was performed on model samples of chicken meat spiked with silver nanoparticles and a solution of ionic silver. Basic calculations of theoretical distribution of Ag among various silver-containing species were implemented and the results showed that most of the silver is in the form of soluble complexes AgCl2- and AgCl32 - for the optimized composition of the mineralization mixture. Three animal tissue certified reference materials were then analyzed to verify the trueness and precision of the results.

  17. Accurate determination of the orientational distribution of a fluorescent molecule in a phospholipid membrane.

    PubMed

    Timr, Štěpán; Bondar, Alexey; Cwiklik, Lukasz; Štefl, Martin; Hof, Martin; Vazdar, Mario; Lazar, Josef; Jungwirth, Pavel

    2014-01-30

    Orientation of lipophilic dye molecules within a biological membrane can report on the molecular environment, i.e., the physical and chemical properties of the surrounding membrane. This fact, however, remains under-utilized, largely because of our limited quantitative knowledge of molecular orientational distributions and the fact that robust techniques allowing experimental observation of molecular orientations of dyes in biological membranes are only being developed. In order to begin filling this lack of knowledge and to develop appropriate tools, we have investigated the membrane orientational distribution of the 3-hydroxyflavone-based membrane dye F2N12S. Results of our single- and two-photon polarization microscopy observations of linear dichroism of F2N12S-labeled giant unilamellar vesicles are consistent with a Gaussian-like orientational distribution of the transition dipole moment of the dye, with a mean tilt angle of 53.2 ± 0.1° with respect to the bilayer normal and a standard deviation of 13.3 ± 0.6°. Independently, by combining quantum chemical calculations and molecular dynamics simulations, we obtained very similar values; a mean tilt angle of 48 ± 4° and a standard deviation of 13 ± 2°. The good agreement between the experimentally and computationally obtained values cross-validates both approaches and gives confidence to the results obtained. The results open a door to robust quantitative determinations of orientational distributions of fluorescent molecules (ranging from simple synthetic dyes to fluorescent proteins attached to membrane proteins) associated with lipid membranes. Such determinations enable rational development of a novel class of sensitive fluorescent optical probes, reporting on cellular events through changes in linear dichroism.

  18. Accurate Determination of Rotational Energy Levels in the Ground State of ^{12}CH_4

    NASA Astrophysics Data System (ADS)

    Abe, M.; Iwakuni, K.; Okubo, S.; Sasada, H.

    2013-06-01

    We have measured absolute frequencies of saturated absorption of 183 allowed and 21 forbidden transitions in the νb{3} band of ^{12}CH_4 using an optical comb-referenced difference-frequency-generation spectrometer from 86.8 to 93.1 THz (from 2890 to 3100 wn). The pump and signal sources are a 1.06-μ m Nd:YAG laser and a 1.5-μ m extended-cavity laser diode. An enhanced-cavity absorption cell increases the optical electric field and enhances the sensitivity. The typical uncertainty is 3 kHz for the allowed transitions and 12 kHz for the forbidden transitions. Twenty combination differences are precisely determined, and the scalar rotational and centrifugal distortion constants of the ground state are thereby yielded as r@ = l@ r@ = l B_{{s}} (157 122 614.2 ± 1.5) kHz, D_{{s}} (3 328.545 ± 0.031) kHz, H_{{s}} (190.90 ± 0.26) Hz, and L_{{s}} (-13.16 ± 0.76) mHz. Here, B_{{s}} is the rotational constant and D_{{s}}, H_{{s}} and L_{{s}} are the scalar quartic, sextic, octic distortion constants. The relative uncertainties are considerably smaller than those obtained from global analysis of Fourier-transform infrared spectroscopy. S. Okubo, H. Nakayama, K. Iwakuni, H. Inaba and H. Sasada, Opt. Express 19, 23878 (2011). M. Abe, K. Iwakuni, S. Okubo, and H. Sasada, J. Opt. Soc. Am. B (to be published). S. Albert, S. Bauerecker, V. Boudon, L. R. Brown, J. -P. Champion, M. Loëte, A. Nikitin, and M. Quack, Chem. Phys. 356, 131 (2009).

  19. Accurate quantification of two key time points used in the determination of hydroxyl polyaluminum species by ferron timed spectrophotometry.

    PubMed

    Zhang, Jing; Yong, Xiaojing; Zhao, Dongyan; Shi, Qiuyi

    2015-01-01

    The content of mononuclear Al (Ala%) changed with its determination time (ta) under different dosages of Ferron (7-iodo-8-hydroxyquinoline-5-sulfonic acid, [Ferron]), and the change of Ala% with [Ferron] at different ta was systematically investigated for the first time. Thus, the most appropriate ta was found with the optimal [Ferron]. Also, the judgment of the platform (flat or level portion) of the complete reaction on the absorption-time curve determined in the hydroxyl polyaluminum solution by Ferron timed spectrophotometry (Ferron assay) was first digitized. The time point (tb) of complete reaction between the medium polyaluminum (Alb) and Ferron reagent depended on the reaction extent, and time could not be used only to judge. Thus, the tb was accurately determined and reduced to half of original, which improved the experiment efficiency significantly. The Ferron assay was completely optimized.

  20. Multiclass semi-volatile compounds determination in wine by gas chromatography accurate time-of-flight mass spectrometry.

    PubMed

    Rodríguez-Cabo, T; Rodríguez, I; Ramil, M; Silva, A; Cela, R

    2016-04-15

    The performance of gas chromatography (GC) with accurate, high resolution mass spectrometry (HRMS) for the determination of a group of 39 semi-volatile compounds related to wine quality (pesticide residues, phenolic off-flavours, phenolic pollutants and bioactive stilbenes) is investigated. Solid-phase extraction (SPE) was used as extraction technique, previously to acetylation (phenolic compounds) and dispersive liquid-liquid microextraction (DLLME) concentration. Compounds were determined by GC coupled to a quadrupole time-of-flight (QTOF) MS system through an electron ionization (EI) source. The final method attained limits of quantification (LOQs) at the very low ng mL(-1) level, covering the range of expected concentrations for target compounds in red and white wines. For 38 out of 39 compounds, performance of sample preparation and determination steps were hardly affected by the wine matrix; thus, accurate recoveries were achieved by using pseudo-external calibration. Levels of target compounds in a set of 25 wine samples are reported. The capabilities of the described approach for the post-run identification of species not considered during method development, without retention time information, are illustrated and discussed with selected examples of compounds from different classes.

  1. A FIB-nanotomography method for accurate 3D reconstruction of open nanoporous structures.

    PubMed

    Mangipudi, K R; Radisch, V; Holzer, L; Volkert, C A

    2016-04-01

    We present an automated focused ion beam nanotomography method for nanoporous microstructures with open porosity, and apply it to reconstruct nanoporous gold (np-Au) structures with ligament sizes on the order of a few tens of nanometers. This method uses serial sectioning of a well-defined wedge-shaped geometry to determine the thickness of individual slices from the changes in the sample width in successive cross-sectional images. The pore space of a selected region of the np-Au is infiltrated with ion-beam-deposited Pt composite before serial sectioning. The cross-sectional images are binarized and stacked according to the individual slice thicknesses, and then processed using standard reconstruction methods. For the image conditions and sample geometry used here, we are able to determine the thickness of individual slices with an accuracy much smaller than a pixel. The accuracy of the new method based on actual slice thickness is assessed by comparing it with (i) a reconstruction using the same cross-sectional images but assuming a constant slice thickness, and (ii) a reconstruction using traditional FIB-tomography method employing constant slice thickness. The morphology and topology of the structures are characterized using ligament and pore size distributions, interface shape distribution functions, interface normal distributions, and genus. The results suggest that the morphology and topology of the final reconstructions are significantly influenced when a constant slice thickness is assumed. The study reveals grain-to-grain variations in the morphology and topology of np-Au. PMID:26906523

  2. Fast and accurate determination of 3D temperature distribution using fraction-step semi-implicit method

    NASA Astrophysics Data System (ADS)

    Cen, Wei; Hoppe, Ralph; Gu, Ning

    2016-09-01

    In this paper, we proposed a method to numerically determinate 3-dimensional thermal response due to electromagnetic exposure quickly and accurately. Due to the stability criterion the explicit finite-difference time-domain (FDTD) method works fast only if the spatial step is not set very small. In this paper, the semi-implicit Crank-Nicholson method for time domain discretization with unconditional time stability is proposed, where the idea of fractional steps method was utilized in 3-dimension so that an efficient numerical implementation is obtained. Compared with the explicit FDTD, with similar numerical precision, the proposed method takes less than 1/200 of the execution time.

  3. Note: Accurate determination of thickness of multiple layers of thin film deposited on a piezoelectric quartz crystal.

    PubMed

    Wajid, Abdul

    2013-10-01

    Modern day piezoelectric quartz crystal microbalances for thin film deposition control are based on Z-match equation, which is mathematically valid for deposition of a single material on a given quartz crystal. When multiple layers are deposited, thickness and deposition rate errors accumulate due to mismatch of acoustic impedance of different materials. Here we present a novel method, based on the acoustic transfer matrix formalism, for accurate determination of thickness of an arbitrary number of layers of dissimilar materials deposited on a quartz crystal. Laboratory data show excellent accuracy of the method compared to conventional Z-match equation. PMID:24182174

  4. Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

    SciTech Connect

    Park, Min-Sun; Park, Sung Yong; Miller, Keith R.; Collins, Edward J.; Lee, Ha Youn

    2013-11-01

    Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.

  5. Accurate localization of supernumerary mediastinal parathyroid adenomas by a combination of structural and functional imaging.

    PubMed

    Mackie, G C; Schlicht, S M

    2004-09-01

    Reoperation for refractory or recurrent hyperparathyroidism following parathyroidectomy carries the potential for increased morbidity and the possibility of failure to localize and remove the lesion intraoperatively. Reported herein are three cases demonstrating the combined use of sestamibi scintigraphy, CT and MR for accurate localization of mediastinal parathyroid adenomas.

  6. Rapid and accurate determination of total lung capacity (TLC) from routine chest radiograms using a programmable hand-held calculator.

    PubMed

    Rodgers, R P; Tannen, R

    1983-01-01

    Since its appearance in 1960, the method of Barnhard and associates for the determination of total lung capacity (TLC) from routine chest radiograms has been widely studied in normal and diseased subjects. The method appears to be as accurate as the current definitive procedure, total body plethysmography. The method is in routine use in major medical institutions where the procedure has been automated, but the method does not seem to have gained the wide use it deserves. This is likely due to the tedium of the technique when performed manually--a single determination can require 30 min. We present here an implementation of the Barnhard method for the HP41-C hand-held programmable calculator. In conjunction with the use of a transparent reticle used for obtaining the required measurements, the program allows a single measurement to be made in under 12 minutes. We hope this technique will make radiographic TLC measurements more broadly accessible to the medical profession. PMID:6872526

  7. Two-dimensional flow nanometry of biological nanoparticles for accurate determination of their size and emission intensity

    PubMed Central

    Block, Stephan; Fast, Björn Johansson; Lundgren, Anders; Zhdanov, Vladimir P.; Höök, Fredrik

    2016-01-01

    Biological nanoparticles (BNPs) are of high interest due to their key role in various biological processes and use as biomarkers. BNP size and composition are decisive for their functions, but simultaneous determination of both properties with high accuracy remains challenging. Optical microscopy allows precise determination of fluorescence/scattering intensity, but not the size of individual BNPs. The latter is better determined by tracking their random motion in bulk, but the limited illumination volume for tracking this motion impedes reliable intensity determination. Here, we show that by attaching BNPs to a supported lipid bilayer, subjecting them to hydrodynamic flows and tracking their motion via surface-sensitive optical imaging enable determination of their diffusion coefficients and flow-induced drifts, from which accurate quantification of both BNP size and emission intensity can be made. For vesicles, the accuracy of this approach is demonstrated by resolving the expected radius-squared dependence of their fluorescence intensity for radii down to 15 nm. PMID:27658367

  8. Structural determinants of hospital closure.

    PubMed

    Longo, D R; Chase, G A

    1984-05-01

    In a retrospective case-control study, structural characteristics of hospitals that closed during the years 1976-1980 were contrasted with three comparison groups: hospitals that were acquired in a merger; hospitals that joined a multihospital system; and hospitals that remained autonomously opened, to investigate these characteristics as predictors of closure. Characteristics investigated included environmental, structural, and process variables. The independent variables were measured 5 years prior to outcome. Findings indicate that closed hospitals resemble hospitals acquired in a merger ("failure"), and likewise autonomous hospitals resemble hospitals that join a multihospital system ("success"). The most important predictors of hospital failure were the physician-to-population ratio, the East North Central and West North Central census regions, the level of diversification, low occupancy rate, location in a standard metropolitan statistical area, the chief executive officer's lack of affiliation in the American College of Hospital Administrators, profit status, bed size of less than 50, and presence in a state with a rate-setting agency. Surprisingly, this study shows the bed-to-population ratio to be unrelated to closure. In addition, the findings strongly support the open-system perspective, which, unlike the closed-system perspective, is concerned with the vulnerability of the organization to the uncontrollable and often unpredictable influences of the environment.

  9. Dielectric-dependent Density Functionals for Accurate Electronic Structure Calculations of Molecules and Solids

    NASA Astrophysics Data System (ADS)

    Skone, Jonathan; Govoni, Marco; Galli, Giulia

    Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.

  10. Accurate retention time determination of co-eluting proteins in analytical chromatography by means of spectral data.

    PubMed

    Dismer, Florian; Hansen, Sigrid; Oelmeier, Stefan Alexander; Hubbuch, Jürgen

    2013-03-01

    Chromatography is the method of choice for the separation of proteins, at both analytical and preparative scale. Orthogonal purification strategies for industrial use can easily be implemented by combining different modes of adsorption. Nevertheless, with flexibility comes the freedom of choice and optimal conditions for consecutive steps need to be identified in a robust and reproducible fashion. One way to address this issue is the use of mathematical models that allow for an in silico process optimization. Although this has been shown to work, model parameter estimation for complex feedstocks becomes the bottleneck in process development. An integral part of parameter assessment is the accurate measurement of retention times in a series of isocratic or gradient elution experiments. As high-resolution analytics that can differentiate between proteins are often not readily available, pure protein is mandatory for parameter determination. In this work, we present an approach that has the potential to solve this problem. Based on the uniqueness of UV absorption spectra of proteins, we were able to accurately measure retention times in systems of up to four co-eluting compounds. The presented approach is calibration-free, meaning that prior knowledge of pure component absorption spectra is not required. Actually, pure protein spectra can be determined from co-eluting proteins as part of the methodology. The approach was tested for size-exclusion chromatograms of 38 mixtures of co-eluting proteins. Retention times were determined with an average error of 0.6 s (1.6% of average peak width), approximated and measured pure component spectra showed an average coefficient of correlation of 0.992.

  11. Surface structure determines dynamic wetting

    PubMed Central

    Wang, Jiayu; Do-Quang, Minh; Cannon, James J.; Yue, Feng; Suzuki, Yuji; Amberg, Gustav; Shiomi, Junichiro

    2015-01-01

    Liquid wetting of a surface is omnipresent in nature and the advance of micro-fabrication and assembly techniques in recent years offers increasing ability to control this phenomenon. Here, we identify how surface roughness influences the initial dynamic spreading of a partially wetting droplet by studying the spreading on a solid substrate patterned with microstructures just a few micrometers in size. We reveal that the roughness influence can be quantified in terms of a line friction coefficient for the energy dissipation rate at the contact line, and that this can be described in a simple formula in terms of the geometrical parameters of the roughness and the line-friction coefficient of the planar surface. We further identify a criterion to predict if the spreading will be controlled by this surface roughness or by liquid inertia. Our results point to the possibility of selectively controlling the wetting behavior by engineering the surface structure. PMID:25683872

  12. THE EFFECT OF STARSPOTS ON ACCURATE RADIUS DETERMINATION OF THE LOW-MASS DOUBLE-LINED ECLIPSING BINARY GU Boo

    SciTech Connect

    Windmiller, G.; Orosz, J. A.; Etzel, P. B. E-mail: orosz@sciences.sdsu.ed

    2010-04-01

    GU Boo is one of only a relatively small number of well-studied double-lined eclipsing binaries that contain low-mass stars. Lopez-Morales and Ribas present a comprehensive analysis of multi-color light and radial velocity curves for this system. The GU Boo light curves presented by Lopez-Morales and Ribas had substantial asymmetries, which were attributed to large spots. In spite of the asymmetry, Lopez-Morales and Ribas derived masses and radii accurate to {approx_equal}2%. We obtained additional photometry of GU Boo using both a CCD and a single-channel photometer and modeled the light curves with the ELC software to determine if the large spots in the light curves give rise to systematic errors at the few percent level. We also modeled the original light curves from the work of Lopez-Morales and Ribas using models with and without spots. We derived a radius of the primary of 0.6329 +- 0.0026 R{sub sun}, 0.6413 +- 0.0049 R{sub sun}, and 0.6373 +- 0.0029 R{sub sun} from the CCD, photoelectric, and Lopez-Morales and Ribas data, respectively. Each of these measurements agrees with the value reported by Lopez-Morales and Ribas (R{sub 1} = 0.623 +- 0.016 R{sub sun}) at the level of {approx}2%. In addition, the spread in these values is {approx}1%-2% from the mean. For the secondary, we derive radii of 0.6074 +- 0.0035 R{sub sun}, 0.5944 +- 0.0069 R{sub sun}, and 0.5976 +- 0.0059 R{sub sun} from the three respective data sets. The Lopez-Morales and Ribas value is R{sub 2} = 0.620 +- 0.020 R{sub sun}, which is {approx}2%-3% larger than each of the three values we found. The spread in these values is {approx}2% from the mean. The systematic difference between our three determinations of the secondary radius and that of Lopez-Morales and Ribas might be attributed to differences in the modeling process and codes used. Our own fits suggest that, for GU Boo at least, using accurate spot modeling of a single set of multi-color light curves results in radii determinations

  13. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  14. Algorithms for Determining Physical Responses of Structures Under Load

    NASA Technical Reports Server (NTRS)

    Richards, W. Lance; Ko, William L.

    2012-01-01

    Ultra-efficient real-time structural monitoring algorithms have been developed to provide extensive information about the physical response of structures under load. These algorithms are driven by actual strain data to measure accurately local strains at multiple locations on the surface of a structure. Through a single point load calibration test, these structural strains are then used to calculate key physical properties of the structure at each measurement location. Such properties include the structure s flexural rigidity (the product of the structure's modulus of elasticity, and its moment of inertia) and the section modulus (the moment of inertia divided by the structure s half-depth). The resulting structural properties at each location can be used to determine the structure s bending moment, shear, and structural loads in real time while the structure is in service. The amount of structural information can be maximized through the use of highly multiplexed fiber Bragg grating technology using optical time domain reflectometry and optical frequency domain reflectometry, which can provide a local strain measurement every 10 mm on a single hair-sized optical fiber. Since local strain is used as input to the algorithms, this system serves multiple purposes of measuring strains and displacements, as well as determining structural bending moment, shear, and loads for assessing real-time structural health. The first step is to install a series of strain sensors on the structure s surface in such a way as to measure bending strains at desired locations. The next step is to perform a simple ground test calibration. For a beam of length l (see example), discretized into n sections and subjected to a tip load of P that places the beam in bending, the flexural rigidity of the beam can be experimentally determined at each measurement location x. The bending moment at each station can then be determined for any general set of loads applied during operation.

  15. Surface structure determines dynamic wetting

    NASA Astrophysics Data System (ADS)

    Shiomi, Junichiro; Wang, Jiayu; Do-Quang, Minh; Cannon, James; Yue, Feng; Suzuki, Yuji; Amberg, Gustav

    2014-11-01

    Dynamic wetting, the spontaneous spreading process after droplet contacts a solid surface, is important in various engineering processes, such as in printing, coating, and lubrication. In the recent years, experiments and numerical simulations have greatly progressed the understanding in the dynamic wetting particularly on ``flat'' substrates. To gain further insight into the governing physics of the dynamic wetting, we perform droplet-wetting experiments on microstructured surfaces, just a few micrometers in size, with complementary numerical simulations, and investigate the dependence of the spreading rate on the microstructure geometries and fluid properties. We reveal that the influence of microstructures can be quantified in terms of a line friction coefficient for the energy dissipation rate at the contact line, and that this can be described in a simple formula in terms of the geometrical parameters of the roughness and the line-friction coefficient of the planar surface. The systematic study is also of practical importance since structures and roughness are omnipresent and their influence on spreading rate would give us additional degrees of freedom to control the dynamic wetting. This work was financially supported in part by, the Japan Society for the Promotion of Science (J.W., J.C., and J.S) and Swedish Governmental Agency for Innovation Systems (M.D.-Q. and G.A.).

  16. Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry.

    PubMed

    Ryde, Ulf

    2007-02-14

    The use of molecular mechanics calculations to supplement experimental data in standard X-ray crystallography and NMR refinements is discussed and it is shown that structures can be locally improved by the use of quantum chemical calculations. Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. They have shown that metal sites in crystal structures are frequently photoreduced or disordered, which makes the interpretation of the structures hard. Similar methods can be used for EXAFS refinements to obtain a full atomic structure, rather than a set of metal-ligand distances.

  17. Accurate determination of the valence band edge in hard x-ray photoemission spectra using GW theory

    NASA Astrophysics Data System (ADS)

    Lischner, Johannes; Nemšák, Slavomír; Conti, Giuseppina; Gloskovskii, Andrei; Pálsson, Gunnar Karl; Schneider, Claus M.; Drube, Wolfgang; Louie, Steven G.; Fadley, Charles

    2016-04-01

    We introduce a new method for determining accurate values of the valence-band maximum in x-ray photoemission spectra. Specifically, we align the sharpest peak in the valence-band region of the experimental spectrum with the corresponding feature of a theoretical valence-band density of states curve from ab initio GW theory calculations. This method is particularly useful for soft and hard x-ray photoemission studies of materials with a mixture of valence-band characters, where strong matrix element effects can render standard methods for extracting the valence-band maximum unreliable. We apply our method to hydrogen-terminated boron-doped diamond, which is a promising substrate material for novel solar cell devices. By carrying out photoemission experiments with variable light polarizations, we verify the accuracy of our analysis and the general validity of the method.

  18. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

    PubMed

    Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

    2014-01-15

    Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.

  19. Accurate Determination of Radionuclidic Purity and Half-Life of Reactor Produced LU-177G for Metabolic Radioimmunotherapy

    NASA Astrophysics Data System (ADS)

    Groppi, F.; Canella, L.; Bonardi, M. L.; Zona, C.; Morzenti, S.; Menapace, E.; Alfassi, Z. B.; Chinol, M.; Papi, S.; Tosi, G.

    2006-04-01

    The accurate determination of radionuclidic purity and half-life of the beta emitter 177gLu used for metabolic radioimmunotherapy is presented. High-resolution gamma spectrometry, as well as deconvolution of beta decay curve measured by spectrometry with liquid scintillation counting, have been adopted for quality control of different samples available on the market. A simple method was developed to distinguish between the different methods available for production of 177gLu: i.e. either direct (n,γ) reactions of enriched 176Lu or indirect (n,γ) activation of enriched 176Yb followed by β- decay. In the first case, the long-lived metastable level 177mLu is present in the radioactive preparation and a low specific activity radionuclide is obtained, in the latter a very high purity and high specific activity 177gLu is produced.

  20. Seeking: Accurate Measurement Techniques for Deep-Bone Density and Structure

    NASA Technical Reports Server (NTRS)

    Sibonga, Jean

    2009-01-01

    We are seeking a clinically-useful technology with enough sensitivity to assess the microstructure of "spongy" bone that is found in the marrow cavities of whole bones. However, this technology must be for skeletal sites surrounded by layers of soft tissues, such as the spine and the hip. Soft tissue interferes with conventional imaging and using a more accessible area -- for example, the wrist or the ankle of limbs-- as a proxy for the less accessible skeletal regions, will not be accurate. A non-radioactive technology is strongly preferred.

  1. Ion chromatography as highly suitable method for rapid and accurate determination of antibiotic fosfomycin in pharmaceutical wastewater.

    PubMed

    Zeng, Ping; Xie, Xiaolin; Song, Yonghui; Liu, Ruixia; Zhu, Chaowei; Galarneau, Anne; Pic, Jean-Stéphane

    2014-01-01

    A rapid and accurate ion chromatography (IC) method (limit of detection as low as 0.06 mg L(-1)) for fosfomycin concentration determination in pharmaceutical industrial wastewater was developed. This method was compared with the performance of high performance liquid chromatography determination (with a high detection limit of 96.0 mg L(-1)) and ultraviolet spectrometry after reacting with alizarin (difficult to perform in colored solutions). The accuracy of the IC method was established in the linear range of 1.0-15.0 mg L(-1) and a linear correlation was found with a correlation coefficient of 0.9998. The recoveries of fosfomycin from industrial pharmaceutical wastewater at spiking concentrations of 2.0, 5.0 and 8.0 mg L(-1) ranged from 81.91 to 94.74%, with a relative standard deviation (RSD) from 1 to 4%. The recoveries of effluent from a sequencing batch reactor treated fosfomycin with activated sludge at spiking concentrations of 5.0, 8.0, 10.0 mg L(-1) ranging from 98.25 to 99.91%, with a RSD from 1 to 2%. The developed IC procedure provided a rapid, reliable and sensitive method for the determination of fosfomycin concentration in industrial pharmaceutical wastewater and samples containing complex components.

  2. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L.; Perdew, John P.

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

  3. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

    PubMed

    Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science. PMID:27554409

  4. Determining crystal structures through crowdsourcing and coursework

    NASA Astrophysics Data System (ADS)

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  5. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-09-16

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  6. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  7. Determining crystal structures through crowdsourcing and coursework

    PubMed Central

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  8. A vector boundary matching technique for efficient and accurate determination of photonic bandgaps in photonic bandgap fibers.

    PubMed

    Dong, Liang

    2011-06-20

    A vector boundary matching technique has been proposed and demonstrated for finding photonic bandgaps in photonic bandgap fibers with circular nodes. Much improved accuracy, comparing to earlier works, comes mostly from using more accurate cell boundaries for each mode at the upper and lower edges of the band of modes. It is recognized that the unit cell boundary used for finding each mode at band edges of the 2D cladding lattice is not only dependent on whether it is a mode at upper or lower band edge, but also on the azimuthal mode number and lattice arrangements. Unit cell boundaries for these modes are determined by mode symmetries which are governed by the azimuthal mode number as well as lattice arrangement due to mostly geometrical constrains. Unit cell boundaries are determined for modes at both upper and lower edges of bands of modes dominated by m = 1 and m = 2 terms in their longitudinal field Fourier-Bessel expansion series, equivalent to LP0s and LP1s modes in the approximate LP mode representations, for hexagonal lattice to illustrate the technique. The novel technique is also implemented in vector form and incorporates a transfer matrix algorithm for the consideration of nodes with arbitrary refractive index profiles. Both are desired new capabilities for further explorations of advanced new designs of photonic bandgap fibers. PMID:21716499

  9. Nonlinear Optical Properties of Fluorescent Dyes Allow for Accurate Determination of Their Molecular Orientations in Phospholipid Membranes.

    PubMed

    Timr, Štěpán; Brabec, Jiří; Bondar, Alexey; Ryba, Tomáš; Železný, Miloš; Lazar, Josef; Jungwirth, Pavel

    2015-07-30

    Several methods based on single- and two-photon fluorescence detected linear dichroism have recently been used to determine the orientational distributions of fluorescent dyes in lipid membranes. However, these determinations relied on simplified descriptions of nonlinear anisotropic properties of the dye molecules, using a transition dipole-moment-like vector instead of an absorptivity tensor. To investigate the validity of the vector approximation, we have now carried out a combination of computer simulations and polarization microscopy experiments on two representative fluorescent dyes (DiI and F2N12S) embedded in aqueous phosphatidylcholine bilayers. Our results indicate that a simplified vector-like treatment of the two-photon transition tensor is applicable for molecular geometries sampled in the membrane at ambient conditions. Furthermore, our results allow evaluation of several distinct polarization microscopy techniques. In combination, our results point to a robust and accurate experimental and computational treatment of orientational distributions of DiI, F2N12S, and related dyes (including Cy3, Cy5, and others), with implications to monitoring physiologically relevant processes in cellular membranes in a novel way.

  10. Polyallelic structural variants can provide accurate, highly informative genetic markers focused on diagnosis and therapeutic targets: Accuracy vs. Precision.

    PubMed

    Roses, A D

    2016-02-01

    Structural variants (SVs) include all insertions, deletions, and rearrangements in the genome, with several common types of nucleotide repeats including single sequence repeats, short tandem repeats, and insertion-deletion length variants. Polyallelic SVs provide highly informative markers for association studies with well-phenotyped cohorts. SVs can influence gene regulation by affecting epigenetics, transcription, splicing, and/or translation. Accurate assays of polyallelic SV loci are required to define the range and allele frequency of variable length alleles. PMID:26517180

  11. Fine structure in proton radioactivity: An accurate tool to ascertain the breaking of axial symmetry in {sup 145}Tm

    SciTech Connect

    Arumugam, P.; Ferreira, L. S.; Maglione, E.

    2008-10-15

    With a proper formalism for proton emission from triaxially deformed nuclei, we perform exact calculations of decay widths for the decays to ground and first excited 2{sup +} states in the daughter nucleus. Our results for rotational spectrum, decay width and fine structure in the case of the nucleus {sup 145}Tm lead for the first time to an accurate identification of triaxial deformation using proton emission. This work also puts in evidence the advantage of proton emission over the conventional probes to study nuclear structure at the proton drip-line.

  12. SCAN: An Efficient Density Functional Yielding Accurate Structures and Energies of Diversely-Bonded Materials

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei

    The accuracy and computational efficiency of the widely used Kohn-Sham density functional theory (DFT) are limited by the approximation to its exchange-correlation energy Exc. The earliest local density approximation (LDA) overestimates the strengths of all bonds near equilibrium (even the vdW bonds). By adding the electron density gradient to model Exc, generalized gradient approximations (GGAs) generally soften the bonds to give robust and overall more accurate descriptions, except for the vdW interaction which is largely lost. Further improvement for covalent, ionic, and hydrogen bonds can be obtained by the computationally more expensive hybrid GGAs, which mix GGAs with the nonlocal exact exchange. Meta-GGAs are still semilocal in computation and thus efficient. Compared to GGAs, they add the kinetic energy density that enables them to recognize and accordingly treat different bonds, which no LDA or GGA can. We show here that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-GGA improves significantly over LDA and the standard Perdew-Burke-Ernzerhof GGA for geometries and energies of diversely-bonded materials (including covalent, metallic, ionic, hydrogen, and vdW bonds) at comparable efficiency. Often SCAN matches or improves upon the accuracy of a hybrid functional, at almost-GGA cost. This work has been supported by NSF under DMR-1305135 and CNS-09-58854, and by DOE BES EFRC CCDM under DE-SC0012575.

  13. Accurate determination of the thickness or mass per unit area of thin foils and single-crystal wafers for x-ray attenuation measurements

    NASA Astrophysics Data System (ADS)

    Tran, C. Q.; Chantler, C. T.; Barnea, Z.; de Jonge, M. D.

    2004-09-01

    The determination of the local mass per unit area m/A=∫ρdt and the thickness of a specimen is an important aspect of its characterization and is often required for material quality control in fabrication. We discuss common methods which have been used to determine the local thickness of thin specimens. We then propose an x-ray technique which is capable of determining the local thickness and the x-ray absorption profile of a foil or wafer to high accuracy. This technique provides an accurate integration of the column density which is not affected by the presence of voids and internal defects in the material. The technique is best suited to specimens with thickness substantially greater than the dimensions of the surface and void structure. We also show that the attenuation of an x-ray beam by a nonuniform specimen is significantly different from that calculated by using a simple linear average of the mass per unit area and quantify this effect. For much thinner specimens or in the presence of a very structured surface profile we propose a complementary technique capable of attaining high accuracy by the use of a secondary standard. The technique is demonstrated by absolute measurements of the x-ray mass attenuation coefficient of copper and silver.

  14. Accurate determination of the thickness or mass per unit area of thin foils and single-crystal wafers for x-ray attenuation measurements

    SciTech Connect

    Tran, C.Q.; Chantler, C.T.; Barnea, Z.; Jonge, M.D. de

    2004-09-01

    The determination of the local mass per unit area m/A={integral}{rho}dt and the thickness of a specimen is an important aspect of its characterization and is often required for material quality control in fabrication. We discuss common methods which have been used to determine the local thickness of thin specimens. We then propose an x-ray technique which is capable of determining the local thickness and the x-ray absorption profile of a foil or wafer to high accuracy. This technique provides an accurate integration of the column density which is not affected by the presence of voids and internal defects in the material. The technique is best suited to specimens with thickness substantially greater than the dimensions of the surface and void structure. We also show that the attenuation of an x-ray beam by a nonuniform specimen is significantly different from that calculated by using a simple linear average of the mass per unit area and quantify this effect. For much thinner specimens or in the presence of a very structured surface profile we propose a complementary technique capable of attaining high accuracy by the use of a secondary standard. The technique is demonstrated by absolute measurements of the x-ray mass attenuation coefficient of copper and silver.

  15. Accurate Fabrication of Hydroxyapatite Bone Models with Porous Scaffold Structures by Using Stereolithography

    NASA Astrophysics Data System (ADS)

    Maeda, Chiaki; Tasaki, Satoko; Kirihara, Soshu

    2011-05-01

    Computer graphic models of bioscaffolds with four-coordinate lattice structures of solid rods in artificial bones were designed by using a computer aided design. The scaffold models composed of acryl resin with hydroxyapatite particles at 45vol. % were fabricated by using stereolithography of a computer aided manufacturing. After dewaxing and sintering heat treatment processes, the ceramics scaffold models with four-coordinate lattices and fine hydroxyapatite microstructures were obtained successfully. By using a computer aided analysis, it was found that bio-fluids could flow extensively inside the sintered scaffolds. This result shows that the lattice structures will realize appropriate bio-fluid circulations and promote regenerations of new bones.

  16. Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction.

    PubMed

    Braun, Tatjana; Koehler Leman, Julia; Lange, Oliver F

    2015-12-01

    Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts. Following this seminal result, much effort is put into the improvement of contact predictions. However, there is also a substantial need to develop structure prediction protocols tailored to the type of restraints gained by contact predictions. Here, we present a structure prediction protocol that combines evolutionary information with the resolution-adapted structural recombination approach of Rosetta, called RASREC. Compared to the classic Rosetta ab initio protocol, RASREC achieves improved sampling, better convergence and higher robustness against incorrect distance restraints, making it the ideal sampling strategy for the stated problem. To demonstrate the accuracy of our protocol, we tested the approach on a diverse set of 28 globular proteins. Our method is able to converge for 26 out of the 28 targets and improves the average TM-score of the entire benchmark set from 0.55 to 0.72 when compared to the top ranked models obtained by the EVFold web server using identical contact predictions. Using a smaller benchmark, we furthermore show that the prediction accuracy of our method is only slightly reduced when the contact prediction accuracy is comparatively low. This observation is of special interest for protein sequences that only have a limited number of homologs.

  17. Direct atomic structure determination by the inspection of structural phase.

    PubMed

    Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne

    2013-08-27

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

  18. CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.

    PubMed

    Mizianty, Marcin J; Kurgan, Lukasz A

    2012-01-01

    Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies. PMID:21919861

  19. CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.

    PubMed

    Mizianty, Marcin J; Kurgan, Lukasz A

    2012-01-01

    Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies.

  20. High Fidelity Non-Gravitational Force Models for Precise and Accurate Orbit Determination of TerraSAR-X

    NASA Astrophysics Data System (ADS)

    Hackel, Stefan; Montenbruck, Oliver; Steigenberger, -Peter; Eineder, Michael; Gisinger, Christoph

    Remote sensing satellites support a broad range of scientific and commercial applications. The two radar imaging satellites TerraSAR-X and TanDEM-X provide spaceborne Synthetic Aperture Radar (SAR) and interferometric SAR data with a very high accuracy. The increasing demand for precise radar products relies on sophisticated validation methods, which require precise and accurate orbit products. Basically, the precise reconstruction of the satellite’s trajectory is based on the Global Positioning System (GPS) measurements from a geodetic-grade dual-frequency receiver onboard the spacecraft. The Reduced Dynamic Orbit Determination (RDOD) approach utilizes models for the gravitational and non-gravitational forces. Following a proper analysis of the orbit quality, systematics in the orbit products have been identified, which reflect deficits in the non-gravitational force models. A detailed satellite macro model is introduced to describe the geometry and the optical surface properties of the satellite. Two major non-gravitational forces are the direct and the indirect Solar Radiation Pressure (SRP). Due to the dusk-dawn orbit configuration of TerraSAR-X, the satellite is almost constantly illuminated by the Sun. Therefore, the direct SRP has an effect on the lateral stability of the determined orbit. The indirect effect of the solar radiation principally contributes to the Earth Radiation Pressure (ERP). The resulting force depends on the sunlight, which is reflected by the illuminated Earth surface in the visible, and the emission of the Earth body in the infrared spectra. Both components of ERP require Earth models to describe the optical properties of the Earth surface. Therefore, the influence of different Earth models on the orbit quality is assessed within the presentation. The presentation highlights the influence of non-gravitational force and satellite macro models on the orbit quality of TerraSAR-X.

  1. Accurate Focal Depth Determination of Oceanic Earthquakes Using Water-column Reverberation and Some Implications for the Shrinking Plate Hypothesis

    NASA Astrophysics Data System (ADS)

    Niu, F.; Huang, J.; Gordon, R. G.

    2015-12-01

    Investigation of oceanic earthquakes can play an important role in constraining the lateral and depth variations of the stress and strain-rate fields in oceanic lithosphere and of the thickness of the seismogenic layer as a function of lithosphere age, thereby providing us with critical insight into thermal and dynamic processes associated with the cooling and evolution of oceanic lithosphere. With the goal of estimating hypocentral depths more accurately, we observe clear water reverberations after the direct P wave on teleseismic records of oceanic earthquakes and develop a technique to estimate earthquake depths by using these reverberations. The Z-H grid search method allows the simultaneous determination of the sea floor depth (H) and earthquake depth (Z) with an uncertainty less than 1 km, which compares favorably with alternative approaches. We apply this method to two closely located earthquakes beneath the eastern Pacific. These earthquakes occur in ≈25 Ma-old lithosphere and were previously estimated to have very similar depths of ≈10-12 km. We find that the two events actually occurred at dissimilar depths of 2.5 km and 16.8 km beneath the seafloor, respectively within the oceanic crust and lithospheric mantle. The shallow and deep events are determined to be a thrust and normal earthquake, respectively, indicating that the stress field within the oceanic lithosphere changes from horizontal compression to horizontal extension as depth increases, which is consistent with the prediction of the lithospheric cooling model. Furthermore, we show that the P-axis of the newly investigated thrust-faulting earthquake is roughly perpendicular to that of the previously studied thrust event, consistent with the predictions of the shrinking-plate hypothesis.

  2. Accurate focal depth determination of oceanic earthquakes using water-column reverberation and some implications for the shrinking plate hypothesis

    NASA Astrophysics Data System (ADS)

    Huang, Jianping; Niu, Fenglin; Gordon, Richard G.; Cui, Chao

    2015-12-01

    Investigation of oceanic earthquakes is useful for constraining the lateral and depth variations of the stress and strain-rate fields in oceanic lithosphere, and the thickness of the seismogenic layer as a function of lithosphere age, thereby providing us with critical insight into thermal and dynamic processes associated with the cooling and evolution of oceanic lithosphere. With the goal of estimating hypocentral depths more accurately, we observe clear water reverberations after the direct P wave on teleseismic records of oceanic earthquakes and develop a technique to estimate earthquake depths by using these reverberations. The Z-H grid search method allows the simultaneous determination of the sea floor depth (H) and earthquake depth (Z) with an uncertainty less than 1 km, which compares favorably with alternative approaches. We apply this method to two closely located earthquakes beneath the eastern Pacific. These earthquakes occurred in ∼25 Ma-old lithosphere and were previously estimated to have similar depths of ∼10-12 km. We find that the two events actually occurred at dissimilar depths of 2.5 km and 16.8 km beneath the seafloor, respectively, within the oceanic crust and lithospheric mantle. The shallow and deep events are determined to be a thrust and normal earthquake, respectively, indicating that the stress field within the oceanic lithosphere changes from horizontal deviatoric compression to horizontal deviatoric tension as depth increases, which is consistent with the prediction of lithospheric cooling models. Furthermore, we show that the P-axis of the newly investigated thrust-faulting earthquake is perpendicular to that of the previously studied thrust event, consistent with the predictions of the shrinking-plate hypothesis.

  3. Development and validation of a novel, simple, and accurate spectrophotometric method for the determination of lead in human serum.

    PubMed

    Shayesteh, Tavakol Heidari; Khajavi, Farzad; Khosroshahi, Abolfazl Ghafuri; Mahjub, Reza

    2016-01-01

    The determination of blood lead levels is the most useful indicator of the determination of the amount of lead that is absorbed by the human body. Various methods, like atomic absorption spectroscopy (AAS), have already been used for the detection of lead in biological fluid, but most of these methods are based on complicated, expensive, and highly instructed instruments. In this study, a simple and accurate spectroscopic method for the determination of lead has been developed and applied for the investigation of lead concentration in biological samples. In this study, a silica gel column was used to extract lead and eliminate interfering agents in human serum samples. The column was washed with deionized water. The pH was adjusted to the value of 8.2 using phosphate buffer, and then tartrate and cyanide solutions were added as masking agents. The lead content was extracted into the organic phase containing dithizone as a complexion reagent and the dithizone-Pb(II) complex was formed and approved by visible spectrophotometry at 538 nm. The recovery was found to be 84.6 %. In order to validate the method, a calibration curve involving the use of various concentration levels was calculated and proven to be linear in the range of 0.01-1.5 μg/ml, with an R (2) regression coefficient of 0.9968 by statistical analysis of linear model validation. The largest error % values were found to be -5.80 and +11.6 % for intra-day and inter-day measurements, respectively. The largest RSD % values were calculated to be 6.54 and 12.32 % for intra-day and inter-day measurements, respectively. Further, the limit of detection (LOD) was calculated to be 0.002 μg/ml. The developed method was applied to determine the lead content in the human serum of voluntary miners, and it has been proven that there is no statistically significant difference between the data provided from this novel method and the data obtained from previously studied AAS. PMID:26631397

  4. Development and validation of a novel, simple, and accurate spectrophotometric method for the determination of lead in human serum.

    PubMed

    Shayesteh, Tavakol Heidari; Khajavi, Farzad; Khosroshahi, Abolfazl Ghafuri; Mahjub, Reza

    2016-01-01

    The determination of blood lead levels is the most useful indicator of the determination of the amount of lead that is absorbed by the human body. Various methods, like atomic absorption spectroscopy (AAS), have already been used for the detection of lead in biological fluid, but most of these methods are based on complicated, expensive, and highly instructed instruments. In this study, a simple and accurate spectroscopic method for the determination of lead has been developed and applied for the investigation of lead concentration in biological samples. In this study, a silica gel column was used to extract lead and eliminate interfering agents in human serum samples. The column was washed with deionized water. The pH was adjusted to the value of 8.2 using phosphate buffer, and then tartrate and cyanide solutions were added as masking agents. The lead content was extracted into the organic phase containing dithizone as a complexion reagent and the dithizone-Pb(II) complex was formed and approved by visible spectrophotometry at 538 nm. The recovery was found to be 84.6 %. In order to validate the method, a calibration curve involving the use of various concentration levels was calculated and proven to be linear in the range of 0.01-1.5 μg/ml, with an R (2) regression coefficient of 0.9968 by statistical analysis of linear model validation. The largest error % values were found to be -5.80 and +11.6 % for intra-day and inter-day measurements, respectively. The largest RSD % values were calculated to be 6.54 and 12.32 % for intra-day and inter-day measurements, respectively. Further, the limit of detection (LOD) was calculated to be 0.002 μg/ml. The developed method was applied to determine the lead content in the human serum of voluntary miners, and it has been proven that there is no statistically significant difference between the data provided from this novel method and the data obtained from previously studied AAS.

  5. Caregiver's Country of Birth Is a Significant Determinant of Accurate Perception of Preschool-Age Children's Weight

    ERIC Educational Resources Information Center

    Natale, Ruby; Uhlhorn, Susan B.; Lopez-Mitnik, Gabriela; Camejo, Stephanie; Englebert, Nicole; Delamater, Alan M.; Messiah, Sarah E.

    2016-01-01

    Background: One in four preschool-age children in the United States are currently overweight or obese. Previous studies have shown that caregivers of this age group often have difficulty accurately recognizing their child's weight status. The purpose of this study was to examine factors associated with accurate/inaccurate perception of child body…

  6. RNA Secondary Structure Determination by NMR.

    PubMed

    Chen, Jonathan L; Bellaousov, Stanislav; Turner, Douglas H

    2016-01-01

    Dynamic programming methods for predicting RNA secondary structure often use thermodynamics and experimental restraints and/or constraints to limit folding space. Chemical mapping results typically restrain certain nucleotides not to be in AU or GC pairs. Two-dimensional nuclear magnetic resonance (NMR) spectra can reveal the order of AU, GC, and GU pairs in double helixes. This chapter describes a program, NMR-assisted prediction of secondary structure and chemical shifts (NAPSS-CS), that constrains possible secondary structures on the basis of the NMR determined order and 5'-3' direction of AU, GC, and GU pairs in helixes. NAPSS-CS minimally requires input of the order of base pairs as determined from nuclear Overhauser effect spectroscopy (NOESY) of imino protons. The program deduces the 5'-3' direction of the base pairs if certain chemical shifts are also input. Secondary structures predicted by the program provide assignments of input chemical shifts to particular nucleotides in the sequence, thus facilitating an important step for determination of the three dimensional structure by NMR. The method is particularly useful for revealing pseudoknots and an example is provided. The method may also allow determination of secondary structures when a sequence folds into two structures that exchange slowly. PMID:27665599

  7. Accurate determination of selected pesticides in soya beans by liquid chromatography coupled to isotope dilution mass spectrometry.

    PubMed

    Huertas Pérez, J F; Sejerøe-Olsen, B; Fernández Alba, A R; Schimmel, H; Dabrio, M

    2015-05-01

    A sensitive, accurate and simple liquid chromatography coupled with mass spectrometry method for the determination of 10 selected pesticides in soya beans has been developed and validated. The method is intended for use during the characterization of selected pesticides in a reference material. In this process, high accuracy and appropriate uncertainty levels associated to the analytical measurements are of utmost importance. The analytical procedure is based on sample extraction by the use of a modified QuEChERS (quick, easy, cheap, effective, rugged, safe) extraction and subsequent clean-up of the extract with C18, PSA and Florisil. Analytes were separated on a C18 column using gradient elution with water-methanol/2.5 mM ammonium acetate mobile phase, and finally identified and quantified by triple quadrupole mass spectrometry in the multiple reaction monitoring mode (MRM). Reliable and accurate quantification of the analytes was achieved by means of stable isotope-labelled analogues employed as internal standards (IS) and calibration with pure substance solutions containing both, the isotopically labelled and native compounds. Exceptions were made for thiodicarb and malaoxon where the isotopically labelled congeners were not commercially available at the time of analysis. For the quantification of those compounds methomyl-(13)C2(15)N and malathion-D10 were used respectively. The method was validated according to the general principles covered by DG SANCO guidelines. However, validation criteria were set more stringently. Mean recoveries were in the range of 86-103% with RSDs lower than 8.1%. Repeatability and intermediate precision were in the range of 3.9-7.6% and 1.9-8.7% respectively. LODs were theoretically estimated and experimentally confirmed to be in the range 0.001-0.005 mg kg(-1) in the matrix, while LOQs established as the lowest spiking mass fractionation level were in the range 0.01-0.05 mg kg(-1). The method reliably identifies and quantifies the

  8. The Dirac equation in electronic structure calculations: Accurate evaluation of DFT predictions for actinides

    SciTech Connect

    Wills, John M; Mattsson, Ann E

    2012-06-06

    Brooks, Johansson, and Skriver, using the LMTO-ASA method and considerable insight, were able to explain many of the ground state properties of the actinides. In the many years since this work was done, electronic structure calculations of increasing sophistication have been applied to actinide elements and compounds, attempting to quantify the applicability of DFT to actinides and actinide compounds and to try to incorporate other methodologies (i.e. DMFT) into DFT calculations. Through these calculations, the limits of both available density functionals and ad hoc methodologies are starting to become clear. However, it has also become clear that approximations used to incorporate relativity are not adequate to provide rigorous tests of the underlying equations of DFT, not to mention ad hoc additions. In this talk, we describe the result of full-potential LMTO calculations for the elemental actinides, comparing results obtained with a full Dirac basis with those obtained from scalar-relativistic bases, with and without variational spin-orbit. This comparison shows that the scalar relativistic treatment of actinides does not have sufficient accuracy to provide a rigorous test of theory and that variational spin-orbit introduces uncontrolled errors in the results of electronic structure calculations on actinide elements.

  9. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  10. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  11. Simple approach for ranking structure determining residues.

    PubMed

    Luna-Martínez, Oscar D; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N; Becerril, Baltazar

    2016-01-01

    Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

  12. Simple approach for ranking structure determining residues

    PubMed Central

    Luna-Martínez, Oscar D.; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I.; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N.

    2016-01-01

    Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology. PMID:27366642

  13. Distributed structure determination at the JCSG

    SciTech Connect

    Bedem, Henry van den Wolf, Guenter; Xu, Qingping; Deacon, Ashley M.

    2011-04-01

    The software suite Xsolve semi-exhaustively explores key parameters of the X-ray structure-determination process to compute multiple three-dimensional protein structures independently and in parallel from a set of diffraction images. An optimal consensus model for subsequent manual refinement is computed from these structures. The Joint Center for Structural Genomics (JCSG), one of four large-scale structure-determination centers funded by the US Protein Structure Initiative (PSI) through the National Institute for General Medical Sciences, has been operating an automated distributed structure-solution pipeline, Xsolve, for well over half a decade. During PSI-2, Xsolve solved, traced and partially refined 90% of the JCSG’s nearly 770 MAD/SAD structures at an average resolution of about 2 Å without human intervention. Xsolve executes many well established publicly available crystallography software programs in parallel on a commodity Linux cluster, resulting in multiple traces for any given target. Additional software programs have been developed and integrated into Xsolve to further minimize human effort in structure refinement. ConsensusModeler exploits complementarities in traces from Xsolve to compute a single optimal model for manual refinement. Xpleo is a powerful robotics-inspired algorithm to build missing fragments and qFit automatically identifies and fits alternate conformations.

  14. Accurate determination of the Gibbs energy of Cu-Zr melts using the thermodynamic integration method in Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Harvey, J.-P.; Gheribi, A. E.; Chartrand, P.

    2011-08-01

    The design of multicomponent alloys used in different applications based on specific thermo-physical properties determined experimentally or predicted from theoretical calculations is of major importance in many engineering applications. A procedure based on Monte Carlo simulations (MCS) and the thermodynamic integration (TI) method to improve the quality of the predicted thermodynamic properties calculated from classical thermodynamic calculations is presented in this study. The Gibbs energy function of the liquid phase of the Cu-Zr system at 1800 K has been determined based on this approach. The internal structure of Cu-Zr melts and amorphous alloys at different temperatures, as well as other physical properties were also obtained from MCS in which the phase trajectory was modeled by the modified embedded atom model formalism. A rigorous comparison between available experimental data and simulated thermo-physical properties obtained from our MCS is presented in this work. The modified quasichemical model in the pair approximation was parameterized using the internal structure data obtained from our MCS and the precise Gibbs energy function calculated at 1800 K from the TI method. The predicted activity of copper in Cu-Zr melts at 1499 K obtained from our thermodynamic optimization was corroborated by experimental data found in the literature. The validity of the amplitude of the entropy of mixing obtained from the in silico procedure presented in this work was analyzed based on the thermodynamic description of hard sphere mixtures.

  15. Determination of Baylisascaris schroederi infection in wild giant pandas by an accurate and sensitive PCR/CE-SSCP method.

    PubMed

    Zhang, Wenping; Yie, Shangmian; Yue, Bisong; Zhou, Jielong; An, Renxiong; Yang, Jiangdong; Chen, Wangli; Wang, Chengdong; Zhang, Liang; Shen, Fujun; Yang, Guangyou; Hou, Rong; Zhang, Zhihe

    2012-01-01

    It has been recognized that other than habitat loss, degradation and fragmentation, the infection of the roundworm Baylisascaris schroederi (B. schroederi) is one of the major causes of death in wild giant pandas. However, the prevalence and intensity of the parasite infection has been inconsistently reported through a method that uses sedimentation-floatation followed by a microscope examination. This method fails to accurately determine infection because there are many bamboo residues and/or few B. schroederi eggs in the examined fecal samples. In the present study, we adopted a method that uses PCR and capillary electrophoresis combined with a single-strand conformation polymorphism analysis (PCR/CE-SSCP) to detect B. schroederi infection in wild giant pandas at a nature reserve, and compared it to the traditional microscope approach. The PCR specifically amplified a single band of 279-bp from both fecal samples and positive controls, which was confirmed by sequence analysis to correspond to the mitochondrial COII gene of B. schroederi. Moreover, it was demonstrated that the amount of genomic DNA was linearly correlated with the peak area of the CE-SSCP analysis. Thus, our adopted method can reliably detect the infectious prevalence and intensity of B. schroederi in wild giant pandas. The prevalence of B. schroederi was found to be 54% in the 91 fecal samples examined, and 48% in the fecal samples of 31 identified individual giant pandas. Infectious intensities of the 91 fecal samples were detected to range from 2.8 to 959.2 units/gram, and from 4.8 to 959.2 units/gram in the fecal samples of the 31 identified giant pandas. For comparison, by using the traditional microscope method, the prevalence of B. schroederi was found to be only 33% in the 91 fecal samples, 32% in the fecal samples of the 31 identified giant pandas, and no reliable infectious intensity was observed. PMID:22911871

  16. Determination of Baylisascaris schroederi Infection in Wild Giant Pandas by an Accurate and Sensitive PCR/CE-SSCP Method

    PubMed Central

    Zhang, Wenping; Yie, Shangmian; Yue, Bisong; Zhou, Jielong; An, Renxiong; Yang, Jiangdong; Chen, Wangli; Wang, Chengdong; Zhang, Liang; Shen, Fujun; Yang, Guangyou; Hou, Rong; Zhang, Zhihe

    2012-01-01

    It has been recognized that other than habitat loss, degradation and fragmentation, the infection of the roundworm Baylisascaris schroederi (B. schroederi) is one of the major causes of death in wild giant pandas. However, the prevalence and intensity of the parasite infection has been inconsistently reported through a method that uses sedimentation-floatation followed by a microscope examination. This method fails to accurately determine infection because there are many bamboo residues and/or few B. schroederi eggs in the examined fecal samples. In the present study, we adopted a method that uses PCR and capillary electrophoresis combined with a single-strand conformation polymorphism analysis (PCR/CE-SSCP) to detect B. schroederi infection in wild giant pandas at a nature reserve, and compared it to the traditional microscope approach. The PCR specifically amplified a single band of 279-bp from both fecal samples and positive controls, which was confirmed by sequence analysis to correspond to the mitochondrial COII gene of B. schroederi. Moreover, it was demonstrated that the amount of genomic DNA was linearly correlated with the peak area of the CE-SSCP analysis. Thus, our adopted method can reliably detect the infectious prevalence and intensity of B. schroederi in wild giant pandas. The prevalence of B. schroederi was found to be 54% in the 91 fecal samples examined, and 48% in the fecal samples of 31 identified individual giant pandas. Infectious intensities of the 91 fecal samples were detected to range from 2.8 to 959.2 units/gram, and from 4.8 to 959.2 units/gram in the fecal samples of the 31 identified giant pandas. For comparison, by using the traditional microscope method, the prevalence of B. schroederi was found to be only 33% in the 91 fecal samples, 32% in the fecal samples of the 31 identified giant pandas, and no reliable infectious intensity was observed. PMID:22911871

  17. Determination of Baylisascaris schroederi infection in wild giant pandas by an accurate and sensitive PCR/CE-SSCP method.

    PubMed

    Zhang, Wenping; Yie, Shangmian; Yue, Bisong; Zhou, Jielong; An, Renxiong; Yang, Jiangdong; Chen, Wangli; Wang, Chengdong; Zhang, Liang; Shen, Fujun; Yang, Guangyou; Hou, Rong; Zhang, Zhihe

    2012-01-01

    It has been recognized that other than habitat loss, degradation and fragmentation, the infection of the roundworm Baylisascaris schroederi (B. schroederi) is one of the major causes of death in wild giant pandas. However, the prevalence and intensity of the parasite infection has been inconsistently reported through a method that uses sedimentation-floatation followed by a microscope examination. This method fails to accurately determine infection because there are many bamboo residues and/or few B. schroederi eggs in the examined fecal samples. In the present study, we adopted a method that uses PCR and capillary electrophoresis combined with a single-strand conformation polymorphism analysis (PCR/CE-SSCP) to detect B. schroederi infection in wild giant pandas at a nature reserve, and compared it to the traditional microscope approach. The PCR specifically amplified a single band of 279-bp from both fecal samples and positive controls, which was confirmed by sequence analysis to correspond to the mitochondrial COII gene of B. schroederi. Moreover, it was demonstrated that the amount of genomic DNA was linearly correlated with the peak area of the CE-SSCP analysis. Thus, our adopted method can reliably detect the infectious prevalence and intensity of B. schroederi in wild giant pandas. The prevalence of B. schroederi was found to be 54% in the 91 fecal samples examined, and 48% in the fecal samples of 31 identified individual giant pandas. Infectious intensities of the 91 fecal samples were detected to range from 2.8 to 959.2 units/gram, and from 4.8 to 959.2 units/gram in the fecal samples of the 31 identified giant pandas. For comparison, by using the traditional microscope method, the prevalence of B. schroederi was found to be only 33% in the 91 fecal samples, 32% in the fecal samples of the 31 identified giant pandas, and no reliable infectious intensity was observed.

  18. A structural determinant required for RNA editing

    PubMed Central

    Tian, Nan; Yang, Yun; Sachsenmaier, Nora; Muggenhumer, Dominik; Bi, Jingpei; Waldsich, Christina; Jantsch, Michael F.; Jin, Yongfeng

    2011-01-01

    RNA editing by adenosine deaminases acting on RNAs (ADARs) can be both specific and non-specific, depending on the substrate. Specific editing of particular adenosines may depend on the overall sequence and structural context. However, the detailed mechanisms underlying these preferences are not fully understood. Here, we show that duplex structures mimicking an editing site in the Gabra3 pre-mRNA unexpectedly fail to support RNA editing at the Gabra3 I/M site, although phylogenetic analysis suggest an evolutionarily conserved duplex structure essential for efficient RNA editing. These unusual results led us to revisit the structural requirement for this editing by mutagenesis analysis. In vivo nuclear injection experiments of mutated editing substrates demonstrate that a non-conserved structure is a determinant for editing. This structure contains bulges either on the same or the strand opposing the edited adenosine. The position of these bulges and the distance to the edited base regulate editing. Moreover, elevated folding temperature can lead to a switch in RNA editing suggesting an RNA structural change. Our results indicate the importance of RNA tertiary structure in determining RNA editing. PMID:21427087

  19. Accurate mass determination, quantification and determination of detection limits in liquid chromatography-high-resolution time-of-flight mass spectrometry: challenges and practical solutions.

    PubMed

    Vergeynst, Leendert; Van Langenhove, Herman; Joos, Pieter; Demeestere, Kristof

    2013-07-30

    Uniform guidelines for the data processing and validation of qualitative and quantitative multi-residue analysis using full-spectrum high-resolution mass spectrometry are scarce. Through systematic research, optimal mass accuracy and sensitivity are obtained after refining the post-processing of the HRMS data. For qualitative analysis, transforming the raw profile spectra to centroid spectra is recommended resulting in a 2.3 fold improved precision on the accurate mass determination of spectrum peaks. However, processing centroid data for quantitative purposes could lead to signal interruption when too narrow mass windows are applied for the construction of extracted ion chromatograms. Therefore, peak integration on the raw profile data is recommended. An optimal width of the mass window of 50 ppm, which is a trade-off between sensitivity and selectivity, was obtained for a TOF instrument providing a resolving power of 20,000 at full width at half maximum (FWHM). For the validation of HRMS analytical methods, widespread concepts such as the signal-to-noise ratios for the determination of decision limits and detection capabilities have shown to be not always applicable because in some cases almost no noise can be detected anymore. A statistical methodology providing a reliable alternative is extended and applied. PMID:23856232

  20. Voronoi-cell finite difference method for accurate electronic structure calculation of polyatomic molecules on unstructured grids

    SciTech Connect

    Son, Sang-Kil

    2011-03-01

    We introduce a new numerical grid-based method on unstructured grids in the three-dimensional real-space to investigate the electronic structure of polyatomic molecules. The Voronoi-cell finite difference (VFD) method realizes a discrete Laplacian operator based on Voronoi cells and their natural neighbors, featuring high adaptivity and simplicity. To resolve multicenter Coulomb singularity in all-electron calculations of polyatomic molecules, this method utilizes highly adaptive molecular grids which consist of spherical atomic grids. It provides accurate and efficient solutions for the Schroedinger equation and the Poisson equation with the all-electron Coulomb potentials regardless of the coordinate system and the molecular symmetry. For numerical examples, we assess accuracy of the VFD method for electronic structures of one-electron polyatomic systems, and apply the method to the density-functional theory for many-electron polyatomic molecules.

  1. A Simple and Accurate Analysis of Conductivity Loss in Millimeter-Wave Helical Slow-Wave Structures

    NASA Astrophysics Data System (ADS)

    Datta, S. K.; Kumar, Lalit; Basu, B. N.

    2009-04-01

    Electromagnetic field analysis of a helix slow-wave structure was carried out and a closed form expression was derived for the inductance per unit length of the transmission-line equivalent circuit of the structure, taking into account the actual helix tape dimensions and surface current on the helix over the actual metallic area of the tape. The expression of the inductance per unit length, thus obtained, was used for estimating the increment in the inductance per unit length caused due to penetration of the magnetic flux into the conducting surfaces following Wheeler’s incremental inductance rule, which was subsequently interpreted for the attenuation constant of the propagating structure. The analysis was computationally simple and accurate, and accrues the accuracy of 3D electromagnetic analysis by allowing the use of dispersion characteristics obtainable from any standard electromagnetic modeling. The approach was benchmarked against measurement for two practical structures, and excellent agreement was observed. The analysis was subsequently applied to demonstrate the effects of conductivity on the attenuation constant of a typical broadband millimeter-wave helical slow-wave structure with respect to helix materials and copper plating on the helix, surface finish of the helix, dielectric loading effect and effect of high temperature operation - a comparative study of various such aspects are covered.

  2. Representing Personal Determinants in Causal Structures.

    ERIC Educational Resources Information Center

    Bandura, Albert

    1984-01-01

    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  3. Protein structure determination using a database of interatomic distance probabilities.

    PubMed Central

    Wall, M. E.; Subramaniam, S.; Phillips, G. N.

    1999-01-01

    The accelerated pace of genomic sequencing has increased the demand for structural models of gene products. Improved quantitative methods are needed to study the many systems (e.g., macromolecular assemblies) for which data are scarce. Here, we describe a new molecular dynamics method for protein structure determination and molecular modeling. An energy function, or database potential, is derived from distributions of interatomic distances obtained from a database of known structures. X-ray crystal structures are refined by molecular dynamics with the new energy function replacing the Van der Waals potential. Compared to standard methods, this method improved the atomic positions, interatomic distances, and side-chain dihedral angles of structures randomized to mimic the early stages of refinement. The greatest enhancement in side-chain placement was observed for groups that are characteristically buried. More accurate calculated model phases will follow from improved interatomic distances. Details usually seen only in high-resolution refinements were improved, as is shown by an R-factor analysis. The improvements were greatest when refinements were carried out using X-ray data truncated at 3.5 A. The database potential should therefore be a valuable tool for determining X-ray structures, especially when only low-resolution data are available. PMID:10631988

  4. Accurate determination of human serum transferrin isoforms: Exploring metal-specific isotope dilution analysis as a quantitative proteomic tool.

    PubMed

    Busto, M Estela del Castillo; Montes-Bayón, Maria; Sanz-Medel, Alfredo

    2006-12-15

    Carbohydrate-deficient transferrin (CDT) measurements are considered a reliable marker for chronic alcohol consumption, and its use is becoming extensive in forensic medicine. However, CDT is not a single molecular entity but refers to a group of sialic acid-deficient transferrin isoforms from mono- to trisialotransferrin. Thus, the development of methods to analyze accurately and precisely individual transferrin isoforms in biological fluids such as serum is of increasing importance. The present work illustrates the use of ICPMS isotope dilution analysis for the quantification of transferrin isoforms once saturated with iron and separated by anion exchange chromatography (Mono Q 5/50) using a mobile phase consisting of a gradient of ammonium acetate (0-250 mM) in 25 mM Tris-acetic acid (pH 6.5). Species-specific and species-unspecific spikes have been explored. In the first part of the study, the use of postcolumn addition of a solution of 200 ng mL(-1) isotopically enriched iron (57Fe, 95%) in 25 mM sodium citrate/citric acid (pH 4) permitted the quantification of individual sialoforms of transferrin (from S2 to S5) in human serum samples of healthy individuals as well as alcoholic patients. Second, the species-specific spike method was performed by synthesizing an isotopically enriched standard of saturated transferrin (saturated with 57Fe). The characterization of the spike was performed by postcolumn reverse isotope dilution analysis (this is, by postcolumn addition of a solution of 200 ng mL(-1) natural iron in sodium citrate/citric acid of pH 4). Also, the stability of the transferrin spike was tested during one week with negligible species transformation. Finally, the enriched transferrin was used to quantify the individual isoforms in the same serum samples obtaining results comparative to those of postcolumn isotope dilution and to those previously published in the literature, demonstrating the suitability of both strategies for quantitative transferrin

  5. Method of fan sound mode structure determination

    NASA Technical Reports Server (NTRS)

    Pickett, G. F.; Sofrin, T. G.; Wells, R. W.

    1977-01-01

    A method for the determination of fan sound mode structure in the Inlet of turbofan engines using in-duct acoustic pressure measurements is presented. The method is based on the simultaneous solution of a set of equations whose unknowns are modal amplitude and phase. A computer program for the solution of the equation set was developed. An additional computer program was developed which calculates microphone locations the use of which results in an equation set that does not give rise to numerical instabilities. In addition to the development of a method for determination of coherent modal structure, experimental and analytical approaches are developed for the determination of the amplitude frequency spectrum of randomly generated sound models for use in narrow annulus ducts. Two approaches are defined: one based on the use of cross-spectral techniques and the other based on the use of an array of microphones.

  6. DeconMSn: A Software Tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

    SciTech Connect

    Mayampurath, Anoop M.; Jaitly, Navdeep; Purvine, Samuel O.; Monroe, Matthew E.; Auberry, Kenneth J.; Adkins, Joshua N.; Smith, Richard D.

    2008-04-01

    We present a new software tool for tandem MS analyses that: • accurately calculates the monoisotopic mass and charge of high–resolution parent ions • accurately operates regardless of the mass selected for fragmentation • performs independent of instrument settings • enables optimal selection of search mass tolerance for high mass accuracy experiments • is open source and thus can be tailored to individual needs • incorporates a SVM-based charge detection algorithm for analyzing low resolution tandem MS spectra • creates multiple output data formats (.dta, .MGF) • handles .RAW files and .mzXML formats • compatible with SEQUEST, MASCOT, X!Tandem

  7. Fast and accurate determination of K, Ca, and Mg in human serum by sector field ICP-MS.

    PubMed

    Yu, Lee L; Davis, W Clay; Nuevo Ordonez, Yoana; Long, Stephen E

    2013-11-01

    Electrolytes in serum are important biomarkers for skeletal and cellular health. The levels of electrolytes are monitored by measuring the Ca, Mg, K, and Na in blood serum. Many reference methods have been developed for the determination of Ca, Mg, and K in clinical measurements; however, isotope dilution thermal ionization mass spectrometry (ID-TIMS) has traditionally been the primary reference method serving as an anchor for traceability and accuracy to these secondary reference methods. The sample matrix must be separated before ID-TIMS measurements, which is a slow and tedious process that hindered the adoption of the technique in routine clinical measurements. We have developed a fast and accurate method for the determination of Ca, Mg, and K in serum by taking advantage of the higher mass resolution capability of the modern sector field inductively coupled plasma mass spectrometry (SF-ICP-MS). Each serum sample was spiked with a mixture containing enriched (44)Ca, (26)Mg, and (41)K, and the (42)Ca(+):(44)Ca(+), (24)Mg(+):(26)Mg(+), and (39)K(+):(41)K(+) ratios were measured. The Ca and Mg ratios were measured in medium resolution mode (m/Δm ≈ 4 500), and the K ratio in high resolution mode (m/Δm ≈ 10 000). Residual (40)Ar(1)H(+) interference was still observed but the deleterious effects of the interference were minimized by measuring the sample at K > 100 ng g(-1). The interferences of Sr(++) at the two Ca isotopes were less than 0.25 % of the analyte signal, and they were corrected with the (88)Sr(+) intensity by using the Sr(++):Sr(+) ratio. The sample preparation involved only simple dilutions, and the measurement using this sample preparation approach is known as dilution-and-shoot (DNS). The DNS approach was validated with samples prepared via the traditional acid digestion approach followed by ID-SF-ICP-MS measurement. DNS and digested samples of SRM 956c were measured with ID-SF-ICP-MS for quality assurance, and the results (mean

  8. Structure determination of molecules of biochemical interest

    NASA Astrophysics Data System (ADS)

    Honzatko, R. B.

    1985-10-01

    In the past year we have established a new laboratory for the determination of macromolecular structure. Currently, facilities are in place for data collection, data processing, molecular modeling and X-ray refinement of structures of up to 100,000 molecular weight in their crystallographic asymmetric unit. In parallel with establishing a new laboratory, we have pursued structure investigations of hemoglobin from the sea lamprey, aspartate carbamoyltransferase from Escherichia coli and p-nitrobenzylidine aminoguanidine, a small molecule which is an acceptor of the adenosine diphosphate ribosyl group in an enzyme mediated reaction. In addition to the structural studies above we have made a theoretical study by techniques of energy minimization of possible modes of aggregation of lamprey hemoglobin and the relationship between aggregate formation and cooperativity expressed in solutions by lamprey hemoglobin.

  9. Structure of mutant human oncogene protein determined

    SciTech Connect

    Baum, R.

    1989-01-16

    The protein encoded by a mutant human oncogene differs only slightly in structure from the native protein that initiates normal cell division, a finding that may complicate efforts to develop inhibitors of the mutant protein. Previously, the x-ray structure of the protein encoded by the normal c-Ha-ras gene, a protein believed to signal cells to start or stop dividing through its interaction with guanosine triphosphate (GTP), was reported. The structure of the protein encoded by a transforming c-Ha-ras oncogene, in which a valine codon replaces the normal glycine codon at position 12 in the gene, has now been determined. The differences in the structures of the mutant and normal proteins are located primarily in a loop that interacts with the /beta/-phosphate of a bound guanosine diphosphate (GDP) molecule.

  10. Crystal structure of methane oxidation enzyme determined

    SciTech Connect

    Baum, R.

    1994-01-10

    A team of chemists has determined to 2.2-[angstrom] resolution the crystal structure of the hydroxylase protein of methane monooxygenase, the enzyme system responsible for the biological oxidation of methane. The hydroxylase, at a molecular weight of 251,000 daltons, if by far the largest component of methane monooxygenase. Although the crystal structure of the hydroxylase did not reveal any startling surprises about the enzyme-many features of the hydroxylase had been inferred previously from modeling and spectroscopic studies -- obtaining it is a significant achievement. For one thing, the crystal structure unambiguously confirms aspects of the enzyme structure that been at least somewhat speculative. The three-dimensional structure of the enzyme, the chemist say, also provides important insight into biological methane oxidation, including how methane, a relatively inert gas, might diffuse to and bind near the active site of the enzyme. The structure points to particular amino acid residues that are likely to participate in catalysis, and clarifies the structure of the dinuclear iron core of the enzyme.

  11. Deducing chemical structure from crystallographically determined atomic coordinates

    PubMed Central

    Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

    2011-01-01

    An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

  12. Efficient and accurate linear algebraic methods for large-scale electronic structure calculations with nonorthogonal atomic orbitals

    NASA Astrophysics Data System (ADS)

    Teng, H.; Fujiwara, T.; Hoshi, T.; Sogabe, T.; Zhang, S.-L.; Yamamoto, S.

    2011-04-01

    The need for large-scale electronic structure calculations arises recently in the field of material physics, and efficient and accurate algebraic methods for large simultaneous linear equations become greatly important. We investigate the generalized shifted conjugate orthogonal conjugate gradient method, the generalized Lanczos method, and the generalized Arnoldi method. They are the solver methods of large simultaneous linear equations of the one-electron Schrödinger equation and map the whole Hilbert space to a small subspace called the Krylov subspace. These methods are applied to systems of fcc Au with the NRL tight-binding Hamiltonian [F. Kirchhoff , Phys. Rev. BJCOMEL1098-012110.1103/PhysRevB.63.195101 63, 195101 (2001)]. We compare results by these methods and the exact calculation and show them to be equally accurate. The system size dependence of the CPU time is also discussed. The generalized Lanczos method and the generalized Arnoldi method are the most suitable for the large-scale molecular dynamics simulations from the viewpoint of CPU time and memory size.

  13. Extraction of accurate structure-factor amplitudes from Laue data: wavelength normalization with wiggler and undulator X-ray sources.

    PubMed

    Srajer, V; Crosson, S; Schmidt, M; Key, J; Schotte, F; Anderson, S; Perman, B; Ren, Z; Teng, T Y; Bourgeois, D; Wulff, M; Moffat, K

    2000-07-01

    Wavelength normalization is an essential part of processing of Laue X-ray diffraction data and is critically important for deriving accurate structure-factor amplitudes. The results of wavelength normalization for Laue data obtained in nanosecond time-resolved experiments at the ID09 beamline at the European Synchrotron Radiation Facility, Grenoble, France, are presented. Several wiggler and undulator insertion devices with complex spectra were used. The results show that even in the most challenging cases, such as wiggler/undulator tandems or single-line undulators, accurate wavelength normalization does not require unusually redundant Laue data and can be accomplished using typical Laue data sets. Single-line undulator spectra derived from Laue data compare well with the measured incident X-ray spectra. Successful wavelength normalization of the undulator data was also confirmed by the observed signal in nanosecond time-resolved experiments. Single-line undulators, which are attractive for time-resolved experiments due to their high peak intensity and low polychromatic background, are compared with wigglers, based on data obtained on the same crystal. PMID:16609201

  14. Membrane protein structure determination - the next generation.

    PubMed

    Moraes, Isabel; Evans, Gwyndaf; Sanchez-Weatherby, Juan; Newstead, Simon; Stewart, Patrick D Shaw

    2014-01-01

    The field of Membrane Protein Structural Biology has grown significantly since its first landmark in 1985 with the first three-dimensional atomic resolution structure of a membrane protein. Nearly twenty-six years later, the crystal structure of the beta2 adrenergic receptor in complex with G protein has contributed to another landmark in the field leading to the 2012 Nobel Prize in Chemistry. At present, more than 350 unique membrane protein structures solved by X-ray crystallography (http://blanco.biomol.uci.edu/mpstruc/exp/list, Stephen White Lab at UC Irvine) are available in the Protein Data Bank. The advent of genomics and proteomics initiatives combined with high-throughput technologies, such as automation, miniaturization, integration and third-generation synchrotrons, has enhanced membrane protein structure determination rate. X-ray crystallography is still the only method capable of providing detailed information on how ligands, cofactors, and ions interact with proteins, and is therefore a powerful tool in biochemistry and drug discovery. Yet the growth of membrane protein crystals suitable for X-ray diffraction studies amazingly remains a fine art and a major bottleneck in the field. It is often necessary to apply as many innovative approaches as possible. In this review we draw attention to the latest methods and strategies for the production of suitable crystals for membrane protein structure determination. In addition we also highlight the impact that third-generation synchrotron radiation has made in the field, summarizing the latest strategies used at synchrotron beamlines for screening and data collection from such demanding crystals. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.

  15. Millimeter-wave interferometry: an attractive technique for fast and accurate sensing of civil and mechanical structures

    NASA Astrophysics Data System (ADS)

    Kim, Seoktae; Nguyen, Cam

    2014-04-01

    This paper discusses the RF interferometry at millimeter-wave frequencies for sensing applications and reports the development of a millimeter-wave interferometric sensor operating around 35 GHz. The sensor is completely realized using microwave integrated circuits (MICs) and microwave monolithic integrated circuits (MMICs). It has been used for various sensing including displacement and velocity measurement. The sensor achieves a resolution and maximum error of only 10 μm and 27 μm, respectively, for displacement sensing and can measure velocity as low as 27.7 mm/s with a resolution about 2.7mm/s. Quick response and accurate sensing, as demonstrated by the developed millimeter-wave interferometric sensor, make the millimeter-wave interferometry attractive for sensing of various civil and mechanical structures.

  16. Structural determinants of sigma receptor affinity

    SciTech Connect

    Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.

    1987-12-01

    The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.

  17. High Resolution Powder Diffraction and Structure Determination

    SciTech Connect

    Cox, D. E.

    1999-04-23

    It is clear that high-resolution synchrotrons X-ray powder diffraction is a very powerful and convenient tool for material characterization and structure determination. Most investigations to date have been carried out under ambient conditions and have focused on structure solution and refinement. The application of high-resolution techniques to increasingly complex structures will certainly represent an important part of future studies, and it has been seen how ab initio solution of structures with perhaps 100 atoms in the asymmetric unit is within the realms of possibility. However, the ease with which temperature-dependence measurements can be made combined with improvements in the technology of position-sensitive detectors will undoubtedly stimulate precise in situ structural studies of phase transitions and related phenomena. One challenge in this area will be to develop high-resolution techniques for ultra-high pressure investigations in diamond anvil cells. This will require highly focused beams and very precise collimation in front of the cell down to dimensions of 50 {micro}m or less. Anomalous scattering offers many interesting possibilities as well. As a means of enhancing scattering contrast it has applications not only to the determination of cation distribution in mixed systems such as the superconducting oxides discussed in Section 9.5.3, but also to the location of specific cations in partially occupied sites, such as the extra-framework positions in zeolites, for example. Another possible application is to provide phasing information for ab initio structure solution. Finally, the precise determination of f as a function of energy through an absorption edge can provide useful information about cation oxidation states, particularly in conjunction with XANES data. In contrast to many experiments at a synchrotron facility, powder diffraction is a relatively simple and user-friendly technique, and most of the procedures and software for data analysis

  18. Fast and accurate procedure for the determination of Cr(VI) in solid samples by isotope dilution mass spectrometry.

    PubMed

    Fabregat-Cabello, Neus; Rodríguez-González, Pablo; Castillo, Ángel; Malherbe, Julien; Roig-Navarro, Antoni F; Long, Stephen E; García Alonso, J Ignacio

    2012-11-20

    We present here a new environmental measurement method for the rapid extraction and accurate quantification of Cr(VI) in solid samples. The quantitative extraction of Cr(VI) is achieved in 10 minutes by means of focused microwave assisted extraction using 50 mmol/L Ethylendiamintetraacetic acid (EDTA) at pH 10 as extractant. In addition, it enables the separation of Cr species by anion exchange chromatography using a mobile phase which is a 1:10 dilution of the extracting solution. Thus, neutralization or acidification steps which are prone to cause interconversion of Cr species are not needed. Another benefit of using EDTA is that it allows to measure Cr(III)-EDTA complex and Cr(VI) simultaneously in an alkaline extraction solution. The application of a 10 minutes focused microwave assisted extraction (5 min at 90 °C plus 5 min at 110 °C) has been shown to quantitatively extract all forms of hexavalent chromium from the standard reference materials (SRM) candidate NIST 2700 and NIST 2701. A double spike isotope dilution mass spectrometry (IDMS) procedure was employed to study chromium interconversion reactions. It was observed that the formation of a Cr(III)-EDTA complex avoided Cr(III) oxidation for these two reference materials. Thus, the use of a double spiking strategy for quantification is not required and a single spike IDMS procedure using isotopically enriched Cr(VI) provided accurate results.

  19. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil.

    PubMed

    Puzzarini, Cristina; Barone, Vincenzo

    2011-04-21

    The equilibrium structure of uracil has been investigated using both theoretical and experimental data. With respect to the former, quantum-chemical calculations at the coupled-cluster level in conjunction with a triple-zeta basis set have been carried out. Extrapolation to the basis set limit, performed employing the second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections have also been considered. Based on the available rotational constants for various isotopic species together with corresponding computed vibrational corrections, the semi-experimental equilibrium structure of uracil has been determined for the first time. Theoretical and semi-experimental structures have been found in remarkably good agreement, thus pointing out the limitations of previous experimental determinations. Molecular and spectroscopic properties of uracil have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the revision of the dipole moment. On the whole, it has been proved that the computational procedure presented is able to provide parameters with the proper accuracy to support experimental investigations of large molecules of biological interest.

  20. A rapid, economical, and accurate method to determining the physical risk of storm marine inundations using sedimentary evidence

    NASA Astrophysics Data System (ADS)

    Nott, Jonathan F.

    2015-04-01

    The majority of physical risk assessments from storm surge inundations are derived from synthetic time series generated from short climate records, which can often result in inaccuracies and are time-consuming and expensive to develop. A new method is presented here for the wet tropics region of northeast Australia. It uses lidar-generated topographic cross sections of beach ridge plains, which have been demonstrated to be deposited by marine inundations generated by tropical cyclones. Extreme value theory statistics are applied to data derived from the cross sections to generate return period plots for a given location. The results suggest that previous methods to estimate return periods using synthetic data sets have underestimated the magnitude/frequency relationship by at least an order of magnitude. The new method promises to be a more rapid, economical, and accurate assessment of the physical risk of these events.

  1. A Simple Accurate Alternative to the Minimum-Deviation Method for the Determination of the Refractive Index of a Prism.

    ERIC Educational Resources Information Center

    Waldenstrom, S.; Naqvi, K. Razi

    1978-01-01

    Proposes an alternative to the classical minimum-deviation method for determining the refractive index of a prism. This new "fixed angle of incidence method" may find applications in research. (Author/GA)

  2. Absorption spectroscopy of the rubidium dimer in an overheated vapor: An accurate check of molecular structure and dynamics

    SciTech Connect

    Beuc, R.; Movre, M.; Horvatic, V.; Vadla, C.; Dulieu, O.; Aymar, M.

    2007-03-15

    Experimental studies of the absorption spectrum of the Rb{sub 2} dimer are performed in the 600-1100 nm wavelength range for temperatures between 615 and 745 K. The reduced absorption coefficient is measured by spatially resolved white light absorption in overheated rubidium vapor with a radial temperature gradient, which enables simultaneous measurements at different temperatures. Semiclassical and quantum spectral simulations are obtained by taking into account all possible transitions involving the potential curves stemming from the 5 {sup 2}S+5 {sup 2}S and 5 {sup 2}S+5 {sup 2}P asymptotes. The most accurate experimental potential curves are used where available, and newly calculated potential curves and transition dipole moments otherwise. The overall consistency of the theoretical model with the experimental interpretation is obtained only if the radial dependence of both the calculated transition dipole moments and the spin-orbit coupling is taken into account. This highlights the low-resolution absorption spectroscopy as a valuable tool for checking the accuracy of molecular electronic structure calculations.

  3. Exploiting Microbeams for Membrane Protein Structure Determination.

    PubMed

    Warren, Anna J; Axford, Danny; Paterson, Neil G; Owen, Robin L

    2016-01-01

    A reproducible, and sample independent means of predictably obtaining large, well-ordered crystals has proven elusive in macromolecular crystallography. In the structure determination pipeline, crystallisation often proves to be a rate-limiting step, and the process of obtaining even small or badly ordered crystals can prove time-consuming and laborious. This is particularly true in the field of membrane protein crystallography and this is reflected in the limited number of unique membrane protein structures deposited in the protein data bank (less than 650 by June 2016 - http://blanco.biomol.uci.edu/mpstruc ). Over recent years the requirement for, and time and cost associated with obtaining, large crystals has been partially alleviated through the development of beamline instrumentation allowing data collection, and structure solution, from ever-smaller crystals. Advances in several areas have led to a step change in what might be considered achievable during a synchrotron trip over the last decade. This chapter will briefly review the current status of the field, the tools available to ease data collection and processing, and give some examples of exploitation of these for membrane protein microfocus macromolecular crystallography. PMID:27553238

  4. Communication: Vibrationally resolved photoelectron spectroscopy of the tetracyanoquinodimethane (TCNQ) anion and accurate determination of the electron affinity of TCNQ

    SciTech Connect

    Zhu, Guo-Zhu; Wang, Lai-Sheng

    2015-12-14

    Tetracyanoquinodimethane (TCNQ) is widely used as an electron acceptor to form highly conducting organic charge-transfer solids. Surprisingly, the electron affinity (EA) of TCNQ is not well known and has never been directly measured. Here, we report vibrationally resolved photoelectron spectroscopy (PES) of the TCNQ{sup −} anion produced using electrospray and cooled in a cryogenic ion trap. Photoelectron spectrum taken at 354.7 nm represents the detachment transition from the ground state of TCNQ{sup −} to that of neutral TCNQ with a short vibrational progression. The EA of TCNQ is measured accurately to be 3.383 ± 0.001 eV (27 289 ± 8 cm{sup −1}), compared to the 2.8 ± 0.1 eV value known in the literature and measured previously using collisional ionization technique. In addition, six vibrational peaks are observed in the photoelectron spectrum, yielding vibrational frequencies for three totally symmetric modes of TCNQ. Two-photon PES via a bound electronic excited state of TCNQ{sup −} at 3.100 eV yields a broad low kinetic energy peak due to fast internal conversion to vibrationally excited levels of the anion ground electronic state. The high EA measured for TCNQ underlies its ability as a good electron acceptor.

  5. Communication: Vibrationally resolved photoelectron spectroscopy of the tetracyanoquinodimethane (TCNQ) anion and accurate determination of the electron affinity of TCNQ

    NASA Astrophysics Data System (ADS)

    Zhu, Guo-Zhu; Wang, Lai-Sheng

    2015-12-01

    Tetracyanoquinodimethane (TCNQ) is widely used as an electron acceptor to form highly conducting organic charge-transfer solids. Surprisingly, the electron affinity (EA) of TCNQ is not well known and has never been directly measured. Here, we report vibrationally resolved photoelectron spectroscopy (PES) of the TCNQ- anion produced using electrospray and cooled in a cryogenic ion trap. Photoelectron spectrum taken at 354.7 nm represents the detachment transition from the ground state of TCNQ- to that of neutral TCNQ with a short vibrational progression. The EA of TCNQ is measured accurately to be 3.383 ± 0.001 eV (27 289 ± 8 cm-1), compared to the 2.8 ± 0.1 eV value known in the literature and measured previously using collisional ionization technique. In addition, six vibrational peaks are observed in the photoelectron spectrum, yielding vibrational frequencies for three totally symmetric modes of TCNQ. Two-photon PES via a bound electronic excited state of TCNQ- at 3.100 eV yields a broad low kinetic energy peak due to fast internal conversion to vibrationally excited levels of the anion ground electronic state. The high EA measured for TCNQ underlies its ability as a good electron acceptor.

  6. Structural Determinants of Misfolding in Multidomain Proteins

    PubMed Central

    Tian, Pengfei; Best, Robert B.

    2016-01-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669

  7. 45 CFR 261.64 - How will we determine whether a State's work verification procedures ensure an accurate work...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... interim Work Verification Plan by September 30, 2006 and a complete Work Verification Plan that we approved by September 30, 2007. (b) A “complete” Work Verification Plan means that: (1) The plan includes... 45 Public Welfare 2 2010-10-01 2010-10-01 false How will we determine whether a State's...

  8. Determination of accurate electron chiral asymmetries in fenchone and camphor in the VUV range: sensitivity to isomerism and enantiomeric purity.

    PubMed

    Nahon, Laurent; Nag, Lipsa; Garcia, Gustavo A; Myrgorodska, Iuliia; Meierhenrich, Uwe; Beaulieu, Samuel; Wanie, Vincent; Blanchet, Valérie; Géneaux, Romain; Powis, Ivan

    2016-05-14

    Photoelectron circular dichroism (PECD) manifests itself as an intense forward/backward asymmetry in the angular distribution of photoelectrons produced from randomly-oriented enantiomers by photoionization with circularly-polarized light (CPL). As a sensitive probe of both photoionization dynamics and of the chiral molecular potential, PECD attracts much interest especially with the recent performance of related experiments with visible and VUV laser sources. Here we report, by use of quasi-perfect CPL VUV synchrotron radiation and using a double imaging photoelectron/photoion coincidence (i(2)PEPICO) spectrometer, new and very accurate values of the corresponding asymmetries on showcase chiral isomers: camphor and fenchone. These data have additionally been normalized to the absolute enantiopurity of the sample as measured by a chromatographic technique. They can therefore be used as benchmarking data for new PECD experiments, as well as for theoretical models. In particular we found, especially for the outermost orbital of both molecules, a good agreement with CMS-Xα PECD modeling over the whole VUV range. We also report a spectacular sensitivity of PECD to isomerism for slow electrons, showing large and opposite asymmetries when comparing R-camphor to R-fenchone (respectively -10% and +16% around 10 eV). In the course of this study, we could also assess the analytical potential of PECD. Indeed, the accuracy of the data we provide are such that limited departure from perfect enantiopurity in the sample we purchased could be detected and estimated in excellent agreement with the analysis performed in parallel via a chromatographic technique, establishing a new standard of accuracy, in the ±1% range, for enantiomeric excess measurement via PECD. The i(2)PEPICO technique allows correlating PECD measurements to specific parent ion masses, which would allow its application to analysis of complex mixtures. PMID:27095534

  9. Accurate determination of electronic transport properties of silicon wafers by nonlinear photocarrier radiometry with multiple pump beam sizes

    SciTech Connect

    Wang, Qian; Li, Bincheng

    2015-12-07

    In this paper, photocarrier radiometry (PCR) technique with multiple pump beam sizes is employed to determine simultaneously the electronic transport parameters (the carrier lifetime, the carrier diffusion coefficient, and the front surface recombination velocity) of silicon wafers. By employing the multiple pump beam sizes, the influence of instrumental frequency response on the multi-parameter estimation is totally eliminated. A nonlinear PCR model is developed to interpret the PCR signal. Theoretical simulations are performed to investigate the uncertainties of the estimated parameter values by investigating the dependence of a mean square variance on the corresponding transport parameters and compared to that obtained by the conventional frequency-scan method, in which only the frequency dependences of the PCR amplitude and phase are recorded at single pump beam size. Simulation results show that the proposed multiple-pump-beam-size method can improve significantly the accuracy of the determination of the electronic transport parameters. Comparative experiments with a p-type silicon wafer with resistivity 0.1–0.2 Ω·cm are performed, and the electronic transport properties are determined simultaneously. The estimated uncertainties of the carrier lifetime, diffusion coefficient, and front surface recombination velocity are approximately ±10.7%, ±8.6%, and ±35.4% by the proposed multiple-pump-beam-size method, which is much improved than ±15.9%, ±29.1%, and >±50% by the conventional frequency-scan method. The transport parameters determined by the proposed multiple-pump-beam-size PCR method are in good agreement with that obtained by a steady-state PCR imaging technique.

  10. Structural and functional screening in human induced-pluripotent stem cell-derived cardiomyocytes accurately identifies cardiotoxicity of multiple drug types

    SciTech Connect

    Doherty, Kimberly R. Talbert, Dominique R.; Trusk, Patricia B.; Moran, Diarmuid M.; Shell, Scott A.; Bacus, Sarah

    2015-05-15

    Safety pharmacology studies that evaluate new drug entities for potential cardiac liability remain a critical component of drug development. Current studies have shown that in vitro tests utilizing human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) may be beneficial for preclinical risk evaluation. We recently demonstrated that an in vitro multi-parameter test panel assessing overall cardiac health and function could accurately reflect the associated clinical cardiotoxicity of 4 FDA-approved targeted oncology agents using hiPS-CM. The present studies expand upon this initial observation to assess whether this in vitro screen could detect cardiotoxicity across multiple drug classes with known clinical cardiac risks. Thus, 24 drugs were examined for their effect on both structural (viability, reactive oxygen species generation, lipid formation, troponin secretion) and functional (beating activity) endpoints in hiPS-CM. Using this screen, the cardiac-safe drugs showed no effects on any of the tests in our panel. However, 16 of 18 compounds with known clinical cardiac risk showed drug-induced changes in hiPS-CM by at least one method. Moreover, when taking into account the Cmax values, these 16 compounds could be further classified depending on whether the effects were structural, functional, or both. Overall, the most sensitive test assessed cardiac beating using the xCELLigence platform (88.9%) while the structural endpoints provided additional insight into the mechanism of cardiotoxicity for several drugs. These studies show that a multi-parameter approach examining both cardiac cell health and function in hiPS-CM provides a comprehensive and robust assessment that can aid in the determination of potential cardiac liability. - Highlights: • 24 drugs were tested for cardiac liability using an in vitro multi-parameter screen. • Changes in beating activity were the most sensitive in predicting cardiac risk. • Structural effects add in

  11. The role of cognitive switching in head-up displays. [to determine pilot ability to accurately extract information from either of two sources

    NASA Technical Reports Server (NTRS)

    Fischer, E.

    1979-01-01

    The pilot's ability to accurately extract information from either one or both of two superimposed sources of information was determined. Static, aerial, color 35 mm slides of external runway environments and slides of corresponding static head-up display (HUD) symbology were used as the sources. A three channel tachistoscope was utilized to show either the HUD alone, the scene alone, or the two slides superimposed. Cognitive performance of the pilots was assessed by determining the percentage of correct answers given to two HUD related questions, two scene related questions, or one HUD and one scene related question.

  12. A simple method for the accurate determination of the Henry's law constant for highly sorptive, semivolatile organic compounds.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2016-01-01

    A novel technique is developed to determine the Henry's law constants (HLCs) of seven volatile fatty acids (VFAs) with significantly high solubility using a combined application of thermal desorber/gas chromatography/mass spectrometry (TD/GC/MS). In light of the strong sorptive properties of these semi-volatile organic compounds (SVOCs), their HLCs were determined by properly evaluating the fraction lost on the surface of the materials used to induce equilibrium (vial, gas-tight syringe, and sorption tube). To this end, a total of nine repeated experiments were conducted in a closed (static) system at three different gas/liquid volume ratios. The best estimates for HLCs (M/atm) were thus 7,200 (propionic acid), 4,700 (i-butyric acid), 4,400 (n-butyric acid), 2,700 (i-valeric acid), 2,400 (n-valeric acid), 1,000 (hexanoic acid), and 1,500 (heptanoic acid). The differences in the HLC values between this study and previous studies, if assessed in terms of the percent difference, ranged from 9.2% (n-valeric acid) to 55.7% (i-valeric acid). We overcame the main cause of errors encountered in previous studies by performing the proper correction of the sorptive losses of the SVOCs that inevitably took place, particularly on the walls of the equilibration systems (mainly the headspace vial and/or the glass tight syringe). PMID:26577086

  13. Accurate determination of ⁴¹Ca concentrations in spent resins from the nuclear industry by accelerator mass spectrometry.

    PubMed

    Nottoli, Emmanuelle; Bourlès, Didier; Bienvenu, Philippe; Labet, Alexandre; Arnold, Maurice; Bertaux, Maité

    2013-12-01

    The radiological characterisation of nuclear waste is essential for managing storage sites. Determining the concentration of Long-Lived RadioNuclides (LLRN) is fundamental for their long-term management. This paper focuses on the measurement of low (41)Ca concentrations in ions exchange resins used for primary fluid purification in Pressurised Water Reactors (PWR). (41)Ca concentrations were successfully measured by Accelerator Mass Spectrometry (AMS) after the acid digestion of resin samples, followed by radioactive decontamination and isobaric suppression through successive hydroxide, carbonate, nitrate and final CaF2 precipitations. Measured (41)Ca concentrations ranged from 0.02 to 0.03 ng/g, i.e. from 0.06 to 0.09 Bq/g. The (41)Ca/(60)Co activity ratios obtained were remarkably reproducible and in good agreement with the current ratio used for resins management. PMID:24144617

  14. Accurate determination of ochratoxin A in Korean fermented soybean paste by isotope dilution-liquid chromatography tandem mass spectrometry.

    PubMed

    Ahn, Seonghee; Lee, Suyoung; Lee, Joonhee; Kim, Byungjoo

    2016-01-01

    Ochratoxin A (OTA), a naturally occurring mycotoxin, has been frequently detected in doenjang, a traditional fermented soybean paste, when it is fermented under improper conditions. Reliable screening of OTA in traditional fermented soybean paste (doenjang) is a special food-safety issue in Korea. Our laboratory, the National Metrology Institute of Korea, established an isotope dilution-liquid chromatography tandem mass spectrometry (ID-LC/MS/MS) method as a higher-order reference method to be used for SI-traceable value-assignment of OTA in certified reference materials (CRMs). (13)C20-OTA was used as an internal standard. Sample preparation conditions and LC/MS measurement parameters were optimised for this purpose. The analytical method was validated by measuring samples fortified with OTA at various levels. Repeatability and reproducibility studies showed that the ID-LC/MS/MS method is reliable and reproducible within 2% relative standard deviation. The analytical method was applied to determine OTA in various commercial doenjang products and home-made doenjang products.

  15. A validated high-throughput UHPLC-MS/MS assay for accurate determination of rivaroxaban in plasma sample.

    PubMed

    Iqbal, Muzaffar; Khalil, Nasr Y; Imam, Faisal; Khalid Anwer, Md

    2015-01-01

    Rivaroxaban is a novel, selective and potent oral direct factor Xa inhibitor, therapeutically indicated in the treatment of thromboembolic diseases. Like traditional anticoagulants, routine coagulation monitoring of rivaroxaban is not necessary, but important in some clinical circumstances. In this study, a sensitive UHPLC-MS/MS assay for rapid determination of rivaroxaban in human plasma was developed and validated. Rivaroxaban and its internal standard (IS) were extracted from plasma using acetonitrile as protein precipitating agent. An isocratic mobile phase of acetonitrile: 10 mM ammonium acetate (80:20, v/v) at a flow rate of 0.3 mL/min was used for the separation of rivaroxaban and IS. Both rivaroxaban and IS was eluted within 1 min with a total run time of 1.5 min only. Electrospray ionization source in positive mode was used for the detections of rivaroxaban and IS. Precursor to product ion transition of m/z 436.00 > 144.87 for rivaroxaban and m/z 411.18 > 191.07 for IS were used in multiple reaction monitoring mode. Developed assay was fully validated in terms of selectivity, linearity, accuracy, precision, recovery, matrix effects and stability using official guideline on bioanalytical method. PMID:25106734

  16. Accurate determination of interface trap state parameters by admittance spectroscopy in the presence of a Schottky barrier contact: Application to ZnO-based solar cells

    NASA Astrophysics Data System (ADS)

    Marin, Andrew T.; Musselman, Kevin P.; MacManus-Driscoll, Judith L.

    2013-04-01

    This work shows that when a Schottky barrier is present in a photovoltaic device, such as in a device with an ITO/ZnO contact, equivalent circuit analysis must be performed with admittance spectroscopy to accurately determine the pn junction interface recombination parameters (i.e., capture cross section and density of trap states). Without equivalent circuit analysis, a Schottky barrier can produce an error of ˜4-orders of magnitude in the capture cross section and ˜50% error in the measured density of trap states. Using a solution processed ZnO/Cu2O photovoltaic test system, we apply our analysis to clearly separate the contributions of interface states at the pn junction from the Schottky barrier at the ITO/ZnO contact so that the interface state recombination parameters can be accurately characterized. This work is widely applicable to the multitude of photovoltaic devices, which use ZnO adjacent to ITO.

  17. Accurate determination of small one-bond heteronuclear residual dipolar couplings by F1 coupled HSQC modified with a G-BIRD (r) module

    NASA Astrophysics Data System (ADS)

    Fehér, Krisztina; Berger, Stefan; Kövér, Katalin E.

    2003-08-01

    We report a G-BIRD (r) modified coupled HSQC experiment for the accurate determination of one-bond heteronuclear residual dipolar couplings. The G-BIRD (r) module has been employed to refocus the long-range coupling evolution of the heteronucleus during the t1 frequency labeling period. As a result, the crosspeaks obtained are split by only the direct one-bond coupling that can be extracted by measuring simple frequency differences between singlet maxima. Additionally the decoupling of long-range multiple bond splittings leads to considerable sensitivity enhancement. The modification also has been applied in a TROSY sequence resulting in a significant sensitivity and resolution improvement.

  18. Structural and functional screening in human induced-pluripotent stem cell-derived cardiomyocytes accurately identifies cardiotoxicity of multiple drug types.

    PubMed

    Doherty, Kimberly R; Talbert, Dominique R; Trusk, Patricia B; Moran, Diarmuid M; Shell, Scott A; Bacus, Sarah

    2015-05-15

    Safety pharmacology studies that evaluate new drug entities for potential cardiac liability remain a critical component of drug development. Current studies have shown that in vitro tests utilizing human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) may be beneficial for preclinical risk evaluation. We recently demonstrated that an in vitro multi-parameter test panel assessing overall cardiac health and function could accurately reflect the associated clinical cardiotoxicity of 4 FDA-approved targeted oncology agents using hiPS-CM. The present studies expand upon this initial observation to assess whether this in vitro screen could detect cardiotoxicity across multiple drug classes with known clinical cardiac risks. Thus, 24 drugs were examined for their effect on both structural (viability, reactive oxygen species generation, lipid formation, troponin secretion) and functional (beating activity) endpoints in hiPS-CM. Using this screen, the cardiac-safe drugs showed no effects on any of the tests in our panel. However, 16 of 18 compounds with known clinical cardiac risk showed drug-induced changes in hiPS-CM by at least one method. Moreover, when taking into account the Cmax values, these 16 compounds could be further classified depending on whether the effects were structural, functional, or both. Overall, the most sensitive test assessed cardiac beating using the xCELLigence platform (88.9%) while the structural endpoints provided additional insight into the mechanism of cardiotoxicity for several drugs. These studies show that a multi-parameter approach examining both cardiac cell health and function in hiPS-CM provides a comprehensive and robust assessment that can aid in the determination of potential cardiac liability.

  19. 13C-labeled gluconate tracing as a direct and accurate method for determining the pentose phosphate pathway split ratio in Penicillium chrysogenum.

    PubMed

    Kleijn, Roelco J; van Winden, Wouter A; Ras, Cor; van Gulik, Walter M; Schipper, Dick; Heijnen, Joseph J

    2006-07-01

    In this study we developed a new method for accurately determining the pentose phosphate pathway (PPP) split ratio, an important metabolic parameter in the primary metabolism of a cell. This method is based on simultaneous feeding of unlabeled glucose and trace amounts of [U-13C]gluconate, followed by measurement of the mass isotopomers of the intracellular metabolites surrounding the 6-phosphogluconate node. The gluconate tracer method was used with a penicillin G-producing chemostat culture of the filamentous fungus Penicillium chrysogenum. For comparison, a 13C-labeling-based metabolic flux analysis (MFA) was performed for glycolysis and the PPP of P. chrysogenum. For the first time mass isotopomer measurements of 13C-labeled primary metabolites are reported for P. chrysogenum and used for a 13C-based MFA. Estimation of the PPP split ratio of P. chrysogenum at a growth rate of 0.02 h(-1) yielded comparable values for the gluconate tracer method and the 13C-based MFA method, 51.8% and 51.1%, respectively. A sensitivity analysis of the estimated PPP split ratios showed that the 95% confidence interval was almost threefold smaller for the gluconate tracer method than for the 13C-based MFA method (40.0 to 63.5% and 46.0 to 56.5%, respectively). From these results we concluded that the gluconate tracer method permits accurate determination of the PPP split ratio but provides no information about the remaining cellular metabolism, while the 13C-based MFA method permits estimation of multiple fluxes but provides a less accurate estimate of the PPP split ratio.

  20. Nuclear structure with accurate chiral perturbation theory nucleon-nucleon potential: Application to 6Li and 10B

    SciTech Connect

    Navratil, P; Caurier, E

    2003-10-14

    The authors calculate properties of A = 6 system using the accurate charge-dependent nucleon-nucleon (NN) potential at fourth order of chiral perturbation theory. By application of the ab initio no-core shell model (NCSM) and a variational calculation in the harmonic oscillator basis with basis size up to 16 {h_bar}{Omega} they obtain the {sup 6}Li binding energy of 28.5(5) MeV and a converged excitation spectrum. Also, they calculate properties of {sup 10}B using the same NN potential in a basis space of up to 8 {h_bar}{Omega}. The results are consistent with results obtained by standard accurate NN potentials and demonstrate a deficiency of Hamiltonians consisting of only two-body terms. At this order of chiral perturbation theory three-body terms appear. It is expected that inclusion of such terms in the Hamiltonian will improve agreement with experiment.

  1. Statistically deformable 2D/3D registration for accurate determination of post-operative cup orientation from single standard X-ray radiograph.

    PubMed

    Zheng, Guoyan

    2009-01-01

    The widely used procedure of evaluation of cup orientation following total hip arthroplasty using single standard anteroposterior (AP) radiograph is known inaccurate, largely due to the wide variability in individual pelvic orientation relative to X-ray plate. 2D/3D rigid image registration methods have been introduced for an accurate determination of the post-operative cup alignment with respect to an anatomical reference extracted from the CT data. Although encouraging results have been reported, their extensive usage in clinical routine is still limited. This may be explained by their requirement of a CAD model of the prosthesis, which is often difficult to be organized from the manufacturer due to the proprietary issue, and by their requirement of a pre-operative CT scan, which is not available for most retrospective studies. To address these issues, we developed and validated a statistically deformable 2D/3D registration approach for accurate determination of post-operative cup orientation. No CAD model and pre-operative CT data is required any more. Quantitative and qualitative results evaluated on cadaveric and clinical datasets are given, which indicate the validity of the approach. PMID:20426064

  2. NMR Structure Determination for Larger Proteins Using Backbone-Only Data

    PubMed Central

    Raman, Srivatsan; Lange, Oliver F.; Rossi, Paolo; Tyka, Michael; Wang, Xu; Aramini, James; Liu, Gaohua; Ramelot, Theresa; Eletsky, Alexander; Szyperski, Thomas; Kennedy, Michael; Prestegard, James; Montelione, Gaetano T.; Baker, David

    2010-01-01

    Conventional protein structure determination from nuclear magnetic resonance data relies heavily on side-chain proton-proton distances. The necessary side-chain resonance assignment, however, is labor intensive and prone to error. Here we show that structures can be accurately determined without NMR information on the sidechains for proteins up to 25 kDa by incorporating backbone chemical shifts, residual dipolar couplings, and amide proton distances into the Rosetta protein structure modelling methodology. These data, which are too sparse for conventional methods, serve only to guide conformational search towards the lowest energy conformations in the folding landscape; the details of the computed models are determined by the physical chemistry implicit in the Rosetta all atom energy function. The new method is not hindered by the deuteration required to suppress nuclear relaxation processes for proteins greater than 15 kDa, and should enable routine NMR structure determination for larger proteins. PMID:20133520

  3. Accurate determination of ultra-trace impurities, including europium, in ultra-pure barium carbonate materials through inductively coupled plasma-tandem mass spectrometry

    NASA Astrophysics Data System (ADS)

    Wu, Shuchao; Zeng, Xiangcheng; Dai, Xuefeng; Hu, Yongping; Li, Gang; Zheng, Cunjiang

    2016-09-01

    Impurities, especially ultra-trace europium (Eu), in ultra-pure barium carbonate materials were accurately determined through inductively coupled plasma-tandem mass spectrometry (ICP-MS/MS). Two reaction modes, namely, mass shift (with O2 as reaction gas) and on-mass modes(with NH3/He and He as reaction gases), were extensively investigated using Eu+ as target analyte. The use of Eu+ → EuO2+, instead of Eu+ → EuO+, as ion pairs in mass shift mode eliminated polyatomic interferences based on Ba matrix ions (135Ba16O2+ on 151Eu16O+ and 137Ba16O2+ on 153Eu16O+). This procedure exhibited enhanced sensitivity and selectivity. When the ICP-MS/MS was operated in NH3 on-mass mode, Eu+ can be determined in its original mass in interference-free conditions because NH3 did not react with Eu+ but with BaO+ to form a neutral product (BaO). The two reaction modes, especially NH3 on mass mode, were validated to be accurate because their resultant isotope ratios of 153Eu/151Eu matched well with that of the natural abundance ratio. The proposed ICP-MS/MS method is a sensitive technique with a limit of detection as low as 2.0 ng L- 1 for 153Eu+. Compared with conventional single-quadrupole (SQ) ICP-MS, both NH3 on-mass mode and O2 mass shift mode in ICP-MS/MS can be used to accurately determine Eu+ in ultra-pure BaCO3 materials. The detected concentration of Eu+ was 4.0 ng L- 1 to 15 ng L- 1, with spiked recoveries ranging from 100%-110%. ICP-MS/MS was also used to eliminate polyatomic interferences, particularly Ba-based interferences, prior to measurement of Gd and Sm. Impurities, including Na, Mg, Al, K, Mn, Fe, Cr, Sr, and Cs, in ultra-pure BaCO3 materials were also determined using ICP-MS/MS in conventional SQ mode.

  4. Determining Probabilities by Examining Underlying Structure.

    ERIC Educational Resources Information Center

    Norton, Robert M.

    2001-01-01

    Discusses how dice games pose fairness issues that appeal to students and examines a structure for three games involving two dice in a way that leads directly to the theoretical probabilities for all possible outcomes. (YDS)

  5. CONDENSED MATTER: STRUCTURE, MECHANICAL AND THERMAL PROPERTIES: An Accurate Image Simulation Method for High-Order Laue Zone Effects

    NASA Astrophysics Data System (ADS)

    Cai, Can-Ying; Zeng, Song-Jun; Liu, Hong-Rong; Yang, Qi-Bin

    2008-05-01

    A completely different formulation for simulation of the high order Laue zone (HOLZ) diffractions is derived. It refers to the new method, i.e. the Taylor series (TS) method. To check the validity and accuracy of the TS method, we take polyvinglidene fluoride (PVDF) crystal as an example to calculate the exit wavefunction by the conventional multi-slice (CMS) method and the TS method. The calculated results show that the TS method is much more accurate than the CMS method and is independent of the slice thicknesses. Moreover, the pure first order Laue zone wavefunction by the TS method can reflect the major potential distribution of the first reciprocal plane.

  6. Rapid and Accurate Determination of Lipopolysaccharide O-Antigen Types in Klebsiella pneumoniae with a Novel PCR-Based O-Genotyping Method

    PubMed Central

    Shih, Yun-Jui; Cheong, Cheng-Man; Yi, Wen-Ching

    2015-01-01

    Klebsiella pneumoniae, a Gram-negative bacillus that causes life-threatening infections in both hospitalized patients and ambulatory persons, can be classified into nine lipopolysaccharide (LPS) O-antigen serotypes. The O-antigen type has important clinical and epidemiological significance. However, K. pneumoniae O serotyping is cumbersome, and the reagents are not commercially available. To overcome the limitations of conventional serotyping methods, we aimed to create a rapid and accurate PCR method for K. pneumoniae O genotyping. We sequenced the genetic determinants of LPS O antigen from serotypes O1, O2a, O2ac, O3, O4, O5, O8, O9, and O12. We established a two-step genotyping scheme, based on the two genomic regions associated with O-antigen biosynthesis. The first set of PCR primers, which detects alleles at the wzm-wzt loci of the wb gene cluster, distinguishes between O1/O2, O3, O4, O5, O8, O9, and O12. The second set of PCR primers, which detects alleles at the wbbY region, further differentiates between O1, O2a, and O2ac. We verified the specificity of O genotyping against the O-serotype reference strains. We then tested the sensitivity and specificity of O genotyping in K. pneumoniae, using the 56 K-serotype reference strains with known O serotypes determined by an inhibition enzyme-linked immunosorbent assay (iELISA). There is a very good correlation between the O genotypes and classical O serotypes. Three discrepancies were observed and resolved by nucleotide sequencing—all in favor of O genotyping. The PCR-based O genotyping, which can be easily performed in clinical and research microbiology laboratories, is a rapid and accurate method for determining the LPS O-antigen types of K. pneumoniae isolates. PMID:26719438

  7. A simple and inclusive method to determine the habit plane in transmission electron microscope based on accurate measurement of foil thickness

    SciTech Connect

    Qiu, Dong Zhang, Mingxing

    2014-08-15

    A simple and inclusive method is proposed for accurate determination of the habit plane between bicrystals in transmission electron microscope. Whilst this method can be regarded as a variant of surface trace analysis, the major innovation lies in the improved accuracy and efficiency of foil thickness measurement, which involves a simple tilt of the thin foil about a permanent tilting axis of the specimen holder, rather than cumbersome tilt about the surface trace of the habit plane. Experimental study has been done to validate this proposed method in determining the habit plane between lamellar α{sub 2} plates and γ matrix in a Ti–Al–Nb alloy. Both high accuracy (± 1°) and high precision (± 1°) have been achieved by using the new method. The source of the experimental errors as well as the applicability of this method is discussed. Some tips to minimise the experimental errors are also suggested. - Highlights: • An improved algorithm is formulated to measure the foil thickness. • Habit plane can be determined with a single tilt holder based on the new algorithm. • Better accuracy and precision within ± 1° are achievable using the proposed method. • The data for multi-facet determination can be collected simultaneously.

  8. Photochemical determination of different DNA structures.

    PubMed

    Xu, Yan; Tashiro, Ryu; Sugiyama, Hiroshi

    2007-01-01

    The various conformations of DNA are thought to have important biological roles. Investigation of the local DNA conformational changes associated with biological events is therefore essential to an understanding of the functions of DNA. We have reported the photoreactivities of 5-halouracil in the five characteristic local DNA structures: the A, B and Z forms, protein-induced DNA kinks and the G-quadruplex form. These studies demonstrate the detailed relationships between the local DNA structures and the photochemical products of photoinduced hydrogen abstraction by the resulting uracil-5-yl radicals, and show that this photochemical method can be used to detect DNA structures. Here, we describe in detail procedures that have been developed in our laboratory for probing DNA conformations by product analysis of photoirradiated 5-halouracil-containing DNA. The protocol includes the preparation of 5-halouracil-containing DNA and the characterization of the photoproducts, and it can be completed in 2 weeks.

  9. Determination of hair structure and shape.

    PubMed

    Schlake, Thomas

    2007-04-01

    The hair follicle attracted significant attention as a model for the investigation of diverse biological problems. Whereas its morphology and the structure of the hair shaft are known in detail, the molecular biology of this miniorgan is significantly less characterised. Many efforts focussed on the development of the hair follicle and its stem cell reservoir; by contrast, the follicular product, the hair, which is interesting not only in terms of cosmetics was neglected. This review highlights our current knowledge of the control of hair structure and shape with emphasis on mouse hair follicle biology and discusses continuing problems.

  10. Accurate approach for determining fresh-water carbonate (H2CO3(*)) alkalinity, using a single H3PO4 titration point.

    PubMed

    Birnhack, Liat; Sabach, Sara; Lahav, Ori

    2012-10-15

    A new, simple and accurate method is introduced for determining H(2)CO(3)(*) alkalinity in fresh waters dominated by the carbonate weak-acid system. The method relies on a single H(3)PO(4) dosage and two pH readings (acidic pH value target: pH~4.0). The computation algorithm is based on the concept that the overall alkalinity mass of a solution does not change upon the addition of a non-proton-accepting species. The accuracy of the new method was assessed batch-wise with both synthetic and actual tap waters and the results were compared to those obtained from two widely used alkalinity analysis methods (titration to pH~4.5 and the Gran titration method). The experimental results, which were deliberately obtained with simple laboratory equipment (glass buret, general-purpose pH electrode, magnetic stirrer) proved the method to be as accurate as the conventional methods at a wide range of alkalinity values (20-400 mg L(-1) as CaCO(3)). Analysis of the relative error attained in the proposed method as a function of the target (acidic) pH showed that at the range 4.0

  11. Electron Diffraction Determination of Nanoscale Structures

    SciTech Connect

    Parks, Joel H

    2013-03-01

    Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.

  12. Contemporary Methodology for Protein Structure Determination.

    ERIC Educational Resources Information Center

    Hunkapiller, Michael W.; And Others

    1984-01-01

    Describes the nature and capabilities of methods used to characterize protein and peptide structure, indicating that they have undergone changes which have improved the speed, reliability, and applicability of the process. Also indicates that high-performance liquid chromatography and gel electrophoresis have made purifying proteins and peptides a…

  13. PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations

    PubMed Central

    Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610

  14. Vascular structure determines pulmonary blood flow distribution.

    PubMed

    Hlastala, M P; Glenny, R W

    1999-10-01

    Scientific knowledge develops through the evolution of new concepts. This process is usually driven by new methodologies that provide observations not previously available. Understanding of pulmonary blood flow determinants advanced significantly in the 1960s and is now changing rapidly again, because of increased spatial resolution of regional pulmonary blood flow measurements.

  15. Determining Factor Structure in a Multidimensional Inventory.

    ERIC Educational Resources Information Center

    Deeter, Thomas E.; Gill, Diane L.

    A two-step procedure is described and used to revise a multidimensional inventory in its developmental stages. First, the latent factors influencing the observed variables on the inventory are determined and justified using the following five methods: Kaiser's criterion, root staring, examination of difference values, examination of root mean…

  16. Accurate determination of one-bond heteronuclear coupling constants with “pure shift” broadband proton-decoupled CLIP/CLAP-HSQC experiments

    NASA Astrophysics Data System (ADS)

    Timári, István; Kaltschnee, Lukas; Kolmer, Andreas; Adams, Ralph W.; Nilsson, Mathias; Thiele, Christina M.; Morris, Gareth A.; Kövér, Katalin E.

    2014-02-01

    We report broadband proton-decoupled CLIP/CLAP-HSQC experiments for the accurate determination of one-bond heteronuclear couplings and, by extension, for the reliable measurement of small residual dipolar coupling constants. The combination of an isotope-selective BIRD(d) filter module with a non-selective 1H inversion pulse is employed to refocus proton-proton coupling evolution prior to the acquisition of brief chunks of free induction decay that are subsequently assembled to reconstruct the fully-decoupled signal evolution. As a result, the cross-peaks obtained are split only by the heteronuclear one-bond coupling along the F2 dimension, allowing coupling constants to be extracted by measuring simple frequency differences between singlet maxima. The proton decoupling scheme presented has also been utilized in standard HSQC experiments, resulting in a fully-decoupled pure shift correlation map with significantly improved resolution.

  17. Some structural determinants of melody recall.

    PubMed

    Boltz, M

    1991-05-01

    Sophisticated musicians were asked to recall, using musical notation, a set of unfamiliar folk tunes that varied in rhythmic structure and referents of tonality. The results showed that memory was facilitated by tonic triad members marking phrase endings, but only when their presence was highlighted by a corresponding pattern of temporal accents. Conversely, recall significantly declined when tonal information was either absent or obscured by rhythmic structure. Error analyses further revealed that the retention of overall pitch contour and information at phrase ending points varied as a function of these manipulations. The results are discussed in terms of a framework that links the acts of perceiving and remembering to a common attentional scheme. PMID:1861610

  18. Structural features determining thermal adaptation of esterases.

    PubMed

    Kovacic, Filip; Mandrysch, Agathe; Poojari, Chetan; Strodel, Birgit; Jaeger, Karl-Erich

    2016-02-01

    The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function.

  19. Development of a coal/water-slurry-fueled diesel engine for industrial cogeneration: Task 6. 0 Determination of accurate heat release diagrams and mechanical efficiency

    SciTech Connect

    Nydick, S.E.

    1987-02-01

    Purpose of the program was to foster the long-range development of a coal/water slurry fuel-fired, slow-speed, two-stroke diesel engine for efficient and economical power generation in the 8 to 30 MW range for use in industrial cogeneration applications. This report contains the results of Task 6 of the program, a detailed analysis of heat release diagrams and determination of the mechanical efficiency for a single-cylinder, slow-speed diesel test engine when operated on coal/water slurry and diesel fuels. A digitized technique was utilized to determine the cylinder pressure history. The results of the program showed that the averages of previously reported thermal efficiency values for operation on coal/water slurry fuels were very accurate determinations. In addition, the slight differences in thermal efficiency between diesel and slurry operation are most likely related to changes in the mechanical efficiency resulting from degradation of the piston ring/cylinder liner interface rather than changes in combustion efficiency. Our previous prediction that, at 50% water content, the efficiency of a coal/water slurry engine is comparable to a diesel engine, has been confirmed experimentally and explained analytically.

  20. Structural determinants of proton blockage in aquaporins.

    PubMed

    Chakrabarti, Nilmadhab; Roux, Benoît; Pomès, Régis

    2004-10-15

    Aquaporins are an important class of membrane channels selective for water and linear polyols but impermeable to ions, including protons. Recent computational studies have revealed that the relay of protons through the water-conduction pathway of aquaporin channels is opposed by a substantial free energy barrier peaking at the signature NPA motifs. Here, free-energy simulations and continuum electrostatic calculations are combined to examine the nature and the magnitude of the contribution of specific structural elements to proton blockage in the bacterial glycerol uptake facilitator, GlpF. Potential of mean-force profiles for both hop and turn steps of structural diffusion in the narrow pore are obtained for artificial variants of the GlpF channel in which coulombic interactions between the pore contents and conserved residues Asn68 and Asn203 at the NPA signature motifs, Arg206 at the selectivity filter, and the peptidic backbone of the two half-helices M3 and M7, which are arranged in head-to-head fashion around the NPA motifs, are turned off selectively. A comparison of these results with electrostatic energy profiles for the translocation of a probe cation throughout the water permeation pathway indicates that the free-energy profile for proton movement inside the narrow pore is dominated by static effects arising from the distribution of charged and polar groups of the channel, whereas dielectric effects contribute primarily to opposing the access of H+ to the pore mouths (desolvation penalty). The single most effective way to abolish the free-energy gradients opposing the movement of H+ around the NPA motif is to turn off the dipole moments of helices M3 and M7. Mutation of either of the two NPA Asn residues to Asp compensates for charge-dipole and dipole-dipole effects opposing the hop and turn steps of structural diffusion, respectively, and dramatically reduces the free energy barrier of proton translocation, suggesting that these single mutants could

  1. Method of fan sound mode structure determination computer program user's manual: Microphone location program

    NASA Technical Reports Server (NTRS)

    Pickett, G. F.; Wells, R. A.; Love, R. A.

    1977-01-01

    A computer user's manual describing the operation and the essential features of the microphone location program is presented. The Microphone Location Program determines microphone locations that ensure accurate and stable results from the equation system used to calculate modal structures. As part of the computational procedure for the Microphone Location Program, a first-order measure of the stability of the equation system was indicated by a matrix 'conditioning' number.

  2. Experimental Determination of Structure Factors of Titanium Aluminum and Silicon

    NASA Astrophysics Data System (ADS)

    Subramanian, Swaminathan

    Brittleness of TiAl has been attributed to strong directional bonding by a number of researchers. Their predictions have been based on theoretical calculations of electron charge density distribution. It is necessary to complement these predictions by experimental measurements. The work described in this thesis, aimed towards that end, involves measurement of Debye-Waller factors by four circle x-ray diffraction and of structure factors by energy filtered convergent beam electron diffraction CBED methods. Stoichiometric single crystals are required for the measurement of Debye-Waller factors by the four circle x-ray diffraction method. Because of constraints imposed by the phase diagram only non-stoichiometric single crystal of TiAl are available. Measurement of Debye-Waller parameters have been attempted by using aluminum rich TiAl single crystals of compositions Ti54at%Al and Ti56at%Al. The symmetry of L1_0 structure of TiAl dictates that all reflections with Miller indices (hkl) not satisfying the condition h + k = 2n should be extinct. However, during the x-ray diffraction experiments diffuse diffracted intensities were observed for reflections of h + k = 2n + 1 type. This indicates the possibility of occupation of the excess Al atoms on the Ti-sites. If the excess Al atom preferentially occupies one of the Ti-sites, it would lead to the formation of L1_2 type TiAl_3 unit cells within the TiAl lattice. This notion has been further verified by least-squares refinement of the data obtained from Ti54at%Al single crystal. Also Debye-Waller factor values were different for equivalent Ti-sites in TiAl. The CBED method was developed for accurate structure factor measurement. Factors such as limitation due to the angular resolution of the aperture and complex matrix and perturbation treatment of absorption have been considered. Computer routines, incorporating these factors, have been developed for the calculation of CBED patterns and for matching the rocking curves

  3. Magnetic Structure Determinations at NBS/NIST

    PubMed Central

    Lynn, J. W.; Borchers, J. A.; Huang, Q.; Santoro, A.; Erwin, R. W.

    2001-01-01

    Magnetic neutron scattering plays a central role in determining and understanding the microscopic properties of a vast variety of magnetic systems, from the fundamental nature, symmetry, and dynamics of magnetically ordered materials to elucidating the magnetic characteristics essential in technological applications. From the early days of neutron scattering measurements at NBS/NIST, magnetic diffraction studies have been a central theme involving many universities, industrial and government labs from around the United States and worldwide. Such measurements have been used to determine the spatial arrangement and directions of the atomic magnetic moments, the atomic magnetization density of the individual atoms in the material, and the value of the ordered moments as a function of thermodynamic parameters such as temperature, pressure, and applied magnetic field. These types of measurements have been carried out on single crystals, powders, thin films, and artificially grown multilayers, and often the information collected can be obtained by no other experimental technique. This article presents, in an historical perspective, a few examples of work carried out at the NIST Center for Neutron Research (NCNR), and discusses the key role that the Center can expect to play in future magnetism research. PMID:27500056

  4. Functional connectivity and structural covariance between regions of interest can be measured more accurately using multivariate distance correlation.

    PubMed

    Geerligs, Linda; Cam-Can; Henson, Richard N

    2016-07-15

    Studies of brain-wide functional connectivity or structural covariance typically use measures like the Pearson correlation coefficient, applied to data that have been averaged across voxels within regions of interest (ROIs). However, averaging across voxels may result in biased connectivity estimates when there is inhomogeneity within those ROIs, e.g., sub-regions that exhibit different patterns of functional connectivity or structural covariance. Here, we propose a new measure based on "distance correlation"; a test of multivariate dependence of high dimensional vectors, which allows for both linear and non-linear dependencies. We used simulations to show how distance correlation out-performs Pearson correlation in the face of inhomogeneous ROIs. To evaluate this new measure on real data, we use resting-state fMRI scans and T1 structural scans from 2 sessions on each of 214 participants from the Cambridge Centre for Ageing & Neuroscience (Cam-CAN) project. Pearson correlation and distance correlation showed similar average connectivity patterns, for both functional connectivity and structural covariance. Nevertheless, distance correlation was shown to be 1) more reliable across sessions, 2) more similar across participants, and 3) more robust to different sets of ROIs. Moreover, we found that the similarity between functional connectivity and structural covariance estimates was higher for distance correlation compared to Pearson correlation. We also explored the relative effects of different preprocessing options and motion artefacts on functional connectivity. Because distance correlation is easy to implement and fast to compute, it is a promising alternative to Pearson correlations for investigating ROI-based brain-wide connectivity patterns, for functional as well as structural data.

  5. Gap between technically accurate information and socially appropriate information for structural health monitoring system installed into tall buildings

    NASA Astrophysics Data System (ADS)

    Mita, Akira

    2016-04-01

    The importance of the structural health monitoring system for tall buildings is now widely recognized by at least structural engineers and managers at large real estate companies to ensure the structural safety immediately after a large earthquake and appeal the quantitative safety of buildings to potential tenants. Some leading real estate companies decided to install the system into all tall buildings. Considering this tendency, a pilot project for the west area of Shinjuku Station supported by the Japan Science and Technology Agency was started by the author team to explore a possibility of using the system to provide safe spaces for commuters and residents. The system was installed into six tall buildings. From our experience, it turned out that viewing only from technological aspects was not sufficient for the system to be accepted and to be really useful. Safe spaces require not only the structural safety but also the soundness of key functions of the building. We need help from social scientists, medical doctors, city planners etc. to further improve the integrity of the system.

  6. Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities.

    PubMed

    Venner, Eric; Lisewski, Andreas Martin; Erdin, Serkan; Ward, R Matthew; Amin, Shivas R; Lichtarge, Olivier

    2010-01-01

    High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome. First, Evolutionary Trace Annotation, or ETA, identifies which proteins have local evolutionary and structural features in common; next, these proteins are linked together into a proteomic network of ETA similarities; then, starting from proteins with known functions, competing functional labels diffuse link-by-link over the entire network. Every node is thus assigned a likelihood z-score for every function, and the most significant one at each node wins and defines its annotation. In high-throughput controls, this competitive diffusion process recovered enzyme activity annotations with 99% and 97% accuracy at half-coverage for the third and fourth Enzyme Commission (EC) levels, respectively. This corresponds to false positive rates 4-fold lower than nearest-neighbor and 5-fold lower than sequence-based annotations. In practice, experimental validation of the predicted carboxylesterase activity in a protein from Staphylococcus aureus illustrated the effectiveness of this approach in the context of an increasingly drug-resistant microbe. This study further links molecular function to a small number of evolutionarily important residues recognizable by Evolutionary Tracing and it points to the specificity and sensitivity of functional annotation by competitive global network diffusion. A web server is at http://mammoth.bcm.tmc.edu/networks.

  7. A Pure-Phase Homonuclear J-Modulated HMQC Experiment with Tilted Cross-Peak Patterns for an Accurate Determination of Homonuclear Coupling Constants

    NASA Astrophysics Data System (ADS)

    Koź Miń Ski, Wiktor

    1999-11-01

    A new HMQC-based experiment is presented which allows for an efficient determination of accurate homonuclear coupling-constant values. Pure absorption lineshapes with tilted cross-peak patterns are obtained by a combination of the active-coupling-pattern tilting (ACT) scheme with J-scaling. Characteristic features include separate heteronuclear echo and antiecho acquisition with a BIRDy pulse positioned before or after the t1 period, respectively, to refocus I-spin homonuclear coupling evolution. Additionally, due to the incorporation of J-scaling the relative spacing of the S-spin chemical-shift differences and I-spin homonuclear coupling splittings in the F1 domain is largely under experimental control. The most important advantage of the proposed method is that the I-spin homonuclear coupling evolution occurs simultaneously with the evolution of the heteronuclear zero and double-quantum coherences, which exhibit a slower transverse relaxation than I-spin single-quantum coherences. The effectiveness of the new sequence is demonstrated by a determination of the 3JHN,Hα couplings in a peptide sample. Additionally, the broadband property of the new sequence is verified with a sucrose sample.

  8. An optimized method for the accurate determination of patulin in apple products by isotope dilution-liquid chromatography/mass spectrometry.

    PubMed

    Seo, Miyeong; Kim, Byungjoo; Baek, Song-Yee

    2015-07-01

    Patulin, a mycotoxin produced by several molds in fruits, has been frequently detected in apple products. Therefore, regulatory bodies have established recommended maximum permitted patulin concentrations for each type of apple product. Although several analytical methods have been adopted to determine patulin in food, quality control of patulin analysis is not easy, as reliable certified reference materials (CRMs) are not available. In this study, as a part of a project for developing CRMs for patulin analysis, we developed isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC/MS/MS) as a higher-order reference method for the accurate value-assignment of CRMs. (13)C7-patulin was used as internal standard. Samples were extracted with ethyl acetate to improve recovery. For further sample cleanup with solid-phase extraction (SPE), the HLB SPE cartridge was chosen after comparing with several other types of SPE cartridges. High-performance liquid chromatography was performed on a multimode column for proper retention and separation of highly polar and water-soluble patulin from sample interferences. Sample extracts were analyzed by LC/MS/MS with electrospray ionization in negative ion mode with selected reaction monitoring of patulin and (13)C7-patulin at m/z 153→m/z 109 and m/z 160→m/z 115, respectively. The validity of the method was tested by measuring gravimetrically fortified samples of various apple products. In addition, the repeatability and the reproducibility of the method were tested to evaluate the performance of the method. The method was shown to provide accurate measurements in the 3-40 μg/kg range with a relative expanded uncertainty of around 1%.

  9. Analytical method for the accurate determination of tricothecenes in grains using LC-MS/MS: a comparison between MRM transition and MS3 quantitation.

    PubMed

    Lim, Chee Wei; Tai, Siew Hoon; Lee, Lin Min; Chan, Sheot Harn

    2012-07-01

    The current food crisis demands unambiguous determination of mycotoxin contamination in staple foods to achieve safer food for consumption. This paper describes the first accurate LC-MS/MS method developed to analyze tricothecenes in grains by applying multiple reaction monitoring (MRM) transition and MS(3) quantitation strategies in tandem. The tricothecenes are nivalenol, deoxynivalenol, deoxynivalenol-3-glucoside, fusarenon X, 3-acetyl-deoxynivalenol, 15-acetyldeoxynivalenol, diacetoxyscirpenol, and HT-2 and T-2 toxins. Acetic acid and ammonium acetate were used to convert the analytes into their respective acetate adducts and ammonium adducts under negative and positive MS polarity conditions, respectively. The mycotoxins were separated by reversed-phase LC in a 13.5-min run, ionized using electrospray ionization, and detected by tandem mass spectrometry. Analyte-specific mass-to-charge (m/z) ratios were used to perform quantitation under MRM transition and MS(3) (linear ion trap) modes. Three experiments were made for each quantitation mode and matrix in batches over 6 days for recovery studies. The matrix effect was investigated at concentration levels of 20, 40, 80, 120, 160, and 200 μg kg(-1) (n = 3) in 5 g corn flour and rice flour. Extraction with acetonitrile provided a good overall recovery range of 90-108% (n = 3) at three levels of spiking concentration of 40, 80, and 120 μg kg(-1). A quantitation limit of 2-6 μg kg(-1) was achieved by applying an MRM transition quantitation strategy. Under MS(3) mode, a quantitation limit of 4-10 μg kg(-1) was achieved. Relative standard deviations of 2-10% and 2-11% were reported for MRM transition and MS(3) quantitation, respectively. The successful utilization of MS(3) enabled accurate analyte fragmentation pattern matching and its quantitation, leading to the development of analytical methods in fields that demand both analyte specificity and fragmentation fingerprint-matching capabilities that are

  10. Accurate and self-consistent procedure for determining pH in seawater desalination brines and its manifestation in reverse osmosis modeling.

    PubMed

    Nir, Oded; Marvin, Esra; Lahav, Ori

    2014-11-01

    Measuring and modeling pH in concentrated aqueous solutions in an accurate and consistent manner is of paramount importance to many R&D and industrial applications, including RO desalination. Nevertheless, unified definitions and standard procedures have yet to be developed for solutions with ionic strength higher than ∼0.7 M, while implementation of conventional pH determination approaches may lead to significant errors. In this work a systematic yet simple methodology for measuring pH in concentrated solutions (dominated by Na(+)/Cl(-)) was developed and evaluated, with the aim of achieving consistency with the Pitzer ion-interaction approach. Results indicate that the addition of 0.75 M of NaCl to NIST buffers, followed by assigning a new standard pH (calculated based on the Pitzer approach), enabled reducing measured errors to below 0.03 pH units in seawater RO brines (ionic strength up to 2 M). To facilitate its use, the method was developed to be both conceptually and practically analogous to the conventional pH measurement procedure. The method was used to measure the pH of seawater RO retentates obtained at varying recovery ratios. The results matched better the pH values predicted by an accurate RO transport model. Calibrating the model by the measured pH values enabled better boron transport prediction. A Donnan-induced phenomenon, affecting pH in both retentate and permeate streams, was identified and quantified.

  11. Determining 3-D motion and structure from image sequences

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

    A method of determining three-dimensional motion and structure from two image frames is presented. The method requires eight point correspondences between the two frames, from which motion and structure parameters are determined by solving a set of eight linear equations and a singular value decomposition of a 3x3 matrix. It is shown that the solution thus obtained is unique.

  12. Determining building interior structures using compressive sensing

    NASA Astrophysics Data System (ADS)

    Lagunas, Eva; Amin, Moeness G.; Ahmad, Fauzia; Nájar, Montse

    2013-04-01

    We consider imaging of the building interior structures using compressive sensing (CS) with applications to through-the-wall imaging and urban sensing. We consider a monostatic synthetic aperture radar imaging system employing stepped frequency waveform. The proposed approach exploits prior information of building construction practices to form an appropriate sparse representation of the building interior layout. We devise a dictionary of possible wall locations, which is consistent with the fact that interior walls are typically parallel or perpendicular to the front wall. The dictionary accounts for the dominant normal angle reflections from exterior and interior walls for the monostatic imaging system. CS is applied to a reduced set of observations to recover the true positions of the walls. Additional information about interior walls can be obtained using a dictionary of possible corner reflectors, which is the response of the junction of two walls. Supporting results based on simulation and laboratory experiments are provided. It is shown that the proposed sparsifying basis outperforms the conventional through-the-wall CS model, the wavelet sparsifying basis, and the block sparse model for building interior layout detection.

  13. Structural determinants of criticality in biological networks

    PubMed Central

    Valverde, Sergi; Ohse, Sebastian; Turalska, Malgorzata; West, Bruce J.; Garcia-Ojalvo, Jordi

    2015-01-01

    Many adaptive evolutionary systems display spatial and temporal features, such as long-range correlations, typically associated with the critical point of a phase transition in statistical physics. Empirical and theoretical studies suggest that operating near criticality enhances the functionality of biological networks, such as brain and gene networks, in terms for instance of information processing, robustness, and evolvability. While previous studies have explained criticality with specific system features, we still lack a general theory of critical behavior in biological systems. Here we look at this problem from the complex systems perspective, since in principle all critical biological circuits have in common the fact that their internal organization can be described as a complex network. An important question is how self-similar structure influences self-similar dynamics. Modularity and heterogeneity, for instance, affect the location of critical points and can be used to tune the system toward criticality. We review and discuss recent studies on the criticality of neuronal and genetic networks, and discuss the implications of network theory when assessing the evolutionary features of criticality. PMID:26005422

  14. Structural Determinants of Sleeping Beauty Transposase Activity.

    PubMed

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

    2016-08-01

    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold.

  15. Structural Determinants of Sleeping Beauty Transposase Activity.

    PubMed

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

    2016-08-01

    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold. PMID:27401040

  16. Structure of catalase determined by MicroED

    PubMed Central

    Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

    2014-01-01

    MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

  17. Structure of catalase determined by MicroED.

    PubMed

    Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

    2014-01-01

    MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. PMID:25303172

  18. Language Structure Is Partly Determined by Social Structure

    PubMed Central

    Lupyan, Gary; Dale, Rick

    2010-01-01

    Background Languages differ greatly both in their syntactic and morphological systems and in the social environments in which they exist. We challenge the view that language grammars are unrelated to social environments in which they are learned and used. Methodology/Principal Findings We conducted a statistical analysis of >2,000 languages using a combination of demographic sources and the World Atlas of Language Structures— a database of structural language properties. We found strong relationships between linguistic factors related to morphological complexity, and demographic/socio-historical factors such as the number of language users, geographic spread, and degree of language contact. The analyses suggest that languages spoken by large groups have simpler inflectional morphology than languages spoken by smaller groups as measured on a variety of factors such as case systems and complexity of conjugations. Additionally, languages spoken by large groups are much more likely to use lexical strategies in place of inflectional morphology to encode evidentiality, negation, aspect, and possession. Our findings indicate that just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in which they are being learned and used. As adults learn a language, features that are difficult for them to acquire, are less likely to be passed on to subsequent learners. Languages used for communication in large groups that include adult learners appear to have been subjected to such selection. Conversely, the morphological complexity common to languages used in small groups increases redundancy which may facilitate language learning by infants. Conclusions/Significance We hypothesize that language structures are subjected to different evolutionary pressures in different social environments. Just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in

  19. Structural determinants of Tau aggregation inhibitor potency.

    PubMed

    Schafer, Kelsey N; Cisek, Katryna; Huseby, Carol J; Chang, Edward; Kuret, Jeff

    2013-11-01

    Small-molecule Tau aggregation inhibitors are under investigation as potential therapeutic agents against Alzheimer disease. Many such inhibitors have been identified in vitro, but their potency-driving features, and their molecular targets in the Tau aggregation pathway, have resisted identification. Previously we proposed ligand polarizability, a measure of electron delocalization, as a candidate descriptor of inhibitor potency. Here we tested this hypothesis by correlating the ground state polarizabilities of cyanine, phenothiazine, and arylmethine derivatives calculated using ab initio quantum methods with inhibitory potency values determined in the presence of octadecyl sulfate inducer under reducing conditions. A series of rhodanine analogs was analyzed as well using potency values disclosed in the literature. Results showed that polarizability and inhibitory potency directly correlated within all four series. To identify putative binding targets, representative members of the four chemotypes were added to aggregation reactions, where they were found to stabilize soluble, but SDS-resistant Tau species at the expense of filamentous aggregates. Using SDS resistance as a secondary assay, and a library of Tau deletion and missense mutants as targets, interaction with cyanine was localized to the microtubule binding repeat region. Moreover, the SDS-resistant phenotype was completely dependent on the presence of octadecyl sulfate inducer, but not intact PHF6/PH6* hexapeptide motifs, indicating that cyanine interacted with a species in the aggregation pathway prior to nucleus formation. Together the data suggest that flat, highly polarizable ligands inhibit Tau aggregation by interacting with folded species in the aggregation pathway and driving their assembly into soluble but highly stable Tau oligomers.

  20. Structural Determinants of Tau Aggregation Inhibitor Potency*

    PubMed Central

    Schafer, Kelsey N.; Cisek, Katryna; Huseby, Carol J.; Chang, Edward; Kuret, Jeff

    2013-01-01

    Small-molecule Tau aggregation inhibitors are under investigation as potential therapeutic agents against Alzheimer disease. Many such inhibitors have been identified in vitro, but their potency-driving features, and their molecular targets in the Tau aggregation pathway, have resisted identification. Previously we proposed ligand polarizability, a measure of electron delocalization, as a candidate descriptor of inhibitor potency. Here we tested this hypothesis by correlating the ground state polarizabilities of cyanine, phenothiazine, and arylmethine derivatives calculated using ab initio quantum methods with inhibitory potency values determined in the presence of octadecyl sulfate inducer under reducing conditions. A series of rhodanine analogs was analyzed as well using potency values disclosed in the literature. Results showed that polarizability and inhibitory potency directly correlated within all four series. To identify putative binding targets, representative members of the four chemotypes were added to aggregation reactions, where they were found to stabilize soluble, but SDS-resistant Tau species at the expense of filamentous aggregates. Using SDS resistance as a secondary assay, and a library of Tau deletion and missense mutants as targets, interaction with cyanine was localized to the microtubule binding repeat region. Moreover, the SDS-resistant phenotype was completely dependent on the presence of octadecyl sulfate inducer, but not intact PHF6/PH6* hexapeptide motifs, indicating that cyanine interacted with a species in the aggregation pathway prior to nucleus formation. Together the data suggest that flat, highly polarizable ligands inhibit Tau aggregation by interacting with folded species in the aggregation pathway and driving their assembly into soluble but highly stable Tau oligomers. PMID:24072703

  1. A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination.

    PubMed

    Li, Xiaowei; Liu, Taigang; Tao, Peiying; Wang, Chunhua; Chen, Lanming

    2015-12-01

    Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique based on auto cross covariance (ACC) transformation of position-specific score matrix (PSSM) to represent a protein sequence. Then support vector machine-recursive feature elimination (SVM-RFE) is adopted to select top K features according to their importance and these features are input to a support vector machine (SVM) to conduct the prediction. Performance evaluation of the proposed method is performed using the jackknife test on three low-similarity datasets, i.e., D640, 1189 and 25PDB. By means of this method, the overall accuracies of 97.2%, 96.2%, and 93.3% are achieved on these three datasets, which are higher than those of most existing methods. This suggests that the proposed method could serve as a very cost-effective tool for predicting protein structural class especially for low-similarity datasets.

  2. Accurate flexible fitting of high-resolution protein structures to small-angle x-ray scattering data using a coarse-grained model with implicit hydration shell.

    PubMed

    Zheng, Wenjun; Tekpinar, Mustafa

    2011-12-21

    Small-angle x-ray scattering (SAXS) is a powerful technique widely used to explore conformational states and transitions of biomolecular assemblies in solution. For accurate model reconstruction from SAXS data, one promising approach is to flexibly fit a known high-resolution protein structure to low-resolution SAXS data by computer simulations. This is a highly challenging task due to low information content in SAXS data. To meet this challenge, we have developed what we believe to be a novel method based on a coarse-grained (one-bead-per-residue) protein representation and a modified form of the elastic network model that allows large-scale conformational changes while maintaining pseudobonds and secondary structures. Our method optimizes a pseudoenergy that combines the modified elastic-network model energy with a SAXS-fitting score and a collision energy that penalizes steric collisions. Our method uses what we consider a new implicit hydration shell model that accounts for the contribution of hydration shell to SAXS data accurately without explicitly adding waters to the system. We have rigorously validated our method using five test cases with simulated SAXS data and three test cases with experimental SAXS data. Our method has successfully generated high-quality structural models with root mean-squared deviation of 1 ∼ 3 Å from the target structures.

  3. A new methodology for non-contact accurate crack width measurement through photogrammetry for automated structural safety evaluation

    NASA Astrophysics Data System (ADS)

    Jahanshahi, Mohammad R.; Masri, Sami F.

    2013-03-01

    In mechanical, aerospace and civil structures, cracks are important defects that can cause catastrophes if neglected. Visual inspection is currently the predominant method for crack assessment. This approach is tedious, labor-intensive, subjective and highly qualitative. An inexpensive alternative to current monitoring methods is to use a robotic system that could perform autonomous crack detection and quantification. To reach this goal, several image-based crack detection approaches have been developed; however, the crack thickness quantification, which is an essential element for a reliable structural condition assessment, has not been sufficiently investigated. In this paper, a new contact-less crack quantification methodology, based on computer vision and image processing concepts, is introduced and evaluated against a crack quantification approach which was previously developed by the authors. The proposed approach in this study utilizes depth perception to quantify crack thickness and, as opposed to most previous studies, needs no scale attachment to the region under inspection, which makes this approach ideal for incorporation with autonomous or semi-autonomous mobile inspection systems. Validation tests are performed to evaluate the performance of the proposed approach, and the results show that the new proposed approach outperforms the previously developed one.

  4. Accurate extraction of Lagrangian coherent structures over finite domains with application to flight data analysis over Hong Kong International Airport.

    PubMed

    Tang, Wenbo; Chan, Pak Wai; Haller, George

    2010-03-01

    Locating Lagrangian coherent structures (LCS) for dynamical systems defined on a spatially limited domain present a challenge because trajectory integration must be stopped at the boundary for lack of further velocity data. This effectively turns the domain boundary into an attractor, introduces edge effects resulting in spurious ridges in the associated finite-time Lyapunov exponent (FTLE) field, and causes some of the real ridges of the FTLE field to be suppressed by strong spurious ridges. To address these issues, we develop a finite-domain FTLE method that renders LCS with an accuracy and fidelity that is suitable for automated feature detection. We show the application of this technique to the analysis of velocity data from aircraft landing at the Hong Kong International Airport.

  5. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  6. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure.

    PubMed

    Piquemal, Jean-Philip; Perera, Lalith; Cisneros, G Andrés; Ren, Pengyu; Pedersen, Lee G; Darden, Thomas A

    2006-08-01

    Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.

  7. A binary image reconstruction technique for accurate determination of the shape and location of metal objects in x-ray computed tomography.

    PubMed

    Wang, Jing; Xing, Lei

    2010-01-01

    The presence of metals in patients causes streaking artifacts in X-ray CT and has been recognized as a problem that limits various applications of CT imaging. Accurate localization of metals in CT images is a critical step for metal artifacts reduction in CT imaging and many practical applications of CT images. The purpose of this work is to develop a method of auto-determination of the shape and location of metallic object(s) in the image space. The proposed method is based on the fact that when a metal object is present in a patient, a CT image can be divided into two prominent components: high density metal and low density normal tissues. This prior knowledge is incorporated into an objective function as the regularization term whose role is to encourage the solution to take a form of two intensity levels. A computer simulation study and four experimental studies are performed to evaluate the proposed approach. Both simulation and experimental studies show that the presented algorithm works well even in the presence of complicated shaped metal objects. For a hexagonally shaped metal embedded in a water phantom, for example, it is found that the accuracy of metal reconstruction is within sub-millimeter.

  8. Selective and Accurate Determination Method of Propofol in Human Plasma by Mixed-Mode Cation Exchange Cartridge and GC-MS

    PubMed Central

    2016-01-01

    A gas chromatography-mass spectrometry (GC-MS) method for the determination of propofol in human plasma has been developed and validated. Propofol was extracted from human plasma by using mixed-mode cation exchange/reversed-phase (MCX) cartridges. As propofol easily volatilizes during concentration, 100% methanol was injected directly into GC-MS to elute propofol. Despite avoiding concentration process of the eluted solution, lower limit of quantization (LLOQ) of propofol was 25 ng/mL. The validated method exhibited good linearity (R2 = 0.9989) with accuracy and precision −5.8%~11.7% and 3.7%~11.6%, respectively. The other validation parameters, recovery and matrix effect, ranged from 96.6% to 99.4% and 95.3% to 101.4%, respectively. Propofol standard was quantified to evaluate possible loss due to the concentration processes, nitrogen gas and centrifugal vacuum. These two concentration processes resulted in notable decrease in the quantity of propofol, signifying avoiding any concentration processes during propofol quantification. Also, to confirm suitability of the developed method, authentic human plasma samples were analyzed. The selective assay method using MCX cartridge and GC-MS facilitated quantification of propofol in plasma sample accurately by preventing any losses due to the concentration processes.

  9. Selective and Accurate Determination Method of Propofol in Human Plasma by Mixed-Mode Cation Exchange Cartridge and GC-MS

    PubMed Central

    2016-01-01

    A gas chromatography-mass spectrometry (GC-MS) method for the determination of propofol in human plasma has been developed and validated. Propofol was extracted from human plasma by using mixed-mode cation exchange/reversed-phase (MCX) cartridges. As propofol easily volatilizes during concentration, 100% methanol was injected directly into GC-MS to elute propofol. Despite avoiding concentration process of the eluted solution, lower limit of quantization (LLOQ) of propofol was 25 ng/mL. The validated method exhibited good linearity (R2 = 0.9989) with accuracy and precision −5.8%~11.7% and 3.7%~11.6%, respectively. The other validation parameters, recovery and matrix effect, ranged from 96.6% to 99.4% and 95.3% to 101.4%, respectively. Propofol standard was quantified to evaluate possible loss due to the concentration processes, nitrogen gas and centrifugal vacuum. These two concentration processes resulted in notable decrease in the quantity of propofol, signifying avoiding any concentration processes during propofol quantification. Also, to confirm suitability of the developed method, authentic human plasma samples were analyzed. The selective assay method using MCX cartridge and GC-MS facilitated quantification of propofol in plasma sample accurately by preventing any losses due to the concentration processes. PMID:27597928

  10. Selective and Accurate Determination Method of Propofol in Human Plasma by Mixed-Mode Cation Exchange Cartridge and GC-MS.

    PubMed

    Pyo, Jae Sung

    2016-01-01

    A gas chromatography-mass spectrometry (GC-MS) method for the determination of propofol in human plasma has been developed and validated. Propofol was extracted from human plasma by using mixed-mode cation exchange/reversed-phase (MCX) cartridges. As propofol easily volatilizes during concentration, 100% methanol was injected directly into GC-MS to elute propofol. Despite avoiding concentration process of the eluted solution, lower limit of quantization (LLOQ) of propofol was 25 ng/mL. The validated method exhibited good linearity (R (2) = 0.9989) with accuracy and precision -5.8%~11.7% and 3.7%~11.6%, respectively. The other validation parameters, recovery and matrix effect, ranged from 96.6% to 99.4% and 95.3% to 101.4%, respectively. Propofol standard was quantified to evaluate possible loss due to the concentration processes, nitrogen gas and centrifugal vacuum. These two concentration processes resulted in notable decrease in the quantity of propofol, signifying avoiding any concentration processes during propofol quantification. Also, to confirm suitability of the developed method, authentic human plasma samples were analyzed. The selective assay method using MCX cartridge and GC-MS facilitated quantification of propofol in plasma sample accurately by preventing any losses due to the concentration processes. PMID:27597928

  11. A rapid and accurate method for determining protein content in dairy products based on asynchronous-injection alternating merging zone flow-injection spectrophotometry.

    PubMed

    Liang, Qin-Qin; Li, Yong-Sheng

    2013-12-01

    An accurate and rapid method and a system to determine protein content using asynchronous-injection alternating merging zone flow-injection spectrophotometry based on reaction between coomassie brilliant blue G250 (CBBG) and protein was established. Main merit of our approach is that it can avoid interferences of other nitric-compounds in samples, such as melamine and urea. Optimized conditions are as follows: Concentrations of CBBG, polyvinyl alcohol (PVA), NaCl and HCl are 150 mg/l, 30 mg/l, 0.1 mol/l and 1.0% (v/v), respectively; volumes of the sample and reagent are 150 μl and 30 μl, respectively; length of a reaction coil is 200 cm; total flow rate is 2.65 ml/min. The linear range of the method is 0.5-15 mg/l (BSA), its detection limit is 0.05 mg/l, relative standard deviation is less than 1.87% (n=11), and analytical speed is 60 samples per hour.

  12. Accurate determination of Curium and Californium isotopic ratios by inductively coupled plasma quadrupole mass spectrometry (ICP-QMS) in 248Cm samples for transmutation studies

    SciTech Connect

    Gourgiotis, A.; Isnard, H.; Aubert, M.; Dupont, E.; AlMahamid, I.; Cassette, P.; Panebianco, S.; Letourneau, A.; Chartier, F.; Tian, G.; Rao, L.; Lukens, W.

    2011-02-01

    The French Atomic Energy Commission has carried out several experiments including the mini-INCA (INcineration of Actinides) project for the study of minor-actinide transmutation processes in high intensity thermal neutron fluxes, in view of proposing solutions to reduce the radiotoxicity of long-lived nuclear wastes. In this context, a Cm sample enriched in {sup 248}Cm ({approx}97 %) was irradiated in thermal neutron flux at the High Flux Reactor (HFR) of the Laue-Langevin Institute (ILL). This work describes a quadrupole ICP-MS (ICP-QMS) analytical procedure for precise and accurate isotopic composition determination of Cm before sample irradiation and of Cm and Cf after sample irradiation. The factors that affect the accuracy and reproducibility of isotopic ratio measurements by ICP-QMS, such as peak centre correction, detector dead time, mass bias, abundance sensitivity and hydrides formation, instrumental background, and memory blank were carefully evaluated and corrected. Uncertainties of the isotopic ratios, taking into account internal precision of isotope ratio measurements, peak tailing, and hydrides formations ranged from 0.3% to 1.3%. This uncertainties range is quite acceptable for the nuclear data to be used in transmutation studies.

  13. Accurate experimental determination of the isotope effects on the triple point temperature of water. I. Dependence on the 2H abundance

    NASA Astrophysics Data System (ADS)

    Faghihi, V.; Peruzzi, A.; Aerts-Bijma, A. T.; Jansen, H. G.; Spriensma, J. J.; van Geel, J.; Meijer, H. A. J.

    2015-12-01

    Variation in the isotopic composition of water is one of the major contributors to uncertainty in the realization of the triple point of water (TPW). Although the dependence of the TPW on the isotopic composition of the water has been known for years, there is still a lack of a detailed and accurate experimental determination of the values for the correction constants. This paper is the first of two articles (Part I and Part II) that address quantification of isotope abundance effects on the triple point temperature of water. In this paper, we describe our experimental assessment of the 2H isotope effect. We manufactured five triple point cells with prepared water mixtures with a range of 2H isotopic abundances encompassing widely the natural abundance range, while the 18O and 17O isotopic abundance were kept approximately constant and the 18O  -  17O ratio was close to the Meijer-Li relationship for natural waters. The selected range of 2H isotopic abundances led to cells that realised TPW temperatures between approximately  -140 μK to  +2500 μK with respect to the TPW temperature as realized by VSMOW (Vienna Standard Mean Ocean Water). Our experiment led to determination of the value for the δ2H correction parameter of A2H  =  673 μK / (‰ deviation of δ2H from VSMOW) with a combined uncertainty of 4 μK (k  =  1, or 1σ).

  14. Towards Efficient and Accurate Description of Many-Electron Problems: Developments of Static and Time-Dependent Electronic Structure Methods

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi

    Understanding electronic behavior in molecular and nano-scale systems is fundamental to the development and design of novel technologies and materials for application in a variety of scientific contexts from fundamental research to energy conversion. This dissertation aims to provide insights into this goal by developing novel methods and applications of first-principle electronic structure theory. Specifically, we will present new methods and applications of excited state multi-electron dynamics based on the real-time (RT) time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) formalism, and new development of the multi-configuration self-consist field theory (MCSCF) for modeling ground-state electronic structure. The RT-TDHF/TDDFT based developments and applications can be categorized into three broad and coherently integrated research areas: (1) modeling of the interaction between moleculars and external electromagnetic perturbations. In this part we will first prove both analytically and numerically the gauge invariance of the TDHF/TDDFT formalisms, then we will present a novel, efficient method for calculating molecular nonlinear optical properties, and last we will study quantum coherent plasmon in metal namowires using RT-TDDFT; (2) modeling of excited-state charge transfer in molecules. In this part, we will investigate the mechanisms of bridge-mediated electron transfer, and then we will introduce a newly developed non-equilibrium quantum/continuum embedding method for studying charge transfer dynamics in solution; (3) developments of first-principles spin-dependent many-electron dynamics. In this part, we will present an ab initio non-relativistic spin dynamics method based on the two-component generalized Hartree-Fock approach, and then we will generalized it to the two-component TDDFT framework and combine it with the Ehrenfest molecular dynamics approach for modeling the interaction between electron spins and nuclear

  15. Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).

    PubMed

    Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

    2015-02-01

    The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp.

  16. An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation.

    PubMed

    Imai, Shunsuke; Kumar, Parimal; Hellen, Christopher U T; D'Souza, Victoria M; Wagner, Gerhard

    2016-09-01

    Many viruses bypass canonical cap-dependent translation in host cells by using internal ribosomal entry sites (IRESs) in their transcripts; IRESs hijack initiation factors for the assembly of initiation complexes. However, it is currently unknown how IRES RNAs recognize initiation factors that have no endogenous RNA binding partners; in a prominent example, the IRES of encephalomyocarditis virus (EMCV) interacts with the HEAT-1 domain of eukaryotic initiation factor 4G (eIF4G). Here we report the solution structure of the J-K region of this IRES and show that its stems are precisely organized to position protein-recognition bulges. This multisite interaction mechanism operates on an all-or-nothing principle in which all domains are required. This preorganization is accomplished by an 'adjuster module': a pentaloop motif that acts as a dual-sided docking station for base-pair receptors. Because subtle changes in the orientation abrogate protein capture, our study highlights how a viral RNA acquires affinity for a target protein. PMID:27525590

  17. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    PubMed

    Fromm, S A; Sachse, C

    2016-01-01

    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method.

  18. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    PubMed

    Fromm, S A; Sachse, C

    2016-01-01

    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. PMID:27572732

  19. Ambiguity of structure determination from a minimum of diffraction intensities.

    PubMed

    Al-Asadi, Ahmed; Leggas, Dimitri; Tsodikov, Oleg V

    2014-07-01

    Although the ambiguity of the crystal structures determined directly from diffraction intensities has been historically recognized, it is not well understood in quantitative terms. Bernstein's theorem has recently been used to obtain the number of one-dimensional crystal structures of equal point atoms, given a minimum set of diffraction intensities. By a similar approach, the number of two- and three-dimensional crystal structures that can be determined from a minimum intensity data set is estimated herein. The ambiguity of structure determination from the algebraic minimum of data increases at least exponentially fast with the increasing structure size. Substituting lower-resolution intensities by higher-resolution ones in the minimum data set has little or no effect on this ambiguity if the number of such substitutions is relatively small. PMID:25970192

  20. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.

    PubMed

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination.

  1. NMRFAM-SDF: a protein structure determination framework.

    PubMed

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C; Cornilescu, Gabriel; Assadi-Porter, Fariba M; Westler, William M; Eghbalnia, Hamid R; Markley, John L

    2015-08-01

    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm).

  2. Accurate structure, thermodynamics and spectroscopy of medium-sized radicals by hybrid Coupled Cluster/Density Functional Theory approaches: the case of phenyl radical

    PubMed Central

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Egidi, Franco; Puzzarini, Cristina

    2015-01-01

    The CCSD(T) model coupled with extrapolation to the complete basis-set limit and additive approaches represents the “golden standard” for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed. PMID:23802956

  3. Introducing Chemists to X-Ray Structure Determination.

    ERIC Educational Resources Information Center

    Enemark, John H.

    1988-01-01

    Presents the organization of a one-semester graduate course in structural chemistry including lectures and problems. Discusses the coverage of diffraction from real crystals and structure determination. Summarizes experiments on real crystals conducted by students in the X-ray laboratory. (CW)

  4. Labor Market Structure and Salary Determination among Professional Basketball Players.

    ERIC Educational Resources Information Center

    Wallace, Michael

    1988-01-01

    The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

  5. Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

    PubMed Central

    Levin, Igor; Vanderah, Terrell

    2008-01-01

    The functional responses (e.g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure—a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale—the so-called “nanostructure problem”—at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem—an ultimate frontier in materials characterization—necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed “institute” would provide an intellectual infrastructure for local structure determination by (1) developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2), (2) connecting industrial and academic users with experts in measurement techniques, (3

  6. Investigation of mass dependence effects for the accurate determination of molybdenum isotope amount ratios by MC-ICP-MS using synthetic isotope mixtures.

    PubMed

    Malinovsky, Dmitry; Dunn, Philip J H; Petrov, Panayot; Goenaga-Infante, Heidi

    2015-01-01

    Methodology for absolute Mo isotope amount ratio measurements by multicollector inductively coupled plasma-mass spectrometry (MC-ICP-MS) using calibration with synthetic isotope mixtures (SIMs) is presented. For the first time, synthetic isotope mixtures prepared from seven commercially available isotopically enriched molybdenum metal powders ((92)Mo, (94)Mo, (95)Mo, (96)Mo, (97)Mo, (98)Mo, and (100)Mo) are used to investigate whether instrumental mass discrimination of Mo isotopes in MC-ICP-MS is consistent with mass-dependent isotope distribution. The parent materials were dissolved and mixed as solutions to obtain mixtures with accurately known isotope amount ratios. The level of elemental impurities in the isotopically enriched molybdenum metal powders was quantified by ICP-MS by using both high-resolution and reaction cell instruments to completely resolve spectral interferences. The Mo isotope amount ratio values with expanded uncertainty (k = 2), determined by MC-ICP-MS for a high-purity Mo rod from Johnson Matthey, were as follows: (92)Mo/(95)Mo = 0.9235(9), (94)Mo/(95)Mo = 0.5785(8), (96)Mo/(95)Mo = 1.0503(9), (97)Mo/(95)Mo = 0.6033(6), (98)Mo/(95)Mo = 1.5291(20), and (100)Mo/(95)Mo = 0.6130(7). A full uncertainty budget for the measurements is presented which shows that the largest contribution to the uncertainty budget comes from correction for elemental impurities (∼51%), followed by the contribution from weighing operations (∼26 %). The atomic weight of molybdenum was calculated to be 95.947(2); the uncertainty in parentheses is expanded uncertainty with the coverage factor of 2. A particular advantage of the developed method is that calibration factors for all six Mo isotope amount ratios, involving the (95)Mo isotope, were experimentally determined. This allows avoiding any assumption on mass-dependent isotope fractions in MC-ICP-MS, inherent to the method of double spike previously used for Mo isotope amount ratio

  7. Structure Determination of Natural Products by Mass Spectrometry.

    PubMed

    Biemann, Klaus

    2015-01-01

    I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts. PMID:26161970

  8. Structural determination of intact proteins using mass spectrometry

    DOEpatents

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  9. Structure Determination of Natural Products by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Biemann, Klaus

    2015-07-01

    I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.

  10. The progress made in determining the Mycobacterium tuberculosis structural proteome

    PubMed Central

    Hecker, Michael

    2011-01-01

    Mycobacterium tuberculosis is a highly infectious pathogen that is still responsible for millions of deaths annually. Effectively treating this disease typically requires a course of antibiotics, most of which were developed decades ago. These drugs are, however, not effective against persistent tubercle bacilli and the emergence of drug-resistant stains threatens to make many of them obsolete. The identification of new drug targets, allowing the development of new potential drugs, is therefore imperative. Both proteomics and structural biology have important roles to play in this process, the former as a means of identifying promising drug targets and the latter allowing understanding of protein function and protein–drug interactions at atomic resolution. The determination of M. tuberculosis protein structures has been a goal of the scientific community for the last decade, who have aimed to supply a large amount of structural data that can be used in structure-based approaches for drug discovery and design. Only since the genome sequence of M. tuberculosis has been available has the determination of large numbers of tuberculosis protein structures been possible. Currently, the molecular structures of 8.5% of all the pathogen's protein-encoding ORFs have been determined. In this review, we look at the progress made in determining the M. tuberculosis structural proteome and the impact this has had on the development of potential new drugs, as well as the discovery of the function of crucial mycobaterial proteins. PMID:21674801

  11. Surface structures and surface-atom vibrations determined using photoelectron diffraction

    SciTech Connect

    Wang, L.Q. . Dept. of Chemistry Lawrence Berkeley Lab., CA )

    1991-07-01

    Surface structures of {radical}3 {times} {radical}3 R30{degrees} Cl/Ni(111) and c(2 {times} 2)Cl/Cu(001) were determined using low- temperature angle-resolved photoemission extended fine structure (ARPEFS), which yields both more accurate surface and near-surface structural information for deeper substrate layers. A study of surface-atom vibrations for {radical}3 {times} {radical}3 R30{degrees} Cl/Ni(111) and c(2 {times} 2)Cl/Cu(001) was made using temperature-dependent ARPEFS. A model for predicting the adsorbate vibrational anisotropy from surface structures was proposed and also successfully applied to several adsorbate systems. This model offered a simple and straightforward physical picture for understanding different types of vibrational anisotropy.

  12. Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile, and accurate RNA structure analysis

    PubMed Central

    Smola, Matthew J.; Rice, Greggory M.; Busan, Steven; Siegfried, Nathan A.; Weeks, Kevin M.

    2016-01-01

    SHAPE chemistries exploit small electrophilic reagents that react with the 2′-hydroxyl group to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues based on the ability of reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as for simple model RNAs. This protocol describes the experimental steps, implemented over three days, required to perform SHAPE probing and construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. These steps include RNA folding and SHAPE structure probing, mutational profiling by reverse transcription, library construction, and sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides useful troubleshooting information, often within an hour. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures, and visualize probable and alternative helices, often in under a day. We illustrate these algorithms with the E. coli thiamine pyrophosphate riboswitch, E. coli 16S rRNA, and HIV-1 genomic RNAs. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles, and entire transcriptomes. The straightforward MaP strategy greatly expands the number, length, and complexity of analyzable RNA structures. PMID:26426499

  13. In cellulo structure determination of a novel cypovirus polyhedrin

    SciTech Connect

    Axford, Danny; Ji, Xiaoyun; Stuart, David I.; Sutton, Geoff

    2014-05-01

    The crystal structure of a previously unsolved type of cypovirus polyhedrin has been determined from data collected directly from frozen live insect cells. This work demonstrates that with the use of a microfocus synchrotron beam the structure of a novel viral polyhedrin could be successfully determined from microcrystals within cells, removing the preparatory step of sample isolation and maintaining a favourable biological environment. The data obtained are of high quality, comparable to that obtained from isolated crystals, and enabled a facile structure determination. A small but significant difference is observed between the unit-cell parameters and the mosaic spread of in cellulo and isolated crystals, suggesting that even these robust crystals are adversely affected by removal from the cell.

  14. Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

    SciTech Connect

    Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani; Fox, Daniel A.; Sim, Adelene Y.L.; Doniach, Sebastian; Lesley, Scott A.

    2009-10-21

    One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based on these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.

  15. Optimizing an emperical scoring function for transmembrane protein structure determination.

    SciTech Connect

    Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne; Kolda, Tamara Gibson

    2003-10-01

    We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.

  16. Determinants of Market Structure and the Airline Industry

    NASA Technical Reports Server (NTRS)

    Raduchel, W.

    1972-01-01

    The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

  17. A Bayesian View on Cryo-EM Structure Determination

    PubMed Central

    Scheres, Sjors H.W.

    2012-01-01

    Three-dimensional (3D) structure determination by single-particle analysis of cryo-electron microscopy (cryo-EM) images requires many parameters to be determined from extremely noisy data. This makes the method prone to overfitting, that is, when structures describe noise rather than signal, in particular near their resolution limit where noise levels are highest. Cryo-EM structures are typically filtered using ad hoc procedures to prevent overfitting, but the tuning of arbitrary parameters may lead to subjectivity in the results. I describe a Bayesian interpretation of cryo-EM structure determination, where smoothness in the reconstructed density is imposed through a Gaussian prior in the Fourier domain. The statistical framework dictates how data and prior knowledge should be combined, so that the optimal 3D linear filter is obtained without the need for arbitrariness and objective resolution estimates may be obtained. Application to experimental data indicates that the statistical approach yields more reliable structures than existing methods and is capable of detecting smaller classes in data sets that contain multiple different structures. PMID:22100448

  18. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  19. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.

    PubMed

    Borbulevych, Oleg; Martin, Roger I; Tickle, Ian J; Westerhoff, Lance M

    2016-04-01

    Gaining an understanding of the protein-ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  20. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement

    PubMed Central

    Borbulevych, Oleg; Martin, Roger I.; Tickle, Ian J.; Westerhoff, Lance M.

    2016-01-01

    Gaining an understanding of the protein–ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  1. 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.

  2. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

    PubMed Central

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

    2013-01-01

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

  3. High-resolution protein structure determination by serial femtosecond crystallography.

    PubMed

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J; Barends, Thomas R M; Aquila, Andrew; Doak, R Bruce; Weierstall, Uwe; DePonte, Daniel P; Steinbrener, Jan; Shoeman, Robert L; Messerschmidt, Marc; Barty, Anton; White, Thomas A; Kassemeyer, Stephan; Kirian, Richard A; Seibert, M Marvin; Montanez, Paul A; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M; Philipp, Hugh T; Tate, Mark W; Hromalik, Marianne; Koerner, Lucas J; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y; Hunter, Mark S; Johansson, Linda C; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C H; Chapman, Henry N; Schlichting, Ilme

    2012-07-20

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  4. High-resolution protein structure determination by serial femtosecond crystallography.

    PubMed

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J; Barends, Thomas R M; Aquila, Andrew; Doak, R Bruce; Weierstall, Uwe; DePonte, Daniel P; Steinbrener, Jan; Shoeman, Robert L; Messerschmidt, Marc; Barty, Anton; White, Thomas A; Kassemeyer, Stephan; Kirian, Richard A; Seibert, M Marvin; Montanez, Paul A; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M; Philipp, Hugh T; Tate, Mark W; Hromalik, Marianne; Koerner, Lucas J; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y; Hunter, Mark S; Johansson, Linda C; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C H; Chapman, Henry N; Schlichting, Ilme

    2012-07-20

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

  5. Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins.

    PubMed

    Brookes, David H; Head-Gordon, Teresa

    2016-04-01

    We develop a Bayesian approach to determine the most probable structural ensemble model from candidate structures for intrinsically disordered proteins (IDPs) that takes full advantage of NMR chemical shifts and J-coupling data, their known errors and variances, and the quality of the theoretical back-calculation from structure to experimental observables. Our approach differs from previous formulations in the optimization of experimental and back-calculation nuisance parameters that are treated as random variables with known distributions, as opposed to structural or ensemble weight optimization or use of a reference ensemble. The resulting experimental inferential structure determination (EISD) method is size extensive with O(N) scaling, with N = number of structures, that allows for the rapid ranking of large ensemble data comprising tens of thousands of conformations. We apply the EISD approach on singular folded proteins and a corresponding set of ∼25 000 misfolded states to illustrate the problems that can arise using Boltzmann weighted priors. We then apply the EISD method to rank IDP ensembles most consistent with the NMR data and show that the primary error for ranking or creating good IDP ensembles resides in the poor back-calculation from structure to simulated experimental observable. We show that a reduction by a factor of 3 in the uncertainty of the back-calculation error can improve the discrimination among qualitatively different IDP ensembles for the amyloid-beta peptide.

  6. High-throughput determination of RNA structure by proximity ligation.

    PubMed

    Ramani, Vijay; Qiu, Ruolan; Shendure, Jay

    2015-09-01

    We present an unbiased method to globally resolve RNA structures through pairwise contact measurements between interacting regions. RNA proximity ligation (RPL) uses proximity ligation of native RNA followed by deep sequencing to yield chimeric reads with ligation junctions in the vicinity of structurally proximate bases. We apply RPL in both baker's yeast (Saccharomyces cerevisiae) and human cells and generate contact probability maps for ribosomal and other abundant RNAs, including yeast snoRNAs, the RNA subunit of the signal recognition particle and the yeast U2 spliceosomal RNA homolog. RPL measurements correlate with established secondary structures for these RNA molecules, including stem-loop structures and long-range pseudoknots. We anticipate that RPL will complement the current repertoire of computational and experimental approaches in enabling the high-throughput determination of secondary and tertiary RNA structures. PMID:26237516

  7. Magnifying endoscopy with narrow-band imaging is more accurate for determination of horizontal extent of early gastric cancers than chromoendoscopy

    PubMed Central

    Asada-Hirayama, Itsuko; Kodashima, Shinya; Sakaguchi, Yoshiki; Ono, Satoshi; Niimi, Keiko; Mochizuki, Satoshi; Tsuji, Yosuke; Minatsuki, Chihiro; Shichijo, Satoki; Matsuzaka, Keisuke; Ushiku, Tetsuo; Fukayama, Masashi; Yamamichi, Nobutake; Fujishiro, Mitsuhiro; Koike, Kazuhiko

    2016-01-01

    Background and study aims: Although magnifying endoscopy with narrow-band imaging (ME-NBI) is reported to be useful for delineating the horizontal extent of early gastric cancers (EGCs), there are few reports which have objectively demonstrated the superiority of ME-NBI over chromoendoscopy with indigo carmine for this purpose. We conducted an exploratory comparison of the diagnostic accuracy of both modalities for the delineation of EGCs using prospectively collected data, and clarified the clinicopathological features related to inaccurate evaluation of the horizontal extent of EGCs. Patients and methods: EGCs were assigned to the oral narrow-band imaging (O-NBI) group or the oral chromoendoscopy (O-CE) group before endoscopic submucosal dissection (ESD). The oral border was observed according to assignment, and the anal border with the other modality. The horizontal extent of the tumor was evaluated by each modality and a marking dot was placed on the visible delineation line. After ESD, the marking dots were identified pathologically and defined as “accurate evaluation” if they were located within 1 mm of the pathological tumor border. We compared the rate of accurate evaluation of ME-NBI and chromoendoscopy, and analyzed the clinicopathological features related to inaccurate evaluation. Results: A total of 113 marking dots evaluated by ME-NBI and 116 evaluated by chromoendoscopy were analyzed. The rate of accurate evaluation by ME-NBI was significantly higher than that by chromoendoscopy (89.4 % vs 75.9 %, P = 0.0071). The EGCs with flat borders and large EGCs were significantly related to inaccurate evaluation using ME-NBI. There were no significant factors related to inaccurate evaluation with chromoendoscopy. Conclusions: The accurate evaluation rate of the horizontal extent of EGCs by ME-NBI is significantly higher than that by chromoendoscopy. Study registration: UMIN000007641 PMID:27556080

  8. The Determination of Molecular Structure from Rotational Spectra

    DOE R&D Accomplishments Database

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  9. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    ERIC Educational Resources Information Center

    Mariana, Neni

    2010-01-01

    Few researches have been concerned about relation between children's spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was…

  10. A Laboratory Exercise in the Determination of Carbohydrate Structures.

    ERIC Educational Resources Information Center

    White, Bernard J.; Robyt, John F.

    1988-01-01

    Describes an experiment in which students are given a naturally occurring oligosaccharide as an unknown and are asked to determine both its monosaccharide composition and its structure. Discusses methods and experimental techniques including thin layer chromatography and the use of enzymes. (CW)

  11. From bacterial to human dihydrouridine synthase: automated structure determination

    SciTech Connect

    Whelan, Fiona Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

    2015-06-30

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  12. Does the genetic type of collagen determine fibril structure

    SciTech Connect

    Eikenberry, E.; Brodsky, B.; Cassidy, K.

    1980-10-01

    A number of genetic types of collagen, all triple-helical but with significant variations in their amino acid sequences, have been found and the distribution of these genetic types is tissue specific. For example, tendon is composed only of type I collagen, while cartilage contains largely type II collagen. Skin contains a large amount of type I, but has a significant fraction, approx. 15%, of type III. Each of these types can form fibrils, but it is not known whether they form distinctive fibril structures that are important in determining tissue organization. We are using x-ray diffraction to analyze a variety of tissues with different collagen genetic types to compare the fibril structures and thus investigate whether genetic type is an important determinant of this structure.

  13. Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T{sub 6} bovine insulin derivatives

    SciTech Connect

    Frankaer, Christian Grundahl; Mossin, Susanne; Ståhl, Kenny; Harris, Pernille

    2014-01-01

    The level of structural detail around the metal sites in Ni{sup 2+} and Cu{sup 2+} T{sub 6} insulin derivatives was significantly improved by using a combination of single-crystal X-ray crystallography and X-ray absorption spectroscopy. Photoreduction and subsequent radiation damage of the Cu{sup 2+} sites in Cu insulin was followed by XANES spectroscopy. Using synchrotron radiation (SR), the crystal structures of T{sub 6} bovine insulin complexed with Ni{sup 2+} and Cu{sup 2+} were solved to 1.50 and 1.45 Å resolution, respectively. The level of detail around the metal centres in these structures was highly limited, and the coordination of water in Cu site II of the copper insulin derivative was deteriorated as a consequence of radiation damage. To provide more detail, X-ray absorption spectroscopy (XAS) was used to improve the information level about metal coordination in each derivative. The nickel derivative contains hexacoordinated Ni{sup 2+} with trigonal symmetry, whereas the copper derivative contains tetragonally distorted hexacoordinated Cu{sup 2+} as a result of the Jahn–Teller effect, with a significantly longer coordination distance for one of the three water molecules in the coordination sphere. That the copper centre is of type II was further confirmed by electron paramagnetic resonance (EPR). The coordination distances were refined from EXAFS with standard deviations within 0.01 Å. The insulin derivative containing Cu{sup 2+} is sensitive towards photoreduction when exposed to SR. During the reduction of Cu{sup 2+} to Cu{sup +}, the coordination geometry of copper changes towards lower coordination numbers. Primary damage, i.e. photoreduction, was followed directly by XANES as a function of radiation dose, while secondary damage in the form of structural changes around the Cu atoms after exposure to different radiation doses was studied by crystallography using a laboratory diffractometer. Protection against photoreduction and subsequent

  14. Molecular determination by electron microscopy of the dynein-microtubule complex structure.

    PubMed

    Narita, Akihiro; Mizuno, Naoko; Kikkawa, Masahide; Maéda, Yuichiro

    2007-10-01

    Dynein is a minus-end-directed microtubule (MT) motor that is responsible for the wide range of MT-based motility in eukaryotic cells. Detailed mechanism of the dynein chemomechanical conversion is still unknown, partly because the structure of dynein is not studied at high resolution. To address this problem and reconstruct the dynein-MT complex at higher resolution, we have developed new procedures based on single particle analysis. To accurately determine the orientation of the dynein-MT complex, we introduced a "dynein track model" to restrict the possible dynein positions on the images. We tested our procedures by reconstructing structures from simulated dynein-MT complex images. Starting from the simulated noisy images generated using three different models of the dynein-MT complex, we have successfully recovered the original three-dimensional (3-D) structure. We also showed that our procedure is robust against fluctuation of the dynein molecules and can determine the structure even when the dynein position fluctuates to a certain extent. Convergence of the final 3-D structure can be tested with a "two-dimensional (2-D) agreement value," which we introduced to see whether the final structure is a result of overfit from fluctuating dynein or not. When the procedures did not work well due to the fluctuation, we could recognize the failure by this 2-D agreement value. Finally, the actual structure of the dynein-MT complex was determined from actual cryoelectron micrographs of Dictyostelium cytoplasmic dynein-MT complex. This method has revealed the detailed 3-D structures of the dynein-MT complex and will shed light on the motor mechanism of the dynein molecule. PMID:17761194

  15. Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

    PubMed Central

    Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; Collazo, Michael J.; Shi, Dan; Reyes, Francis E.; Gonen, Tamir; Eisenberg, David S.

    2016-01-01

    Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods. PMID:27647903

  16. Observation and Structure Determination of an Oxide Quasicrystal Approximant

    NASA Astrophysics Data System (ADS)

    Förster, S.; Trautmann, M.; Roy, S.; Adeagbo, W. A.; Zollner, E. M.; Hammer, R.; Schumann, F. O.; Meinel, K.; Nayak, S. K.; Mohseni, K.; Hergert, W.; Meyerheim, H. L.; Widdra, W.

    2016-08-01

    We report on the first observation of an approximant structure to the recently discovered two-dimensional oxide quasicrystal. Using scanning tunneling microscopy, low-energy electron diffraction, and surface x-ray diffraction in combination with ab initio calculations, the atomic structure and the bonding scheme are determined. The oxide approximant follows a 32 .4.3.4 Archimedean tiling. Ti atoms reside at the corners of each tiling element and are threefold coordinated to oxygen atoms. Ba atoms separate the TiO3 clusters, leading to a fundamental edge length of the tiling 6.7 Å.

  17. Observation and Structure Determination of an Oxide Quasicrystal Approximant.

    PubMed

    Förster, S; Trautmann, M; Roy, S; Adeagbo, W A; Zollner, E M; Hammer, R; Schumann, F O; Meinel, K; Nayak, S K; Mohseni, K; Hergert, W; Meyerheim, H L; Widdra, W

    2016-08-26

    We report on the first observation of an approximant structure to the recently discovered two-dimensional oxide quasicrystal. Using scanning tunneling microscopy, low-energy electron diffraction, and surface x-ray diffraction in combination with ab initio calculations, the atomic structure and the bonding scheme are determined. The oxide approximant follows a 3^{2}.4.3.4 Archimedean tiling. Ti atoms reside at the corners of each tiling element and are threefold coordinated to oxygen atoms. Ba atoms separate the TiO_{3} clusters, leading to a fundamental edge length of the tiling 6.7 Å. PMID:27610863

  18. Direct structure determination by atomic-resolution incoherent STEM imaging

    SciTech Connect

    Nellist, P.D.; Xin, Y.; Pennycook, S.J.

    1997-11-01

    Use of a large, annular dark-field (ADF) detector in a scanning transmission electron microscope is shown to give images that can allow direct structure determination, being a convolution between the illuminating probe intensity and an object function localized at the atomic column positions. The ADF image is also shown to resolve crystal spacings more than twice smaller than the phase contrast point resolution limit of the microscope used, with sub-angstrom structural information being retrieved. ADF image of several semiconductor materials are studied.

  19. Accurate crystal-structure refinement of Ca3Ga2Ge4O14 at 295 and 100 K and analysis of the disorder in the atomic positions

    NASA Astrophysics Data System (ADS)

    Dudka, A. P.; Mill', B. V.

    2013-07-01

    The accurate X-ray diffraction study of a Ca3Ga2Ge4O14 crystal (sp. gr. P321, Z = 1) has been performed using repeated X-ray diffraction data sets collected on a diffractometer equipped with a CCD area detector at 295 and 100 K. The asymmetric disorder in the atomic positions in Ca3Ga2Ge4O14 is described in two alternative ways: with the use of anharmonic atomic displacements (at 295 K R/wR = 0.68/0.60%, 3754 reflections; at 100 K R/wR = 0.90/0.70%, 3632 reflections) and using a split model (SM) (at 295 K R/wR = 0.74/0.67%; at 100 K R/wR = 0.95/0.74%). An analysis of the probability density function that defines the probability of finding an atom at a particular point in space shows that, at 295 K, five of the seven independent atoms in the unit cell are asymmetrically disordered in the vicinity of their sites, whereas only three atoms are disordered at 100 K. At both temperatures the largest disorder is observed at the 3 f site on a twofold axis, which is a prerequisite for the formation of helicoidal chains of atoms along the c axis of the crystal and can serve as a structural basis for multiferroic properties of this family of crystals with magnetic ions.

  20. Team Assembly Mechanisms Determine Collaboration Network Structure and Team Performance

    PubMed Central

    Guimerà, Roger; Uzzi, Brian; Spiro, Jarrett; Nunes Amaral, Luís A.

    2007-01-01

    Agents in creative enterprises are embedded in networks that inspire, support, and evaluate their work. Here, we investigate how the mechanisms by which creative teams self-assemble determine the structure of these collaboration networks. We propose a model for the self-assembly of creative teams that has its basis in three parameters: team size, the fraction of newcomers in new productions, and the tendency of incumbents to repeat previous collaborations. The model suggests that the emergence of a large connected community of practitioners can be described as a phase transition. We find that team assembly mechanisms determine both the structure of the collaboration network and team performance for teams derived from both artistic and scientific fields. PMID:15860629

  1. Team assembly mechanisms determine collaboration network structure and team performance.

    PubMed

    Guimerà, Roger; Uzzi, Brian; Spiro, Jarrett; Amaral, Luís A Nunes

    2005-04-29

    Agents in creative enterprises are embedded in networks that inspire, support, and evaluate their work. Here, we investigate how the mechanisms by which creative teams self-assemble determine the structure of these collaboration networks. We propose a model for the self-assembly of creative teams that has its basis in three parameters: team size, the fraction of newcomers in new productions, and the tendency of incumbents to repeat previous collaborations. The model suggests that the emergence of a large connected community of practitioners can be described as a phase transition. We find that team assembly mechanisms determine both the structure of the collaboration network and team performance for teams derived from both artistic and scientific fields.

  2. High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure.

    PubMed

    Darby, B J; Todd, T C; Herman, M A

    2013-11-01

    Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available. PMID:24103081

  3. High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure.

    PubMed

    Darby, B J; Todd, T C; Herman, M A

    2013-11-01

    Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available.

  4. The potential for biological structure determination with pulsed neutrons

    SciTech Connect

    Wilson, C.C.

    1994-12-31

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed.

  5. Determination of the Basin Structure Beneath European Side of Istanbul

    NASA Astrophysics Data System (ADS)

    Karabulut, Savas; Cengiz Cinku, Mulla; Thomas, Michael; Lamontagne, Maurice

    2016-04-01

    Istanbul (near North Anatolian Fault Zone:NAFZ, Turkey) is located in northern part of Sea of Marmara, an area that has been influenced by possible Marmara Earthquakes. The general geology of Istanbul divided into two stratigraphic unit such as sedimentary (from Oligocene to Quaternary Deposits) and bedrock (Paleozoic and Eocene). The bedrock units consists of sand stone, clay stone to Paleozoic age and limestone to Eocene age and sedimentary unit consist of sand, clay, mil and gravel from Oligocene to Quaternary age. Earthquake disaster mitigation studies divided into two important phases, too. Firstly, earthquake, soil and engineering structure problems identify for investigation area, later on strategic emergency plan can prepare for these problems. Soil amplification play important role the disaster mitigation and the site effect analysis and basin structure is also a key parameter for determining of site effect. Some geophysical, geological and geotechnical measurements are requeired to defined this relationship. Istanbul Megacity has been waiting possible Marmara Earthquake and their related results. In order to defined to possible damage potential related to site effect, gravity measurements carried out for determining to geological structure, basin geometry and faults in Istanbul. Gravity data were collected at 640 sites by using a Scientrex CG-5 Autogravity meter Standard corrections applied to the gravity data include those for instrumental drift, Earth tides and latitude, and the free-air and Bouguer corrections. The corrected gravity data were imported into a Geosoft database to create a grid and map of the Bouguer gravity anomaly (grid cell size of 200 m). As a previously results, we determined some lineminants, faults and basins beneath Istanbul City. Especially, orientation of faults were NW-SE direction and some basin structures determined on between Buyukcekmece and Kucukcekmece Lake.

  6. Strain-Based Damage Determination Using Finite Element Analysis for Structural Health Management

    NASA Technical Reports Server (NTRS)

    Hochhalter, Jacob D.; Krishnamurthy, Thiagaraja; Aguilo, Miguel A.

    2016-01-01

    A damage determination method is presented that relies on in-service strain sensor measurements. The method employs a gradient-based optimization procedure combined with the finite element method for solution to the forward problem. It is demonstrated that strains, measured at a limited number of sensors, can be used to accurately determine the location, size, and orientation of damage. Numerical examples are presented to demonstrate the general procedure. This work is motivated by the need to provide structural health management systems with a real-time damage characterization. The damage cases investigated herein are characteristic of point-source damage, which can attain critical size during flight. The procedure described can be used to provide prognosis tools with the current damage configuration.

  7. PlaneWave Admittance Method- a novel approach for determining the electromagnetic modes in photonic structures.

    PubMed

    Dems, Maciej; Kotynski, Rafal; Panajotov, Krassimir

    2005-05-01

    In this article we present a novel approach for determining the electromagnetic modes of photonic multilayer structures. We combine the plane wave expansion method with the method of lines resulting in a fast and accurate computational technique which we named the plane wave admittance method. In addition, we incorporate perfectly matched layers at the boundaries parallel to the multilayer surfaces which allow for easy determination of leaky modes. The convergence of the method is verified for the case of photonic crystal slab showing very good agreement with the results obtained with full three-dimensional plane wave expansion method while the numerical effort is largely reduced. The numerical implementation of the method will be soon available on the web.

  8. A form-factor method for determining the structure of distorted stars

    NASA Technical Reports Server (NTRS)

    Wolfe, R. H., Jr.; Kern, J. W.

    1979-01-01

    The equilibrium equations of a uniformly rotating and tidally distorted star are reduced to the same form as for a spherical star except for the inclusion of two form factors. One factor, expressing the buoyancy effects of centrifugal force, is determined directly from the integrated structure variables. The other factor, expressing the deviation from spherical shape, is shown to be relatively insensitive to errors in the assumed shape, so that accurate solutions are obtained in spite of the use of an a priori shape. The method is employed by adding computations for the factors to an existing spherical model program. Upper Main Sequence models determined by this method compare closely with results from the double approximation method even for critical rotation and tidal distortion.

  9. MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

    PubMed

    Ünlü, Ali; Dettweiler, Ulrich

    2015-12-01

    Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure. PMID:26595290

  10. MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

    PubMed

    Ünlü, Ali; Dettweiler, Ulrich

    2015-12-01

    Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure.

  11. Extension of the AMBER force field for nitroxide radicals and combined QM/MM/PCM approach to the accurate determination of EPR parameters of DMPOH in solution

    PubMed Central

    Hermosilla, Laura; Prampolini, Giacomo; Calle, Paloma; García de la Vega, José Manuel; Brancato, Giuseppe; Barone, Vincenzo

    2015-01-01

    A computational strategy that combines both time-dependent and time-independent approaches is exploited to accurately model molecular dynamics and solvent effects on the isotropic hyperfine coupling constants of the DMPO-H nitroxide. Our recent general force field for nitroxides derived from AMBER ff99SB is further extended to systems involving hydrogen atoms in β-positions with respect to NO. The resulting force-field has been employed in a series of classical molecular dynamics simulations, comparing the computed EPR parameters from selected molecular configurations to the corresponding experimental data in different solvents. The effect of vibrational averaging on the spectroscopic parameters is also taken into account, by second order vibrational perturbation theory involving semi-diagonal third energy derivatives together first and second property derivatives. PMID:26584116

  12. Sectional power-law correction for the accurate determination of lutetium by isotope dilution multiple collector-inductively coupled plasma-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Yuan, Hong-Lin; Gao, Shan; Zong, Chun-Lei; Dai, Meng-Ning

    2009-11-01

    In this study, we employ a sectional power-law (SPL) correction that provides accurate and precise measurements of 176Lu/ 175Lu ratios in geological samples using multiple collector-inductively coupled plasma-mass spectrometry (MC-ICP-MS). Three independent power laws were adopted based on the 176Lu/ 176Yb ratios of samples measured after chemical chromatography. Using isotope dilution (ID) techniques and the SPL correction method, the measured lutetium contents of United States Geological Survey rock standards (BHVO-1, BHVO-2, BCR-2, AGV-1, and G-2) agree well with the recommended values. Results obtained by conventional ICP-MS and INAA are generally higher than those obtained by ID-TIMS and ID-MC-ICP-MS; this discrepancy probably reflects oxide interference and inaccurate corrections.

  13. Determination of the stretch tensor for structural transformations

    NASA Astrophysics Data System (ADS)

    Chen, Xian; Song, Yintao; Tamura, Nobumichi; James, Richard D.

    2016-08-01

    Structural transformations in crystalline solids are increasingly the basis of the functional behavior of materials. Recently, in diverse alloy systems, both low hysteresis and reversibility of phase transformations have been linked to the satisfaction of the nongeneric conditions of compatibility between phases. According to the Cauchy-Born rule, these conditions are expressed as properties of transformation stretch tensor. The transformation stretch tensor is difficult to measure directly due to the lack of knowledge about the exact transforming pathway during the structural change, and the complicating effects of microstructure. In this paper we give a rigorous algorithmic approach for determining the transformation stretch tensor from X-ray measurements of structure and lattice parameters. For some traditional and emerging phase transformations, the results given by the algorithm suggest unexpected transformation mechanisms.

  14. Local magnetic structure determination using polarized neutron holography

    SciTech Connect

    Szakál, Alex Markó, Márton Cser, László

    2015-05-07

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  15. Optimal isotope labelling for NMR protein structure determinations.

    PubMed

    Kainosho, Masatsune; Torizawa, Takuya; Iwashita, Yuki; Terauchi, Tsutomu; Mei Ono, Akira; Güntert, Peter

    2006-03-01

    Nuclear-magnetic-resonance spectroscopy can determine the three-dimensional structure of proteins in solution. However, its potential has been limited by the difficulty of interpreting NMR spectra in the presence of broadened and overlapping resonance lines and low signal-to-noise ratios. Here we present stereo-array isotope labelling (SAIL), a technique that can overcome many of these problems by applying a complete stereospecific and regiospecific pattern of stable isotopes that is optimal with regard to the quality and information content of the resulting NMR spectra. SAIL uses exclusively chemically and enzymatically synthesized amino acids for cell-free protein expression. We demonstrate for the 17-kDa protein calmodulin and the 41-kDa maltodextrin-binding protein that SAIL offers sharpened lines, spectral simplification without loss of information, and the ability to rapidly collect the structural restraints required to solve a high-quality solution structure for proteins twice as large as commonly solved by NMR. It thus makes a large class of proteins newly accessible to detailed solution structure determination.

  16. Method and apparatus for determining material structural integrity

    DOEpatents

    Pechersky, M.J.

    1994-01-01

    Disclosed are a nondestructive method and apparatus for determining the structural integrity of materials by combining laser vibrometry with damping analysis to determine the damping loss factor. The method comprises the steps of vibrating the area being tested over a known frequency range and measuring vibrational force and velocity vs time over the known frequency range. Vibrational velocity is preferably measured by a laser vibrometer. Measurement of the vibrational force depends on the vibration method: if an electromagnetic coil is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by the coil current. If a reciprocating transducer is used, the vibrational force is determined by a force gauge in the transducer. Using vibrational analysis, a plot of the drive point mobility of the material over the preselected frequency range is generated from the vibrational force and velocity data. Damping loss factor is derived from a plot of the drive point mobility over the preselected frequency range using the resonance dwell method and compared with a reference damping loss factor for structural integrity evaluation.

  17. Method and apparatus for determining material structural integrity

    DOEpatents

    Pechersky, Martin

    1996-01-01

    A non-destructive method and apparatus for determining the structural integrity of materials by combining laser vibrometry with damping analysis techniques to determine the damping loss factor of a material. The method comprises the steps of vibrating the area being tested over a known frequency range and measuring vibrational force and velocity as a function of time over the known frequency range. Vibrational velocity is preferably measured by a laser vibrometer. Measurement of the vibrational force depends on the vibration method. If an electromagnetic coil is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by the amount of coil current used in vibrating the magnet. If a reciprocating transducer is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by a force gauge in the reciprocating transducer. Using known vibrational analysis methods, a plot of the drive point mobility of the material over the preselected frequency range is generated from the vibrational force and velocity measurements. The damping loss factor is derived from a plot of the drive point mobility over the preselected frequency range using the resonance dwell method and compared with a reference damping loss factor for structural integrity evaluation.

  18. Single Crystal Structure Determination of Alumina to 1 Mbar

    NASA Astrophysics Data System (ADS)

    Dong, H.; Zhang, L.; Prakapenka, V.; Mao, H.

    2014-12-01

    Aluminum oxide (Al2O3) is an important ceramic material and a major oxide in the earth. Additionally, alumina is a widely used pressure standard in static high-pressure experiments (Cr3+-bearing corundum, ruby). The changes of its crystal structure with pressure (P) and temperature (T) are important for its applications and understanding its physical properties in the deep Earth. There have been numerous reports on the high P-T polymorphs of alumina. Previous theoretical calculations and experiments suggest that the crystal structure of Al2O3 evolves greatly at high P-T. In this study, we used the newly developed multigrain crystallography method combined with single-crystal x-ray diffraction analysis technique for the structure determination of alumina at high P-T to provide single-crystal structure refinement for high-pressure phases of Al2O3. Alumina powder was mixed with ~10% Pt and Ne was used as both pressure transmitting media and thermal insulating layers during laser-heating. Coarse-grained aggregates of Al2O3 were synthesized in a laser-heated diamond anvil cell. The structure change of Al2O3 was monitored by in situ x-ray diffraction at ~1 Mbar and 2700 K. The results allow us to distinguish the structural differences between the Rh2O3 (II) structure (space group Pbcn) and perovskite structure (space group Pbnm) for the first high-pressure phase of Al2O3. More detailed results will be discussed in the later work.

  19. Sexing the Sciuridae: a simple and accurate set of molecular methods to determine sex in tree squirrels, ground squirrels and marmots.

    PubMed

    Gorrell, Jamieson C; Boutin, Stan; Raveh, Shirley; Neuhaus, Peter; Côté, Steeve D; Coltman, David W

    2012-09-01

    We determined the sequence of the male-specific minor histocompatibility complex antigen (Smcy) from the Y chromosome of seven squirrel species (Sciuridae, Rodentia). Based on conserved regions inside the Smcy intron sequence, we designed PCR primers for sex determination in these species that can be co-amplified with nuclear loci as controls. PCR co-amplification yields two products for males and one for females that are easily visualized as bands by agarose gel electrophoresis. Our method provides simple and reliable sex determination across a wide range of squirrel species.

  20. Study on the applicability of a precise, accurate method for rapid evaluation of engine and lubricant performance. [determination of wear metal in used lubricating oils

    NASA Technical Reports Server (NTRS)

    Kinard, J. T.

    1975-01-01

    The development of a procedure for obtaining data related to wear metal determinations in used lubricants is discussed. The procedure makes it possible to obtain rapid, simultaneous determinations of a number of wear metals at levels of parts per thousand to low parts per billion using a small amount of sample. The electrode assembly and instrumentation used in the process are described. Samples of data obtained from tests conducted under controlled conditions are tabulated.

  1. Determinants of femoral geometry and structure during adolescent growth.

    PubMed

    van der Meulen, M C; Ashford, M W; Kiratli, B J; Bachrach, L K; Carter, D R

    1996-01-01

    Our goal was to understand developmental determinants of femoral structure during growth and sexual maturation by relating femoral measurements to gender and developmental factors (age, pubertal stage, height, and body mass). The bone mineral content of the femur was measured by dual energy x-ray absorptiometry in 101 healthy Caucasian adolescents and young adults, 9-26 years of age. After some simplifying assumptions had been made, cross-sectional geometric properties of the femoral midshaft were estimated. Two geometry-based structural indicators, the section modulus and whole bone strength index, were calculated to assess the structural characteristics of the femur. Femoral strength, as described by these structural indicators, increased dramatically from childhood through young adulthood. Regressions were performed between these femoral measurements and the developmental factors. Our data show that of age, pubertal stage, body mass, and height, body mass is the strongest predictor of femoral cross-sectional properties, and the correlation of body mass with femoral cross-sectional structure is independent of gender. A model including all four developmental factors and gender did not substantially increase the accuracy of predictions compared with the model with body mass alone. In light of previous research, we hypothesize that body mass is an indicator of in vivo loading and that this in vivo loading influences the cross-sectional growth of the long bones.

  2. Databases of Conformations and NMR Structures of Glycan Determinants.

    PubMed

    Sarkar, Anita; Drouillard, Sophie; Rivet, Alain; Perez, Serge

    2015-12-01

    The present study reports a comprehensive nuclear magnetic resonance (NMR) characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large-scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B and O), core structures (Types 1, 2 and 4), fucosylated oligosaccharides (core and lacto-series), sialylated oligosaccharides (Types 1 and 2), Lewis antigens, GPI-anchors and globosides. A complementary set of about 100 glycan determinants occurring in glycoproteins and glycosaminoglycans has also been structurally characterized using molecular mechanics-based computation. The experimental and computational data generated are organized in two relational databases that can be queried by the user through a user-friendly search engine. The NMR ((1)H and (13)C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats. Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to cope with the different usages in chemistry and biology. These web-based databases were developed with non-proprietary software and are open access for the scientific community available at http://glyco3d.cermav.cnrs.fr.

  3. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Technical Reports Server (NTRS)

    Nandhakumar, N.; Smith, Philip W.

    1993-01-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

  4. On the determination of the crystal-vapor surface free energy, and why a Gaussian expression can be accurate for a system far from Gaussian

    NASA Astrophysics Data System (ADS)

    Modak, Viraj P.; Wyslouzil, Barbara E.; Singer, Sherwin J.

    2016-08-01

    The crystal-vapor surface free energy γ is an important physical parameter governing physical processes, such as wetting and adhesion. We explore exact and approximate routes to calculate γ based on cleaving an intact crystal into non-interacting sub-systems with crystal-vapor interfaces. We do this by turning off the interactions, ΔV, between the sub-systems. Using the soft-core scheme for turning off ΔV, we find that the free energy varies smoothly with the coupling parameter λ, and a single thermodynamic integration yields the exact γ. We generate another exact method, and a cumulant expansion for γ by expressing the surface free energy in terms of an average of e-βΔV in the intact crystal. The second cumulant, or Gaussian approximation for γ is surprisingly accurate in most situations, even though we find that the underlying probability distribution for ΔV is clearly not Gaussian. We account for this fact by developing a non-Gaussian theory for γ and find that the difference between the non-Gaussian and Gaussian expressions for γ consist of terms that are negligible in many situations. Exact and approximate methods are applied to the (111) surface of a Lennard-Jones crystal and are also tested for more complex molecular solids, the surface of octane and nonadecane. Alkane surfaces were chosen for study because their crystal-vapor surface free energy has been of particular interest for understanding surface freezing in these systems.

  5. On the determination of the crystal-vapor surface free energy, and why a Gaussian expression can be accurate for a system far from Gaussian.

    PubMed

    Modak, Viraj P; Wyslouzil, Barbara E; Singer, Sherwin J

    2016-08-01

    The crystal-vapor surface free energy γ is an important physical parameter governing physical processes, such as wetting and adhesion. We explore exact and approximate routes to calculate γ based on cleaving an intact crystal into non-interacting sub-systems with crystal-vapor interfaces. We do this by turning off the interactions, ΔV, between the sub-systems. Using the soft-core scheme for turning off ΔV, we find that the free energy varies smoothly with the coupling parameter λ, and a single thermodynamic integration yields the exact γ. We generate another exact method, and a cumulant expansion for γ by expressing the surface free energy in terms of an average of e(-βΔV) in the intact crystal. The second cumulant, or Gaussian approximation for γ is surprisingly accurate in most situations, even though we find that the underlying probability distribution for ΔV is clearly not Gaussian. We account for this fact by developing a non-Gaussian theory for γ and find that the difference between the non-Gaussian and Gaussian expressions for γ consist of terms that are negligible in many situations. Exact and approximate methods are applied to the (111) surface of a Lennard-Jones crystal and are also tested for more complex molecular solids, the surface of octane and nonadecane. Alkane surfaces were chosen for study because their crystal-vapor surface free energy has been of particular interest for understanding surface freezing in these systems.

  6. Tackling the crystallographic structure determination of the COP9 signalosome

    PubMed Central

    Bunker, Richard D.

    2016-01-01

    The COP9 signalosome (CSN) is an essential multi-protein complex in eukaryotes. CSN is a master regulator of intracellular protein degradation, controlling the vast family of cullin–RING ubiquitin (E3) ligases (CRLs). Important in many cellular processes, CSN has prominent roles in DNA repair, cell-cycle control and differentiation. The recent crystal structure of human CSN provides insight into its exquisite regulation and functionality [Lingaraju et al. (2014 ▸), Nature (London), 512, 161–165]. Structure determination was complicated by low-resolution diffraction from crystals affected by twinning and rotational pseudo-symmetry. Crystal instability and non-isomorphism strongly influenced by flash-cooling, radiation damage and difficulty in obtaining heavy-atom derivatives, were overcome. Many different subunits of the same fold class were distinguished at low resolution aided by combinatorial selenomethionine labelling. As an example of how challenging projects can be approached, the structure determination of CSN is described as it unfolded using cluster-compound MIRAS phasing, MR-SAD with electron-density models and cross-crystal averaging exploiting non-isomorphism among unit-cell variants of the same crystal form. PMID:26960120

  7. Tackling the crystallographic structure determination of the COP9 signalosome.

    PubMed

    Bunker, Richard D

    2016-03-01

    The COP9 signalosome (CSN) is an essential multi-protein complex in eukaryotes. CSN is a master regulator of intracellular protein degradation, controlling the vast family of cullin-RING ubiquitin (E3) ligases (CRLs). Important in many cellular processes, CSN has prominent roles in DNA repair, cell-cycle control and differentiation. The recent crystal structure of human CSN provides insight into its exquisite regulation and functionality [Lingaraju et al. (2014), Nature (London), 512, 161-165]. Structure determination was complicated by low-resolution diffraction from crystals affected by twinning and rotational pseudo-symmetry. Crystal instability and non-isomorphism strongly influenced by flash-cooling, radiation damage and difficulty in obtaining heavy-atom derivatives, were overcome. Many different subunits of the same fold class were distinguished at low resolution aided by combinatorial selenomethionine labelling. As an example of how challenging projects can be approached, the structure determination of CSN is described as it unfolded using cluster-compound MIRAS phasing, MR-SAD with electron-density models and cross-crystal averaging exploiting non-isomorphism among unit-cell variants of the same crystal form. PMID:26960120

  8. X-ray structure determination and deuteration of nattokinase

    PubMed Central

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

    2013-01-01

    Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis. PMID:24121331

  9. X-ray structure determination and deuteration of nattokinase.

    PubMed

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

    2013-11-01

    Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  10. Effect of chemical fixatives on accurate preservation of Escherichia coli and Bacillus subtilis structure in cells prepared by freeze-substitution

    SciTech Connect

    Graham, L.L.; Beveridge, T.J. )

    1990-04-01

    Five chemical fixatives were evaluated for their ability to accurately preserve bacterial ultrastructure during freeze-substitution of select Escherichia coli and Bacillus subtilis strains. Radioisotopes were specifically incorporated into the peptidoglycan, lipopolysaccharide, and nucleic acids of E. coli SFK11 and W7 and into the peptidoglycan and RNA of B. subtilis 168 and W23. The ease of extraction of radiolabels, as assessed by liquid scintillation counting during all stages of processing for freeze-substitution, was used as an indicator of cell structural integrity and retention of cellular chemical composition. Subsequent visual examination by electron microscopy was used to confirm ultrastructural conformation. The fixatives used were: 2% (wt/vol) osmium tetroxide and 2% (wt/vol) uranyl acetate; 2% (vol/vol) glutaraldehyde and 2% (wt/vol) uranyl acetate; 2% (vol/vol) acrolein and 2% (wt/vol) uranyl acetate; 2% (wt/vol) gallic acid; and 2% (wt/vol) uranyl acetate. All fixatives were prepared in a substitution solvent of anhydrous acetone. Extraction of cellular constituents depended on the chemical fixative used. A combination of 2% osmium tetroxide-2% uranyl acetate or 2% gallic acid alone resulted in optimum fixation as ascertained by least extraction of radiolabels. In both gram-positive and gram-negative organisms, high levels of radiolabel were detected in the processing fluids in which 2% acrolein-2% uranyl acetate, 2% glutaraldehyde-2% uranyl acetate, or 2% uranyl acetate alone were used as fixatives. Ultrastructural variations were observed in cells freeze-substituted in the presence of different chemical fixatives. We recommend the use of osmium tetroxide and uranyl acetate in acetone for routine freeze-substitution of eubacteria, while gallic acid is recommended for use when microanalytical processing necessitates the omission of osmium.

  11. Velocity Structure Determination Through Seismic Waveform Modeling and Time Deviations

    NASA Astrophysics Data System (ADS)

    Savage, B.; Zhu, L.; Tan, Y.; Helmberger, D. V.

    2001-12-01

    Through the use of seismic waveforms recorded by TriNet, a dataset of earthquake focal mechanisms and deviations (time shifts) relative to a standard model facilitates the investigation of the crust and uppermost mantle of southern California. The CAP method of focal mechanism determination, in use by TriNet on a routine basis, provides time shifts for surface waves and Pnl arrivals independently relative to the reference model. These shifts serve as initial data for calibration of local and regional seismic paths. Time shifts from the CAP method are derived by splitting the Pnl section of the waveform, the first arriving Pn to just before the arrival of the S wave, from the much slower surface waves then cross-correlating the data with synthetic waveforms computed from a standard model. Surface waves interact with the entire crust, but the upper crust causes the greatest effect. Whereas, Pnl arrivals sample the deeper crust, upper mantle, and source region. This natural division separates the upper from lower crust for regional calibration and structural modeling and allows 3-D velocity maps to be created using the resulting time shifts. Further examination of Pnl and other arrivals which interact with the Moho illuminate the complex nature of this boundary. Initial attempts at using the first 10 seconds of the Pnl section to determine upper most mantle structure have proven insightful. Two large earthquakes north of southern California in Nevada and Mammoth Lakes, CA allow the creation of record sections from 200 to 600 km. As the paths swing from east to west across southern California, simple 1-D models turn into complex structure, dramatically changing the waveform character. Using finite difference models to explain the structure, we determine that a low velocity zone is present at the base of the crust and extends to 100 km in depth. Velocity variations of 5 percent of the mantle in combination with steeply sloping edges produces complex waveform variations

  12. A flow cytometry-based immuno-titration assay for rapid and accurate titer determination of modified vaccinia Ankara virus vectors.

    PubMed

    Li, Zengji; Ling, Loni; Liu, Xiaohui; Laus, Reiner; Delcayre, Alain

    2010-10-01

    A flow cytometry-based immuno-titration titer assay was established to determine infectious unit (IU) and transducing unit (TU) of modified vaccinia Ankara (MVA) virus vectors. This titration method enumerates infected cells by measuring the expression of viral protein for IU and transgene protein for TU in individual cells after staining with fluorophore-conjugated antibodies. It presents many advantages over standard virus titration approaches, such as TCID(50) or plaque assay, for its convenience, rapidity and accuracy as illustrated by excellent assay linearity and reproducibility. Importantly, the IU and the TCID(50) assays generated similar batch-specific titer values when testing varied MVA-derived virus preparations. Assay development revealed that the post-infection time at which viral protein expression is evaluated, host cell type, and blocking the formation and release of progeny virion with nocodazole, an anti-microtubule agent or rifampin, a specific vaccinia virus assembly inhibitor, are critical parameters for the precision, robustness, and accuracy of IU titer determination. An added advantage of this assay is that it enables the concurrent determination of IU and transducing units (TU) by measuring the expression of a transgene product when testing recombinant viruses. The latter was demonstrated using a MVA vector carrying a human HER-2 gene fragment as model. Hence, this assay is very versatile in that it can be used to determine IU as well as multiple TU titers simultaneously. Furthermore, it can readily be adapted to other poxvirus vectors.

  13. Development and validation of a sensitive solid phase extraction/hydrophilic interaction liquid chromatography/mass spectrometry method for the accurate determination of glucosamine in dog plasma.

    PubMed

    Hubert, C; Houari, S; Lecomte, F; Houbart, V; De Bleye, C; Fillet, M; Piel, G; Rozet, E; Hubert, Ph

    2010-05-01

    A sensitive and accurate LC/MS method was developed for the monitoring of glucosamine (GLcN) dog plasmatic concentration. In this scope, relatively low plasmatic concentrations of GLcN were expected, ranging from 50 to 1000 ng/mL. Liquid chromatography coupled to simple quadrupole mass spectrometry detection (LC/MS) was selected bringing the selectivity and the sensitivity needed for this application. Additionally, a solid phase extraction (SPE) step was performed to reduce matrix and ion suppression effects. Due to the ionisable character of the compound of interest, a mixed-mode strong cation exchange (Plexa PCX) disposable extraction cartridge (DEC) was selected. The separation was carried out on a Zorbax SB-CN column (5 microm, 4.6mm i.d. x 250 mm), considering hydrophilic interaction liquid chromatography (HILIC). Indeed, the mobile phase was made of methanol and 5mM ammonium hydrogen carbonate buffer at pH 7.5 (95/5, v/v). The detection was led at m/z ratios of 180.0 and 417.0, for GLcN and IS, respectively. Reliability of the results was demonstrated through the validation of the method using an approach based on the accuracy profile allowing managing the risk associated to the use of these methods in routine analysis: it is thus guaranteed that each future result will fall in the +/-30% acceptance limits with a probability of at least 90%. Successful application of the method to a preliminary pharmacokinetic study illustrated the usefulness of the method for pre-clinical studies.

  14. Combining DSMC Simulations and ROSINA/COPS Data of Comet 67P/Churyumov-Gerasimenko to Develop a Realistic Empirical Coma Model and to Determine Accurate Production Rates

    NASA Astrophysics Data System (ADS)

    Hansen, K. C.; Fougere, N.; Bieler, A. M.; Altwegg, K.; Combi, M. R.; Gombosi, T. I.; Huang, Z.; Rubin, M.; Tenishev, V.; Toth, G.; Tzou, C. Y.

    2015-12-01

    We have previously published results from the AMPS DSMC (Adaptive Mesh Particle Simulator Direct Simulation Monte Carlo) model and its characterization of the neutral coma of comet 67P/Churyumov-Gerasimenko through detailed comparison with data collected by the ROSINA/COPS (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis/COmet Pressure Sensor) instrument aboard the Rosetta spacecraft [Bieler, 2015]. Results from these DSMC models have been used to create an empirical model of the near comet coma (<200 km) of comet 67P. The empirical model characterizes the neutral coma in a comet centered, sun fixed reference frame as a function of heliocentric distance, radial distance from the comet, local time and declination. The model is a significant improvement over more simple empirical models, such as the Haser model. While the DSMC results are a more accurate representation of the coma at any given time, the advantage of a mean state, empirical model is the ease and speed of use. One use of such an empirical model is in the calculation of a total cometary coma production rate from the ROSINA/COPS data. The COPS data are in situ measurements of gas density and velocity along the ROSETTA spacecraft track. Converting the measured neutral density into a production rate requires knowledge of the neutral gas distribution in the coma. Our empirical model provides this information and therefore allows us to correct for the spacecraft location to calculate a production rate as a function of heliocentric distance. We will present the full empirical model as well as the calculated neutral production rate for the period of August 2014 - August 2015 (perihelion).

  15. Structure Determination of a Membrane Protein in Proteoliposomes

    PubMed Central

    Das, Bibhuti B.; Nothnagel, Henry J.; Lu, George J.; Son, Woo Sung; Tian, Ye; Marassi, Francesca M.; Opella, Stanley J.

    2012-01-01

    An NMR method for determining the three-dimensional structures of membrane proteins in proteoliposomes is demonstrated by determining the structure of MerFt, the 60-residue helix–loop–helix integral membrane core of the 81-residue mercury transporter MerF. The method merges elements of oriented sample (OS) solid-state NMR and magic angle spinning (MAS) solid-state NMR techniques to measure orientation restraints relative to a single external axis (the bilayer normal) from individual residues in a uniformly 13C/15N labeled protein in unoriented liquid crystalline phospholipid bilayers. The method relies on the fast (>105 Hz) rotational diffusion of membrane proteins in bilayers to average the static chemical shift anisotropy and heteronuclear dipole–dipole coupling powder patterns to axially symmetric powder patterns with reduced frequency spans. The frequency associated with the parallel edge of such motionally averaged powder patterns is exactly the same as that measured from the single line resonance in the spectrum of a stationary sample that is macroscopically aligned parallel to the direction of the applied magnetic field. All data are collected on unoriented samples undergoing MAS. Averaging of the homonuclear 13C/13C dipolar couplings, by MAS of the sample, enables the use of uniformly 13C/15N labeled proteins, which provides enhanced sensitivity through direct 13C detection as well as the use of multidimensional MAS solid-state NMR methods for resolving and assigning resonances. The unique feature of this method is the measurement of orientation restraints that enable the protein structure and orientation to be determined in unoriented proteoliposomes. PMID:22217388

  16. Structure Determination of Natural Products by Nuclear Magnetic Resonance Spectroscopy

    NASA Astrophysics Data System (ADS)

    Li, Du.

    High-field NMR experiments were used to determine the full structures of six new natural products extracted from plants. These are: four saponins (PT-2, P1, P2 and P3) from the plant Alphitonia zizyphoides found in Samoa; one sesquiterpene (DF-4) from Douglas fir and one diterpene derivative (E-2) from a Chinese medicinal herb. By concerted use of various 1D and 2D NMR techniques, the structures of the above compounds were established and complete resonance assignments were achieved. The 2D INADEQUATE technique coupled with a computerized spectral analysis was extensively used. When carried out on concentrations as low as 60 mg of sample, this technique provided absolute confirmation of the assignments for 35 of the possible 53 C-C bonds for PT-2. On 30 mg of sample of E-21, it revealed 22 of 28 possible C-C bonds.

  17. Theoretical challenge to the experimentally determined geometrical structure of dimethylsilaethylene

    SciTech Connect

    Yoshioka, Yasunori; Goddard, John D.; Schaefer, III, Henry F.

    1981-05-01

    The equilibrium geometries of (CH3)2Si=CH2 and H{2Si=CH2 have been determined at the self-consistent-field level of electronic structure theory using a double zeta basis set augmented with d functions on all heavy atoms. For the parent silaethylene, large scale configuration interaction (6920 configurations) demonstrates that electron correlation effects do not qualitatively alter the predicted structure. Because of this, it is concluded that the experimental electron diffraction geometry of Mahaffy, Gutowsky, and Montgomery is likely to be seriously incorrect. Specifically the theoretical prediction for the dimethylsilaethylene Si=C distance is 1.692 Å, while the range of experimental values presented was 1.815 - 1.835 Å.

  18. The determinants of health: structure, context and agency.

    PubMed

    Williams, Gareth H

    2003-01-01

    The concept of social structure is one of the main building blocks of the social sciences, but it lacks any precise technical definition within general sociological theory. This paper reviews the way in which the concept has been deployed within medical sociology, arguing that in recent times it has been used primarily as a frame for the sociological interpretation of health inequalities and their social determinants. It goes on to examine the contribution that medical sociologists have made to the debate over health inequalities, giving particular attention to contributions to Sociology of Health and Illness. These have often provided a focus for discussions outside or critical of the mainstream debates that have been driven primarily by epidemiologists. The paper reviews some of the main points of criticism of epidemiological approaches, focusing in particular on the methodological constraints that limit the capacity of epidemiologists to develop more theoretically satisfactory accounts of the inter-relationships of social structure, context and agency in their impact on health and well being. Some recent examples from the Journal of more theoretically innovative and analytically fine-grained approaches to understanding the impact of social structure on health are then explored. The paper concludes with an argument for a more historically-informed analysis of the relationships between social structure and health, using the knowledgeable narratives of people in places as a window onto those relationships. PMID:14498934

  19. Mathematical aspects of protein structure determination with NMR orientational restraints.

    PubMed

    Quine, J R; Cross, Timothy A; Chapman, Michael S; Bertram, Richard

    2004-11-01

    The field of structural biology is becoming increasingly important as new technological developments facilitate the collection of data on the atomic structures of proteins and nucleic acids. The solid-state NMR method is a relatively new biophysical technique that holds particular promise for determining the structures of peptides and proteins that are located within the cell membrane. This method provides information on the orientation of the peptide planes relative to an external magnetic field. In this article, we discuss some of the mathematical methods and tools that are useful in deriving the atomic structure from these orientational data. We first discuss how the data are viewed as tensors, and how these tensors can be used to construct an initial atomic model, assuming ideal stereochemistry. We then discuss methods for refining the models using global optimization, with stereochemistry constraints treated as penalty functions. These two processes, initial model building followed by refinement, are the two crucial steps between data collection and the final atomic model.

  20. Structural and energetic determinants of proton transfer in bacteriorhodopsin

    SciTech Connect

    Bondar, A.N.; Smith, Jeremy C; Fischer, S.

    2006-05-01

    In the light-driven bacteriorhodopsin proton pump, the first proton transfer step is from the retinal Schiff base to a nearby carboxylate group. The mechanism of this transfer step is highly controversial, in particular whether a direct proton jump is allowed. Here, we review the structural and energetic determinants of the direct proton transfer path computed by using a combined quantum mechanical/molecular mechanical approach. Both protein flexibility and electrostatic interactions play an important role in shaping the proton transfer energy profile. Detailed analysis of the energetics of putative transitions in the first half of the photocycle focuses on two elements that determine the likelihood that a given configuration of the active site is populated during the proton-pumping cycle. First, the rate-limiting barrier for proton transfer must be consistent with the kinetics of the photocycle. Second, the active-site configuration must be compatible with a productive overall pumping cycle.

  1. Shallow lunar structure determined from the passive seismic experiment

    NASA Technical Reports Server (NTRS)

    Nakamura, Y.; Dorman, J.; Duennebier, F.; Lammlein, D.; Latham, G.

    1975-01-01

    Data relevant to the shallow structure of the moon obtained at the Apollo seismic stations are compared with previously published results of the active seismic experiments. It is concluded that the lunar surface is covered by a layer of low seismic velocity which appears to be equivalent to the lunar regolith defined previously by geological observations. This layer is underlain by a zone of distinctly higher seismic velocity at all of the Apollo landing sites. The regolith thicknesses at the Apollo 11, 12, and 15 sites are estimated from the shear-wave resonance to be 4.4, 3.7, and 4.4 m, respectively. These thicknesses and those determined at the other Apollo sites by the active seismic experiments appear to be correlated with the age determinations and the abundances of extralunar components at the sites.

  2. Purification and primary structure determination of human lysosomal dipeptidase.

    PubMed

    Dolenc, Iztok; Mihelic, Marko

    2003-02-01

    The lysosomal metallopeptidase is an enzyme that acts preferentially on dipeptides with unsubstituted N- and C-termini. Its activity is highest in slightly acidic pH. Here we describe the isolation and characterization of lysosomal dipeptidase from human kidney. The isolated enzyme has the amino-terminal sequence DVAKAIINLAVY and is a homodimer with a molecular mass of 100 kDa. So far no amino acid sequence has been determined for this metallopeptidase. The complete primary structure as deduced from the nucleotide sequence revealed that the isolated dipeptidase is similar to blood plasma glutamate carboxypeptidase.

  3. Crystal structure determination of anti-DNA Fab A52.

    PubMed

    Stanfield, Robyn L; Eilat, Dan

    2014-08-01

    A52 is a murine monoclonal antibody isolated from autoimmune New Zealand Black/New Zealand White F1 mice that recognizes single and double stranded DNA. This mouse strain spontaneously develops systemic lupus erythematosus-like symptoms and has served as a model for that disease for many years. The 1.62 Å crystal structure of the A52 Fab fragment reveals an H3 complementarity determining region with four closely spaced arginine residues, creating a positively charged surface to accommodate bound DNA.

  4. Toward structure determination using membrane-protein nanocrystals and microcrystals

    PubMed Central

    Hunter, Mark S.; Fromme, Petra

    2012-01-01

    Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet brought fully-hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses (~ 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. During the initial experiments at the AMO beamline using 6.9-Å wavelength, Bragg peaks were recorded to 8.5-Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage [Chapman H.N., et al. Femtosecond X-ray protein nanocrystallography, Nature 470 (2011) 73–81]. Many additional techniques still need to be developed to explore the

  5. Accurate determination of ¹²⁹I concentrations and ¹²⁹I/¹³⁷Cs ratios in spent nuclear resins by Accelerator Mass Spectrometry.

    PubMed

    Nottoli, Emmanuelle; Bienvenu, Philippe; Labet, Alexandre; Bourlès, Didier; Arnold, Maurice; Bertaux, Maité

    2014-04-01

    Determining long-lived radionuclide concentrations in radioactive waste has fundamental implications for the long-term management of storage sites. This paper focuses on the measurement of low (129)I contents in ion exchange resins used for primary fluid purification in Pressurised Water Reactors (PWR). Iodine-129 concentrations were successfully determined using Accelerator Mass Spectrometry (AMS) following a chemical procedure which included (1) acid digestion of resin samples in HNO3/HClO4, (2) radioactive decontamination by selective iodine extraction using a new chromatographic resin (CL Resin), and (3) AgI precipitation. Measured (129)I concentrations ranged from 4 to 12 ng/g, i.e. from 0.03 to 0.08 Bq/g. The calculation of (129)I/(137)Cs activity ratios used for routine waste management produced values in agreement with the few available data for PWR resin samples. PMID:24525301

  6. Eddy current measurement system evaluation for corrosion depth determination on cast aluminum aircraft structure

    NASA Astrophysics Data System (ADS)

    Singh, Surendra; Greving, Dan; Kinney, Andy; Vensel, Fred; Ohm, Jim; Peeler, Mike

    2013-01-01

    An eddy current (EC) technique was developed to determine the corrosion depth on a bare flange face of a cast aluminum A356-T6 aircraft engine structure. The EC response and the corrosion depths determined through metallurgical cross sections were used to develop an empirical relation between EC response and depth. The EC technique and depth determination are used to inspect the engine structures during overhaul to determine if they are fit for continued service. An accurate and reliable Non-Destructive Inspection is required to ensure that structures returned to service are safe for continued operation. NDE system reliability demonstrations of the eddy current technique are traditionally reported in terms of Probability of Detection (POD) data using MIL-HDBK-1823A. However, the calculation of POD data is based on a simple linear predictive model that is valid only if certain criteria are met. These are: 1) NDE system response is measurable (i.e. continuous data), 2) Flaw size is known and measurable (i.e. continuous data), 3) relationship between the NDE system response and flaw size is linear (or linear on a log scale), 4) variation in measured responseresponse around a predicted response for a given flaw size is normally distributed, 5) the variation around the predicted response is constant (i.e. variation does not change with flaw size), and 6) inherent variability in the NDE system is known and fully understood. In this work, a Measurement System Evaluation (MSE) of the Eddy Current System was used to address some of these concerns. This work was completed on two aircraft structures having varying corrosion depths. The data were acquired in a random manner at fifty regions of interests (ROIs). Three operators participated in this study, and each operator measured Eddy Current response three times in each ROI. In total, there were four hundred and fifty data points collected. Following this, the two structures were sectioned for measuring corrosion depth. The

  7. Structural determinants of tobacco vein mottling virus protease substrate specificity

    SciTech Connect

    Sun, Ping; Austin, Brian P.; Tozer, Jozsef; Waugh, David

    2010-10-28

    Tobacco vein mottling virus (TVMV) is a member of the Potyviridae, one of the largest families of plant viruses. The TVMV genome is translated into a single large polyprotein that is subsequently processed by three virally encoded proteases. Seven of the nine cleavage events are carried out by the NIa protease. Its homolog from the tobacco etch virus (TEV) is a widely used reagent for the removal of affinity tags from recombinant proteins. Although TVMV protease is a close relative of TEV protease, they exhibit distinct sequence specificities. We report here the crystal structure of a catalytically inactive mutant TVMV protease (K65A/K67A/C151A) in complex with a canonical peptide substrate (Ac-RETVRFQSD) at 1.7-{angstrom} resolution. As observed in several crystal structures of TEV protease, the C-terminus ({approx}20 residues) of TVMV protease is disordered. Unexpectedly, although deleting the disordered residues from TEV protease reduces its catalytic activity by {approx}10-fold, an analogous truncation mutant of TVMV protease is significantly more active. Comparison of the structures of TEV and TVMV protease in complex with their respective canonical substrate peptides reveals that the S3 and S4 pockets are mainly responsible for the differing substrate specificities. The structure of TVMV protease suggests that it is less tolerant of variation at the P1{prime} position than TEV protease. This conjecture was confirmed experimentally by determining kinetic parameters k{sub cat} and K{sub m} for a series of oligopeptide substrates. Also, as predicted by the cocrystal structure, we confirm that substitutions in the P6 position are more readily tolerated by TVMV than TEV protease.

  8. Application of double-spike isotope dilution for the accurate determination of Cr(III), Cr(VI) and total Cr in yeast.

    PubMed

    Yang, Lu; Ciceri, Elena; Mester, Zoltán; Sturgeon, Ralph E

    2006-11-01

    A method is presented for the simultaneous determination of Cr(III) and Cr(VI) in yeast using species-specific double-spike isotope dilution (SSDSID) with anion-exchange liquid chromatography (LC) separation and sector field inductively coupled plasma mass spectrometric (SF-ICP-MS) detection. Total Cr is quantitated using ID SF-ICP-MS. Samples were digested on a hot plate at 95+/-2 degrees C for 6 h in an alkaline solution of 0.5 M NaOH and 0.28 M Na2CO3 for the determination of Cr(III) and Cr(VI), whereas microwave-assisted decomposition with HNO3 and H2O2 was used for the determination of total Cr. Concentrations of 2,014+/-16, 1,952+/-103 and 76+/-48 mg kg-1 (one standard deviation, n=4, 3, 3), respectively were obtained for total Cr, Cr(III) and Cr(VI) in the yeast sample. Significant oxidation of Cr(III) to Cr(VI) (24.2+/-7.6% Cr(III) oxidized, n=3) and reduction of Cr(VI) to Cr(III) (37.6+/-6.5% Cr(VI) reduced, n=3) occurred during alkaline extraction and subsequent chromatographic separation at pH 7. Despite this significant bidirectional redox transformation, quantitative recoveries for both Cr(III) and Cr(VI) were achieved using the SSDSID method. In addition, mass balance between total Cr and the sum of Cr(III) and Cr(VI) concentrations was achieved. Method detection limits of 0.3, 2 and 30 mg kg-1 were obtained for total Cr, Cr(VI) and Cr(III), respectively, based on a 0.2-g sub-sample.

  9. Distribution of nuclear bomb Pu in Nishiyama area, Nagasaki, estimated by accurate and precise determination of 240Pu/239Pu ratio in soils.

    PubMed

    Yoshida, S; Muramatsu, Y; Yamazaki, S; Ban-Nai, T

    2007-01-01

    Plutonium isotopes in forest soils collected in Nishiyama area, Nagasaki, were successfully determined by high resolution inductively coupled plasma mass spectrometry after the treatment with a microwave decomposition system. The (240)Pu/(239)Pu atom ratios observed in the samples in the Nishiyama area were obviously lower than the range of the global fallout. The low ratios (minimum 0.032) observed in Nishiyama area indicated the influence of detonation of the Pu nuclear weapon in 1945. Since the area is contaminated also by global fallout, the (240)Pu/(239)Pu atom ratio can be more sensitive indicator of bomb-derived Pu than Pu activity concentration.

  10. Accurate determination of 2,4,6-trichloroanisole in wines at low parts per trillion by solid-phase microextraction followed by GC-ECD.

    PubMed

    Alzaga, Roberto; Ortiz, Laura; Sánchez-Baeza, Francisco; Marco, M-Pilar; Bayona, Josep Maria

    2003-06-01

    A headspace solid-phase microextraction (HS-SPME) procedure at 30 degrees C with a 100 microm PDMS fiber of a saturated NaCl solution stirred at 1100 rpm combined to GC-ECD for the 2,4,6-trichloroanisol (TCA) determination in wines has been developed. Due to the matrix complexity and ethanol absorption into the fiber, the internal standard selection was crucial to obtain unbiased results. Thus, matrix effects were observed when analyzing different types of Spanish wines (white, early, and vintage red wines) spiked with TCA at low concentration levels (i.e., <40 ng L(-)(1)). In contrast, the use of 2,4,6-tribromoanisole (TBA) as internal standard overcame these matrix effects, whereas the use of 2,4,6-trichlorophenyl ethyl ether led to inconsistent results. The developed HS-SPME-GC-ECD methodology reaches a limit of quantitation for TCA in wine within 2.9-18 ng L(-)(1), with a relative standard deviation of 2.5-13.4%, depending on the TCA concentration level and wine characteristics. This analytical method is comparable to the existing methodologies based on HS-SPME followed by GC-MS in terms of accuracy, precision, length of determination, and length of quantification; however, analysis cost is reduced.

  11. Accurate determination of the anisotropy factors and the phase differences of Raman polarizabilities in some uniaxial crystals: the case of lithium niobate.

    PubMed

    Djiedeu, N; Mohamadou, B; Bourson, P; Aillerie, M

    2009-01-01

    The present study highlights self-consistently helpful improvements dedicated to overcoming the difficulty resulting from the fitting procedure of integrated Raman intensities recorded according to the rotation crystal method described earlier. To this end, the anisotropy factors of Raman polarizabilities and the corresponding relative phases are determined within the framework of the exact mathematical derivation of the phase factors. These are the relevant parameters of the Raman efficiency relations which are numerically difficult to obtain from the fitting of the integrated areas. The present theoretical approach is then applied to the modes of the A(1) and Ey symmetry species of the lithium niobate (LN) crystal point group. All the expressions of the Raman absolute intensities of the A(1) and Ey irreducible representations initially imply three parameters to be determined from the fitting computations. However, from the derived analytical expressions of the phase differences, the number of parameters involved in the fitting procedure is reduced from 3 to 2, thus improving the statistics of the numerical treatment.

  12. Simple surface structure determination from Fourier transforms of angle-resolved photoemission extended fine structure

    SciTech Connect

    Zheng, Y. |; Shirley, D.A.

    1995-02-01

    The authors show by Fourier analyses of experimental data, with no further treatment, that the positions of all the strong peaks in Fourier transforms of angle-resolved photoemission extended fine structure (ARPEFS) from adsorbed surfaces can be explicitly predicted from a trial structure with an accuracy of about {+-} 0.3 {angstrom} based on a single-scattering cluster model together with the concept of a strong backscattering cone, and without any additional analysis. This characteristic of ARPEFS Fourier transforms can be developed as a simple method for determining the structures of adsorbed surfaces to an accuracy of about {+-} 0.1 {angstrom}.

  13. New methods of structure refinement for macromolecular structure determination by NMR

    PubMed Central

    Clore, G. Marius; Gronenborn, Angela M.

    1998-01-01

    Recent advances in multidimensional NMR methodology have permitted solution structures of proteins in excess of 250 residues to be solved. In this paper, we discuss several methods of structure refinement that promise to increase the accuracy of macromolecular structures determined by NMR. These methods include the use of a conformational database potential and direct refinement against three-bond coupling constants, secondary 13C shifts, 1H shifts, T1/T2 ratios, and residual dipolar couplings. The latter two measurements provide long range restraints that are not accessible by other solution NMR parameters. PMID:9600889

  14. Structures of Large RNAs and RNA-Protein Complexes: Toward Structure Determination of Riboswitches.

    PubMed

    Grigg, Jason C; Ke, Ailong

    2015-01-01

    Riboswitches are widespread and important regulatory elements. They are typically present in the mRNA of the gene under their regulation, where they form complex three-dimensional structures that can bind an effector and regulate either transcription or translation of the mRNA. Structural biology has been essential to our understanding of their ligand recognition and conformational switching mechanisms, but riboswitch determination presents several important complications. Overcoming these challenges requires a synergistic approach using rational design of the constructs and supporting methods to biochemically validate the designs and resulting structures. PMID:26068743

  15. Feasibility of ultra-high performance liquid and gas chromatography coupled to mass spectrometry for accurate determination of primary and secondary phthalate metabolites in urine samples.

    PubMed

    Herrero, Laura; Calvarro, Sagrario; Fernández, Mario A; Quintanilla-López, Jesús Eduardo; González, María José; Gómara, Belén

    2015-01-01

    Phthalates (PAEs) are ubiquitous toxic chemical compounds. During the last few years, some phthalate metabolites (MPAEs) have been proposed as appropriate biomarkers in human urine samples to determine PAE human intake and exposure. So, it is necessary to have fast, easy, robust and validated analytical methods to determine selected MPAEs in urine human samples. Two different instrumental methods based on gas (GC) and ultra-high performance liquid (UHPLC) chromatography coupled to mass spectrometry (MS) have been optimized, characterized and validated for the simultaneous determination of nine primary and secondary phthalate metabolites in urine samples. Both instrumental methods have similar sensitivity (detection limits ranged from 0.03 to 8.89 pg μL(-1) and from 0.06 to 0.49 pg μL(-1) in GC-MS and UHPLC-MS(2), respectively), precision (repeatability, expressed as relative standard deviation, which was lower than 8.4% in both systems, except for 5OH-MEHP in the case of GC-MS) and accuracy. But some advantages of the UHPLC-MS(2) method, such as more selectivity and lower time in the chromatographic runs (6.8 min vs. 28.5 min), have caused the UHPLC-MS(2) method to be chosen to analyze the twenty one human urine samples from the general Spanish population. Regarding these samples, MEP showed the highest median concentration (68.6 μg L(-1)), followed by MiBP (23.3 μg L(-1)), 5cx-MEPP (22.5 μg L(-1)) and MBP (19.3μgL(-1)). MMP (6.99 μg L(-1)), 5oxo-MEHP (6.15 μg L(-1)), 5OH-MEHP (5.30 μg L(-1)) and MEHP (4.40 μg L(-1)) showed intermediate levels. Finally, the lowest levels were found for MBzP (2.55 μg L(-1)). These data are within the same order of magnitude as those found in other similar populations. PMID:25467512

  16. Feasibility of ultra-high performance liquid and gas chromatography coupled to mass spectrometry for accurate determination of primary and secondary phthalate metabolites in urine samples.

    PubMed

    Herrero, Laura; Calvarro, Sagrario; Fernández, Mario A; Quintanilla-López, Jesús Eduardo; González, María José; Gómara, Belén

    2015-01-01

    Phthalates (PAEs) are ubiquitous toxic chemical compounds. During the last few years, some phthalate metabolites (MPAEs) have been proposed as appropriate biomarkers in human urine samples to determine PAE human intake and exposure. So, it is necessary to have fast, easy, robust and validated analytical methods to determine selected MPAEs in urine human samples. Two different instrumental methods based on gas (GC) and ultra-high performance liquid (UHPLC) chromatography coupled to mass spectrometry (MS) have been optimized, characterized and validated for the simultaneous determination of nine primary and secondary phthalate metabolites in urine samples. Both instrumental methods have similar sensitivity (detection limits ranged from 0.03 to 8.89 pg μL(-1) and from 0.06 to 0.49 pg μL(-1) in GC-MS and UHPLC-MS(2), respectively), precision (repeatability, expressed as relative standard deviation, which was lower than 8.4% in both systems, except for 5OH-MEHP in the case of GC-MS) and accuracy. But some advantages of the UHPLC-MS(2) method, such as more selectivity and lower time in the chromatographic runs (6.8 min vs. 28.5 min), have caused the UHPLC-MS(2) method to be chosen to analyze the twenty one human urine samples from the general Spanish population. Regarding these samples, MEP showed the highest median concentration (68.6 μg L(-1)), followed by MiBP (23.3 μg L(-1)), 5cx-MEPP (22.5 μg L(-1)) and MBP (19.3μgL(-1)). MMP (6.99 μg L(-1)), 5oxo-MEHP (6.15 μg L(-1)), 5OH-MEHP (5.30 μg L(-1)) and MEHP (4.40 μg L(-1)) showed intermediate levels. Finally, the lowest levels were found for MBzP (2.55 μg L(-1)). These data are within the same order of magnitude as those found in other similar populations.

  17. Size and concentration determination of (functionalised) fullerenes in surface and sewage water matrices using field flow fractionation coupled to an online accurate mass spectrometer: method development and validation.

    PubMed

    Herrero, Pol; Bäuerlein, Patrick S; Emke, Erik; Marcé, Rosa M; de Voogt, Pim

    2015-04-29

    In order to assess the environmental risks of a compound it is imperative to have suitable and reliable techniques for its determination in environmental matrices. In this paper, we focused on a method development for the recently introduced online coupling of a field flow fractionation (FFF) system to an Orbitrap-HRMS, that allows the simultaneous size and concentration determination of different aqueous fullerene aggregates and their concentrations in different size fractions. A 0.05% NH4OH solution in water was identified as the best carrier liquid for the analysis of the three different aqueous fullerene suspensions (C60 [60], [6,6]-phenyl-C61 butyric acid methyl ester ([60]PCBM) and [6,6]-(bis)phenyl-C61 butyric acid methyl ester ([60]bisPCBM)). The multi-angle light scattering (MALS) data received after employing the ammonia solution was consistent with both the theory and calibration using well defined Au and latex particles. The LODs obtained using Orbitrap HRMS detection were 0.1 μg L(-1) for an injection volume of 100 μL which are significantly better than the LODs obtained by using UV (20 μg L(-1)) and MALS detectors (5 μg L(-1)). However, these LODs can be further improved as in theory there is no limit to the amount of sample that can be injected into the FFF. Environmental samples (river and sewage water) were spiked with fullerenes and the fractograms obtained for these samples revealed that the matrix does affect the size of fullerene aggregates. Information on the size distribution can be useful for the risk assessment of these particles.

  18. WE-E-18A-03: How Accurately Can the Peak Skin Dose in Fluoroscopy Be Determined Using Indirect Dose Metrics?

    SciTech Connect

    Jones, A; Pasciak, A

    2014-06-15

    Purpose: Skin dosimetry is important for fluoroscopically-guided interventions, as peak skin doses (PSD) that Result in skin reactions can be reached during these procedures. The purpose of this study was to assess the accuracy of different indirect dose estimates and to determine if PSD can be calculated within ±50% for embolization procedures. Methods: PSD were measured directly using radiochromic film for 41 consecutive embolization procedures. Indirect dose metrics from procedures were collected, including reference air kerma (RAK). Four different estimates of PSD were calculated and compared along with RAK to the measured PSD. The indirect estimates included a standard method, use of detailed information from the RDSR, and two simplified calculation methods. Indirect dosimetry was compared with direct measurements, including an analysis of uncertainty associated with film dosimetry. Factors affecting the accuracy of the indirect estimates were examined. Results: PSD calculated with the standard calculation method were within ±50% for all 41 procedures. This was also true for a simplified method using a single source-to-patient distance (SPD) for all calculations. RAK was within ±50% for all but one procedure. Cases for which RAK or calculated PSD exhibited large differences from the measured PSD were analyzed, and two causative factors were identified: ‘extreme’ SPD and large contributions to RAK from rotational angiography or runs acquired at large gantry angles. When calculated uncertainty limits [−12.8%, 10%] were applied to directly measured PSD, most indirect PSD estimates remained within ±50% of the measured PSD. Conclusions: Using indirect dose metrics, PSD can be determined within ±50% for embolization procedures, and usually to within ±35%. RAK can be used without modification to set notification limits and substantial radiation dose levels. These results can be extended to similar procedures, including vascular and interventional oncology

  19. Nanoscale structural features determined by AFM for single virus particles.

    PubMed

    Chen, Shu-wen W; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc

    2013-11-21

    In this work, we propose "single-image analysis", as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis. PMID:24056758

  20. More accurate determination of the quantity of ice crystallized at low cooling rates in the glycerol and 1,2-propanediol aqueous solutions: comparison with equilibrium.

    PubMed

    Boutron, P

    1984-04-01

    It is generally assumed that when cells are cooled at rates close to those corresponding to the maximum of survival, once supercooling has ceased, above the eutectic melting temperature the extracellular ice is in equilibrium with the residual solution. This did not seem evident to us due to the difficulty of ice crystallization in cryoprotective solutions. The maximum quantities of ice crystallized in glycerol and 1,2-propanediol solutions have been calculated from the area of the solidification and fusion peaks obtained with a Perkin-Elmer DSC-2 differential scanning calorimeter. The accuracy has been improved by several corrections: better defined baseline, thermal variation of the heat of fusion of the ice, heat of solution of the water from its melting with the residual solution. More ice crystallizes in the glycerol than in the 1,2-propanediol solutions, of which the amorphous residue contains about 40 to 55% 1,2-propanediol. The equilibrium values are unknown in the presence of 1,2-propanediol. With glycerol, in our experiments, the maximum is first lower than the equilibrium but approaches it as the concentration increases. It is not completely determined by the colligative properties of the solutes.

  1. Optimization of Stripping Voltammetric Sensor by a Back Propagation Artificial Neural Network for the Accurate Determination of Pb(II) in the Presence of Cd(II)

    PubMed Central

    Zhao, Guo; Wang, Hui; Liu, Gang; Wang, Zhiqiang

    2016-01-01

    An easy, but effective, method has been proposed to detect and quantify the Pb(II) in the presence of Cd(II) based on a Bi/glassy carbon electrode (Bi/GCE) with the combination of a back propagation artificial neural network (BP-ANN) and square wave anodic stripping voltammetry (SWASV) without further electrode modification. The effects of Cd(II) in different concentrations on stripping responses of Pb(II) was studied. The results indicate that the presence of Cd(II) will reduce the prediction precision of a direct calibration model. Therefore, a two-input and one-output BP-ANN was built for the optimization of a stripping voltammetric sensor, which considering the combined effects of Cd(II) and Pb(II) on the SWASV detection of Pb(II) and establishing the nonlinear relationship between the stripping peak currents of Pb(II) and Cd(II) and the concentration of Pb(II). The key parameters of the BP-ANN and the factors affecting the SWASV detection of Pb(II) were optimized. The prediction performance of direct calibration model and BP-ANN model were tested with regard to the mean absolute error (MAE), root mean square error (RMSE), average relative error (ARE), and correlation coefficient. The results proved that the BP-ANN model exhibited higher prediction accuracy than the direct calibration model. Finally, a real samples analysis was performed to determine trace Pb(II) in some soil specimens with satisfactory results. PMID:27657083

  2. Structure determination of trans-cinnamaldehyde by broadband microwave spectroscopy.

    PubMed

    Zinn, Sabrina; Betz, Thomas; Medcraft, Chris; Schnell, Melanie

    2015-06-28

    The rotational spectrum of trans-cinnamaldehyde ((E)-3-phenyl-2-propenal, C9H8O) was recorded by chirped-pulse Fourier transform microwave spectroscopy in the frequency range of 2-8.5 GHz. The odourant molecule is the essential component of cinnamon oil and causes the characteristic smell. The rotational signatures of two conformers were observed: s-trans-trans- and s-cis-trans-cinnamaldehyde. The rotational spectra of s-trans-trans-cinnamaldehyde and all of its (13)C-monosubstituted species in natural abundance were assigned and the corresponding carbon backbone structure was determined. The second conformer s-cis-trans-cinnamaldehyde is about 9 kJ mol(-1) higher in energy and could also be identified in the spectrum.

  3. Annular dark field transmission electron microscopy for protein structure determination.

    PubMed

    Koeck, Philip J B

    2016-02-01

    Recently annular dark field (ADF) transmission electron microscopy (TEM) has been advocated as a means of recording images of biological specimens with better signal to noise ratio (SNR) than regular bright field images. I investigate whether and how such images could be used to determine the three-dimensional structure of proteins given that an ADF aperture with a suitable pass-band can be manufactured and used in practice. I develop an approximate theory of ADF-TEM image formation for weak amplitude and phase objects and test this theory using computer simulations. I also test whether these simulated images can be used to calculate a three-dimensional model of the protein using standard software and discuss problems and possible ways to overcome these. PMID:26656466

  4. Shape determination and control for large space structures

    NASA Technical Reports Server (NTRS)

    Weeks, C. J.

    1981-01-01

    An integral operator approach is used to derive solutions to static shape determination and control problems associated with large space structures. Problem assumptions include a linear self-adjoint system model, observations and control forces at discrete points, and performance criteria for the comparison of estimates or control forms. Results are illustrated by simulations in the one dimensional case with a flexible beam model, and in the multidimensional case with a finite model of a large space antenna. Modal expansions for terms in the solution algorithms are presented, using modes from the static or associated dynamic mode. These expansions provide approximated solutions in the event that a used form analytical solution to the system boundary value problem is not available.

  5. Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity

    SciTech Connect

    Pruitt, Rory N.; Chumbler, Nicole M.; Rutherford, Stacey A.; Farrow, Melissa A.; Friedman, David B.; Spiller, Ben; Lacy, D. Borden

    2012-03-28

    The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.

  6. Novel, Precise, Accurate Ion-Pairing Method to Determine the Related Substances of the Fondaparinux Sodium Drug Substance: Low-Molecular-Weight Heparin

    PubMed Central

    Deshpande, Amol A.; Madhavan, P.; Deshpande, Girish R.; Chandel, Ravi Kumar; Yarbagi, Kaviraj M.; Joshi, Alok R.; Moses Babu, J.; Murali Krishna, R.; Rao, I. M.

    2016-01-01

    Fondaparinux sodium is a synthetic low-molecular-weight heparin (LMWH). This medication is an anticoagulant or a blood thinner, prescribed for the treatment of pulmonary embolism and prevention and treatment of deep vein thrombosis. Its determination in the presence of related impurities was studied and validated by a novel ion-pair HPLC method. The separation of the drug and its degradation products was achieved with the polymer-based PLRPs column (250 mm × 4.6 mm; 5 μm) in gradient elution mode. The mixture of 100 mM n-hexylamine and 100 mM acetic acid in water was used as buffer solution. Mobile phase A and mobile phase B were prepared by mixing the buffer and acetonitrile in the ratio of 90:10 (v/v) and 20:80 (v/v), respectively. Mobile phases were delivered in isocratic mode (2% B for 0–5 min) followed by gradient mode (2–85% B in 5–60 min). An Evaporative Light Scattering Detector (ELSD) was connected to the LC system to detect the responses of chromatographic separation. Further, the drug was subjected to stress studies for acidic, basic, oxidative, photolytic, and thermal degradations as per ICH guidelines and the drug was found to be labile in acid, base hydrolysis, and oxidation, while stable in neutral, thermal, and photolytic degradation conditions. The method provided linear responses over the concentration range of the LOQ to 0.30% for each impurity with respect to the analyte concentration of 12.5 mg/mL, and regression analysis showed a correlation coefficient value (r2) of more than 0.99 for all the impurities. The LOD and LOQ were found to be 1.4 µg/mL and 4.1 µg/mL, respectively, for fondaparinux. The developed ion-pair method was validated as per ICH guidelines with respect to accuracy, selectivity, precision, linearity, and robustness. PMID:27110496

  7. Novel, Precise, Accurate Ion-Pairing Method to Determine the Related Substances of the Fondaparinux Sodium Drug Substance: Low-Molecular-Weight Heparin.

    PubMed

    Deshpande, Amol A; Madhavan, P; Deshpande, Girish R; Chandel, Ravi Kumar; Yarbagi, Kaviraj M; Joshi, Alok R; Moses Babu, J; Murali Krishna, R; Rao, I M

    2016-01-01

    Fondaparinux sodium is a synthetic low-molecular-weight heparin (LMWH). This medication is an anticoagulant or a blood thinner, prescribed for the treatment of pulmonary embolism and prevention and treatment of deep vein thrombosis. Its determination in the presence of related impurities was studied and validated by a novel ion-pair HPLC method. The separation of the drug and its degradation products was achieved with the polymer-based PLRPs column (250 mm × 4.6 mm; 5 μm) in gradient elution mode. The mixture of 100 mM n-hexylamine and 100 mM acetic acid in water was used as buffer solution. Mobile phase A and mobile phase B were prepared by mixing the buffer and acetonitrile in the ratio of 90:10 (v/v) and 20:80 (v/v), respectively. Mobile phases were delivered in isocratic mode (2% B for 0-5 min) followed by gradient mode (2-85% B in 5-60 min). An Evaporative Light Scattering Detector (ELSD) was connected to the LC system to detect the responses of chromatographic separation. Further, the drug was subjected to stress studies for acidic, basic, oxidative, photolytic, and thermal degradations as per ICH guidelines and the drug was found to be labile in acid, base hydrolysis, and oxidation, while stable in neutral, thermal, and photolytic degradation conditions. The method provided linear responses over the concentration range of the LOQ to 0.30% for each impurity with respect to the analyte concentration of 12.5 mg/mL, and regression analysis showed a correlation coefficient value (r(2)) of more than 0.99 for all the impurities. The LOD and LOQ were found to be 1.4 µg/mL and 4.1 µg/mL, respectively, for fondaparinux. The developed ion-pair method was validated as per ICH guidelines with respect to accuracy, selectivity, precision, linearity, and robustness. PMID:27110496

  8. Protein structure determination with paramagnetic solid-state NMR spectroscopy.

    PubMed

    Sengupta, Ishita; Nadaud, Philippe S; Jaroniec, Christopher P

    2013-09-17

    Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2

  9. The Structural Determinants behind the Epigenetic Role of Histone Variants

    PubMed Central

    Cheema, Manjinder S.; Ausió, Juan

    2015-01-01

    Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism. PMID:26213973

  10. Comparison of different torsion angle approaches for NMR structure determination.

    PubMed

    Bardiaux, Benjamin; Malliavin, Thérèse E; Nilges, Michael; Mazur, Alexey K

    2006-03-01

    A new procedure for NMR structure determination, based on the Internal Coordinate Molecular Dynamics (ICMD) approach, is presented. The method finds biopolymer conformations that satisfy usual NMR-derived restraints by using high temperature dynamics in torsion angle space. A variable target function algorithm gradually increases the number of NOE-based restraints applied, with the treatment of ambiguous and floating restraints included. This soft procedure allows combining artificially high temperature with a general purpose force-field including Coulombic and Lennard-Jones non-bonded interactions, which improves the quality of the ensemble of conformations obtained in the gas-phase. The new method is compared to existing algorithms by using the structures of eight ribosomal proteins earlier obtained with state-of-the-art procedures and included into the RECOORD database [Nederveen, A., Doreleijers, J., Vranken, W., Miller, Z., Spronk, C., Nabuurs, S., Guntert, P., Livny, M., Markley, M., Nilges, M., Ulrich, E., Kaptein, R. and Bonvin, A.M. (2005) Proteins, 59, 662-672]. For the majority of tested proteins, the ICMD algorithm shows similar convergence and somewhat better quality Z scores for the phi, psi distributions. The new method is more computationally demanding although the overall load is reasonable.

  11. Determining the structure of supersymmetry breaking with renormalization group invariants

    SciTech Connect

    Carena, Marcela; Draper, Patrick; Shah, Nausheen R.; Wagner, Carlos E. M.

    2010-10-01

    If collider experiments demonstrate that the minimal supersymmetric standard model (MSSM) is a good description of nature at the weak scale, the experimental priority will be the precise determination of superpartner masses. These masses are governed by the weak scale values of the soft supersymmetry-breaking (SUSY-breaking) parameters, which are in turn highly dependent on the SUSY-breaking scheme present at high scales. It is therefore of great interest to find patterns in the soft parameters that can distinguish different high-scale SUSY-breaking structures, identify the scale at which the breaking is communicated to the visible sector, and determine the soft breaking parameters at that scale. In this work, we demonstrate that 1-loop renormalization group invariant quantities present in the MSSM may be used to answer each of these questions. We apply our method first to generic flavor-blind models of SUSY breaking, and then we examine in detail the subset of these models described by general gauge mediation and the constrained MSSM with nonuniversal Higgs masses. As renormalization group invariance generally does not hold beyond leading-log order, we investigate the magnitude and direction of the 2-loop corrections. We find that with superpartners at the TeV scale, these 2-loop effects are either negligible, or they are of the order of optimistic experimental uncertainties and have definite signs, which allows them to be easily accounted for in the overall uncertainty.

  12. Determination of the object surface function by structured light: application to the study of spinal deformities

    NASA Astrophysics Data System (ADS)

    Buendía, M.; Salvador, R.; Cibrián, R.; Laguia, M.; Sotoca, J. M.

    1999-01-01

    The projection of structured light is a technique frequently used to determine the surface shape of an object. In this paper, a new procedure is described that efficiently resolves the correspondence between the knots of the projected grid and those obtained on the object when the projection is made. The method is based on the use of three images of the projected grid. In two of them the grid is projected over a flat surface placed, respectively, before and behind the object; both images are used for calibration. In the third image the grid is projected over the object. It is not reliant on accurate determination of the camera and projector pair relative to the grid and object. Once the method is calibrated, we can obtain the surface function by just analysing the projected grid on the object. The procedure is especially suitable for the study of objects without discontinuities or large depth gradients. It can be employed for determining, in a non-invasive way, the patient's back surface function. Symmetry differences permit a quantitative diagnosis of spinal deformities such as scoliosis.

  13. The Devil is in the Details: Using X-Ray Computed Tomography to Develop Accurate 3D Grain Characteristics and Bed Structure Metrics for Gravel Bed Rivers

    NASA Astrophysics Data System (ADS)

    Voepel, H.; Hodge, R. A.; Leyland, J.; Sear, D. A.; Ahmed, S. I.

    2014-12-01

    Uncertainty for bedload estimates in gravel bed rivers is largely driven by our inability to characterize the arrangement and orientation of the sediment grains within the bed. The characteristics of the surface structure are produced by the water working of grains, which leads to structural differences in bedforms through differential patterns of grain sorting, packing, imbrication, mortaring and degree of bed armoring. Until recently the technical and logistical difficulties of characterizing the arrangement of sediment in 3D have prohibited a full understanding of how grains interact with stream flow and the feedback mechanisms that exist. Micro-focus X-ray CT has been used for non-destructive 3D imaging of grains within a series of intact sections of river bed taken from key morphological units (see Figure 1). Volume, center of mass, points of contact, protrusion and spatial orientation of individual surface grains are derived from these 3D images, which in turn, facilitates estimates of 3D static force properties at the grain-scale such as pivoting angles, buoyancy and gravity forces, and grain exposure. By aggregating representative samples of grain-scale properties of localized interacting sediment into overall metrics, we can compare and contrast bed stability at a macro-scale with respect to stream bed morphology. Understanding differences in bed stability through representative metrics derived at the grain-scale will ultimately lead to improved bedload estimates with reduced uncertainty and increased understanding of interactions between grain-scale properties on channel morphology. Figure 1. CT-Scans of a water worked gravel-filled pot. a. 3D rendered scan showing the outer mesh, and b. the same pot with the mesh removed. c. vertical change in porosity of the gravels sampled in 5mm volumes. Values are typical of those measured in the field and lab. d. 2-D slices through the gravels at 20% depth from surface (porosity = 0.35), and e. 75% depth from

  14. Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles.

    PubMed

    Singharoy, Abhishek; Venkatakrishnan, Balasubramanian; Liu, Yun; Mayne, Christopher G; Lee, Semin; Chen, Chun-Hsing; Zlotnick, Adam; Schulten, Klaus; Flood, Amar H

    2015-07-15

    Crystal structure determination has long provided insight into structure and bonding of small molecules. When those same small molecules are designed to come together in multimolecular assemblies, such as in coordination cages, supramolecular architectures and organic-based frameworks, their crystallographic characteristics closely resemble biological macromolecules. This resemblance suggests that biomacromolecular refinement approaches be used for structure determination of abiological molecular complexes that arise in an aggregate state. Following this suggestion we investigated the crystal structure of a pentagonal macrocycle, cyanostar, by means of biological structure analysis methods and compared results to traditional small molecule methods. Cyanostar presents difficulties seen in supramolecular crystallography including whole molecule disorder and highly flexible solvent molecules sitting in macrocyclic and intermolecule void spaces. We used the force-field assisted refinement method, molecular dynamics flexible fitting algorithm for X-ray crystallography (xMDFF), along with tools from the macromolecular structure determination suite PHENIX. We found that a standard implementation of PHENIX, namely one without xMDFF, either fails to produce a solution by molecular replacement alone or produces an inaccurate structure when using generic geometry restraints, even at a very high diffraction data resolution of 0.84 Å. The problems disappear when taking advantage of xMDFF, which applies an optimized force field to realign molecular models during phasing by providing accurate restraints. The structure determination for this model system shows excellent agreement with the small-molecule methods. Therefore, the joint xMDFF-PHENIX refinement protocol provides a new strategy that uses macromolecule methods for structure determination of small molecules and their assemblies. PMID:26121416

  15. Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles

    PubMed Central

    Singharoy, Abhishek; Venkatakrishnan, Balasubramanian; Liu, Yun; Mayne, Christopher G.; Lee, Semin; Chen, Chun-Hsing; Zlotnick, Adam; Schulten, Klaus; Flood, Amar H.

    2015-01-01

    Crystal structure determination has long provided insight into structure and bonding of small molecules. When those same small molecules are designed to come together in multi-molecular assemblies, such as in coordination cages, supramolecular architectures and organic-based frameworks, their crystallographic characteristics closely resemble biological macromolecules. This resemblance suggests that bio-macromolecular refinement approaches be used for structure determination of abiological molecular complexes that arise in an aggregate state. Following this suggestion we investigated the crystal structure of a pentagonal macrocycle, cyanostar, by means of biological structure analysis methods and compared results to traditional small molecule methods. Cyanostar presents difficulties seen in supramolecular crystallography including whole molecule disorder and highly flexible solvent molecules sitting in macrocyclic and intermolecule void spaces. We used the force-field assisted refinement method, molecular dynamics flexible fitting algorithm for X-ray crystallography (xMDFF), along with tools from the macromolecular structure determination suite PHENIX. We found that a standard implementation of PHENIX, namely one without xMDFF, either fails to produce a solution by molecular replacement alone or produces an inaccurate structure when using generic geometry restraints, even at a very high diffraction data resolution of 0.84 Å. The problems disappear when taking advantage of xMDFF, which applies an optimized force field to re-align molecular models during phasing by providing accurate restraints. The structure determination for this model system shows excellent agreement with the small-molecule methods. Therefore, the joint xMDFF-PHENIX refinement protocol provides a new strategy that uses macromolecule methods for structure determination of small molecules and their assemblies. PMID:26121416

  16. A facile method to determine the absolute structure of achiral molecules: supramolecular-tilt structures.

    PubMed

    Tejedor, Rosa María; Uriel, Santiago; Graus, Sara; Sierra, Teresa; Serrano, José Luis; Claramunt, Rosa M; López, Concepción; Pérez-Torralba, Marta; Alkorta, Ibon; Elguero, José

    2013-05-01

    Achiral compounds 4-methoxy-4-(p-methoxyphenyl)cyclohexanoneethylene ketal (2), 4-hydroxy-4-(p-methoxy phenyl)cyclohexanoneethylene ketal (3), and 3,5-dimethyl-4-nitropyrazole (4) crystallized in chiral structures and the samples showed an enantiomeric excess. We have determined the absolute structures of these compounds by using X-ray diffraction with copper radiation at low temperatures. Moreover, we have also established the prevalent absolute structures in these samples, by comparing their calculated and solid-state vibrational circular dichroism (VCD) spectra. The consistency of this method was confirmed by using (R,R)-2,8-diiodo-4,10-dimethyl-6 H,12H-5,11-methano-dibenzo[b,f][1,5]diazocine, Tröger's base, (R,R)-1, as a chiral compound of known absolute configuration.

  17. Determining cleanup levels in bioremediation: Quantitative structure activity relationship techniques

    SciTech Connect

    Arulgnanendran, V.R.J.; Nirmalakhandan, N.

    1995-12-31

    An important feature in the process of planning and initiating bioremediation is the quantification of the toxicity of either an individual chemical or a group of chemicals when multiple chemicals are involved. A laboratory protocol was developed to test the toxicity of single chemicals and mixtures of organic chemicals in a soil medium. Portions of these chemicals are used as a training set to develop Quantitative Structure Activity Relationship (QSAR) models. These predictive models are tested using the chemicals in the testing set, i.e., the remaining chemicals. Moreover mixtures with 10 contaminants in each mixture are tested experimentally to determine joint toxicity for mixtures of chemicals. Using the concepts of Toxic Units, Additivity Index, and Mixture Toxicity Index, the laboratory results are tested for additive, synergistic, or antagonistic effects of the contaminants. These concepts are further validated on mixtures containing eight chemicals that are tested in the laboratory. In addition to the use of the predictive models in evaluating cleanup levels for hazardous waste locations, they are useful to predict microbial toxicity in soils of new chemicals from a congeneric group acting by the same mode of toxicity. These models are applicable when the contaminants act singly or jointly in a mixture.

  18. Using NMR to Determine Protein Structure in Solution

    NASA Astrophysics Data System (ADS)

    Cavagnero, Silvia

    2003-02-01

    Nuclear magnetic resonance (NMR) is a marvelous spectroscopic technique that chemists, physicists, and biochemists routinely employ for their research around the world. This year half of the Nobel Prize for chemistry went to Kurt Wüthrich, who was recognized for the development of NMR-based techniques that lead to the structure determination of biomolecules in solution. In addition to implementing novel pulse sequences and software packages, Wüthrich also applied his methods to several biological systems of key importance to human health. These include the prion protein, which is heavily involved in the spongiform encephalopathy (best known as 'mad cow disease'), which recently caused numerous human deaths, particularly in the UK, due to ingestion of contaminated meat. Transverse relaxation optimized spectroscopy (TROSY) is the most intriguing new NMR method recently developed by Wüthrich and coworkers. This and other closely related pulse sequences promise to play a pivotal role in the extension of NMR to the conformational analysis of very large (up to the megadalton range) macromolecules and macromolecular complexes. More exciting new developments are expected in the near future.

  19. Accurate determination of pair potentials for a C{sub w}H{sub x}N{sub y}O{sub z} system of molecules: A semiempirical method

    SciTech Connect

    Thiel, M. van; Ree, F.H.; Haselman, L.C.

    1995-03-01

    Statistical mechanical chemical equilibrium calculations of the properties of high-pressure high-temperature reactive C,H,N,O mixtures are made to derive an accurate self-consistent set of inter-molecular potentials for the product molecules. Previous theoretical efforts to predict such properties relied in part on Corresponding States theory and shock wave data of argon. More recent high-pressure Hugoniot measurements on a number of elements and molecules allow more accurate determination of the potentials of these materials, and explicit inclusion of additional dissociation products. The present discussion briefly reviews the previous analysis and the method used to produce a self-consistent set of potentials from shock data on N{sub 2}, O{sub 2}, H{sub 2}, NO, an N{sub 2} + O{sub 2} mixture, carbon, CO{sub 2}, and CO, as well as some simple explosive product mixtures from detonation of hexanitrobenzene, PETN, and a mixture of hydrazine nitrate, hydrazine and water. The results are tested using the data from an HMX explosive formulations. The effect of the non-equilibrium nature of carbon clusters is estimated using data for TNT as a standard to determine a nonequilibrium equation of state for carbon. The resulting parameter set is used in a survey of 27 explosives. For the subset that contains no fluorine or two-phase carbon effects the rms deviation from experimental detonation velocity is 1.2%.

  20. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus. Purification, Crystallization and Structure Determination

    SciTech Connect

    Clemons, William M.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki

    2009-10-07

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 {angstrom} resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 {angstrom} resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  1. NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins.

    PubMed

    Zook, James; Mo, Gina; Sisco, Nicholas J; Craciunescu, Felicia M; Hansen, Debra T; Baravati, Bobby; Cherry, Brian R; Sykes, Kathryn; Wachter, Rebekka; Van Horn, Wade D; Fromme, Petra

    2015-06-01

    Tularemia is a potentially fatal bacterial infection caused by Francisella tularensis, and is endemic to North America and many parts of northern Europe and Asia. The outer membrane lipoprotein, Flpp3, has been identified as a virulence determinant as well as a potential subunit template for vaccine development. Here we present the first structure for the soluble domain of Flpp3 from the highly infectious Type A SCHU S4 strain, derived through high-resolution solution nuclear magnetic resonance (NMR) spectroscopy; the first structure of a lipoprotein from the genus Francisella. The Flpp3 structure demonstrates a globular protein with an electrostatically polarized surface containing an internal cavity-a putative binding site based on the structurally homologous Bet v1 protein family of allergens. NMR-based relaxation studies suggest loop regions that potentially modulate access to the internal cavity. The Flpp3 structure may add to the understanding of F. tularensis virulence and contribute to the development of effective vaccines.

  2. Determination of interface structure and bonding at atomic resolution in the stem

    SciTech Connect

    Pennycook, S.J.; McGibbon, A.J.; McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.; Jesson, D.E.

    1994-03-01

    The scanning transmission electron microscope now routinely produces probes of atomic dimensions, 2.2{Angstrom} at 100 kV and 1.3{Angstrom} at 300 kV. This capability opens up a new strategy for determining the structure and bonding of materials at the atomic scale, which is particularly advantageous for complex interfaces such as grain boundaries. The Z-contrast image allows the high-Z column locations to be determined by direct inspection, and quantified through maximum entropy methods to a positional accuracy of currently {approximately}0.2{Angstrom}. With the same electron probe, located to sub-Angstrom precision with reference to the Z-contrast image, parallel detection EELS can determine light element coordination from core edge fine structure, in principle around a single atomic column. There are several attractive features to combining Z-contrast imaging with EELS. First, the incoherent nature of Z-contrast imaging provides higher resolution, compared with 0.66 for phase contrast imaging, freedom from contrast reversals and a highly local image. This allows a greatly extended regieme of intuitive image interpretation. For example, the presence of dumbbells, with a spacing of 1.36{Angstrom}, in a Si<110> image is seen directly at 2.2{Angstrom} resolution from the elongation of the image features. For microanalysis, the Z-contrast image facilitates the accurate placement of the probe over selected atomic columns, either a single atomic column or using a line scan to reduce the effects of beam damage. Column-by-column analysis by EELS is possible, without beam broadening, through the columnar channeling effect that occurs when a highly convergent coherent probe is incident along a low order crystal zone axis.

  3. Fluid bilayer structure determination: Joint refinement in composition space using X-ray and neutron diffraction data

    SciTech Connect

    White, S.H.; Wiener, M.C.

    1994-12-31

    Experimentally-determined structural models of fluid lipid bilayers are essential for verifying molecular dynamics simulations of bilayers and for understanding the structural consequences of peptide interactions. The extreme thermal motion of bilayers precludes the possibility of atomic-level structural models. Defining {open_quote}the structure{close_quote} of a bilayer as the time-averaged transbilayer distribution of the water and the principal lipid structural groups such as the carbonyls and double-bonds (quasimolecular fragments), one can represent the bilayer structure as a sum of Gaussian functions referred to collectively as the quasimolecular structure. One method of determining the structure is by neutron diffraction combined with exhaustive specific deuteration. This method is impractical because of the expense of the chemical syntheses and the limited amount of neutron beam time currently available. We have therefore developed the composition space refinement method for combining X-ray and minimal neutron diffraction data to arrive at remarkably detailed and accurate structures of fluid bilayers. The composition space representation of the bilayer describes the probability of occupancy per unit length across the width of the bilayer of each quasimolecular component and permits the joint refinement of X-ray and neutron lamellar diffraction data by means of a single quasimolecular structure that is fitted simultaneously to both data sets. Scaling of each component by the appropriate neutron or X-ray scattering length maps the composition-space profile to the appropriate scattering length space for comparison to experimental data. The difficulty with the method is that fluid bilayer structures are generally only marginally determined by the experimental data. This means that the space of possible solutions must be extensively explored in conjunction with a thorough analysis of errors.

  4. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  5. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  6. Decoupling structural and environmental determinants of sap velocity

    NASA Astrophysics Data System (ADS)

    Caylor, K. K.; Dragoni, D.

    2007-12-01

    Characterization of transpiration based on the water use of individual tress has the advantage of preserving vital information on the plant-environment functional links and flux partitioning between species and landscape areas. Whole-tree transpiration has been estimated by means of sap velocity probes, which offer the dual advantages of practicality and repeatability. However, the assumptions underlying the technique require careful verification in order to determine total sap flow from point-based estimates of sap velocity. Our work presents a novel theoretical framework for the study of individual tree sap flow that incorporates both spatial and temporal variability in sap velocities. The instantaneous sap velocity at any point in the radial profile of xylem tissue is defined as the product of two components: (1) a time-invariant sap velocity distribution linked to the species- specific anatomical and structural properties of the conducting xylem, and (2) a time-varying term linked to the dynamics of the atmospheric water demand and available soil moisture. The separation of structural and temporal variation in sap velocity observations provides a direct mechanism for investigating how sap flow is governed by variation in environmental conditions as well as a means for comparing characteristic rates of plant water use among individuals of varying size. Most critically, this approach allows for a consistent and physically meaningful method for extrapolating point observations of sap velocity across the entire depth of conducting xylem. Experimental evidence supports our theoretical framework in the case of a population of sugar maples in a mixed deciduous forest, where observations were taken from a wide range of tree sizes, under varying soil water availability and atmospheric transpiration demand. We have also applied our approach to a small homogeneous sample of dwarf apple trees in a managed orchard, with favorable results. While these results require further

  7. Discovery and Structure Determination of the Orphan Enzyme Isoxanthopterin Deaminase

    SciTech Connect

    Hall, R.S.; Swaminathan, S.; Agarwal, R.; Hitchcock, D.; Sauder, J. M.; Burley, S. K.; Raushel, F. M.

    2010-05-25

    Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a (gi|44585104) and NYSGXRC-9236b (gi|44611670), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 {angstrom} resolution (Protein Data Bank entry 2PAJ). This protein folds as a distorted ({beta}/{alpha}){sub 8} barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s{sup -1}, 8.0 {micro}M, and 1.3 x 10{sup 5} M{sup -1} s{sup -1} (k{sub cat}, K{sub m}, and k{sub cat}/K{sub m}, respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site

  8. Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase .

    PubMed

    Hall, Richard S; Agarwal, Rakhi; Hitchcock, Daniel; Sauder, J Michael; Burley, Stephen K; Swaminathan, Subramanyam; Raushel, Frank M

    2010-05-25

    Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a ( gi|44585104 ) and NYSGXRC-9236b ( gi|44611670 ), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 A resolution (Protein Data Bank entry 2PAJ ). This protein folds as a distorted (beta/alpha)(8) barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s(-1), 8.0 muM, and 1.3 x 10(5) M(-1) s(-1) (k(cat), K(m), and k(cat)/K(m), respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9 ). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site residues were used to identify 24 other genes

  9. Determination of boiling point of petrochemicals by gas chromatography-mass spectrometry and multivariate regression analysis of structural activity relationship.

    PubMed

    Fakayode, Sayo O; Mitchell, Breanna S; Pollard, David A

    2014-08-01

    Accurate understanding of analyte boiling points (BP) is of critical importance in gas chromatographic (GC) separation and crude oil refinery operation in petrochemical industries. This study reported the first combined use of GC separation and partial-least-square (PLS1) multivariate regression analysis of petrochemical structural activity relationship (SAR) for accurate BP determination of two commercially available (D3710 and MA VHP) calibration gas mix samples. The results of the BP determination using PLS1 multivariate regression were further compared with the results of traditional simulated distillation method of BP determination. The developed PLS1 regression was able to correctly predict analytes BP in D3710 and MA VHP calibration gas mix samples, with a root-mean-square-%-relative-error (RMS%RE) of 6.4%, and 10.8% respectively. In contrast, the overall RMS%RE of 32.9% and 40.4%, respectively obtained for BP determination in D3710 and MA VHP using a traditional simulated distillation method were approximately four times larger than the corresponding RMS%RE of BP prediction using MRA, demonstrating the better predictive ability of MRA. The reported method is rapid, robust, and promising, and can be potentially used routinely for fast analysis, pattern recognition, and analyte BP determination in petrochemical industries.

  10. Determination of boiling point of petrochemicals by gas chromatography-mass spectrometry and multivariate regression analysis of structural activity relationship.

    PubMed

    Fakayode, Sayo O; Mitchell, Breanna S; Pollard, David A

    2014-08-01

    Accurate understanding of analyte boiling points (BP) is of critical importance in gas chromatographic (GC) separation and crude oil refinery operation in petrochemical industries. This study reported the first combined use of GC separation and partial-least-square (PLS1) multivariate regression analysis of petrochemical structural activity relationship (SAR) for accurate BP determination of two commercially available (D3710 and MA VHP) calibration gas mix samples. The results of the BP determination using PLS1 multivariate regression were further compared with the results of traditional simulated distillation method of BP determination. The developed PLS1 regression was able to correctly predict analytes BP in D3710 and MA VHP calibration gas mix samples, with a root-mean-square-%-relative-error (RMS%RE) of 6.4%, and 10.8% respectively. In contrast, the overall RMS%RE of 32.9% and 40.4%, respectively obtained for BP determination in D3710 and MA VHP using a traditional simulated distillation method were approximately four times larger than the corresponding RMS%RE of BP prediction using MRA, demonstrating the better predictive ability of MRA. The reported method is rapid, robust, and promising, and can be potentially used routinely for fast analysis, pattern recognition, and analyte BP determination in petrochemical industries. PMID:24881546

  11. Determination of the fine structure constant based on BLOCH oscillations of ultracold atoms in a vertical optical lattice.

    PubMed

    Cladé, Pierre; de Mirandes, Estefania; Cadoret, Malo; Guellati-Khélifa, Saïda; Schwob, Catherine; Nez, François; Julien, Lucile; Biraben, François

    2006-01-27

    We report an accurate measurement of the recoil velocity of 87Rb atoms based on Bloch oscillations in a vertical accelerated optical lattice. We transfer about 900 recoil momenta with an efficiency of 99.97% per recoil. A set of 72 measurements of the recoil velocity, each one with a relative uncertainty of about 33 ppb in 20 min integration time, leads to a determination of the fine structure constant with a statistical relative uncertainty of 4.4 ppb. The detailed analysis of the different systematic errors yields to a relative uncertainty of 6.7 ppb. The deduced value of alpha-1 is 137.035 998 78(91).

  12. The Combination of Laser Scanning and Structure from Motion Technology for Creation of Accurate Exterior and Interior Orthophotos of ST. Nicholas Baroque Church

    NASA Astrophysics Data System (ADS)

    Koska, B.; Křemen, T.

    2013-02-01

    Terrestrial laser scanning technology is used for creation of building documentation and 3D building model from its emerging at the turn of the millennium. Photogrammetry has even longer tradition in this field. Both technologies have some technical limitations if they are used for creation of a façade or even an interior orthophoto, but combination of both technologies seems profitable. Laser scanning can be used for creation of an accurate 3D model and photogrammetry for consequent application of high quality colour information. Both technologies were used in synergy to create the building plans, 2D drawing documentation of facades and interior views and the orthophotos of St. Nicholas Baroque church in Prague. The case study is described in details in the paper.

  13. Determination of Paleoseismic Ground Motions from Inversion of Block Failures in Masonry Structures

    NASA Astrophysics Data System (ADS)

    Yagoda-Biran, G.; Hatzor, Y. H.

    2010-12-01

    Accurate estimation of ground motion parameters such as expected peak ground acceleration (PGA), predominant frequency and duration of motion in seismically active regions, is crucial for hazard preparedness and sound engineering design. The best way to estimate quantitatively these parameters would be to investigate long term recorded data of past strong earthquakes in a studied region. In some regions of the world however recorded data are scarce due to lack of seismic network infrastructure, and in all regions the availability of recorded data is restricted to the late 19th century and onwards. Therefore, existing instrumental data are hardly representative of the true seismicity of a region. When recorded data are scarce or not available, alternative methods may be applied, for example adopting a quantitative paleoseismic approach. In this research we suggest the use of seismically damaged masonry structures as paleoseismic indicators. Visitors to archeological sites all over the world are often struck by structural failure features which seem to be "seismically driven", particularly when inspecting old masonry structures. While it is widely accepted that no other loading mechanism can explain the preserved damage, the actual driving mechanism remains enigmatic even now. In this research we wish to explore how such failures may be triggered by earthquake induced ground motions and use observed block displacements to determine the characteristic parameters of the paleoseismic earthquake motion, namely duration, frequency, and amplitude. This is performed utilizing a 3D, fully dynamic, numerical analysis performed with the Discontinuous Deformation Analysis (DDA) method. Several case studies are selected for 3D numerical analysis. First we study a simple structure in the old city of L'Aquila, Italy. L'Aquila was hit by an earthquake on April 6th, 2009, with over 300 casualties and many of its medieval buildings damaged. This case study is an excellent opportunity

  14. Phase Determination by Multiple-Wavelength X-ray Diffraction: Crystal Structure of a Basic ``Blue'' Copper Protein from Cucumbers

    NASA Astrophysics Data System (ADS)

    Guss, J. Mitchell; Merritt, Ethan A.; Phizackerley, R. Paul; Hedman, Britt; Murata, Mitsuo; Hodgson, Keith O.; Freeman, Hans C.

    1988-08-01

    A novel x-ray diffraction technique, multiple-wavelength anomalous dispersion (MAD) phasing, has been applied to the de novo determination of an unknown protein structure, that of the ``blue'' copper protein isolated from cucumber seedlings. This method makes use of crystallographic phases determined from measurements made at several wavelengths and has recently been made technically feasible through the use of intense, polychromatic synchrotron radiation together with accurate data collection from multiwire electronic area detectors. In contrast with all of the conventional methods of solving protein structures, which require either multiple isomorphous derivatives or coordinates of a similar structure for molecular replacement, this technique allows direct solution of the classical ``phase problem'' in x-ray crystallography. MAD phase assignment should be particularly useful for determining structures of small to medium-sized metalloproteins for which isomorphous derivatives are difficult or impossible to make. The structure of this particular protein provides new insights into the spectroscopic and redox properties of blue copper proteins, an important class of metalloproteins widely distributed in nature.

  15. Accurate documentation and wound measurement.

    PubMed

    Hampton, Sylvie

    This article, part 4 in a series on wound management, addresses the sometimes routine yet crucial task of documentation. Clear and accurate records of a wound enable its progress to be determined so the appropriate treatment can be applied. Thorough records mean any practitioner picking up a patient's notes will know when the wound was last checked, how it looked and what dressing and/or treatment was applied, ensuring continuity of care. Documenting every assessment also has legal implications, demonstrating due consideration and care of the patient and the rationale for any treatment carried out. Part 5 in the series discusses wound dressing characteristics and selection.

  16. Accurate absolute frequencies of the {nu}{sub 1}+{nu}{sub 3} band of {sup 13}C{sub 2}H{sub 2} determined using an infrared mode-locked Cr:YAG laser frequency comb

    SciTech Connect

    Madej, Alan A.; Bernard, John E.; John Alcock, A.; Czajkowski, Andrzej; Chepurov, Sergei

    2006-04-15

    Absolute frequency measurements, with up to 1x10{sup -11} level accuracies, are presented for 60 lines of the P and R branches for the {nu}{sub 1}+{nu}{sub 3} band of {sup 13}C{sub 2}H{sub 2} at 1.5 {mu}m (194 THz). The measurements were made using cavity-enhanced, diode-laser-based saturation spectroscopy. With one laser system stabilized to the P(16) line and a second laser system stabilized to the line whose frequency was to be determined, a Cr:YAG frequency comb was employed to accurately measure the tetrahertz level frequency intervals. The results are compared with recent work from other groups and indicate that these lines would form a basis for a high-quality atlas of reference frequencies for this region of the spectrum.

  17. Determining the Mechanical Properties of Lattice Block Structures

    NASA Technical Reports Server (NTRS)

    Wilmoth, Nathan

    2013-01-01

    Lattice block structures and shape memory alloys possess several traits ideal for solving intriguing new engineering problems in industries such as aerospace, military, and transportation. Recent testing at the NASA Glenn Research Center has investigated the material properties of lattice block structures cast from a conventional aerospace titanium alloy as well as lattice block structures cast from nickel-titanium shape memory alloy. The lattice block structures for both materials were sectioned into smaller subelements for tension and compression testing. The results from the cast conventional titanium material showed that the expected mechanical properties were maintained. The shape memory alloy material was found to be extremely brittle from the casting process and only compression testing was completed. Future shape memory alloy lattice block structures will utilize an adjusted material composition that will provide a better quality casting. The testing effort resulted in baseline mechanical property data from the conventional titanium material for comparison to shape memory alloy materials once suitable castings are available.

  18. Negative chemical ionization gas chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry and automated accurate mass data processing for determination of pesticides in fruit and vegetables.

    PubMed

    Besil, Natalia; Uclés, Samanta; Mezcúa, Milagros; Heinzen, Horacio; Fernández-Alba, Amadeo R

    2015-08-01

    Gas chromatography coupled to high resolution hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS), operating in negative chemical ionization (NCI) mode and combining full scan with MSMS experiments using accurate mass analysis, has been explored for the automated determination of pesticide residues in fruit and vegetables. Seventy compounds were included in this approach where 50 % of them are not approved by the EU legislation. A global 76 % of the analytes could be identified at 1 μg kg(-1). Recovery studies were developed at three concentration levels (1, 5, and 10 μg kg(-1)). Seventy-seven percent of the detected pesticides at the lowest level yielded recoveries within the 70 %-120 % range, whereas 94 % could be quantified at 5 μg kg(-1), and the 100 % were determined at 10 μg kg(-1). Good repeatability, expressed as relative standard deviation (RSD <20 %), was obtained for all compounds. The main drawback of the method was the limited dynamic range that was observed for some analytes that can be overcome either diluting the sample or lowering the injection volume. A home-made database was developed and applied to an automatic accurate mass data processing. Measured mass accuracies of the generated ions were mainly less than 5 ppm for at least one diagnostic ion. When only one ion was obtained in the single-stage NCI-MS, a representative product ion from MSMS experiments was used as identification criterion. A total of 30 real samples were analyzed and 67 % of the samples were positive for 12 different pesticides in the range 1.0-1321.3 μg kg(-1). PMID:25694145

  19. GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features

    PubMed Central

    Li, Fuyi; Li, Chen; Revote, Jerico; Zhang, Yang; Webb, Geoffrey I.; Li, Jian; Song, Jiangning; Lithgow, Trevor

    2016-01-01

    Glycosylation plays an important role in cell-cell adhesion, ligand-binding and subcellular recognition. Current approaches for predicting protein glycosylation are primarily based on sequence-derived features, while little work has been done to systematically assess the importance of structural features to glycosylation prediction. Here, we propose a novel bioinformatics method called GlycoMinestruct(http://glycomine.erc.monash.edu/Lab/GlycoMine_Struct/) for improved prediction of human N- and O-linked glycosylation sites by combining sequence and structural features in an integrated computational framework with a two-step feature-selection strategy. Experiments indicated that GlycoMinestruct outperformed NGlycPred, the only predictor that incorporated both sequence and structure features, achieving AUC values of 0.941 and 0.922 for N- and O-linked glycosylation, respectively, on an independent test dataset. We applied GlycoMinestruct to screen the human structural proteome and obtained high-confidence predictions for N- and O-linked glycosylation sites. GlycoMinestruct can be used as a powerful tool to expedite the discovery of glycosylation events and substrates to facilitate hypothesis-driven experimental studies. PMID:27708373

  20. Using Surface NMR Nuclear Magnetic Resonance to Determine Sediment Structure and Properties Beneath Thermokarst Lakes

    NASA Astrophysics Data System (ADS)

    Creighton, A.; Parsekian, A.; Arp, C. D.; Jones, B. M.; Walter Anthony, K. M.; Bondurant, A.

    2015-12-01

    Thermokarst lakes form following the subsidence of ice-rich permafrost terrain and concurrent infilling of the depression with water. Areas of unfrozen sediment, called taliks, can form under lakes that have a mean annual bottom temperature greater than 0°C. Taliks are thought to play an important role in permafrost hydrology and carbon cycling. Sub-lake taliks can extend to depths of tens of meters, making them difficult and costly to measure by direct methods such as boreholes. Surface nuclear magnetic resonance (NMR) provides an unambiguous measurement of the liquid water content associated with unfrozen taliks; however, limitations of the measurements and the interpretation of the data still remain. Forward models were created to test the effect of varying water column thicknesses on the ability to resolve the depth and water content of taliks with parameters similar to geometries measured in late-winter field studies in the Arctic and Boreal regions of Alaska. The results of the forward modeling show that talik depth resolution decreases with a larger water column thickness, a shallower talik depth, and a lower water content. These results place constraints on our field measurements, with lakes greater than 9 m deep yielding potentially misleading inversion results. Field data was collected at a small, 4.6 m deep thermokarst lake near Fairbanks, Alaska, which had a known subsurface structure including talik depth, and available talik sediments from cores. Known subsurface structure was not used to inform the inversion model to determine how well talik depth could be resolved in lakes with unknown structure. With constraints placed on ice and water thickness, which are easily measured in the field, the blocky inversion model was able to accurately resolve the talik depth and water content for lakes less than 9 m deep.

  1. Environmental filtering determines metacommunity structure in wetland microcrustaceans.

    PubMed

    Gascón, Stéphanie; Arranz, Ignasi; Cañedo-Argüelles, Miguel; Nebra, Alfonso; Ruhí, Albert; Rieradevall, Maria; Caiola, Nuno; Sala, Jordi; Ibàñez, Carles; Quintana, Xavier D; Boix, Dani

    2016-05-01

    Metacommunity approaches are becoming popular when analyzing factors driving species distribution at the regional scale. However, until the popularization of the variation partitioning technique it was difficult to assess the main drivers of the observed patterns (spatial or environmental). Here we propose a new framework linking the emergence of different metacommunity structures (e.g., nested, Gleasonian, Clementsian) to spatial and environmental filters. This is a novel approach that provides a more profound analysis of how both drivers could lead to similar metacommunity structures. We tested this framework on 110 sites covering a strong environmental gradient (i.e., microcrustacean assemblages organized along a salinity gradient, from freshwater to brackish water wetlands). First we identified the metacommunity structure that better fitted these microcrustacean assemblages. Then, we used hierarchical variation partitioning to quantify the relative influences of environmental filters and the distance among wetlands on the identified structure. Our results showed that under strong environmental filtering metacommunity structures were non-random. We also noted that even passive dispersers, that are supposed to be poorly spatially filtered, showed spatial signals at a large geographical scale. However, some difficulties arose when inferring biotic interactions at finer-scale spatial signals. Overall, our study shows the potential of elements of metacommunity structure combined with variation partition techniques to detect environmental drivers and broadscale patterns of metacommunity structure, and that some caution is needed when interpreting finer-scale spatial signals. PMID:26781303

  2. Environmental filtering determines metacommunity structure in wetland microcrustaceans.

    PubMed

    Gascón, Stéphanie; Arranz, Ignasi; Cañedo-Argüelles, Miguel; Nebra, Alfonso; Ruhí, Albert; Rieradevall, Maria; Caiola, Nuno; Sala, Jordi; Ibàñez, Carles; Quintana, Xavier D; Boix, Dani

    2016-05-01

    Metacommunity approaches are becoming popular when analyzing factors driving species distribution at the regional scale. However, until the popularization of the variation partitioning technique it was difficult to assess the main drivers of the observed patterns (spatial or environmental). Here we propose a new framework linking the emergence of different metacommunity structures (e.g., nested, Gleasonian, Clementsian) to spatial and environmental filters. This is a novel approach that provides a more profound analysis of how both drivers could lead to similar metacommunity structures. We tested this framework on 110 sites covering a strong environmental gradient (i.e., microcrustacean assemblages organized along a salinity gradient, from freshwater to brackish water wetlands). First we identified the metacommunity structure that better fitted these microcrustacean assemblages. Then, we used hierarchical variation partitioning to quantify the relative influences of environmental filters and the distance among wetlands on the identified structure. Our results showed that under strong environmental filtering metacommunity structures were non-random. We also noted that even passive dispersers, that are supposed to be poorly spatially filtered, showed spatial signals at a large geographical scale. However, some difficulties arose when inferring biotic interactions at finer-scale spatial signals. Overall, our study shows the potential of elements of metacommunity structure combined with variation partition techniques to detect environmental drivers and broadscale patterns of metacommunity structure, and that some caution is needed when interpreting finer-scale spatial signals.

  3. Structure determination of Fe-Al-Ge alloys

    NASA Astrophysics Data System (ADS)

    Gargicevich, D.; Galván Josa, V. M.; Blanco, C.; Lambri, A.; Cuello, G. J.

    2015-11-01

    We studied the crystalline structure of Fe - 8at.%Al - 4at.%Ge alloy between 300 and 1300 K and its relation to the mechanical response by means of neutron diffraction and mechanical spectroscopy. At room temperature we observe a Fe3Al-type ordered structure with a deficiency of Al in the 8c sites. The Ge atoms are distributed in the 4a and Al atoms in 8c sites. At high temperature we observe an order-disorder transformation when the crystal structure becomes Fe-α type. This loss of order gives rise to the hysteresis behavior of damping between the heating and cooling runs.

  4. Determinants of structural choice in visually situated sentence production.

    PubMed

    Myachykov, Andriy; Garrod, Simon; Scheepers, Christoph

    2012-11-01

    Three experiments investigated how perceptual, structural, and lexical cues affect structural choices during English transitive sentence production. Participants described transitive events under combinations of visual cueing of attention (toward either agent or patient) and structural priming with and without semantic match between the notional verb in the prime and the target event. Speakers had a stronger preference for passive-voice sentences (1) when their attention was directed to the patient, (2) upon reading a passive-voice prime, and (3) when the verb in the prime matched the target event. The verb-match effect was the by-product of an interaction between visual cueing and verb match: the increase in the proportion of passive-voice responses with matching verbs was limited to the agent-cued condition. Persistence of visual cueing effects in the presence of both structural and lexical cues suggests a strong coupling between referent-directed visual attention and Subject assignment in a spoken sentence.

  5. Structural determinants of SMAD function in TGF-β signaling

    PubMed Central

    Macias, Maria J.; Martin-Malpartida, Pau; Massagué, Joan

    2015-01-01

    Smad transcription factors are central to the signal transduction pathway that mediates the numerous effects of the TGF-β superfamily of cytokines in metazoan embryo development and adult tissue regeneration and homeostasis. Although Smad proteins are conserved, recent genome-sequencing projects have revealed their sequence variation in metazoan evolution, human polymorphism, and cancer. Structural studies of Smads bound to partner proteins and target DNA provided a framework to understand the significance of these evolutionary and pathologic sequence variations. Here we synthesize the extant mutational and structural data to suggest how genetic variation in Smads may affect the structure, regulation, and function of these proteins. Furthermore, we present a web-app that compares Smad sequences and displays Smad protein structures and their disease-associated variants. PMID:25935112

  6. Structural determinants of Smad function in TGF-β signaling.

    PubMed

    Macias, Maria J; Martin-Malpartida, Pau; Massagué, Joan

    2015-06-01

    Smad transcription factors are central to the signal transduction pathway that mediates the numerous effects of the transforming growth factor β (TGF-β) superfamily of cytokines in metazoan embryo development as well as in adult tissue regeneration and homeostasis. Although Smad proteins are conserved, recent genome-sequencing projects have revealed their sequence variation in metazoan evolution, human polymorphisms, and cancer. Structural studies of Smads bound to partner proteins and target DNA provide a framework for understanding the significance of these evolutionary and pathologic sequence variations. We synthesize the extant mutational and structural data to suggest how genetic variation in Smads may affect the structure, regulation, and function of these proteins. We also present a web application that compares Smad sequences and displays Smad protein structures and their disease-associated variants.

  7. Structure Determination and Improved Model of Plant Photosystem I*

    PubMed Central

    Amunts, Alexey; Toporik, Hila; Borovikova, Anna; Nelson, Nathan

    2010-01-01

    Photosystem I functions as a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae, and higher plants. Functionally, Photosystem I captures sunlight and transfers the excitation energy through an intricate and precisely organized antenna system, consisting of a pigment network, to the center of the molecule, where it is used in the transmembrane electron transfer reaction. Our current understanding of the sophisticated mechanisms underlying these processes has profited greatly from elucidation of the crystal structures of the Photosystem I complex. In this report, we describe the developments that ultimately led to enhanced structural information of plant Photosystem I. In addition, we report an improved crystallographic model at 3.3-Å resolution, which allows analysis of the structure in more detail. An improved electron density map yielded identification and tracing of subunit PsaK. The location of an additional ten β-carotenes as well as five chlorophylls and several loop regions, which were previously uninterpretable, are now modeled. This represents the most complete plant Photosystem I structure obtained thus far, revealing the locations of and interactions among 17 protein subunits and 193 non-covalently bound photochemical cofactors. Using the new crystal structure, we examine the network of contacts among the protein subunits from the structural perspective, which provide the basis for elucidating the functional organization of the complex. PMID:19923216

  8. Scaling up the Single Transducer Thickness-Independent Ultrasonic Imaging Method for Accurate Characterization of Microstructural Gradients in Monolithic and Composite Tubular Structures

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Carney, Dorothy V.; Baaklini, George Y.; Bodis, James R.; Rauser, Richard W.

    1998-01-01

    Ultrasonic velocity/time-of-flight imaging that uses back surface reflections to gauge volumetric material quality is highly suited for quantitative characterization of microstructural gradients including those due to pore fraction, density, fiber fraction, and chemical composition variations. However, a weakness of conventional pulse-echo ultrasonic velocity/time-of-flight imaging is that the image shows the effects of thickness as well as microstructural variations unless the part is uniformly thick. This limits this imaging method's usefulness in practical applications. Prior studies have described a pulse-echo time-of-flight-based ultrasonic imaging method that requires using a single transducer in combination with a reflector plate placed behind samples that eliminates the effect of thickness variation in the image. In those studies, this method was successful at isolating ultrasonic variations due to material microstructure in plate-like samples of silicon nitride, metal matrix composite, and polymer matrix composite. In this study, the method is engineered for inspection of more complex-shaped structures-those having (hollow) tubular/curved geometry. The experimental inspection technique and results are described as applied to (1) monolithic mullite ceramic and polymer matrix composite 'proof-of-concept' tubular structures that contain machined patches of various depths and (2) as-manufactured monolithic silicon nitride ceramic and silicon carbide/silicon carbide composite tubular structures that might be used in 'real world' applications.

  9. Insights in the electronic structure and redox reaction energy in LiFePO{sub 4} battery material from an accurate Tran-Blaha modified Becke Johnson potential

    SciTech Connect

    Araujo, Rafael B.; Almeida, J. de S; Ferreira da Silva, A.; Ahuja, Rajeev

    2015-09-28

    The main goals of this paper are to investigate the accuracy of the Tran-Blaha modified Becke Johnson (TB-mBJ) potential to predict the electronic structure of lithium iron phosphate and the related redox reaction energy with the lithium deintercalation process. The computed electronic structures show that the TB-mBJ method is able to partially localize Fe-3d electrons in LiFePO{sub 4} and FePO{sub 4} which usually is a problem for the generalized gradient approximation (GGA) due to the self interaction error. The energy band gap is also improved by the TB-mBJ calculations in comparison with the GGA results. It turned out, however, that the redox reaction energy evaluated by the TB-mBJ technique is not in good agreement with the measured one. It is speculated that this disagreement in the computed redox energy and the experimental value is due to the lack of a formal expression to evaluate the exchange and correlation energy. Therefore, the TB-mBJ is an efficient method to improve the prediction of the electronic structures coming form the standard GGA functional in LiFePO{sub 4} and FePO{sub 4}. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.

  10. Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

    ERIC Educational Resources Information Center

    Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

    2012-01-01

    This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

  11. Determination of Structural and Morphological Parameters of Human Bulbar Conjunctiva from Optical Diffuse Reflectance Spectra

    NASA Astrophysics Data System (ADS)

    Lisenko, S. A.; Firago, V. A.; Kugeiko, M. M.; Kubarko, A. I.

    2016-09-01

    We have developed a method for on-the-fl y retrieval of the volume concentration of blood vessels, the average diameter of the blood vessels, the blood oxygenation level, and the molar concentrations of chromophores in the bulbar conjunctiva from its diffuse reflectance spectra, measured when the radiation delivery and detection channels are spatially separated. The relationship between the diffuse reflectance spectrum of the conjunctiva and its unknown parameters is described in terms of an analytical model, constructed on the basis of a highly accurate approximation analog of the Monte Carlo method. We have studied the effect of localization of hemoglobin in erythrocytes and localization of erythrocytes in the blood vessels on the power of the retrieval of structural and morphological parameters for the conjunctiva. We developed a device for obtaining video images of the conjunctiva and contactless measurements of its diffuse reflectance spectrum. By comparing simulated diffuse reflectance spectra of the conjunctiva with the experimental measurements, we established a set of chromophores which must be taken into account in the model for reproducing the experimental data within the measurement error. We observed absorption bands for neuroglobin in the experimental spectra, and provided a theoretical basis for the possibility of determining its absolute concentrations in the conjunctiva. We have shown that our method can detect low bilirubin concentrations in blood.

  12. Determining population structure and hybridization for two iris species

    PubMed Central

    Hamlin, Jennafer A P; Arnold, Michael L

    2014-01-01

    Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up “species boundaries” can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping-by-sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species. PMID:24683457

  13. SHELXT - integrated space-group and crystal-structure determination.

    PubMed

    Sheldrick, George M

    2015-01-01

    The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.

  14. Structural Determinants of Cadherin-23 Function in Hearing and Deafness

    SciTech Connect

    Sotomayor, Marcos; Weihofen, Wilhelm A.; Gaudet, Rachelle; Corey, David P.

    2010-06-21

    The hair-cell tip link, a fine filament directly conveying force to mechanosensitive transduction channels, is composed of two proteins, protocadherin-15 and cadherin-23, whose mutation causes deafness. However, their molecular structure, elasticity, and deafness-related structural defects are unknown. We present crystal structures of the first and second extracellular cadherin repeats of cadherin-23. Overall, structures show typical cadherin folds, but reveal an elongated N terminus that precludes classical cadherin interactions and contributes to an N-terminal Ca{sup 2+}-binding site. The deafness mutation D101G, in the linker region between the repeats, causes a slight bend between repeats and decreases Ca{sup 2+} affinity. Molecular dynamics simulations suggest that cadherin-23 repeats are stiff and that either removing Ca{sup 2+} or mutating Ca{sup 2+}-binding residues reduces rigidity and unfolding strength. The structures define an uncharacterized cadherin family and, with simulations, suggest mechanisms underlying inherited deafness and how cadherin-23 may bind with itself and with protocadherin-15 to form the tip link.

  15. An integrated strategy for rapid and accurate determination of free and cell-bound microcystins and related peptides in natural blooms by liquid chromatography-electrospray-high resolution mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry using both positive and negative ionization modes.

    PubMed

    Flores, Cintia; Caixach, Josep

    2015-08-14

    An integrated high resolution mass spectrometry (HRMS) strategy has been developed for rapid and accurate determination of free and cell-bound microcystins (MCs) and related peptides in water blooms. The natural samples (water and algae) were filtered for independent analysis of aqueous and sestonic fractions. These fractions were analyzed by MALDI-TOF/TOF-MS and ESI-Orbitrap-HCD-MS. MALDI, ESI and the study of fragmentation sequences have been provided crucial structural information. The potential of combined positive and negative ionization modes, full scan and fragmentation acquisition modes (TOF/TOF and HCD) by HRMS and high resolution and accurate mass was investigated in order to allow unequivocal determination of MCs. Besides, a reliable quantitation has been possible by HRMS. This composition helped to decrease the probability of false positives and negatives, as alternative to commonly used LC-ESI-MS/MS methods. The analysis was non-target, therefore covered the possibility to analyze all MC analogs concurrently without any pre-selection of target MC. Furthermore, archived data was subjected to retrospective "post-targeted" analysis and a screening of other potential toxins and related peptides as anabaenopeptins in the samples was done. Finally, the MS protocol and identification tools suggested were applied to the analysis of characteristic water blooms from Spanish reservoirs. PMID:26141269

  16. An integrated strategy for rapid and accurate determination of free and cell-bound microcystins and related peptides in natural blooms by liquid chromatography-electrospray-high resolution mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry using both positive and negative ionization modes.

    PubMed

    Flores, Cintia; Caixach, Josep

    2015-08-14

    An integrated high resolution mass spectrometry (HRMS) strategy has been developed for rapid and accurate determination of free and cell-bound microcystins (MCs) and related peptides in water blooms. The natural samples (water and algae) were filtered for independent analysis of aqueous and sestonic fractions. These fractions were analyzed by MALDI-TOF/TOF-MS and ESI-Orbitrap-HCD-MS. MALDI, ESI and the study of fragmentation sequences have been provided crucial structural information. The potential of combined positive and negative ionization modes, full scan and fragmentation acquisition modes (TOF/TOF and HCD) by HRMS and high resolution and accurate mass was investigated in order to allow unequivocal determination of MCs. Besides, a reliable quantitation has been possible by HRMS. This composition helped to decrease the probability of false positives and negatives, as alternative to commonly used LC-ESI-MS/MS methods. The analysis was non-target, therefore covered the possibility to analyze all MC analogs concurrently without any pre-selection of target MC. Furthermore, archived data was subjected to retrospective "post-targeted" analysis and a screening of other potential toxins and related peptides as anabaenopeptins in the samples was done. Finally, the MS protocol and identification tools suggested were applied to the analysis of characteristic water blooms from Spanish reservoirs.

  17. RNA structure determination by solid-state NMR spectroscopy

    PubMed Central

    Marchanka, Alexander; Simon, Bernd; Althoff-Ospelt, Gerhard; Carlomagno, Teresa

    2015-01-01

    Knowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines—independent of their ability to crystallize— and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies. PMID:25960310

  18. Surface structure determination of black phosphorus using photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    de Lima, Luis Henrique; Barreto, Lucas; Landers, Richard; de Siervo, Abner

    2016-01-01

    The atomic structure of single-crystalline black phosphorus is studied using high-resolution synchrotron-based photoelectron diffraction (XPD). The results show that the topmost phosphorene layer in the black phosphorus is slightly displaced compared to the bulk structure and presents a small contraction in the direction perpendicular to the surface. Furthermore, the XPD results show the presence of a small buckling among the surface atoms, in agreement with previously reported scanning tunneling microscopy results. The contraction of the surface layer added to the presence of the buckling indicates a uniformity in the size of the s p3 bonds between P atoms at the surface.

  19. Theoretical determination of the structure of acetylene on Pt(111)

    NASA Astrophysics Data System (ADS)

    Anderson, Alfred B.; Hubbard, Arthur T.

    1980-09-01

    An atom superposition and electron delocalization technique applied to acetylene chemisorption on small cluster models for the Pt(111) surface shows preference for the triangular site as deduced from electron energy loss analyses by Ibach and Lehwald. This confirms the applicability of Badger's and related rules in this instance. Calculations on CCH 3 produce a structure in agreement with a dynamic LEED analysis at 400 K by Kesmodel, Dubois and Somorjai. Structures of CCH 2 and CHCH 2 are calculated and these species are found to be less stable than acetylene and CCH 3, respectively, when chemisorbed on Pt(111).

  20. First-principles determination of the structure of magnesium borohydride.

    PubMed

    Zhou, Xiang-Feng; Oganov, Artem R; Qian, Guang-Rui; Zhu, Qiang

    2012-12-14

    The energy landscape of Mg(BH(4))(2) under pressure is explored by ab initio evolutionary calculations. Two new tetragonal structures, with space groups P4 and I4(1)/acd, are predicted to be lower in enthalpy by 15.4 and 21.2 kJ/mol, respectively, than the earlier proposed P4(2)nm phase. We have simulated x-ray diffraction spectra, lattice dynamics, and equations of state of these phases. The density, volume contraction, bulk modulus, and simulated x-ray diffraction patterns of I4(1)/acd and P4 structures are in excellent agreement with the experimental results.

  1. Polybrominated Diphenyl Ethers: Structure Determination and Trends in Antibacterial Activity.

    PubMed

    Liu, Hongbing; Lohith, Katheryn; Rosario, Margaret; Pulliam, Thomas H; O'Connor, Robert D; Bell, Lori J; Bewley, Carole A

    2016-07-22

    Antibacterial-guided fractionation of the Dictyoceratid sponges Lamellodysidea sp. and two samples of Dysidea granulosa yielded 14 polybrominated, diphenyl ethers including one new methoxy-containing compound (8). Their structures were elucidated by interpretation of spectroscopic data of the natural product and their methoxy derivatives. Most of the compounds showed strong antimicrobial activity with low- to sub-microgram mL(-1) minimum inhibitory concentrations against drug-susceptible and drug-resistant strains of Staphylococcus aureus and Enterococcus faecium, and two compounds inhibited Escherichia coli in a structure-dependent manner. PMID:27399938

  2. Recent advances in thermal desorption-gas chromatography-mass spectrometery method to eliminate the matrix effect between air and water samples: application to the accurate determination of Henry's law constant.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2014-05-16

    Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2).

  3. Recent advances in thermal desorption-gas chromatography-mass spectrometery method to eliminate the matrix effect between air and water samples: application to the accurate determination of Henry's law constant.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2014-05-16

    Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2). PMID:24704185

  4. Active and accurate trans-translation requires distinct determinants in the C-terminal tail of SmpB protein and the mRNA-like domain of transfer messenger RNA (tmRNA).

    PubMed

    Camenares, Devin; Dulebohn, Daniel P; Svetlanov, Anton; Karzai, A Wali

    2013-10-18

    Unproductive ribosome stalling in eubacteria is resolved by the actions of SmpB protein and transfer messenger (tm) RNA. We examined the functional significance of conserved regions of SmpB and tmRNA to the trans-translation process. Our investigations reveal that the N-terminal 20 residues of SmpB, which are located near the ribosomal decoding center, are dispensable for all known SmpB activities. In contrast, a set of conserved residues that reside at the junction between the tmRNA-binding core and the C-terminal tail of SmpB play an important role in tmRNA accommodation. Our data suggest that the highly conserved glycine 132 acts as a flexible hinge that enables movement of the C-terminal tail, thus permitting proper positioning and establishment of the tmRNA open reading frame (ORF) as the surrogate template. To gain further insights into the function of the SmpB C-terminal tail, we examined the tagging activity of hybrid variants of tmRNA and the SmpB protein, in which the tmRNA ORF or the SmpB C-terminal tail was substituted with the equivalent but highly divergent sequences from Francisella tularensis. We observed that the hybrid tmRNA was active but resulted in less accurate selection of the resume codon. Cognate hybrid SmpB was necessary to restore activity. Furthermore, accurate tagging was observed when the identity of the resume codon was reverted from GGC to GCA. Taken together, these data suggest that the engagement of the tmRNA ORF and the selection of the correct translation resumption point are distinct activities that are influenced by independent tmRNA and SmpB determinants.

  5. Compressed Sensing Electron Tomography for Determining Biological Structure

    NASA Astrophysics Data System (ADS)

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.

    2016-06-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets.

  6. Structural Determinants of Intergroup Association: Interracial Marriage and Crime.

    ERIC Educational Resources Information Center

    South, Scott J.; Messner, Steven F.

    1986-01-01

    Using data from a sample of 25 U. S. metropolitan cities, this study investigates the relationship between interracial marriage and violent interracial crime. Results show a positive relationship, one which was predicted by Blau's macrosociological theory of social structure. (Author/JDH)

  7. Compressed Sensing Electron Tomography for Determining Biological Structure

    PubMed Central

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.

    2016-01-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets. PMID:27291259

  8. A Discovery Mission to Determine the Interior Structure of Gas- and Ice-Giants

    NASA Astrophysics Data System (ADS)

    Hofstadter, Mark D.; Murphy, N.; Matousek, S.; Bairstow, S.; Maiwald, F.; Jeffries, S.; Schmider, F.; Guillot, T.

    2013-10-01

    The Ice Giants (Uranus and Neptune) are fundamentally different than the better-known Gas Giants (Jupiter and Saturn). Ice Giants are roughly 65% water by mass, compared to Gas Giants which are ~95% hydrogen and helium. Knowing the interior structure of both types of planets is a key measurement needed to advance our understanding of the formation and evolution of planetary systems, particularly in light of recent findings that Ice Giants are far more abundant in our galaxy than Gas Giants (Borucki et al., ApJ 2011). In the past, gravity measurements from spacecraft in low orbits have been the primary way to tease out information on interior structure. A new approach, Doppler imaging, can provide detailed information on interior structure from great distances (Gaulme et al., A&A 2011). A planetary Doppler Imager (DI) builds on the well-established fields of helio- and stellar-seismology, which have revolutionized our understanding of the interior of stars. The great advantage of a DI is that its observations do not require the spacecraft to enter orbit. We have designed a Discovery mission around such an instrument to determine the interior structures of Jupiter and Uranus during flybys of each planet. The data collected at Jupiter (after a 1.5 year flight) will compliment observations to be made by the Juno spacecraft in 2016, creating a much more accurate picture of the interior than is possible from the gravity technique alone. Roughly 6.5 years after the Jupiter flyby, DI measurements of Uranus will open that planet's interior for the first time. At both planets, measurements of the interior structure are made over a 4-month period centered on closest approach (CA), but with a ~1 week gap at CA when the planet is too close for whole-disk imaging. This allows other measurements to be made at that time, such as of small-scale weather features or satellites. We note that the DI technique, while enabling a Discovery-class mission, can also benefit larger missions

  9. Spatial and temporal determinants of genetic structure in Gentianella bohemica

    PubMed Central

    Königer, Julia; Rebernig, Carolin A; Brabec, Jiří; Kiehl, Kathrin; Greimler, Josef

    2012-01-01

    The biennial plant Gentianella bohemica is a subendemic of the Bohemian Massif, where it occurs in seminatural grasslands. It has become rare in recent decades as a result of profound changes in land use. Using amplified fragment length polymorphisms (AFLP) fingerprint data, we investigated the genetic structure within and among populations of G. bohemica in Bavaria, the Czech Republic, and the Austrian border region. The aim of our study was (1) to analyze the genetic structure among populations and to discuss these findings in the context of present and historical patterns of connectivity and isolation of populations, (2) to analyze genetic structure among consecutive generations (cohorts of two consecutive years), and (3) to investigate relationships between intrapopulational diversity and effective population size (Ne) as well as plant traits. (1) The German populations were strongly isolated from each other (pairwise FST= 0.29–0.60) and from all other populations (FST= 0.24–0.49). We found a pattern of near panmixis among the latter (FST= 0.15–0.35) with geographical distance explaining only 8% of the genetic variance. These results were congruent with a principal coordinate analysis (PCoA) and analysis using STRUCTURE to identify genetically coherent groups. These findings are in line with the strong physical barrier and historical constraints, resulting in separation of the German populations from the others. (2) We found pronounced genetic differences between consecutive cohorts of the German populations (pairwise FST= 0.23 and 0.31), which can be explained by local population history (land use, disturbance). (3) Genetic diversity within populations (Shannon index, HSh) was significantly correlated with Ne (RS= 0.733) and reflected a loss of diversity due to several demographic bottlenecks. Overall, we found that the genetic structure in G. bohemica is strongly influenced by historical periods of high connectivity and isolation as well as by marked

  10. Non-iterative determination of pattern phase in structured illumination microscopy using auto-correlations in Fourier space.

    PubMed

    Wicker, Kai

    2013-10-21

    The artefact-free reconstruction of structured illumination microscopy images requires precise knowledge of the pattern phases in the raw images. If this parameter cannot be controlled precisely enough in an experimental setup, the phases have to be determined a posteriori from the acquired data. While an iterative optimisation based on cross-correlations between individual Fourier images yields accurate results, it is rather time-consuming. Here I present a fast non-iterative technique which determines each pattern phase from an auto-correlation of the respective Fourier image. In addition to improving the speed of the reconstruction, simulations show that this method is also more robust, yielding errors of typically less than λ/500 under realistic signal-to-noise levels.

  11. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

    PubMed

    Lindert, Steffen; Alexander, Nathan; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L; Meiler, Jens

    2012-03-01

    Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy or X-ray crystallography. In these density maps, the general arrangement of secondary structure elements (SSEs) is revealed, whereas their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å.

  12. Iron phosphate glasses: Structure determination and radiation tolerance

    NASA Astrophysics Data System (ADS)

    Jolley, Kenny; Smith, Roger

    2016-05-01

    Iron phosphate glass (IPG) has gained recent interest for use in encapsulating radioactive waste for long term storage. In this work, we investigate 5 different compositions of iron phosphate glass. We consider amorphous structures of 3 known crystalline phases: Fe2+ Fe23+ (P2O7)2, Fe43 + (P2O7)3 and Fe3+(PO3)3, and structures of IPG (40 mol% Fe2O3 and 60 mol% P2O5), with 4% and 17% Fe2+ ion concentrations. Using constant volume molecular dynamics (MD), we quench a set of structures for each glass composition, to find the optimal density structure. We found that the lowest energy structures of IPG with 4% and 17% concentration of Fe2+, have a density of 3.25 and 3.28 g/cm3 respectively. This is slightly higher than the experimentally measured values of 2.9 and 2.95 g/cm3 respectively. We also estimate an upper and lower bound on the melting temperatures of each glass, then for each glass, we simulate radiation damage cascades at 4 keV. The cascade structures can be in the form of either a concentrated thermal spike or more diffuse with sub-cascade branching. We found that the glass compositions with a higher Fe/P atomic ratio, contained a greater number of displacements after the cascade. We also found that the IPG with 4% Fe2+, contained slightly fewer displacements than the IPG with 17% Fe2+. This is consistent with our previous work, which showed that the threshold displacement energies are lower for glasses with a lower Fe2+ content. In all the simulations, many PO4 polyhedra are destroyed during the early stages of irradiation, but recover strongly over a time scale of picoseconds, leaving very few over or under co-ordinated P atoms at the end of the ballistic phase. This is in contrast to recent work in apatite. The strong recovery indicates that phosphate glasses with a low Fe2+ content could be good materials for waste encapsulation.

  13. Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

    PubMed

    Potrzebowski, Wojciech; André, Ingemar

    2015-07-01

    For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.

  14. Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

    PubMed

    Potrzebowski, Wojciech; André, Ingemar

    2015-07-01

    For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints. PMID:25961412

  15. Structural Determinants of Oligomerization of the Aquaporin-4 Channel.

    PubMed

    Kitchen, Philip; Conner, Matthew T; Bill, Roslyn M; Conner, Alex C

    2016-03-25

    The aquaporin (AQP) family of integral membrane protein channels mediate cellular water and solute flow. Although qualitative and quantitative differences in channel permeability, selectivity, subcellular localization, and trafficking responses have been observed for different members of the AQP family, the signature homotetrameric quaternary structure is conserved. Using a variety of biophysical techniques, we show that mutations to an intracellular loop (loop D) of human AQP4 reduce oligomerization. Non-tetrameric AQP4 mutants are unable to relocalize to the plasma membrane in response to changes in extracellular tonicity, despite equivalent constitutive surface expression levels and water permeability to wild-type AQP4. A network of AQP4 loop D hydrogen bonding interactions, identified using molecular dynamics simulations and based on a comparative mutagenic analysis of AQPs 1, 3, and 4, suggest that loop D interactions may provide a general structural framework for tetrameric assembly within the AQP family. PMID:26786101

  16. Computer program for determining mass properties of a rigid structure

    NASA Technical Reports Server (NTRS)

    Hull, R. A.; Gilbert, J. L.; Klich, P. J.

    1978-01-01

    A computer program was developed for the rapid computation of the mass properties of complex structural systems. The program uses rigid body analyses and permits differences in structural material throughout the total system. It is based on the premise that complex systems can be adequately described by a combination of basic elemental shapes. Simple geometric data describing size and location of each element and the respective material density or weight of each element were the only required input data. From this minimum input, the program yields system weight, center of gravity, moments of inertia and products of inertia with respect to mutually perpendicular axes through the system center of gravity. The program also yields mass properties of the individual shapes relative to component axes.

  17. Structural Determinants of Oligomerization of the Aquaporin-4 Channel*

    PubMed Central

    Kitchen, Philip; Conner, Matthew T.; Bill, Roslyn M.; Conner, Alex C.

    2016-01-01

    The aquaporin (AQP) family of integral membrane protein channels mediate cellular water and solute flow. Although qualitative and quantitative differences in channel permeability, selectivity, subcellular localization, and trafficking responses have been observed for different members of the AQP family, the signature homotetrameric quaternary structure is conserved. Using a variety of biophysical techniques, we show that mutations to an intracellular loop (loop D) of human AQP4 reduce oligomerization. Non-tetrameric AQP4 mutants are unable to relocalize to the plasma membrane in response to changes in extracellular tonicity, despite equivalent constitutive surface expression levels and water permeability to wild-type AQP4. A network of AQP4 loop D hydrogen bonding interactions, identified using molecular dynamics simulations and based on a comparative mutagenic analysis of AQPs 1, 3, and 4, suggest that loop D interactions may provide a general structural framework for tetrameric assembly within the AQP family. PMID:26786101

  18. Structural determinants of reductive terpene cyclization in iridoid biosynthesis.

    PubMed

    Kries, Hajo; Caputi, Lorenzo; Stevenson, Clare E M; Kamileen, Mohammed O; Sherden, Nathaniel H; Geu-Flores, Fernando; Lawson, David M; O'Connor, Sarah E

    2016-01-01

    The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (from Catharanthus roseus) bound to a mechanism-inspired inhibitor that illuminates substrate binding and catalytic function of the enzyme. Key features that distinguish iridoid synthase from its close homolog progesterone 5β-reductase are highlighted.

  19. Determinants of fish assemblage structure in Northwestern Great Plains streams

    USGS Publications Warehouse

    Mullen, J.A.; Bramblett, R.G.; Guy, C.S.; Zale, A.V.; Roberts, D.W.

    2011-01-01

    Prairie streams are known for their harsh and stochastic physical conditions, and the fish assemblages therein have been shown to be temporally variable. We assessed the spatial and temporal variation in fish assemblage structure in five intermittent, adventitious northwestern Great Plains streams representing a gradient of watershed areas. Fish assemblages and abiotic conditions varied more spatially than temporally. The most important variables explaining fish assemblage structure were longitudinal position and the proportion of fine substrates. The proportion of fine substrates increased proceeding upstream, approaching 100% in all five streams, and species richness declined upstream with increasing fine substrates. High levels of fine substrate in the upper reaches appeared to limit the distribution of obligate lithophilic fish species to reaches further downstream. Species richness and substrates were similar among all five streams at the lowermost and uppermost sites. However, in the middle reaches, species richness increased, the amount of fine substrate decreased, and connectivity increased as watershed area increased. Season and some dimensions of habitat (including thalweg depth, absolute distance to the main-stem river, and watershed size) were not essential in explaining the variation in fish assemblages. Fish species richness varied more temporally than overall fish assemblage structure did because common species were consistently abundant across seasons, whereas rare species were sometimes absent or perhaps not detected by sampling. The similarity in our results among five streams varying in watershed size and those from other studies supports the generalization that spatial variation exceeds temporal variation in the fish assemblages of prairie and warmwater streams. Furthermore, given longitudinal position, substrate, and stream size, general predictions regarding fish assemblage structure and function in prairie streams are possible. ?? American

  20. Structural determinants of reductive terpene cyclization in iridoid biosynthesis

    PubMed Central

    Stevenson, Clare E. M.; Kamileen, Mohammed O.; Sherden, Nathaniel H.; Geu-Flores, Fernando; Lawson, David M.; O’Connor, Sarah E.

    2015-01-01

    The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (Catharanthus roseus) bound to a mechanism-inspired inhibitor that illuminates substrate binding and catalytic function of the enzyme. Key features that distinguish iridoid synthase from its close homologue, progesterone 5β-reductase, are highlighted. PMID:26551396