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Sample records for causap csar pedrocchi

  1. Copernicus Sentinel-1 Satellite And C-SAR Instrument

    NASA Astrophysics Data System (ADS)

    Panetti, Aniceto; Rostan, Friedhelm; L'Abbate, Michelangelo; Bruno, Claudio; Bauleo, Antonio; Catalano, Toni; Cotogni, Marco; Galvagni, Luigi; Pietropaolo, Andrea; Taini, Giacomo; Venditti, Paolo; Huchler, Markus; Torres, Ramon; Lokaas, Svein; Bibby, David

    2013-12-01

    The Copernicus Sentinel-1 Earth Radar Observatory, a mission funded by the European Union and developed by ESA, is a constellation of two C-band radar satellites. The satellites have been conceived to be a continuous and reliable source of C-band SAR imagery for operational applications such as mapping of global landmasses, coastal zones and monitoring of shipping routes. The Sentinel-1 satellites are built by an industrial consortium led by Thales Alenia Space Italia as Prime Contractor and with Astrium GmbH as SAR Instrument Contractor. The paper describes the general satellite architecture, the spacecraft subsystems, AIT flow and the satellite key performances. It provides also an overview on the C-SAR Instrument, its development status and pre- launch SAR performance prediction.

  2. CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma.

    PubMed

    Carlson, Heather A; Smith, Richard D; Damm-Ganamet, Kelly L; Stuckey, Jeanne A; Ahmed, Aqeel; Convery, Maire A; Somers, Donald O; Kranz, Michael; Elkins, Patricia A; Cui, Guanglei; Peishoff, Catherine E; Lambert, Millard H; Dunbar, James B

    2016-06-27

    The 2014 CSAR Benchmark Exercise was the last community-wide exercise that was conducted by the group at the University of Michigan, Ann Arbor. For this event, GlaxoSmithKline (GSK) donated unpublished crystal structures and affinity data from in-house projects. Three targets were used: tRNA (m1G37) methyltransferase (TrmD), Spleen Tyrosine Kinase (SYK), and Factor Xa (FXa). A particularly strong feature of the GSK data is its large size, which lends greater statistical significance to comparisons between different methods. In Phase 1 of the CSAR 2014 Exercise, participants were given several protein-ligand complexes and asked to identify the one near-native pose from among 200 decoys provided by CSAR. Though decoys were requested by the community, we found that they complicated our analysis. We could not discern whether poor predictions were failures of the chosen method or an incompatibility between the participant's method and the setup protocol we used. This problem is inherent to decoys, and we strongly advise against their use. In Phase 2, participants had to dock and rank/score a set of small molecules given only the SMILES strings of the ligands and a protein structure with a different ligand bound. Overall, docking was a success for most participants, much better in Phase 2 than in Phase 1. However, scoring was a greater challenge. No particular approach to docking and scoring had an edge, and successful methods included empirical, knowledge-based, machine-learning, shape-fitting, and even those with solvation and entropy terms. Several groups were successful in ranking TrmD and/or SYK, but ranking FXa ligands was intractable for all participants. Methods that were able to dock well across all submitted systems include MDock,1 Glide-XP,2 PLANTS,3 Wilma,4 Gold,5 SMINA,6 Glide-XP2/PELE,7 FlexX,8 and MedusaDock.9 In fact, the submission based on Glide-XP2/PELE7 cross-docked all ligands to many crystal structures, and it was particularly impressive to see

  3. Blind Pose Prediction, Scoring, and Affinity Ranking of the CSAR 2014 Dataset.

    PubMed

    Martiny, Virginie Y; Martz, François; Selwa, Edithe; Iorga, Bogdan I

    2016-06-27

    The 2014 CSAR Benchmark Exercise was focused on three protein targets: coagulation factor Xa, spleen tyrosine kinase, and bacterial tRNA methyltransferase. Our protocol involved a preliminary analysis of the structural information available in the Protein Data Bank for the protein targets, which allowed the identification of the most appropriate docking software and scoring functions to be used for the rescoring of several docking conformations datasets, as well as for pose prediction and affinity ranking. The two key points of this study were (i) the prior evaluation of molecular modeling tools that are most adapted for each target and (ii) the increased search efficiency during the docking process to better explore the conformational space of big and flexible ligands. PMID:26391724

  4. CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection.

    PubMed

    Nedumpully-Govindan, Praveen; Jemec, Domen B; Ding, Feng

    2016-06-27

    While molecular docking with both ligand and receptor flexibilities can help capture conformational changes upon binding, correct ranking of nativelike binding poses and accurate estimation of binding affinities remains a major challenge. In addition to the commonly used scoring approach with intermolecular interaction energies, we included the contribution of intramolecular energies changes upon binding in our flexible docking method, MedusaDock. In CSAR 2013-2014 binding prediction benchmark exercises, the new scoring function MScomplex was found to better recapitulate experimental binding affinities and correctly identify ligand-binding sequences from decoy receptors. Our further analysis with the DUD data sets indicates significant improvement of virtual screening enrichment using the new scoring function when compared to the previous intermolecular energy based scoring method. Our postanalysis also suggests a new approach to select nativelike poses in the clustering-based pose ranking approach by MedusaDock. Since the calculation of intramolecular energy changes and clustering-based pose ranking and selection are not MedusaDock specific, we expect a broad application in force-field based estimation of binding affinities and pose ranking using flexible ligand-receptor docking. PMID:26252196

  5. Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment.

    PubMed

    Baumgartner, Matthew P; Camacho, Carlos J

    2016-06-27

    The 2013/2014 Community Structure-Activity Resource (CSAR) challenge was designed to prospectively validate advancement in the field of docking and scoring receptor-small molecule interactions. Purely computational methods have been found to be quite limiting. Thus, the challenges assessed methods that combined both experimental data and computational approaches. Here, we describe our contribution to solve three important challenges in rational drug discovery: rank-ordering protein primary sequences based on affinity to a compound, determining close-to-native bound conformations out of a set of decoy poses, and rank-ordering sets of congeneric compounds based on affinity to a given protein. We showed that the most significant contribution to a meaningful enrichment of native-like models was the identification of the best receptor structure for docking and scoring. Depending on the target, the optimal receptor for cross-docking and scoring was identified by a self-consistent docking approach that used the Vina scoring function, by aligning compounds to the closest cocrystal or by selecting the cocrystal receptor with the largest pocket. For tRNA (m1G37) methyltransferase (TRMD), ranking a set of 31 congeneric binding compounds cross-docked to the optimal receptor resulted in a R(2) = 0.67; whereas, using any other of the 13 receptor structures led to almost no enrichment of native-like complex structures. Furthermore, although redocking predicted lower RMSDs relative to the bound structures, the ranking based on multiple receptor structures did not improve the correlation coefficient. Our predictions highlight the role of rational structure-based modeling in maximizing the outcome of virtual screening, as well as limitations scoring multiple receptors. PMID:26222931

  6. Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark.

    PubMed

    Ding, Feng; Dokholyan, Nikolay V

    2013-08-26

    Solution of the structures of ligand-receptor complexes via computational docking is an integral step in many structural modeling efforts as well as in rational drug discovery. A major challenge in ligand-receptor docking is the modeling of both receptor and ligand flexibilities in order to capture receptor conformational changes induced by ligand binding. In the molecular docking suite MedusaDock, both ligand and receptor side chain flexibilities are modeled simultaneously with sets of discrete rotamers, where the ligand rotamer library is generated "on the fly" in a stochastic manner. Here, we introduce backbone flexibility into MedusaDock by implementing ensemble docking in a sequential manner for a set of distinct receptor backbone conformations. We generate corresponding backbone ensembles to capture backbone changes upon binding to different ligands, as observed experimentally. We develop a simple clustering and ranking approach to select the top poses as blind predictions. We applied our method in the CSAR2011 benchmark exercise. In 28 out of 35 cases (80%) where the ligand-receptor complex structures were released, we were able to predict near-native poses (<2.5 Å RMSD), the highest success rate reported for CSAR2011. This result highlights the importance of modeling receptor backbone flexibility to the accurate docking of ligands to flexible targets. We expect a broad application of our fully flexible docking approach in biological studies as well as in rational drug design. PMID:23237273

  7. Study of the new CSAR62 positive tone electron-beam resist at 40 keV electron energy

    NASA Astrophysics Data System (ADS)

    Andok, R.; Bencurova, A.; Vutova, K.; Koleva, E.; Nemec, P.; Hrkut, P.; Kostic, I.; Mladenov, G.

    2016-03-01

    One of the few "top-down" methods for nano-device fabrication is the electron-beam lithography, which allows flexible patterning of various structures with a nanoscale resolution down to less than 10 nm. Thinner, more etching durable, and more sensitive e-beam resists are required for the better control, linearity, and uniformity of critical dimensions of structures for nano-device fabrication. Within the last decade, researchers have made significant efforts to improve the resolution of the nanoscale e-beam lithography. The resist material properties are an important factor governing the resolution. Only the e-beam resist ZEP 520 of the Japanese manufacturer ZEON is characterized by relatively good properties and thus meets most users' expectations. This paper deals with the investigation and simulation of the characteristics of the new less-expensive AR-P 6200 (CSAR 62) positive e-beam resist (available since May 2013, manufactured by Allresist GmbH company).

  8. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.

    PubMed

    Smith, Richard D; Damm-Ganamet, Kelly L; Dunbar, James B; Ahmed, Aqeel; Chinnaswamy, Krishnapriya; Delproposto, James E; Kubish, Ginger M; Tinberg, Christine E; Khare, Sagar D; Dou, Jiayi; Doyle, Lindsey; Stuckey, Jeanne A; Baker, David; Carlson, Heather A

    2016-06-27

    Community Structure-Activity Resource (CSAR) conducted a benchmark exercise to evaluate the current computational methods for protein design, ligand docking, and scoring/ranking. The exercise consisted of three phases. The first phase required the participants to identify and rank order which designed sequences were able to bind the small molecule digoxigenin. The second phase challenged the community to select a near-native pose of digoxigenin from a set of decoy poses for two of the designed proteins. The third phase investigated the ability of current methods to rank/score the binding affinity of 10 related steroids to one of the designed proteins (pKd = 4.1 to 6.7). We found that 11 of 13 groups were able to correctly select the sequence that bound digoxigenin, with most groups providing the correct three-dimensional structure for the backbone of the protein as well as all atoms of the active-site residues. Eleven of the 14 groups were able to select the appropriate pose from a set of plausible decoy poses. The ability to predict absolute binding affinities is still a difficult task, as 8 of 14 groups were able to correlate scores to affinity (Pearson-r > 0.7) of the designed protein for congeneric steroids and only 5 of 14 groups were able to correlate the ranks of the 10 related ligands (Spearman-ρ > 0.7). PMID:26419257

  9. CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

    PubMed Central

    2013-01-01

    The Community Structure–Activity Resource (CSAR) recently held its first blinded exercise based on data provided by Abbott, Vertex, and colleagues at the University of Michigan, Ann Arbor. A total of 20 research groups submitted results for the benchmark exercise where the goal was to compare different improvements for pose prediction, enrichment, and relative ranking of congeneric series of compounds. The exercise was built around blinded high-quality experimental data from four protein targets: LpxC, Urokinase, Chk1, and Erk2. Pose prediction proved to be the most straightforward task, and most methods were able to successfully reproduce binding poses when the crystal structure employed was co-crystallized with a ligand from the same chemical series. Multiple evaluation metrics were examined, and we found that RMSD and native contact metrics together provide a robust evaluation of the predicted poses. It was notable that most scoring functions underpredicted contacts between the hetero atoms (i.e., N, O, S, etc.) of the protein and ligand. Relative ranking was found to be the most difficult area for the methods, but many of the scoring functions were able to properly identify Urokinase actives from the inactives in the series. Lastly, we found that minimizing the protein and correcting histidine tautomeric states positively trended with low RMSD for pose prediction but minimizing the ligand negatively trended. Pregenerated ligand conformations performed better than those that were generated on the fly. Optimizing docking parameters and pretraining with the native ligand had a positive effect on the docking performance as did using restraints, substructure fitting, and shape fitting. Lastly, for both sampling and ranking scoring functions, the use of the empirical scoring function appeared to trend positively with the RMSD. Here, by combining the results of many methods, we hope to provide a statistically relevant evaluation and elucidate specific shortcomings

  10. Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks.

    PubMed

    Yan, Chengfei; Grinter, Sam Z; Merideth, Benjamin Ryan; Ma, Zhiwei; Zou, Xiaoqin

    2016-06-27

    In this study, we developed two iterative knowledge-based scoring functions, ITScore_pdbbind(rigid) and ITScore_pdbbind(flex), using rigid decoy structures and flexible decoy structures, respectively, that were generated from the protein-ligand complexes in the refined set of PDBbind 2012. These two scoring functions were evaluated using the 2013 and 2014 CSAR benchmarks. The results were compared with the results of two other scoring functions, the Vina scoring function and ITScore, the scoring function that we previously developed from rigid decoy structures for a smaller set of protein-ligand complexes. A graph-based method was developed to evaluate the root-mean-square deviation between two conformations of the same ligand with different atom names and orders due to different file preparations, and the program is freely available. Our study showed that the two new scoring functions developed from the larger training set yielded significantly improved performance in binding mode predictions. For binding affinity predictions, all four scoring functions showed protein-dependent performance. We suggest the development of protein-family-dependent scoring functions for accurate binding affinity prediction. PMID:26389744

  11. Sentinel-1A and Sentinel-1B CSAR status

    NASA Astrophysics Data System (ADS)

    Snoeij, Paul; Brown, Mike; Davidson, Malcolm; Rommen, Bjorn; Floury, Nicolas; Geudtner, Dirk; Torres, Ramon

    2011-11-01

    The ESA Sentinels constitute the first series of operational satellites responding to the Earth Observation needs of the EU-ESA Global Monitoring for Environment and Security programme. The GMES space component relies on existing and planned space assets as well as on new complementary developments by ESA. In particular, as part of the GMES space component, ESA is currently undertaking the development of 3 Sentinels mission families. Each Sentinel is based on a constellation of 2 satellites in the same orbital plane. This configuration allows to fulfil the revisit and coverage requirements and to provide a robust and affordable operational service. The launch of the 2nd satellite is scheduled 18 months after the launch of the 1st spacecraft of the constellation. The lifetime of the individual satellite is specified as 7 years, with consumables allowing mission extension up to 12 years. The lifecycle of the space segment is planned to be in the order of 15-20 years. The strategy for Sentinel procurement and replacement over this period is being elaborated, but will likely result in a need for 4-5 satellites of each type if the desired robustness for the service that GMES will provide is to be achieved. This paper will describe the operational and observational capabilities of the Sentinel-1 mission based on the user requirements, including potential emergency requests. An example of a pre-defined mission timeline for each and every cycle will be given.

  12. Addendum 3 to CSAR 80-027, Use of calorimeter 109B for fissile material measurement

    SciTech Connect

    Chiao, T.

    1994-12-05

    This modification to the Plutonium Finishing Plant (PFP) calorimeter system involves removing current calorimeter No. 3 from the water bath and replacing it with a calorimeter that can accommodate larger diameter items (an oversize can). The inside diameters of both the sample and the reference cells will be increased to 5.835 inches at the top opening and to 5.22 inches at the bottom, the 8 inch high measurement zone. This Addendum 3 to Criticality Safety Analysis Report 80-027 examines criticality safety during the use of the modified calorimeter (Calorimeter 109B) with enlarged cell tube diameters to assure that an adequate margin of subcriticality is maintained for all normal and contingency conditions.

  13. CSAR 79-034 ADDENDUM 2, storing the man-basket in the process cell in 236-Z Building, Plutonium Finishing Plant/Plutonium Reclamation Facility

    SciTech Connect

    Chiao, T.

    1994-10-25

    The man-basket is stored in the Plutonium Reclamation Facility canyon area and this addendum reports on a technical evaluation for the storage inside the canyon to ensure consistency with the requirements of the Nuclear Criticality Safety Manual, WHC-CM-4-29.

  14. Stresses and Strains

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Computerized Structural Analysis and Research Corporation (CSAR) flagship product is CSA/NASTRAN, a Finite Element Analysis program for structural, thermal, aeroelastic and acoustic analysis. CSAR's first products were software products for performing structural optimization in conjuction wtih MSC/NASTRAN. In 1984, CSAR released the first version of CSA/NASTRAN, then merely an enhanced version of COSMIC NASTRAN. In 1988, CSAR purchased the source code outright and released the first "independent" version of CSA/NASTRAN.

  15. Breast tumor detection using UWB circular-SAR tomographic microwave imaging.

    PubMed

    Oloumi, Daniel; Boulanger, Pierre; Kordzadeh, Atefeh; Rambabu, Karumudi

    2015-08-01

    This paper describes the possibility of detecting tumors in human breast using ultra-wideband (UWB) circular synthetic aperture radar (CSAR). CSAR is a subset of SAR which is a radar imaging technique using a circular data acquisition pattern. Tomographic image reconstruction is done using a time domain global back projection technique adapted to CSAR. Experiments are conducted on a breast phantoms made of pork fat emulating normal and cancerous conditions. Preliminary experimental results show that microwave imaging of a breast phantom using UWB-CSAR is a simple and low-cost method, efficiently capable of detecting the presence of tumors. PMID:26737919

  16. Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies.

    PubMed

    Shin, Woong-Hee; Lee, Gyu Rie; Seok, Chaok

    2016-06-27

    We analyze the results of the GalaxyDock protein-ligand docking program in the two recent experiments of Community Structure-Activity Resource (CSAR), CSAR 2013 and 2014. GalaxyDock performs global optimization of a modified AutoDock3 energy function by employing the conformational space annealing method. The energy function of GalaxyDock is quite sensitive to atomic clashes. Such energy functions can be effective for sampling physically correct conformations but may not be effective for scoring when conformations are not fully optimized. In phase 1 of CSAR 2013, we successfully selected all four true binders of digoxigenin along with three false positives. However, the energy values were rather high due to insufficient optimization of the conformations docked to homology models. A posteriori relaxation of the model complex structures by GalaxyRefine improved the docking energy values and differentiated the true binders from the false positives better. In the scoring test of CSAR 2013 phase 2, we selected the best poses for each of the two targets. The results of CSAR 2013 phase 3 suggested that an improved method for generating initial conformations for GalaxyDock is necessary for targets involving bulky ligands. Finally, combining existing binding information with GalaxyDock energy-based optimization may be needed for more accurate binding affinity prediction. PMID:26583962

  17. Investigating Gender-Related Construct-Irrelevant Components of Scores on the Written Assessment Exercise of a High-Stakes Certification Assessment

    ERIC Educational Resources Information Center

    Boulet, John R.; McKinley, Danette W.

    2005-01-01

    The ECFMG[R] Clinical Skills Assessment (CSA[R]) was developed to evaluate whether graduates of international medical schools (IMGs) are ready to enter graduate training programs in the United States. The patient note (PN) exercise is specifically used to assess a candidate's ability to summarize and synthesize the data collected in a simulated…

  18. Does Composition Medium Affect the Psychometric Properties of Scores on an Exercise Designed to Assess Written Medical Communication Skills?

    ERIC Educational Resources Information Center

    Boulet, John R.; McKinley, Danette W.; Rebbecchi, Thomas; Whelan, Gerald P.

    2007-01-01

    The ECFMG[R] Clinical Skills Assessment (CSA[R]) was developed to evaluate whether graduates of international medical schools are ready to enter graduate training programs in the United States. The performance-based patient note exercise is specifically used to assess an examinee's ability to summarize, synthesize and interpret the data collected…

  19. DOCUMENTATION OF NATIONAL WEATHER CONDITIONS AFFECTING LONG-TERM DEGRADATION OF COMMERCIAL SPENT NUCLEAR FUEL AND DOE SPENT NUCLEAR FUEL AND HIGH-LEVEL WASTE

    SciTech Connect

    W. L. Poe, Jr.; P.F. Wise

    1998-11-01

    The U.S. Department of Energy (DOE) is preparing a proposal to construct, operate 2nd monitor, and eventually close a repository at Yucca Mountain in Nye County, Nevada, for the geologic disposal of spent nuclear fuel (SNF) and high-level radioactive waste (HLW). As part of this effort, DOE has prepared a viability assessment and an assessment of potential consequences that may exist if the repository is not constructed. The assessment of potential consequences if the repository is not constructed assumes that all SNF and HLW would be left at the generator sites. These include 72 commercial generator sites (three commercial facility pairs--Salem and Hope Creek, Fitzpatrick and Nine Mile Point, and Dresden and Morris--would share common storage due to their close proximity to each other) and five DOE sites across the country. DOE analyzed the environmental consequences of the effects of the continued storage of these materials at these sites in a report titled Continued Storage Analysis Report (CSAR; Reference 1 ) . The CSAR analysis includes a discussion of the degradation of these materials when exposed to the environment. This document describes the environmental parameters that influence the degradation analyzed in the CSAR. These include temperature, relative humidity, precipitation chemistry (pH and chemical composition), annual precipitation rates, annual number of rain-days, and annual freeze/thaw cycles. The document also tabulates weather conditions for each storage site, evaluates the degradation of concrete storage modules and vaults in different regions of the country, and provides a thermal analysis of commercial SNF in storage.

  20. Design definition study of a lift/cruise fan technology V/STOL aircraft. Volume 1: Navy operational aircraft

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Aircraft were designed and sized to meet Navy mission requirements. Five missions were established for evaluation: anti-submarine warfare (ASW), surface attack (SA), combat search and rescue (CSAR), surveillance (SURV), and vertical on-board delivery (VOD). All missions were performed with a short takeoff and a vertical landing. The aircraft were defined using existing J97-GE gas generators or reasonable growth derivatives in conjunction with turbotip fans reflecting LF460 type technology. The multipurpose aircraft configuration established for U.S. Navy missions utilizes the turbotip driven lift/cruise fan concept for V/STOL aircraft.

  1. Physical states and finite-size effects in Kitaev's honeycomb model: Bond disorder, spin excitations, and NMR line shape

    NASA Astrophysics Data System (ADS)

    Zschocke, Fabian; Vojta, Matthias

    2015-07-01

    Kitaev's compass model on the honeycomb lattice realizes a spin liquid whose emergent excitations are dispersive Majorana fermions and static Z2 gauge fluxes. We discuss the proper selection of physical states for finite-size simulations in the Majorana representation, based on a recent paper by F. L. Pedrocchi, S. Chesi, and D. Loss [Phys. Rev. B 84, 165414 (2011), 10.1103/PhysRevB.84.165414]. Certain physical observables acquire large finite-size effects, in particular if the ground state is not fermion-free, which we prove to generally apply to the system in the gapless phase and with periodic boundary conditions. To illustrate our findings, we compute the static and dynamic spin susceptibilities for finite-size systems. Specifically, we consider random-bond disorder (which preserves the solubility of the model), calculate the distribution of local flux gaps, and extract the NMR line shape. We also predict a transition to a random-flux state with increasing disorder.

  2. The Boson Expansion Theory as the Nuclear Structure Theory for the Heavy Nuclei.

    NASA Astrophysics Data System (ADS)

    Kim, Hyoung-Bae

    1987-09-01

    Sometime ago, Kishimoto and Tamura developed a formalism of boson expansion theory (BET), and then Weeks and Tamura showed that it fitted many experimental data of collective nuclei. This formalism has recently been simplified significantly by Pedrocchi, Jamaluddin and Tamura. The new and old theories are very closely related but are not exactly the same. It has thus been desired to see whether the new theory can also fit data, and to show that it indeed works well constitutes a major part of this thesis. It is in fact seen that a number of data of Sm, Os and Pt isotopes are explained nicely. Since the new form of the theory is rather simple, it permits us to take into account easily the effects of noncollective states to the behavior of collective states. This thesis shows that a remarkably improved fit to data of magnetic moments of Sm isotopes is achieved in this way. The thesis discusses one additional subject. It is a result of an effort made to improve the BET by removing as much as possible the error due to the use of the BCS theory. This was done by applying a method developed by Li to the Dyson form of BET. A way to develop this work further is suggested.

  3. Application of a Boson Expansion formalism based on the Random Phase Approximation to samarium isotopes

    SciTech Connect

    Jamaluddin, M.B.

    1986-01-01

    The Boson Expansion Theory of Kishimoto and Tamura has proved to be very successful in describing quadrupole collective motions in even-even nuclei. This theory, however, involves a complicated transformation from the Tamm-Dancoff phonons to the phonons of the random Phase Approximation. In this thesis a Boson Expansion formalism, derived directly from the Random Phase Approximation and set forth by Pedracchi and Tamura, is used to derive the boson forms of the nuclear Hamiltonian and the electromagnetic transition operator. Detailed discussions of the formalism of Pedrocchi and Tamura and its extension needed to perform realistic calculations are presented. The technique used to deriving the boson forms and the formulae used in the calculations are also given a thorough treatment to demonstrate the simplicity of this approach. Finally, the theory is tested by applying it to calculate the energy levels and some electromagnetic properties of the Samarium isotopes. The results show that the present theory is capable of describing the range of behavior from a vibrational to a rotational character of the Samarium isotopes as well as the previous theory.

  4. The boson expansion theory as the nuclear structure theory for the heavy nuclei

    SciTech Connect

    Kim, H.B.

    1987-01-01

    Sometime sago, Kishimoto and Tamura developed a formalism of boson expansion theory (BET), and then Weeks and Tamura showed that it fitted many experimental data of collective nuclei. This formalism has recently been simplified significantly be Pedrocchi, Jamaluddin and Tamura. The new and old theories are very closely related but are not exactly the same. It has thus been desired to see whether the new theory can also fit data, and to show that it indeed works well constitutes a major part of this thesis. It is in fact seen that a number of data of Sm, Os and Pt isotopes are explained nicely. Since the new form of the theory is rather simple, it permits us to take into account easily the effects of noncollective states to the behavior of collective states. This thesis shows that are remarkably improved fit to data of magnetic moments of SM isotopes is achieved in this way. The thesis discusses one additional subject. It is a result of an effort made to improve the BET by removing as much as possible the error due to the use of the BCS theory. This was done by applying a method developed by Li to the Dyson form of BET. A way to develop this work further is suggested.

  5. Identification and catalytic residues of the arsenite methyltransferase from a sulfate-reducing bacterium, Clostridium sp. BXM.

    PubMed

    Wang, Pei-Pei; Bao, Peng; Sun, Guo-Xin

    2015-01-01

    Arsenic methylation is an important process frequently occurring in anaerobic environments. Anaerobic microorganisms have been implicated as the major contributors for As methylation. However, very little information is available regarding the enzymatic mechanism of As methylation by anaerobes. In this study, one novel sulfate-reducing bacterium isolate, Clostridium sp. BXM, which was isolated from a paddy soil in our laboratory, was demonstrated to have the ability of methylating As. One putative arsenite S-Adenosyl-Methionine methyltransferase (ArsM) gene, CsarsM was cloned from Clostridium sp. BXM. Heterologous expression of CsarsM conferred As resistance and the ability of methylating As to an As-sensitive strain of Escherichia coli. Purified methyltransferase CsArsM catalyzed the formation of methylated products from arsenite, further confirming its function of As methylation. Site-directed mutagenesis studies demonstrated that three conserved cysteine residues at positions 65, 153 and 203 in CsArsM are necessary for arsenite methylation, but only Cysteine 153 and Cysteine 203 are required for the methylation of monomethylarsenic to dimethylarsenic. These results provided the characterization of arsenic methyltransferase from anaerobic sulfate-reducing bacterium. Given that sulfate-reducing bacteria are ubiquitous in various wetlands including paddy soils, enzymatic methylation mediated by these anaerobes is proposed to contribute to the arsenic biogeochemical cycling. PMID:25790486

  6. Analysis of containment performance and radiological consequences under severe accident conditions for the Advanced Neutron Source Reactor at the Oak Ridge National Laboratory

    SciTech Connect

    Kim, S.H.; Taleyarkhan, R.P.

    1994-01-01

    A severe accident study was conducted to evaluate conservatively scoped source terms and radiological consequences to support the Advanced Neutron Source (ANS) Conceptual Safety Analysis Report (CSAR). Three different types of severe accident scenarios were postulated with a view of evaluating conservatively scoped source terms. The first scenario evaluates maximum possible steaming loads and associated radionuclide transport, whereas the next scenario is geared towards evaluating conservative containment loads from releases of radionuclide vapors and aerosols with associated generation of combustible gases. The third scenario follows the prescriptions given by the 10 CFR 100 guidelines. It was included in the CSAR for demonstrating site-suitability characteristics of the ANS. Various containment configurations are considered for the study of thermal-hydraulic and radiological behaviors of the ANS containment. Severe accident mitigative design features such as the use of rupture disks were accounted for. This report describes the postulated severe accident scenarios, methodology for analysis, modeling assumptions, modeling of several severe accident phenomena, and evaluation of the resulting source term and radiological consequences.

  7. Standard review plan for reviewing safety analysis reports for dry metallic spent fuel storage casks

    SciTech Connect

    Not Available

    1988-01-01

    The Cask Standard Review Plan (CSRP) has been prepared as guidance to be used in the review of Cask Safety Analysis Reports (CSARs) for storage packages. The principal purpose of the CSRP is to assure the quality and uniformity of storage cask reviews and to present a well-defined base from which to evaluate proposed changes in the scope and requirements of reviews. The CSRP also sets forth solutions and approaches determined to be acceptable in the past by the NRC staff in dealing with a specific safety issue or safety-related design area. These solutions and approaches are presented in this form so that reviewers can take consistent and well-understood positions as the same safety issues arise in future cases. An applicant submitting a CSAR does not have to follow the solutions or approaches presented in the CSRP. However, applicants should recognize that the NRC staff has spent substantial time and effort in reviewing and developing their positions for the issues. A corresponding amount of time and effort will probably be required to review and accept new or different solutions and approaches.

  8. Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries.

    PubMed

    Li, Liwei; Wang, Bo; Meroueh, Samy O

    2011-09-26

    The community structure-activity resource (CSAR) data sets are used to develop and test a support vector machine-based scoring function in regression mode (SVR). Two scoring functions (SVR-KB and SVR-EP) are derived with the objective of reproducing the trend of the experimental binding affinities provided within the two CSAR data sets. The features used to train SVR-KB are knowledge-based pairwise potentials, while SVR-EP is based on physicochemical properties. SVR-KB and SVR-EP were compared to seven other widely used scoring functions, including Glide, X-score, GoldScore, ChemScore, Vina, Dock, and PMF. Results showed that SVR-KB trained with features obtained from three-dimensional complexes of the PDBbind data set outperformed all other scoring functions, including best performing X-score, by nearly 0.1 using three correlation coefficients, namely Pearson, Spearman, and Kendall. It was interesting that higher performance in rank ordering did not translate into greater enrichment in virtual screening assessed using the 40 targets of the Directory of Useful Decoys (DUD). To remedy this situation, a variant of SVR-KB (SVR-KBD) was developed by following a target-specific tailoring strategy that we had previously employed to derive SVM-SP. SVR-KBD showed a much higher enrichment, outperforming all other scoring functions tested, and was comparable in performance to our previously derived scoring function SVM-SP. PMID:21728360

  9. Safety review of the design, operation, and radiation sections of the General Electric Morris Operation Consolidated Safety Analysis Report

    SciTech Connect

    McBride, J.P.

    1981-01-30

    A safety review was made of Sections 4 through 9 of the Consolidated Safety Analysis Report (CSAR) for the GE Morris Operation spent-fuel storage facility. The sections reviewed include Design Criteria and Compliance, Facility Design and Description, Radiation Protection, Accident Analysis, and Conduct of Operations. The safety review was performed in accordance with the Code of Federal Regulations, Title 10, Part 72, ''Licensing Requirements for the Storage of Spent Fuel in an Independent Spent Fuel Storage Installation'' and contains independent estimations of source terms and dose-commitments from postulated accidents in the storage facility and a structural analysis of the Morris Operation cranes as an appendix. The review confirms that the features of the facility as described in Sections 4 through 9 of the CSAR fulfilled the safety requirements of 10 CFR 72, and it is concluded that spent-fuel handling and storage at the Morris Operation do not present significant risks to public health and safety. 15 refs., 3 tabs.

  10. Observation of the continuous transformation of a four level laser into a two level system

    SciTech Connect

    Hewitt, J. D.; Readle, J. D.; Eden, J. G.

    2012-08-13

    A longstanding and fundamental question of laser and maser physics concerns the energy separation ({Delta}{epsilon}) required between the pumped and lasing states of a three (or four) level system. We observe a four level laser gradually transform into a two level (nonlasing) system by photoassociating Cs-Ar thermal atomic pairs and monitoring subsequent stimulated emission on the 6p{sup 2}P{sub 3/2} {yields} 6s{sup 2}S{sub 1/2} (D{sub 2}) transition of Cs at 852.1 nm. Laser excitation spectra demonstrate that the value of {Delta}{epsilon} below which the system rapidly assumes the form of a two level structure and lasing ceases is {approx}0.7kT which corresponds to a Boltzmann factor (exp[-{Delta}{epsilon}/kT]) of 0.5.

  11. Sentinel-1 Instrument Overview

    NASA Astrophysics Data System (ADS)

    Snoeij, Paul; Torres, Ramon; Geudtner, Dirk; Brown, Michael; Deghaye, Patrick; Navas-Traver, Ignacio; Ostergaard, Allan; Rommen, Bjorn; Floury, Nicolas; Davidson, Malcolm

    2013-03-01

    The forthcoming European Space Agency (ESA) Sentinel-1 (S-1) C-band SAR constellation will provide continuous all-weather day/night global coverage, with six days exact repetition time (near daily coverage over Europe and Canada) and with radar data delivery within 3 to 24 hours. These features open new possibilities for operational maritime services. The Sentinel-1 space segment has been designed and is being built by an industrial consortium with Thales Alenia Space Italia as prime contractor and EADS Astrium GmbH as C-SAR instrument responsible. It is expected that Sentinel-1A be launched in 2013. This paper will provide an overview of the Sentinel-1 system, the status and characteristics of the technical implementation. The key elements of the system supporting the maritime user community will be highlighted.

  12. Heterogeneous propellant internal ballistics: criticism and regeneration

    NASA Astrophysics Data System (ADS)

    Glick, R. L.

    2011-10-01

    Although heterogeneous propellant and its innately nondeterministic, chemically discrete morphology dominates applications, ballisticcharacterization deterministic time-mean burning rate and acoustic admittance measures' absence of explicit, nondeterministic information requires homogeneous propellant with a smooth, uniformly regressing burning surface: inadequate boundary conditions for heterogeneous propellant grained applications. The past age overcame this dichotomy with one-dimensional (1D) models and empirical knowledge from numerous, adequately supported motor developments and supplementary experiments. However, current cost and risk constraints inhibit this approach. Moreover, its fundamental science approach is more sensitive to incomplete boundary condition information (garbage-in still equals garbage-out) and more is expected. This work critiques this situation and sketches a path forward based on enhanced ballistic and motor characterizations in the workplace and approximate model and apparatus developments mentored by CSAR DNS capabilities (or equivalent).

  13. Toward a physical interpretation of substituent effects: the case of fluorine and trifluoromethyl groups.

    PubMed

    Siodła, Tomasz; Ozimiński, Wojciech P; Hoffmann, Marcin; Koroniak, Henryk; Krygowski, Tadeusz M

    2014-08-15

    The application of ab initio and DFT computational methods at six different levels of theory (MP2/cc-pVDZ, MP2/aug-cc-pVTZ, B3LYP/cc-pVDZ, B3LYP/aug-cc-pVTZ, M06/cc-pVDZ, and M06/aug-cc-pVTZ) to meta- and para-substituted fluoro- and trifluoromethylbenzene derivatives and to 1-fluoro- and 1-trifluoromethyl-2-substituted trans-ethenes allowed the study of changes in the electronic and geometric properties of F- and CF3-substituted systems under the impact of other substituents (BeH, BF2, BH2, Br, CFO, CHO, Cl, CN, F, Li, NH2, NMe2, NO, NO2, OH, H, CF3, and CH3). Various parameters of these systems have been investigated, including homodesmotic reactions in terms of the substituent effect stabilization energy (SESE), the π and σ electron donor-acceptor indexes (pEDA and sEDA, respectively), the charge on the substituent active region (cSAR, known earlier as qSAR), and bond lengths, which have been regressed against Hammett constants, resulting mostly in an accurate correspondence except in the case of p-fluorobenzene derivatives. Moreover, changes in the characteristics of the ability of the substituent to attract or donate electrons under the impact of the kind of moiety to which the substituent is attached have been considered as the indirect substituent effect and investigated by means of the cSAR model. Regressions of cSAR(X) versus cSAR(Y) for any systems X and Y allow final results to be obtained on the same scale of magnitude. PMID:25046196

  14. REGIONAL BINNING FOR CONTINUED STORAGE OF SPENT NUCLEAR FUEL AND HIGH-LEVEL WASTES

    SciTech Connect

    W. Lee Poe, Jr

    1998-10-01

    In the Continued Storage Analysis Report (CSAR) (Reference 1), DOE decided to analyze the environmental consequences of continuing to store the commercial spent nuclear fuel (SNF) at 72 commercial nuclear power sites and DOE-owned spent nuclear fuel and high-level waste at five Department of Energy sites by region rather than by individual site. This analysis assumes that three commercial facilities pairs--Salem and Hope Creek, Fitzpatrick and Nine-Mile Point, and Dresden and Moms--share common storage due to their proximity to each other. The five regions selected for this analysis are shown on Figure 1. Regions 1, 2, and 3 are the same as those used by the Nuclear Regulatory Commission in their regulatory oversight of commercial power reactors. NRC Region 4 was subdivided into two regions to more appropriately define the two different climates that exist in NRC Region 4. A single hypothetical site in each region was assumed to store all the SNF and HLW in that region. Such a site does not exist and has no geographic location but is a mathematical construct for analytical purposes. To ensure that the calculated results for the regional analyses reflect appropriate inventory, facility and material degradation, and radionuclide transport, the waste inventories, engineered barriers, and environmental conditions for the hypothetical sites were developed from data for each of the existing sites within the given region. Weighting criteria to account for the amount and types of SNF and HLW at each site were used in the development of the environmental data for the regional site, such that the results of the analyses for the hypothetical site were representative of the sum of the results of each actual site if they had been modeled independently. This report defines the actual site data used in development of this hypothetical site, shows how the individual site data was weighted to develop the regional site, and provides the weighted data used in the CSAR analysis. It is

  15. A New Scoring Function for Molecular Docking Based on AutoDock and AutoDock Vina.

    PubMed

    Tanchuk, Vsevolod Yu; Tanin, Volodymyr O; Vovk, Andriy I; Poda, Gennady

    2015-01-01

    Molecular docking of small molecules in the protein binding sites is the most widely used computational technique in modern structure-based drug discovery. Although accurate prediction of binding modes of small molecules can be achieved in most cases, estimation of their binding affinities remains mediocre at best. As an attempt to improve the correlation between the inhibitory constants, pKi, and scoring, we created a new, hybrid scoring function. The new function is a linear combination of the terms of the scoring functions of AutoDock and AutoDock Vina. It was trained on 2,412 protein-ligand complexes from the PDBbind database (www.pdbbind.org.cn, version 2012) and validated on a set of 313 complexes released in the 2013 version as a test set. The new function was included in a modified version of AutoDock. The hybrid scoring function showed a statistically significant improvement in both training and test sets in terms of correlation with and root mean square and mean absolute errors in prediction of pKi values. It was also tested on the CSAR 2014 Benchmark Exercise dataset (team T) and produced reasonably good results. PMID:26302746

  16. Characterizing geolocation ambiguity responses in synthetic aperture radar: ground moving target indication

    NASA Astrophysics Data System (ADS)

    Holston, Matthew E.; Minardi, Michael J.; Temple, Michael A.; Saville, Michael A.

    2007-04-01

    Single-channel synthetic aperture radar (SAR) can provide high quality, focused images of moving targets by utilizing advanced SAR-GMTI techniques that focus all constant velocity targets into a three-dimensional space indexed by range, cross-range and cross-range velocity. However, an inherent geolocation ambiguity exists in that multiple, distinct moving targets may posses identical range versus time responses relative to a constant velocity collection platform. Although these targets are uniquely located within a four-dimensional space (x-position, y-position, x-velocity, and y-velocity), their responses are focused and mapped to the same three-dimensional position in the SAR-GMTI image cube. Previous research has shown that circular SAR (CSAR) collection geometry is one way to break this ambiguity and creates a four-dimensional detection space. This research determines the target resolution available in the detection space as a function of different collection parameters. A metric is introduced to relate the resolvability of multiple target responses for various parametric combinations, i.e., changes in key collection parameters such as integration time, slant range, look angle, and carrier frequency.

  17. Positive nonlinear pressure shift of Cs in Ne

    NASA Astrophysics Data System (ADS)

    Xia, Tian; McGuyer, Bart; Jau, Yuan-Yu; Happer, William

    2010-03-01

    We demonstrate that the hyperfine resonance frequency of ground state Cs atoms have a nonlinear dependence on the pressure of the buffer gas Ne at a fixed temperature. The hyperfine resonance frequency of alkali-metal atoms is shifted by an amount, which had long been assumed to be linear with the buffer gas pressure until Fei Gong discovered that the shift of Rb and Cs hyperfine resonance frequency has a nonlinear dependence on the pressure of the buffer gas Ar and Kr. While the nonlinear pressure shift of Cs in Ar and Kr is negative, we found that the nonlinear pressure shift of Cs hyperfine frequency in Ne is positive. The reason of the nonlinear shift is the three body collision(eg: Cs-Ne-Ne) and the formation of Van der Waals molecules of a Cs atom and a buffer gas atom of Ar, Kr, or Ne. The hyperfine precession rate of a Cs atom bound in molecule has a shift respect to a free Cs atom. The reversal sign of this nonlinear pressure shift of Cs in Ne respect to Ar and Kr demonstrate that the shift of the hyperfine precession rate of Cs in CsNe is reversed respect to CsAr and CsKr.

  18. M.Y.S.P.A.C.E. : Multinational Youth Studying Practical Applications of Climatic Events

    NASA Astrophysics Data System (ADS)

    Mckay, M.; Arvedson, J. P.; Arvedson, P.

    2014-12-01

    M.Y. S.P.A.C.E. (Multinational Youth Studying Practical Applications of Climatic Events) is an international collaboration of high school students engaged in self-selected research projects on the local impact of global environmental issues. Students work with their own, trained, Teacher Leaders at their school sites using both locally generated and satellite-based remote-sensing data with support from the National Oceanic and Atmospheric Administration (NOAA) and the National Aeronautics and Space Administration (NASA). Teams from each school meet at the annual Satellites & Education Conference to discover global trends in their collective data and present their findings. Students learn and practice techniques of scientific investigation; methods of data processing, analysis and interpretation; leadership; and effective communication. They work with NOAA and NASA scientists and engineers, experience university campus life, and can apply for special internships at selected university research centers such as the Center for Energy and Sustainability (CE&S), the Center for Spatial Analysis and Remote Sensing (CSARS), and graduate research opportunities in Geosciences and Environment. The M.Y. S.P.A.C.E. Program is an initiative of the Satellites & Education Conference, which is produced by the non-profit Satellite Educators Association. It is administered from the campus of California State University, Los Angeles. NOAA, NASA, and the NOAA-CREST West grant support the program. It is aligned with NOAA goals of building excitement about careers in science, math, engineering and technology.

  19. Multiphysics Application Coupling Toolkit

    Energy Science and Technology Software Center (ESTSC)

    2013-12-02

    This particular consortium implementation of the software integration infrastructure will, in large part, refactor portions of the Rocstar multiphysics infrastructure. Development of this infrastructure originated at the University of Illinois DOE ASCI Center for Simulation of Advanced Rockets (CSAR) to support the center's massively parallel multiphysics simulation application, Rocstar, and has continued at IllinoisRocstar, a small company formed near the end of the University-based program. IllinoisRocstar is now licensing these new developments as free, openmore » source, in hopes to help improve their own and others' access to infrastructure which can be readily utilized in developing coupled or composite software systems; with particular attention to more rapid production and utilization of multiphysics applications in the HPC environment. There are two major pieces to the consortium implementation, the Application Component Toolkit (ACT), and the Multiphysics Application Coupling Toolkit (MPACT). The current development focus is the ACT, which is (will be) the substrate for MPACT. The ACT itself is built up from the components described in the technical approach. In particular, the ACT has the following major components: 1.The Component Object Manager (COM): The COM package provides encapsulation of user applications, and their data. COM also provides the inter-component function call mechanism. 2.The System Integration Manager (SIM): The SIM package provides constructs and mechanisms for orchestrating composite systems of multiply integrated pieces.« less

  20. HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches.

    PubMed

    Huang, Sheng-You; Li, Min; Wang, Jianxin; Pan, Yi

    2016-06-27

    Structure-based molecular docking and ligand-based similarity search are two commonly used computational methods in computer-aided drug design. Structure-based docking tries to utilize the structural information on a drug target like protein, and ligand-based screening takes advantage of the information on known ligands for a target. Given their different advantages, it would be desirable to use both protein- and ligand-based approaches in drug discovery when information for both the protein and known ligands is available. Here, we have presented a general hybrid docking protocol, referred to as HybridDock, to utilize both the protein structures and known ligands by combining the molecular docking program MDock and the ligand-based similarity search method SHAFTS, and evaluated our hybrid docking protocol on the CSAR 2013 and 2014 exercises. The results showed that overall our hybrid docking protocol significantly improved the performance in both binding affinity and binding mode predictions, compared to the sole MDock program. The efficacy of the hybrid docking protocol was further confirmed using the combination of DOCK and SHAFTS, suggesting an alternative docking approach for modern drug design/discovery. PMID:26317502

  1. Electron collisions with cesium atoms—benchmark calculations and application to modeling an excimer-pumped alkali laser

    NASA Astrophysics Data System (ADS)

    Zatsarinny, Oleg; Bartschat, Klaus; Babaeva, Natalia Yu; Kushner, Mark J.

    2014-06-01

    The B-spline R-matrix (BSR) with pseudostates method is employed to describe electron collisions with cesium atoms. Over 300 states are kept in the close-coupling expansion, including a large number of pseudostates to model the effect of the Rydberg spectrum and, most importantly, the ionization continuum on the results for transitions between the discrete physical states of interest. Predictions for elastic scattering, momentum transfer, excitation and ionization are presented for incident energies up to 200 eV and compared with results from previous calculations and available experimental data. In a second step, the results are used to model plasma formation in an excimer-pumped alkali laser operating on the Cs (62P3/2,1/2 → 62S1/2) (852 nm and 894 nm) transitions. At sufficiently high operating temperature of a Cs-Ar containing quartz cell, pump power, and repetition rate, plasma formation in excess of 1014-1015 cm-3 occurs. This may reduce laser output power by electron collisional mixing of the upper and lower laser levels.

  2. Multiphysics Application Coupling Toolkit

    SciTech Connect

    Campbell, Michael T.

    2013-12-02

    This particular consortium implementation of the software integration infrastructure will, in large part, refactor portions of the Rocstar multiphysics infrastructure. Development of this infrastructure originated at the University of Illinois DOE ASCI Center for Simulation of Advanced Rockets (CSAR) to support the center's massively parallel multiphysics simulation application, Rocstar, and has continued at IllinoisRocstar, a small company formed near the end of the University-based program. IllinoisRocstar is now licensing these new developments as free, open source, in hopes to help improve their own and others' access to infrastructure which can be readily utilized in developing coupled or composite software systems; with particular attention to more rapid production and utilization of multiphysics applications in the HPC environment. There are two major pieces to the consortium implementation, the Application Component Toolkit (ACT), and the Multiphysics Application Coupling Toolkit (MPACT). The current development focus is the ACT, which is (will be) the substrate for MPACT. The ACT itself is built up from the components described in the technical approach. In particular, the ACT has the following major components: 1.The Component Object Manager (COM): The COM package provides encapsulation of user applications, and their data. COM also provides the inter-component function call mechanism. 2.The System Integration Manager (SIM): The SIM package provides constructs and mechanisms for orchestrating composite systems of multiply integrated pieces.

  3. Benchmarking the QUAD4/TRIA3 element

    NASA Astrophysics Data System (ADS)

    Pitrof, Stephen M.; Venkayya, Vipperla B.

    1993-09-01

    The QUAD4 and TRIA3 elements are the primary plate/shell elements in NASTRAN. These elements enable the user to analyze thin plate/shell structures for membrane, bending and shear phenomena. They are also very new elements in the NASTRAN library. These elements are extremely versatile and constitute a substantially enhanced analysis capability in NASTRAN. However, with the versatility comes the burden of understanding a myriad of modeling implications and their effect on accuracy and analysis quality. The validity of many aspects of these elements were established through a series of benchmark problem results and comparison with those available in the literature and obtained from other programs like MSC/NASTRAN and CSAR/NASTRAN. Never-the-less such a comparison is never complete because of the new and creative use of these elements in complex modeling situations. One of the important features of QUAD4 and TRIA3 elements is the offset capability which allows the midsurface of the plate to be noncoincident with the surface of the grid points. None of the previous elements, with the exception of bar (beam), has this capability. The offset capability played a crucial role in the design of QUAD4 and TRIA3 elements. It allowed modeling layered composites, laminated plates and sandwich plates with the metal and composite face sheets. Even though the basic implementation of the offset capability is found to be sound in the previous applications, there is some uncertainty in relatively simple applications. The main purpose of this paper is to test the integrity of the offset capability and provide guidelines for its effective use. For the purpose of simplicity, references in this paper to the QUAD4 element will also include the TRIA3 element.

  4. A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series

    PubMed Central

    Rapp, Chaya S.; Kalyanaraman, Chakrapani; Schiffmiller, Aviva; Schoenbrun, Esther Leah; Jacobson, Matthew P.

    2011-01-01

    We introduce the “Prime-ligand” method for ranking ligands in congeneric series. The method employs a single scoring function, the OPLS-AA/GBSA molecular mechanics/implicit solvent model, for all stages of sampling and scoring. We evaluate the method using 12 test sets of congeneric series for which experimental binding data is available in the literature, as well as the structure of one member of the series bound to the protein. Ligands are ‘docked’ by superimposing a common stem fragment among the compounds in the series using a crystal complex from the Protein Databank, and sampling the conformational space of the variable region. Our results show good correlation between our predicted rankings and experimental data for cases in which binding affinities differ by at least one order of magnitude. For 11 out of 12 cases, >90% of such ligand pairs could be correctly ranked, while for the remaining case, Factor Xa, 76% of such pairs were correctly ranked. A small number of compounds could not be docked using the current protocol due to the large size of functional groups that could not be accommodated by a rigid receptor. CPU requirements for the method, involving CPU-minutes per ligand, are modest compared with more rigorous methods that use similar force fields, such as free energy perturbation. We also benchmark the scoring function using series of ligand bound to the same protein within the CSAR data set. We demonstrate that energy minimization of ligand in the crystal structures is critical to obtain any correlation with experimentally determined binding affinities. PMID:21780805

  5. Synthesis and Preclinical Evaluation of Sulfonamido-based [11C-Carbonyl]-Carbamates and Ureas for Imaging Monoacylglycerol Lipase

    PubMed Central

    Wang, Lu; Mori, Wakana; Cheng, Ran; Yui, Joji; Hatori, Akiko; Ma, Longle; Zhang, Yiding; Rotstein, Benjamin H.; Fujinaga, Masayuki; Shimoda, Yoko; Yamasaki, Tomoteru; Xie, Lin; Nagai, Yuji; Minamimoto, Takafumi; Higuchi, Makoto; Vasdev, Neil; Zhang, Ming-Rong; Liang, Steven H.

    2016-01-01

    Monoacylglycerol lipase (MAGL) is a 33 kDa member of the serine hydrolase superfamily that preferentially degrades 2-arachidonoylglycerol (2-AG) to arachidonic acid in the endocannabinoid system. Inhibition of MAGL is not only of interest for probing the cannabinoid pathway but also as a therapeutic and diagnostic target for neuroinflammation. Limited attempts have been made to image MAGL in vivo and a suitable PET ligand for this target has yet to be identified and is urgently sought to guide small molecule drug development in this pathway. Herein we synthesized and evaluated the physiochemical properties of an array of eleven sulfonamido-based carbamates and ureas with a series of terminal aryl moieties, linkers and leaving groups. The most potent compounds were a novel MAGL inhibitor, N-((1-(1H-1,2,4-triazole-1-carbonyl)piperidin-4-yl) methyl)-4-chlorobenzenesulfonamide (TZPU; IC50 = 35.9 nM), and the known inhibitor 1,1,1,3,3,3-hexafluoropropan-2-yl 4-(((4-chlorophenyl)sulfonamido) methyl)piperidine-1-carboxylate (SAR127303; IC50 = 39.3 nM), which were also shown to be selective for MAGL over fatty acid amide hydrolase (FAAH), and cannabinoid receptors (CB1 & CB2). Both of these compounds were radiolabeled with carbon-11 via [11C]COCl2, followed by comprehensive ex vivo biodistribution and in vivo PET imaging studies in normal rats to determine their brain permeability, specificity, clearance and metabolism. Whereas TZPU did not show adequate specificity to warrant further evaluation, [11C]SAR127303 was advanced for preliminary PET neuroimaging studies in nonhuman primate. The tracer showed good brain permeability (ca. 1 SUV) and heterogeneous regional brain distribution which is consistent with the distribution of MAGL. PMID:27279908

  6. Excimer-pumped alkali vapor lasers: a new class of photoassociation lasers

    NASA Astrophysics Data System (ADS)

    Readle, J. D.; Wagner, C. J.; Verdeyen, J. T.; Spinka, T. M.; Carroll, D. L.; Eden, J. G.

    2010-02-01

    Excimer-pumped alkali vapor lasers (XPALs) are a new class of photoassociation lasers which take advantage of the spectrally broad absorption profiles of alkali-rare gas collision pairs. In these systems, transient alkali-rare gas molecules are photopumped from the thermal continuum to a dissociative X2Σ+ 1/2 interaction potential, subsequently populating the n2P3/2 state of the alkali. The absorption profiles >=5 nm and quantum efficiencies >98% have been observed in oscillator experiments, indicating XPAL compatibility with conventional high power laser diode arrays. An alternative technique for populating the n2P3/2 state is direct photoexcitation on the n2P3/2<--n2S1/2 atomic transition. However, because the XPAL scheme employs an off-resonant optical pump, the strengths of resonantly-enhanced nonlinear processes are minimized. Additionally, the absorption coefficient may be adjusted by altering the number densities of the lasing species and/or perturbers, a valuable asset in the design of large volume, high power lasers. We present an overview of XPAL lasers and their operation, including the characteristics of recently demonstrated systems photopumped with a pulsed dye laser. Lasing has been observed in Cs at both 894 nm and 852 nm by pumping CsAr or CsKr pairs as well as in Rb at 795 nm by pumping RbKr. These results highlight the important role of the perturbing species in determining the strength and position of the excimer absorption profile. It is expected that similar results may be obtained in other gas mixtures as similar collision pair characteristics have historically been observed in a wide variety of transient diatomic species.

  7. An Ammonia Spectral Map of the L1495-B218 Filaments in the Taurus Molecular Cloud. I. Physical Properties of Filaments and Dense Cores

    NASA Astrophysics Data System (ADS)

    Seo, Young Min; Shirley, Yancy L.; Goldsmith, Paul; Ward-Thompson, Derek; Kirk, Jason M.; Schmalzl, Markus; Lee, Jeong-Eun; Friesen, Rachel; Langston, Glen; Masters, Joe; Garwood, Robert W.

    2015-06-01

    We present deep NH3 observations of the L1495-B218 filaments in the Taurus molecular cloud covering over a 3° angular range using the K-band focal plane array on the 100 m Green Bank Telescope. The L1495-B218 filaments form an interconnected, nearby, large complex extending over 8 pc. We observed NH3 (1, 1) and (2, 2) with a spectral resolution of 0.038 km s-1 and a spatial resolution of 31″. Most of the ammonia peaks coincide with intensity peaks in dust continuum maps at 350 and 500 μm. We deduced physical properties by fitting a model to the observed spectra. We find gas kinetic temperatures of 8-15 K, velocity dispersions of 0.05-0.25 km s-1, and NH3 column densities of 5 × 1012 to 1 × 1014 cm-2. The CSAR algorithm, which is a hybrid of seeded-watershed and binary dendrogram algorithms, identifies a total of 55 NH3 structures, including 39 leaves and 16 branches. The masses of the NH3 sources range from 0.05 to 9.5 {{M}⊙ }. The masses of NH3 leaves are mostly smaller than their corresponding virial mass estimated from their internal and gravitational energies, which suggests that these leaves are gravitationally unbound structures. Nine out of 39 NH3 leaves are gravitationally bound, and seven out of nine gravitationally bound NH3 leaves are associated with star formation. We also found that 12 out of 30 gravitationally unbound leaves are pressure confined. Our data suggest that a dense core may form as a pressure-confined structure, evolve to a gravitationally bound core, and undergo collapse to form a protostar.

  8. Benchmarking the QUAD4/TRIA3 element

    NASA Technical Reports Server (NTRS)

    Pitrof, Stephen M.; Venkayya, Vipperla B.

    1993-01-01

    The QUAD4 and TRIA3 elements are the primary plate/shell elements in NASTRAN. These elements enable the user to analyze thin plate/shell structures for membrane, bending and shear phenomena. They are also very new elements in the NASTRAN library. These elements are extremely versatile and constitute a substantially enhanced analysis capability in NASTRAN. However, with the versatility comes the burden of understanding a myriad of modeling implications and their effect on accuracy and analysis quality. The validity of many aspects of these elements were established through a series of benchmark problem results and comparison with those available in the literature and obtained from other programs like MSC/NASTRAN and CSAR/NASTRAN. Never-the-less such a comparison is never complete because of the new and creative use of these elements in complex modeling situations. One of the important features of QUAD4 and TRIA3 elements is the offset capability which allows the midsurface of the plate to be noncoincident with the surface of the grid points. None of the previous elements, with the exception of bar (beam), has this capability. The offset capability played a crucial role in the design of QUAD4 and TRIA3 elements. It allowed modeling layered composites, laminated plates and sandwich plates with the metal and composite face sheets. Even though the basic implementation of the offset capability is found to be sound in the previous applications, there is some uncertainty in relatively simple applications. The main purpose of this paper is to test the integrity of the offset capability and provide guidelines for its effective use. For the purpose of simplicity, references in this paper to the QUAD4 element will also include the TRIA3 element.

  9. The L1495-B218 filaments in Taurus seen in NH3 & CCS and Dynamical Stability of Filaments and Dense Cores

    NASA Astrophysics Data System (ADS)

    Seo, Youngmin

    2016-01-01

    We present deep NH3 map of L1495-B218 filaments and the dense cores embedded within the filaments in Taurus. The L1495-B218 filaments form an interconnected, nearby, large complex extending 8 pc. We observed the filaments in NH3 (1,1) & (2,2) and CCS 21-10 with spectral resolution of 0.038 km/s and spatial resolution of 31". The CSAR algorithm, which is a hybrid of seeded-watershed and binary dendrogram algorithm, identifies 39 leaves and 16 branches in NH3 (1,1). Applying a virial analysis for the 39 NH3 leaves, we find only 9 out of 39 leaves are gravitationally bound, and 12 out of 30 gravitationally unbound leaves are pressure-confined. Our analysis suggests that a dense core may form as a pressure-confined structure, evolve to a gravitationally bound core, and then undergo collapse to form a protostar (Seo et al. 2015).We also present more realistic dynamic stability conditions for dense cores with converging motions and under the influence of radiation pressure. The critical Bonnor-Ebert sphere and the isothermal cylinder have been widely used to test stability of dense cores and filaments; however, these assume a quiescent environment while actual star forming regions are turbulent and illuminated by radiation. In a new analysis of stability conditions we account for converging motions which have been modeled toward starless cores (Seo et al. 2011) and the effect of radiation fields into account. We find that the critical size of a dense core having a homologous converging motion with its peak speed being the sound speed is roughly half of the critical size of the Bonnor-Ebert sphere (Seo et al. 2013). We also find that the critical mass/line density of a dense core/filament irradiated by radiation are considerably smaller than that of the Bonnor-Ebert sphere/isothermal cylinder when the radiation pressure is stronger than the central gas pressure of dense core/isothermal cylinder. For inner Galactic regions and regions near OB associations, the critical

  10. istar: A Web Platform for Large-Scale Protein-Ligand Docking

    PubMed Central

    Li, Hongjian; Leung, Kwong-Sak; Ballester, Pedro J.; Wong, Man-Hon

    2014-01-01

    Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar

  11. Sentinel-1 Mission Overview and Implementation Status

    NASA Astrophysics Data System (ADS)

    Davidson, M.; Attema, E.; Snoeij, P.; Levrini, G.

    2009-04-01

    Sentinel-1 is an imaging radar mission at C-band consisting of a constellation of two satellites aimed at providing continuity of all-weather day-and-night supply of imagery for user services. Special emphasis is placed on services identified in ESA's GMES service elements program and on projects funded by the European Union Framework Programmes. Three priorities (fast-track services) for the mission have been identified by user consultation working groups of the European Union: Marine Core Services, Land Monitoring and Emergency Services. These cover applications such as: - Monitoring sea ice zones and the arctic environment - Surveillance of marine environment - Monitoring land surface motion risks - Mapping of land surfaces: forest, water and soil, agriculture - Mapping in support of humanitarian aid in crisis situations. The Sentinel 1 space segment will be designed and built by an industrial consortium with Thales Alenia Space Italia as prime contractor and EADS Astrium GmbH as C-SAR instrument responsible. Data products from current and previous ESA missions including ERS-1, ERS-2 and Envisat missions form the basis for many of the pilot GMES services. Consequently Sentinel-1 data maintain data quality levels of the Agency‘s previous SAR missions in terms of spatial resolution, sensitivity, accuracy, polarization and wavelength. Nonetheless, the Sentinel-1 synthetic aperture radar (SAR) constellation represents a completely new approach to SAR mission design by ESA in direct response to the operational needs for SAR data expressed under the EU-ESA Global Monitoring for Environment and Security (GMES) programme. The Sentinel-1 constellation is expected to provide near daily coverage over Europe and Canada, global coverage all independent of weather with delivery of radar data within 1 hour of acquisition - all vast improvements with respect to the existing SAR systems. The continuity of C-band SAR data combined with the greatly improved data provision is